diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 0000000..a3ed7f4 --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,14 @@ +# Codecov configuration to make it a bit less noisy +coverage: + status: + patch: false + project: + default: + threshold: 50% +comment: + layout: "header" + require_changes: false + branches: null + behavior: default + flags: null + paths: null \ No newline at end of file diff --git a/.coveragerc b/.coveragerc index 349ec12..828bdba 100644 --- a/.coveragerc +++ b/.coveragerc @@ -2,9 +2,9 @@ branch = True omit = # omit all tests - src/alchemtest/tests/* + alchemtest/tests/* # omit the versioneer-installed _version.py - src/alchemtest/_version.py + alchemtest/_version.py [report] exclude_lines = diff --git a/.gitattributes b/.gitattributes index e5735d4..f55ab6a 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -src/alchemtest/_version.py export-subst +alchemtest/_version.py export-subst diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 0000000..3cdbaba --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,47 @@ +# How to contribute + +We welcome contributions from external contributors, and this document +describes how to merge code changes into this alchemtest. + +If you want to **contribute a new test files** then please also read the + [Contributing new data sets](https://alchemtest.readthedocs.io/en/latest/contributing.html) +chapter in the documentation. + + +## Getting Started + +* Make sure you have a [GitHub account](https://github.com/signup/free). +* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub. +* On your local machine, + [clone](https://help.github.com/articles/cloning-a-repository/) your fork of + the repository. + +## Making Changes + +* Add some really awesome code to your local fork. It's usually a [good + idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/) + to make changes on a + [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) + with the branch name relating to the feature you are going to add. +* When you are ready for others to examine and comment on your new feature, + navigate to your fork of alchemtest on GitHub and open a [pull + request](https://help.github.com/articles/using-pull-requests/) (PR). Note that + after you launch a PR from one of your fork's branches, all + subsequent commits to that branch will be added to the open pull request + automatically. Each commit added to the PR will be validated for + mergability, compilation and test suite compliance; the results of these tests + will be visible on the PR page. +* If you're providing a new feature, you must add test cases and documentation. +* When the code is ready to go, make sure you run the test suite using pytest. +* When you're ready to be considered for merging, check the "Ready to go" + box on the PR page to let the alchemtest devs know that the changes are complete. + The code will not be merged until this box is checked, the continuous + integration returns checkmarks, + and multiple core developers give "Approved" reviews. + +# Additional Resources + +* [General GitHub documentation](https://help.github.com/) +* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/) +* [A guide to contributing to software packages](http://www.contribution-guide.org) +* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..c772b96 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,12 @@ +## Description +Provide a brief description of the PR's purpose here. + +## Todos +Notable points that this PR has either accomplished or will accomplish. + - [ ] TODO 1 + +## Questions +- [ ] Question1 + +## Status +- [ ] Ready to go \ No newline at end of file diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 1f31978..5dabaef 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -24,63 +24,52 @@ jobs: strategy: matrix: os: [macOS-latest, ubuntu-latest, windows-latest] - python-version: ["3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12"] # Only test lowest and highest version on the expensive/slow # macOS and windows runners (UPDATE when supported versions change): exclude: - - os: macOS-latest - python-version: 3.8 - - os: macOS-latest - python-version: 3.11 - - os: windows-latest - python-version: 3.8 - - os: windows-latest - python-version: 3.11 + - os: macOS-latest + python-version: 3.10 + - os: macOS-latest + python-version: 3.11 + - os: windows-latest + python-version: 3.10 + - os: windows-latest + python-version: 3.11 steps: - - uses: actions/checkout@v2 - - - name: Setup python - uses: actions/setup-python@v2 - with: - python-version: ${{ matrix.python-version }} - - - name: Display Python version - run: python -c "import sys; print(sys.version)" - - - name: Additional info about the build - shell: bash - run: | - uname -a - df -h - ulimit -a - - - name: Install pytest, pytest plugins - run: | - python -m pip install wheel - python -m pip install pytest pytest-cov pytest-pep8 - - - name: Install package - run: | - python -m pip install . - - - name: Run tests - - # conda setup requires this special shell - shell: bash -l {0} - - run: | - pytest -v --cov=alchemtest --cov-report=xml --color=yes src/alchemtest/tests - - - name: CodeCov - uses: codecov/codecov-action@v3 - with: - token: ${{ secrets.CODECOV_TOKEN }} - name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} - file: ./coverage.xml - flags: unittests - fail_ci_if_error: true - + - uses: actions/checkout@v3 + + # More info on options: https://github.com/marketplace/actions/provision-with-micromamba + - uses: mamba-org/provision-with-micromamba@main + with: + environment-file: devtools/conda-envs/test_env.yaml + environment-name: test + channels: conda-forge,defaults + extra-specs: | + python=${{ matrix.python-version }} + + - name: Install package + # conda setup requires this special shell + shell: bash -l {0} + run: | + python -m pip install . --no-deps + micromamba list + + - name: Run tests + # conda setup requires this special shell + shell: bash -l {0} + run: | + pytest -v --cov=alchemtest --cov-report=xml --color=yes alchemtest/tests/ + + - name: CodeCov + uses: codecov/codecov-action@v3 + with: + token: ${{ secrets.CODECOV_TOKEN }} + name: codecov-${{ matrix.os }}-py${{ matrix.python-version }} + file: ./coverage.xml + flags: unittests + fail_ci_if_error: true pypi_check: name: Check source package integrity (for PyPi deployment) @@ -97,12 +86,12 @@ jobs: - name: Install tools run: | - python -m pip install setuptools twine - + python -m pip install twine build + - name: Build alchemtest source dist run: | - python setup.py sdist - + python -m build --sdist --wheel --outdir dist/ + - name: Check package build sdist run: | DISTRIBUTION=$(ls -t1 dist/alchemtest-*.tar.gz | head -n 1) diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index 530e53b..c0b9a3a 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -48,7 +48,7 @@ jobs: - name: build run: | python -m build --sdist --wheel --outdir dist/ - + - name: publish_testpypi # Upload to testpypi on every tag if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/') diff --git a/.gitignore b/.gitignore index 9d77bd3..6f1dfcd 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,111 @@ -docs/_build -src/alchemtest.egg-info -*__pycache__* -.idea -*.DS_Store -build +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +.pytest_cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# dotenv +.env + +# virtualenv +.venv +venv/ +ENV/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ + +# profraw files from LLVM? Unclear exactly what triggers this +# There are reports this comes from LLVM profiling, but also Xcode 9. +*profraw + +# In-tree generated files +*/_version.py +*/.DS_Store +*/.idea/ \ No newline at end of file diff --git a/.lgtm.yml b/.lgtm.yml new file mode 100644 index 0000000..014fb86 --- /dev/null +++ b/.lgtm.yml @@ -0,0 +1,11 @@ +# Configure LGTM for this package + +extraction: + python: # Configure Python + python_setup: # Configure the setup + version: 3 # Specify Version 3 +path_classifiers: + library: + - devtools/* + generated: + - alchemtest/_version.py diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..4842944 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,77 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, +body size, disability, ethnicity, gender identity and expression, level of +experience, nationality, personal appearance, race, religion, or sexual +identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +Moreover, project maintainers will strive to offer feedback and advice to +ensure quality and consistency of contributions to the code. Contributions +from outside the group of project maintainers are strongly welcomed but the +final decision as to whether commits are merged into the codebase rests with +the team of project maintainers. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an +appointed representative at an online or offline event. Representation of a +project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at 'william@zhiyiwu.me'. The project team will +review and investigate all complaints, and will respond in a way that it deems +appropriate to the circumstances. The project team is obligated to maintain +confidentiality with regard to the reporter of an incident. Further details of +specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 1.4, available at +[http://contributor-covenant.org/version/1/4][version] + +[homepage]: http://contributor-covenant.org +[version]: http://contributor-covenant.org/version/1/4/ diff --git a/LICENSE b/LICENSE index 7538305..227850c 100644 --- a/LICENSE +++ b/LICENSE @@ -24,5 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. \ No newline at end of file diff --git a/MANIFEST.in b/MANIFEST.in index 6c503f8..0435778 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,6 +1,6 @@ include *.rst -recursive-include src/alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out *.xvg *.npy +recursive-include alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out *.xvg *.npy include README.rst include LICENSE include versioneer.py -include src/alchemtest/_version.py +include alchemtest/_version.py diff --git a/README.rst b/README.rst index 9e5b974..7a31395 100644 --- a/README.rst +++ b/README.rst @@ -28,7 +28,7 @@ modification, separation, for any purpose and without a charge. :alt: Zenodo DOI :scale: 100% :target: https://zenodo.org/badge/latestdoi/83470847 - + .. |build| image:: https://github.com/alchemistry/alchemtest/actions/workflows/CI.yaml/badge.svg?branch=master :alt: Build Status :scale: 100% diff --git a/src/alchemtest/__init__.py b/alchemtest/__init__.py similarity index 93% rename from src/alchemtest/__init__.py rename to alchemtest/__init__.py index 9661e40..8c57fb2 100644 --- a/src/alchemtest/__init__.py +++ b/alchemtest/__init__.py @@ -1,7 +1,6 @@ +"""The simple alchemistry test set.""" -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions +from ._version import __version__ class Bunch(dict): """Container object for datasets diff --git a/src/alchemtest/amber/__init__.py b/alchemtest/amber/__init__.py similarity index 100% rename from src/alchemtest/amber/__init__.py rename to alchemtest/amber/__init__.py diff --git a/src/alchemtest/amber/access.py b/alchemtest/amber/access.py similarity index 100% rename from src/alchemtest/amber/access.py rename to alchemtest/amber/access.py diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.00/ti-0.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.00/ti-0.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.00/ti-0.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.00/ti-0.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.25/ti-0.25.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.25/ti-0.25.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.25/ti-0.25.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.25/ti-0.25.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.50/ti-0.50.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.50/ti-0.50.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.50/ti-0.50.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.50/ti-0.50.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.75/ti-0.75.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.75/ti-0.75.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.75/ti-0.75.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/0.75/ti-0.75.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/1.00/ti-1.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/1.00/ti-1.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/1.00/ti-1.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/decharge/1.00/ti-1.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.00/ti-0.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.00/ti-0.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.00/ti-0.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.00/ti-0.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.25/ti-0.25.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.25/ti-0.25.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.25/ti-0.25.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.25/ti-0.25.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.50/ti-0.50.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.50/ti-0.50.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.50/ti-0.50.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.50/ti-0.50.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.75/ti-0.75.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.75/ti-0.75.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.75/ti-0.75.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/0.75/ti-0.75.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/1.00/ti-1.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/1.00/ti-1.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/1.00/ti-1.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/recharge/1.00/ti-1.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0/ti-0.0.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0/ti-0.0.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0/ti-0.0.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0/ti-0.0.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0479/ti-0.0479.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0479/ti-0.0479.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0479/ti-0.0479.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.0479/ti-0.0479.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.1150/ti-0.1150.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.1150/ti-0.1150.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.1150/ti-0.1150.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.1150/ti-0.1150.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.2063/ti-0.2063.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.2063/ti-0.2063.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.2063/ti-0.2063.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.2063/ti-0.2063.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.3160/ti-0.3160.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.3160/ti-0.3160.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.3160/ti-0.3160.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.3160/ti-0.3160.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.4373/ti-0.4373.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.4373/ti-0.4373.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.4373/ti-0.4373.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.4373/ti-0.4373.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.5626/ti-0.5626.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.5626/ti-0.5626.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.5626/ti-0.5626.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.5626/ti-0.5626.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.6839/ti-0.6839.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.6839/ti-0.6839.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.6839/ti-0.6839.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.6839/ti-0.6839.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.7936/ti-0.7936.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.7936/ti-0.7936.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.7936/ti-0.7936.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.7936/ti-0.7936.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.8849/ti-0.8849.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.8849/ti-0.8849.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.8849/ti-0.8849.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.8849/ti-0.8849.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.9520/ti-0.9520.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.9520/ti-0.9520.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.9520/ti-0.9520.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/0.9520/ti-0.9520.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/1.0/ti-1.0.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/1.0/ti-1.0.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/1.0/ti-1.0.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/complex/vdw/1.0/ti-1.0.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst b/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst rename to alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.00/ti-0.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.00/ti-0.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.00/ti-0.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.00/ti-0.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.25/ti-0.25.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.25/ti-0.25.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.25/ti-0.25.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.25/ti-0.25.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.50/ti-0.50.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.50/ti-0.50.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.50/ti-0.50.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.50/ti-0.50.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.75/ti-0.75.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.75/ti-0.75.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.75/ti-0.75.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/0.75/ti-0.75.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/1.00/ti-1.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/1.00/ti-1.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/1.00/ti-1.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/decharge/1.00/ti-1.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.00/ti-0.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.00/ti-0.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.00/ti-0.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.00/ti-0.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.25/ti-0.25.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.25/ti-0.25.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.25/ti-0.25.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.25/ti-0.25.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.50/ti-0.50.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.50/ti-0.50.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.50/ti-0.50.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.50/ti-0.50.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.75/ti-0.75.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.75/ti-0.75.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.75/ti-0.75.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/0.75/ti-0.75.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/1.00/ti-1.00.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/1.00/ti-1.00.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/1.00/ti-1.00.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/recharge/1.00/ti-1.00.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0/ti-0.0.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0/ti-0.0.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0/ti-0.0.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0/ti-0.0.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0479/ti-0.0479.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0479/ti-0.0479.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0479/ti-0.0479.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.0479/ti-0.0479.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.1150/ti-0.1150.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.1150/ti-0.1150.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.1150/ti-0.1150.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.1150/ti-0.1150.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.2063/ti-0.2063.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.2063/ti-0.2063.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.2063/ti-0.2063.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.2063/ti-0.2063.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.3160/ti-0.3160.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.3160/ti-0.3160.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.3160/ti-0.3160.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.3160/ti-0.3160.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.4373/ti-0.4373.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.4373/ti-0.4373.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.4373/ti-0.4373.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.4373/ti-0.4373.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.5626/ti-0.5626.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.5626/ti-0.5626.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.5626/ti-0.5626.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.5626/ti-0.5626.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.6839/ti-0.6839.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.6839/ti-0.6839.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.6839/ti-0.6839.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.6839/ti-0.6839.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.7936/ti-0.7936.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.7936/ti-0.7936.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.7936/ti-0.7936.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.7936/ti-0.7936.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.8849/ti-0.8849.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.8849/ti-0.8849.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.8849/ti-0.8849.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.8849/ti-0.8849.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.9520/ti-0.9520.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.9520/ti-0.9520.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.9520/ti-0.9520.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/0.9520/ti-0.9520.out.bz2 diff --git a/src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/1.0/ti-1.0.out.bz2 b/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/1.0/ti-1.0.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/1.0/ti-1.0.out.bz2 rename to alchemtest/amber/bace_CAT-13d~CAT-17a/solvated/vdw/1.0/ti-1.0.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/descr.rst b/alchemtest/amber/bace_improper/descr.rst similarity index 100% rename from src/alchemtest/amber/bace_improper/descr.rst rename to alchemtest/amber/bace_improper/descr.rst diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.0/ti-0.0.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.0/ti-0.0.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.0/ti-0.0.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.0/ti-0.0.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.0479/ti-0.0479.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.0479/ti-0.0479.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.0479/ti-0.0479.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.0479/ti-0.0479.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.1150/ti-0.1150.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.1150/ti-0.1150.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.1150/ti-0.1150.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.1150/ti-0.1150.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.2063/ti-0.2063.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.2063/ti-0.2063.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.2063/ti-0.2063.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.2063/ti-0.2063.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.3160/ti-0.3160.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.3160/ti-0.3160.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.3160/ti-0.3160.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.3160/ti-0.3160.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.4373/ti-0.4373.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.4373/ti-0.4373.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.4373/ti-0.4373.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.4373/ti-0.4373.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.5626/ti-0.5626.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.5626/ti-0.5626.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.5626/ti-0.5626.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.5626/ti-0.5626.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.6839/ti-0.6839.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.6839/ti-0.6839.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.6839/ti-0.6839.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.6839/ti-0.6839.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.7936/ti-0.7936.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.7936/ti-0.7936.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.7936/ti-0.7936.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.7936/ti-0.7936.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.8849/ti-0.8849.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.8849/ti-0.8849.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.8849/ti-0.8849.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.8849/ti-0.8849.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/0.9520/ti-0.9520.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/0.9520/ti-0.9520.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/0.9520/ti-0.9520.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/0.9520/ti-0.9520.out.bz2 diff --git a/src/alchemtest/amber/bace_improper/solvated/vdw/1.0/ti-1.0.out.bz2 b/alchemtest/amber/bace_improper/solvated/vdw/1.0/ti-1.0.out.bz2 similarity index 100% rename from src/alchemtest/amber/bace_improper/solvated/vdw/1.0/ti-1.0.out.bz2 rename to alchemtest/amber/bace_improper/solvated/vdw/1.0/ti-1.0.out.bz2 diff --git a/src/alchemtest/amber/simplesolvated/charge/0.00/ti-0.00.out.tar.bz2 b/alchemtest/amber/simplesolvated/charge/0.00/ti-0.00.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/charge/0.00/ti-0.00.out.tar.bz2 rename to alchemtest/amber/simplesolvated/charge/0.00/ti-0.00.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/charge/0.25/ti-0.25.out.tar.bz2 b/alchemtest/amber/simplesolvated/charge/0.25/ti-0.25.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/charge/0.25/ti-0.25.out.tar.bz2 rename to alchemtest/amber/simplesolvated/charge/0.25/ti-0.25.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/charge/0.50/ti-0.50.out.tar.bz2 b/alchemtest/amber/simplesolvated/charge/0.50/ti-0.50.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/charge/0.50/ti-0.50.out.tar.bz2 rename to alchemtest/amber/simplesolvated/charge/0.50/ti-0.50.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/charge/0.75/ti-0.75.out.tar.bz2 b/alchemtest/amber/simplesolvated/charge/0.75/ti-0.75.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/charge/0.75/ti-0.75.out.tar.bz2 rename to alchemtest/amber/simplesolvated/charge/0.75/ti-0.75.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/charge/1.00/ti-1.00.out.tar.bz2 b/alchemtest/amber/simplesolvated/charge/1.00/ti-1.00.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/charge/1.00/ti-1.00.out.tar.bz2 rename to alchemtest/amber/simplesolvated/charge/1.00/ti-1.00.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/descr.rst b/alchemtest/amber/simplesolvated/descr.rst similarity index 100% rename from src/alchemtest/amber/simplesolvated/descr.rst rename to alchemtest/amber/simplesolvated/descr.rst diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.0/ti-0.0.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.0/ti-0.0.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.0/ti-0.0.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.0/ti-0.0.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.04794/ti-0.04794.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.04794/ti-0.04794.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.04794/ti-0.04794.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.04794/ti-0.04794.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.11505/ti-0.11505.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.11505/ti-0.11505.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.11505/ti-0.11505.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.11505/ti-0.11505.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.20634/ti-0.20634.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.20634/ti-0.20634.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.20634/ti-0.20634.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.20634/ti-0.20634.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.31608/ti-0.31608.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.31608/ti-0.31608.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.31608/ti-0.31608.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.31608/ti-0.31608.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.43738/ti-0.43738.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.43738/ti-0.43738.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.43738/ti-0.43738.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.43738/ti-0.43738.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.56262/ti-0.56262.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.56262/ti-0.56262.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.56262/ti-0.56262.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.56262/ti-0.56262.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.68392/ti-0.68392.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.68392/ti-0.68392.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.68392/ti-0.68392.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.68392/ti-0.68392.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.79366/ti-0.79366.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.79366/ti-0.79366.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.79366/ti-0.79366.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.79366/ti-0.79366.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.88495/ti-0.88495.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.88495/ti-0.88495.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.88495/ti-0.88495.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.88495/ti-0.88495.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/0.95206/ti-0.95206.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/0.95206/ti-0.95206.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/0.95206/ti-0.95206.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/0.95206/ti-0.95206.out.tar.bz2 diff --git a/src/alchemtest/amber/simplesolvated/vdw/1.0/ti-1.0.out.tar.bz2 b/alchemtest/amber/simplesolvated/vdw/1.0/ti-1.0.out.tar.bz2 similarity index 100% rename from src/alchemtest/amber/simplesolvated/vdw/1.0/ti-1.0.out.tar.bz2 rename to alchemtest/amber/simplesolvated/vdw/1.0/ti-1.0.out.tar.bz2 diff --git a/src/alchemtest/amber/testfiles/descr.rst b/alchemtest/amber/testfiles/descr.rst similarity index 100% rename from src/alchemtest/amber/testfiles/descr.rst rename to alchemtest/amber/testfiles/descr.rst diff --git a/src/alchemtest/amber/testfiles/descr_invalid.rst b/alchemtest/amber/testfiles/descr_invalid.rst similarity index 100% rename from src/alchemtest/amber/testfiles/descr_invalid.rst rename to alchemtest/amber/testfiles/descr_invalid.rst diff --git a/src/alchemtest/amber/testfiles/high_and_wrong_number_of_mbar_windows.out.bz2 b/alchemtest/amber/testfiles/high_and_wrong_number_of_mbar_windows.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/high_and_wrong_number_of_mbar_windows.out.bz2 rename to alchemtest/amber/testfiles/high_and_wrong_number_of_mbar_windows.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_atomic_section.out.bz2 b/alchemtest/amber/testfiles/no_atomic_section.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_atomic_section.out.bz2 rename to alchemtest/amber/testfiles/no_atomic_section.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_control_data.out.bz2 b/alchemtest/amber/testfiles/no_control_data.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_control_data.out.bz2 rename to alchemtest/amber/testfiles/no_control_data.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_dHdl_data_points.out.bz2 b/alchemtest/amber/testfiles/no_dHdl_data_points.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_dHdl_data_points.out.bz2 rename to alchemtest/amber/testfiles/no_dHdl_data_points.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_free_energy_info.out.bz2 b/alchemtest/amber/testfiles/no_free_energy_info.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_free_energy_info.out.bz2 rename to alchemtest/amber/testfiles/no_free_energy_info.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_results_section.out.bz2 b/alchemtest/amber/testfiles/no_results_section.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_results_section.out.bz2 rename to alchemtest/amber/testfiles/no_results_section.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_spaces_around_equal.out.bz2 b/alchemtest/amber/testfiles/no_spaces_around_equal.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_spaces_around_equal.out.bz2 rename to alchemtest/amber/testfiles/no_spaces_around_equal.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_starting_simulation_time.out.bz2 b/alchemtest/amber/testfiles/no_starting_simulation_time.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_starting_simulation_time.out.bz2 rename to alchemtest/amber/testfiles/no_starting_simulation_time.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_temp0_set.out.bz2 b/alchemtest/amber/testfiles/no_temp0_set.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_temp0_set.out.bz2 rename to alchemtest/amber/testfiles/no_temp0_set.out.bz2 diff --git a/src/alchemtest/amber/testfiles/no_useful_data.out.bz2 b/alchemtest/amber/testfiles/no_useful_data.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/no_useful_data.out.bz2 rename to alchemtest/amber/testfiles/no_useful_data.out.bz2 diff --git a/src/alchemtest/amber/testfiles/none_in_mbar.out.bz2 b/alchemtest/amber/testfiles/none_in_mbar.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/none_in_mbar.out.bz2 rename to alchemtest/amber/testfiles/none_in_mbar.out.bz2 diff --git a/src/alchemtest/amber/testfiles/not_finished_run.out.bz2 b/alchemtest/amber/testfiles/not_finished_run.out.bz2 similarity index 100% rename from src/alchemtest/amber/testfiles/not_finished_run.out.bz2 rename to alchemtest/amber/testfiles/not_finished_run.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.00922/ti-0.00922.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.00922/ti-0.00922.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.00922/ti-0.00922.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.00922/ti-0.00922.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.04794/ti-0.04794.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.04794/ti-0.04794.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.04794/ti-0.04794.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.04794/ti-0.04794.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.11505/ti-0.11505.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.11505/ti-0.11505.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.11505/ti-0.11505.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.11505/ti-0.11505.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.20634/ti-0.20634.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.20634/ti-0.20634.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.20634/ti-0.20634.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.20634/ti-0.20634.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.31608/ti-0.31608.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.31608/ti-0.31608.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.31608/ti-0.31608.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.31608/ti-0.31608.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.43738/ti-0.43738.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.43738/ti-0.43738.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.43738/ti-0.43738.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.43738/ti-0.43738.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.56262/ti-0.56262.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.56262/ti-0.56262.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.56262/ti-0.56262.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.56262/ti-0.56262.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.68392/ti-0.68392.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.68392/ti-0.68392.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.68392/ti-0.68392.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.68392/ti-0.68392.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.79366/ti-0.79366.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.79366/ti-0.79366.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.79366/ti-0.79366.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.79366/ti-0.79366.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.88495/ti-0.88495.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.88495/ti-0.88495.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.88495/ti-0.88495.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.88495/ti-0.88495.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.95206/ti-0.95206.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.95206/ti-0.95206.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.95206/ti-0.95206.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.95206/ti-0.95206.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.99078/ti-0.99078.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.99078/ti-0.99078.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.99078/ti-0.99078.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/complex/0.99078/ti-0.99078.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst b/alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst rename to alchemtest/amber/tyk2_ejm_47~ejm_31/descr.rst diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.00922/ti-0.00922.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.00922/ti-0.00922.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.00922/ti-0.00922.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.00922/ti-0.00922.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.04794/ti-0.04794.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.04794/ti-0.04794.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.04794/ti-0.04794.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.04794/ti-0.04794.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.11505/ti-0.11505.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.11505/ti-0.11505.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.11505/ti-0.11505.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.11505/ti-0.11505.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.20634/ti-0.20634.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.20634/ti-0.20634.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.20634/ti-0.20634.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.20634/ti-0.20634.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.31608/ti-0.31608.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.31608/ti-0.31608.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.31608/ti-0.31608.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.31608/ti-0.31608.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.43738/ti-0.43738.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.43738/ti-0.43738.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.43738/ti-0.43738.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.43738/ti-0.43738.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.56262/ti-0.56262.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.56262/ti-0.56262.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.56262/ti-0.56262.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.56262/ti-0.56262.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.68392/ti-0.68392.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.68392/ti-0.68392.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.68392/ti-0.68392.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.68392/ti-0.68392.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.79366/ti-0.79366.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.79366/ti-0.79366.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.79366/ti-0.79366.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.79366/ti-0.79366.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.88495/ti-0.88495.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.88495/ti-0.88495.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.88495/ti-0.88495.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.88495/ti-0.88495.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.95206/ti-0.95206.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.95206/ti-0.95206.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.95206/ti-0.95206.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.95206/ti-0.95206.out.bz2 diff --git a/src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.99078/ti-0.99078.out.bz2 b/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.99078/ti-0.99078.out.bz2 similarity index 100% rename from src/alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.99078/ti-0.99078.out.bz2 rename to alchemtest/amber/tyk2_ejm_47~ejm_31/solvated/0.99078/ti-0.99078.out.bz2 diff --git a/src/alchemtest/generic/BFGS/N_k.npy b/alchemtest/generic/BFGS/N_k.npy similarity index 100% rename from src/alchemtest/generic/BFGS/N_k.npy rename to alchemtest/generic/BFGS/N_k.npy diff --git a/src/alchemtest/generic/BFGS/descr.rst b/alchemtest/generic/BFGS/descr.rst similarity index 100% rename from src/alchemtest/generic/BFGS/descr.rst rename to alchemtest/generic/BFGS/descr.rst diff --git a/src/alchemtest/generic/BFGS/u_nk.npy b/alchemtest/generic/BFGS/u_nk.npy similarity index 100% rename from src/alchemtest/generic/BFGS/u_nk.npy rename to alchemtest/generic/BFGS/u_nk.npy diff --git a/src/alchemtest/generic/__init__.py b/alchemtest/generic/__init__.py similarity index 100% rename from src/alchemtest/generic/__init__.py rename to alchemtest/generic/__init__.py diff --git a/src/alchemtest/generic/access.py b/alchemtest/generic/access.py similarity index 100% rename from src/alchemtest/generic/access.py rename to alchemtest/generic/access.py diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_00.xvg b/alchemtest/gmx/ABFE/complex/dhdl_00.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_00.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_00.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_01.xvg b/alchemtest/gmx/ABFE/complex/dhdl_01.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_01.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_01.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_02.xvg b/alchemtest/gmx/ABFE/complex/dhdl_02.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_02.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_02.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_03.xvg b/alchemtest/gmx/ABFE/complex/dhdl_03.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_03.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_03.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_04.xvg b/alchemtest/gmx/ABFE/complex/dhdl_04.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_04.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_04.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_05.xvg b/alchemtest/gmx/ABFE/complex/dhdl_05.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_05.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_05.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_06.xvg b/alchemtest/gmx/ABFE/complex/dhdl_06.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_06.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_06.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_07.xvg b/alchemtest/gmx/ABFE/complex/dhdl_07.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_07.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_07.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_08.xvg b/alchemtest/gmx/ABFE/complex/dhdl_08.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_08.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_08.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_09.xvg b/alchemtest/gmx/ABFE/complex/dhdl_09.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_09.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_09.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_10.xvg b/alchemtest/gmx/ABFE/complex/dhdl_10.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_10.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_10.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_11.xvg b/alchemtest/gmx/ABFE/complex/dhdl_11.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_11.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_11.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_12.xvg b/alchemtest/gmx/ABFE/complex/dhdl_12.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_12.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_12.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_13.xvg b/alchemtest/gmx/ABFE/complex/dhdl_13.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_13.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_13.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_14.xvg b/alchemtest/gmx/ABFE/complex/dhdl_14.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_14.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_14.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_15.xvg b/alchemtest/gmx/ABFE/complex/dhdl_15.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_15.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_15.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_16.xvg b/alchemtest/gmx/ABFE/complex/dhdl_16.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_16.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_16.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_17.xvg b/alchemtest/gmx/ABFE/complex/dhdl_17.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_17.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_17.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_18.xvg b/alchemtest/gmx/ABFE/complex/dhdl_18.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_18.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_18.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_19.xvg b/alchemtest/gmx/ABFE/complex/dhdl_19.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_19.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_19.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_20.xvg b/alchemtest/gmx/ABFE/complex/dhdl_20.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_20.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_20.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_21.xvg b/alchemtest/gmx/ABFE/complex/dhdl_21.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_21.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_21.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_22.xvg b/alchemtest/gmx/ABFE/complex/dhdl_22.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_22.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_22.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_23.xvg b/alchemtest/gmx/ABFE/complex/dhdl_23.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_23.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_23.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_24.xvg b/alchemtest/gmx/ABFE/complex/dhdl_24.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_24.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_24.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_25.xvg b/alchemtest/gmx/ABFE/complex/dhdl_25.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_25.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_25.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_26.xvg b/alchemtest/gmx/ABFE/complex/dhdl_26.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_26.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_26.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_27.xvg b/alchemtest/gmx/ABFE/complex/dhdl_27.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_27.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_27.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_28.xvg b/alchemtest/gmx/ABFE/complex/dhdl_28.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_28.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_28.xvg diff --git a/src/alchemtest/gmx/ABFE/complex/dhdl_29.xvg b/alchemtest/gmx/ABFE/complex/dhdl_29.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/complex/dhdl_29.xvg rename to alchemtest/gmx/ABFE/complex/dhdl_29.xvg diff --git a/src/alchemtest/gmx/ABFE/descr.rst b/alchemtest/gmx/ABFE/descr.rst similarity index 100% rename from src/alchemtest/gmx/ABFE/descr.rst rename to alchemtest/gmx/ABFE/descr.rst diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_00.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_00.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_00.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_00.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_01.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_01.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_01.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_01.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_02.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_02.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_02.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_02.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_03.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_03.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_03.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_03.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_04.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_04.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_04.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_04.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_05.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_05.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_05.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_05.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_06.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_06.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_06.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_06.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_07.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_07.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_07.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_07.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_08.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_08.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_08.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_08.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_09.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_09.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_09.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_09.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_10.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_10.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_10.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_10.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_11.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_11.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_11.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_11.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_12.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_12.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_12.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_12.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_13.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_13.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_13.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_13.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_14.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_14.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_14.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_14.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_15.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_15.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_15.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_15.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_16.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_16.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_16.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_16.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_17.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_17.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_17.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_17.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_18.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_18.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_18.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_18.xvg diff --git a/src/alchemtest/gmx/ABFE/ligand/dhdl_19.xvg b/alchemtest/gmx/ABFE/ligand/dhdl_19.xvg similarity index 100% rename from src/alchemtest/gmx/ABFE/ligand/dhdl_19.xvg rename to alchemtest/gmx/ABFE/ligand/dhdl_19.xvg diff --git a/src/alchemtest/gmx/__init__.py b/alchemtest/gmx/__init__.py similarity index 100% rename from src/alchemtest/gmx/__init__.py rename to alchemtest/gmx/__init__.py diff --git a/src/alchemtest/gmx/access.py b/alchemtest/gmx/access.py similarity index 100% rename from src/alchemtest/gmx/access.py rename to alchemtest/gmx/access.py diff --git a/src/alchemtest/gmx/benzene/Coulomb/0000/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/Coulomb/0000/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/Coulomb/0000/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/Coulomb/0000/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/Coulomb/0250/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/Coulomb/0250/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/Coulomb/0250/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/Coulomb/0250/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/Coulomb/0500/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/Coulomb/0500/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/Coulomb/0500/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/Coulomb/0500/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/Coulomb/0750/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/Coulomb/0750/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/Coulomb/0750/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/Coulomb/0750/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/Coulomb/1000/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/Coulomb/1000/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/Coulomb/1000/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/Coulomb/1000/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0000/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0000/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0000/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0000/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0050/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0050/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0050/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0050/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0100/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0100/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0100/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0100/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0200/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0200/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0200/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0200/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0300/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0300/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0300/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0300/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0400/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0400/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0400/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0400/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0500/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0500/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0500/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0500/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0600/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0600/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0600/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0600/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0650/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0650/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0650/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0650/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0700/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0700/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0700/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0700/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0750/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0750/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0750/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0750/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0800/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0800/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0800/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0800/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0850/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0850/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0850/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0850/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0900/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0900/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0900/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0900/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/0950/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/0950/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/0950/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/0950/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/VDW/1000/dhdl.xvg.bz2 b/alchemtest/gmx/benzene/VDW/1000/dhdl.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/benzene/VDW/1000/dhdl.xvg.bz2 rename to alchemtest/gmx/benzene/VDW/1000/dhdl.xvg.bz2 diff --git a/src/alchemtest/gmx/benzene/descr.rst b/alchemtest/gmx/benzene/descr.rst similarity index 100% rename from src/alchemtest/gmx/benzene/descr.rst rename to alchemtest/gmx/benzene/descr.rst diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.0.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.0.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.0.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.0.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.1.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.1.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.1.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.1.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.10.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.10.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.10.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.10.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.11.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.11.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.11.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.11.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.12.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.12.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.12.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.12.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.13.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.13.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.13.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.13.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.2.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.2.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.2.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.2.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.3.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.3.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.3.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.3.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.4.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.4.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.4.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.4.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.5.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.5.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.5.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.5.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.6.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.6.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.6.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.6.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.7.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.7.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.7.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.7.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.8.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.8.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.8.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.8.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/Coulomb/dhdl.9.xvg.bz2 b/alchemtest/gmx/ethanol/Coulomb/dhdl.9.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/Coulomb/dhdl.9.xvg.bz2 rename to alchemtest/gmx/ethanol/Coulomb/dhdl.9.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.1.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.1.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.1.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.1.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.10.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.10.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.10.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.10.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.11.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.11.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.11.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.11.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.12.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.12.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.12.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.12.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.13.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.13.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.13.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.13.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.2.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.2.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.2.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.2.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.3.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.3.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.3.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.3.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.4.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.4.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.4.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.4.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.5.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.5.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.5.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.5.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.6.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.6.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.6.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.6.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.7.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.7.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.7.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.7.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.8.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.8.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.8.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.8.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/VDW/dhdl.9.xvg.bz2 b/alchemtest/gmx/ethanol/VDW/dhdl.9.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/ethanol/VDW/dhdl.9.xvg.bz2 rename to alchemtest/gmx/ethanol/VDW/dhdl.9.xvg.bz2 diff --git a/src/alchemtest/gmx/ethanol/descr.rst b/alchemtest/gmx/ethanol/descr.rst similarity index 100% rename from src/alchemtest/gmx/ethanol/descr.rst rename to alchemtest/gmx/ethanol/descr.rst diff --git a/src/alchemtest/gmx/expanded_ensemble/case_1/CB7_Guest3_dhdl.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_1/CB7_Guest3_dhdl.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_1/CB7_Guest3_dhdl.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_1/CB7_Guest3_dhdl.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst b/alchemtest/gmx/expanded_ensemble/case_1/descr.rst similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst rename to alchemtest/gmx/expanded_ensemble/case_1/descr.rst diff --git a/src/alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_1.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_1.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_1.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_1.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_2.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_2.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_2.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_2/CB7_Guest3_dhdl_2.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst b/alchemtest/gmx/expanded_ensemble/case_2/descr.rst similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst rename to alchemtest/gmx/expanded_ensemble/case_2/descr.rst diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_00.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_00.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_00.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_00.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_01.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_01.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_01.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_01.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_02.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_02.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_02.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_02.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_03.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_03.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_03.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_03.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_04.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_04.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_04.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_04.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_05.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_05.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_05.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_05.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_06.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_06.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_06.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_06.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_07.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_07.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_07.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_07.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_08.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_08.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_08.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_08.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_09.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_09.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_09.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_09.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_10.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_10.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_10.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_10.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_11.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_11.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_11.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_11.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_12.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_12.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_12.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_12.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_13.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_13.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_13.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_13.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_14.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_14.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_14.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_14.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_15.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_15.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_15.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_15.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_16.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_16.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_16.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_16.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_17.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_17.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_17.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_17.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_18.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_18.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_18.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_18.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_19.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_19.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_19.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_19.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_20.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_20.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_20.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_20.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_21.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_21.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_21.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_21.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_22.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_22.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_22.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_22.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_23.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_23.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_23.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_23.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_24.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_24.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_24.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_24.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_25.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_25.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_25.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_25.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_26.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_26.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_26.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_26.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_27.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_27.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_27.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_27.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_28.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_28.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_28.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_28.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_29.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_29.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_29.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_29.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_30.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_30.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_30.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_30.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_31.xvg.gz b/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_31.xvg.gz similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_31.xvg.gz rename to alchemtest/gmx/expanded_ensemble/case_3/CB7_Guest3_dhdl_31.xvg.gz diff --git a/src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst b/alchemtest/gmx/expanded_ensemble/case_3/descr.rst similarity index 100% rename from src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst rename to alchemtest/gmx/expanded_ensemble/case_3/descr.rst diff --git a/src/alchemtest/gmx/water_particle/descr.rst b/alchemtest/gmx/water_particle/descr.rst similarity index 100% rename from src/alchemtest/gmx/water_particle/descr.rst rename to alchemtest/gmx/water_particle/descr.rst diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_0.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_0.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_0.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_0.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_1.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_1.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_1.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_1.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_10.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_10.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_10.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_10.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_11.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_11.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_11.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_11.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_12.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_12.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_12.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_12.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_13.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_13.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_13.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_13.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_14.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_14.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_14.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_14.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_15.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_15.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_15.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_15.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_16.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_16.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_16.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_16.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_17.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_17.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_17.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_17.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_18.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_18.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_18.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_18.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_19.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_19.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_19.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_19.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_2.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_2.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_2.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_2.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_20.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_20.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_20.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_20.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_21.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_21.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_21.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_21.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_22.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_22.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_22.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_22.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_23.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_23.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_23.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_23.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_24.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_24.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_24.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_24.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_25.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_25.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_25.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_25.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_26.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_26.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_26.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_26.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_27.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_27.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_27.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_27.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_28.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_28.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_28.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_28.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_29.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_29.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_29.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_29.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_3.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_3.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_3.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_3.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_30.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_30.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_30.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_30.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_31.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_31.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_31.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_31.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_32.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_32.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_32.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_32.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_33.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_33.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_33.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_33.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_34.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_34.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_34.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_34.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_35.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_35.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_35.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_35.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_36.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_36.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_36.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_36.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_37.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_37.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_37.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_37.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_4.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_4.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_4.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_4.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_5.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_5.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_5.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_5.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_6.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_6.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_6.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_6.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_7.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_7.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_7.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_7.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_8.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_8.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_8.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_8.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_potential_energy/lambda_9.xvg.bz2 b/alchemtest/gmx/water_particle/with_potential_energy/lambda_9.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_potential_energy/lambda_9.xvg.bz2 rename to alchemtest/gmx/water_particle/with_potential_energy/lambda_9.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_0.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_0.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_0.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_0.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_1.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_1.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_1.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_1.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_10.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_10.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_10.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_10.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_11.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_11.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_11.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_11.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_12.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_12.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_12.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_12.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_13.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_13.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_13.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_13.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_14.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_14.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_14.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_14.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_15.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_15.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_15.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_15.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_16.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_16.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_16.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_16.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_17.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_17.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_17.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_17.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_18.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_18.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_18.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_18.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_19.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_19.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_19.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_19.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_2.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_2.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_2.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_2.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_20.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_20.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_20.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_20.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_21.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_21.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_21.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_21.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_22.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_22.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_22.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_22.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_23.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_23.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_23.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_23.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_24.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_24.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_24.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_24.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_25.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_25.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_25.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_25.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_26.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_26.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_26.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_26.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_27.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_27.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_27.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_27.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_28.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_28.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_28.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_28.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_29.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_29.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_29.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_29.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_3.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_3.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_3.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_3.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_30.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_30.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_30.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_30.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_31.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_31.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_31.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_31.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_32.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_32.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_32.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_32.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_33.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_33.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_33.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_33.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_34.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_34.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_34.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_34.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_35.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_35.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_35.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_35.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_36.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_36.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_36.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_36.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_37.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_37.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_37.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_37.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_4.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_4.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_4.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_4.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_5.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_5.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_5.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_5.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_6.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_6.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_6.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_6.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_7.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_7.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_7.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_7.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_8.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_8.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_8.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_8.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/with_total_energy/lambda_9.xvg.bz2 b/alchemtest/gmx/water_particle/with_total_energy/lambda_9.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/with_total_energy/lambda_9.xvg.bz2 rename to alchemtest/gmx/water_particle/with_total_energy/lambda_9.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_0.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_0.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_0.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_0.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_1.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_1.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_1.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_1.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_10.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_10.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_10.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_10.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_11.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_11.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_11.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_11.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_12.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_12.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_12.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_12.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_13.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_13.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_13.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_13.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_14.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_14.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_14.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_14.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_15.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_15.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_15.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_15.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_16.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_16.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_16.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_16.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_17.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_17.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_17.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_17.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_18.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_18.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_18.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_18.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_19.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_19.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_19.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_19.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_2.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_2.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_2.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_2.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_20.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_20.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_20.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_20.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_21.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_21.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_21.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_21.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_22.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_22.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_22.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_22.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_23.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_23.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_23.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_23.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_24.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_24.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_24.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_24.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_25.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_25.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_25.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_25.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_26.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_26.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_26.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_26.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_27.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_27.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_27.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_27.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_28.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_28.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_28.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_28.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_29.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_29.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_29.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_29.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_3.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_3.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_3.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_3.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_30.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_30.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_30.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_30.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_31.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_31.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_31.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_31.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_32.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_32.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_32.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_32.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_33.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_33.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_33.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_33.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_34.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_34.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_34.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_34.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_35.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_35.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_35.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_35.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_36.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_36.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_36.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_36.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_37.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_37.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_37.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_37.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_4.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_4.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_4.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_4.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_5.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_5.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_5.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_5.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_6.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_6.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_6.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_6.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_7.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_7.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_7.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_7.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_8.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_8.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_8.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_8.xvg.bz2 diff --git a/src/alchemtest/gmx/water_particle/without_energy/lambda_9.xvg.bz2 b/alchemtest/gmx/water_particle/without_energy/lambda_9.xvg.bz2 similarity index 100% rename from src/alchemtest/gmx/water_particle/without_energy/lambda_9.xvg.bz2 rename to alchemtest/gmx/water_particle/without_energy/lambda_9.xvg.bz2 diff --git a/src/alchemtest/gomc/__init__.py b/alchemtest/gomc/__init__.py similarity index 100% rename from src/alchemtest/gomc/__init__.py rename to alchemtest/gomc/__init__.py diff --git a/src/alchemtest/gomc/access.py b/alchemtest/gomc/access.py similarity index 100% rename from src/alchemtest/gomc/access.py rename to alchemtest/gomc/access.py diff --git a/src/alchemtest/gomc/benzene/descr.rst b/alchemtest/gomc/benzene/descr.rst similarity index 100% rename from src/alchemtest/gomc/benzene/descr.rst rename to alchemtest/gomc/benzene/descr.rst diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_00.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_00.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_00.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_00.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_01.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_01.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_01.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_01.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_02.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_02.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_02.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_02.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_03.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_03.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_03.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_03.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_04.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_04.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_04.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_04.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_05.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_05.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_05.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_05.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_06.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_06.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_06.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_06.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_07.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_07.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_07.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_07.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_08.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_08.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_08.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_08.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_09.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_09.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_09.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_09.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_10.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_10.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_10.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_10.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_11.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_11.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_11.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_11.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_12.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_12.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_12.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_12.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_13.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_13.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_13.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_13.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_14.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_14.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_14.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_14.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_15.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_15.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_15.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_15.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_16.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_16.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_16.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_16.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_17.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_17.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_17.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_17.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_18.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_18.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_18.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_18.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_19.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_19.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_19.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_19.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_20.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_20.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_20.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_20.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_21.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_21.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_21.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_21.dat.bz2 diff --git a/src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_22.dat.bz2 b/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_22.dat.bz2 similarity index 100% rename from src/alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_22.dat.bz2 rename to alchemtest/gomc/benzene/inWater/Free_Energy_BOX_0_PRODUCTION_22.dat.bz2 diff --git a/src/alchemtest/namd/__init__.py b/alchemtest/namd/__init__.py similarity index 100% rename from src/alchemtest/namd/__init__.py rename to alchemtest/namd/__init__.py diff --git a/src/alchemtest/namd/access.py b/alchemtest/namd/access.py similarity index 100% rename from src/alchemtest/namd/access.py rename to alchemtest/namd/access.py diff --git a/src/alchemtest/namd/idws/descr.rst b/alchemtest/namd/idws/descr.rst similarity index 100% rename from src/alchemtest/namd/idws/descr.rst rename to alchemtest/namd/idws/descr.rst diff --git a/src/alchemtest/namd/idws/idws1.fepout.bz2 b/alchemtest/namd/idws/idws1.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/idws/idws1.fepout.bz2 rename to alchemtest/namd/idws/idws1.fepout.bz2 diff --git a/src/alchemtest/namd/idws/idws2.fepout.bz2 b/alchemtest/namd/idws/idws2.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/idws/idws2.fepout.bz2 rename to alchemtest/namd/idws/idws2.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/descr.rst b/alchemtest/namd/restarted/descr.rst similarity index 100% rename from src/alchemtest/namd/restarted/descr.rst rename to alchemtest/namd/restarted/descr.rst diff --git a/src/alchemtest/namd/restarted/restarted000.fepout.bz2 b/alchemtest/namd/restarted/restarted000.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted000.fepout.bz2 rename to alchemtest/namd/restarted/restarted000.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted000a.fepout.bz2 b/alchemtest/namd/restarted/restarted000a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted000a.fepout.bz2 rename to alchemtest/namd/restarted/restarted000a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted000b.fepout.bz2 b/alchemtest/namd/restarted/restarted000b.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted000b.fepout.bz2 rename to alchemtest/namd/restarted/restarted000b.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted001.fepout.bz2 b/alchemtest/namd/restarted/restarted001.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted001.fepout.bz2 rename to alchemtest/namd/restarted/restarted001.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted002.fepout.bz2 b/alchemtest/namd/restarted/restarted002.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted002.fepout.bz2 rename to alchemtest/namd/restarted/restarted002.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted002a.fepout.bz2 b/alchemtest/namd/restarted/restarted002a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted002a.fepout.bz2 rename to alchemtest/namd/restarted/restarted002a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted003.fepout.bz2 b/alchemtest/namd/restarted/restarted003.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted003.fepout.bz2 rename to alchemtest/namd/restarted/restarted003.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted003a.fepout.bz2 b/alchemtest/namd/restarted/restarted003a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted003a.fepout.bz2 rename to alchemtest/namd/restarted/restarted003a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted004.fepout.bz2 b/alchemtest/namd/restarted/restarted004.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted004.fepout.bz2 rename to alchemtest/namd/restarted/restarted004.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted005.fepout.bz2 b/alchemtest/namd/restarted/restarted005.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted005.fepout.bz2 rename to alchemtest/namd/restarted/restarted005.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted006.fepout.bz2 b/alchemtest/namd/restarted/restarted006.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted006.fepout.bz2 rename to alchemtest/namd/restarted/restarted006.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted007.fepout.bz2 b/alchemtest/namd/restarted/restarted007.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted007.fepout.bz2 rename to alchemtest/namd/restarted/restarted007.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted008.fepout.bz2 b/alchemtest/namd/restarted/restarted008.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted008.fepout.bz2 rename to alchemtest/namd/restarted/restarted008.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted009.fepout.bz2 b/alchemtest/namd/restarted/restarted009.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted009.fepout.bz2 rename to alchemtest/namd/restarted/restarted009.fepout.bz2 diff --git a/src/alchemtest/namd/restarted/restarted010.fepout.bz2 b/alchemtest/namd/restarted/restarted010.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted/restarted010.fepout.bz2 rename to alchemtest/namd/restarted/restarted010.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/descr.rst b/alchemtest/namd/restarted_reversed/descr.rst similarity index 100% rename from src/alchemtest/namd/restarted_reversed/descr.rst rename to alchemtest/namd/restarted_reversed/descr.rst diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed000.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed000.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed000.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed000.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed001.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed001.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed001.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed001.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed001a.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed001a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed001a.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed001a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed001b.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed001b.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed001b.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed001b.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed002.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed002.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed002.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed002.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed002a.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed002a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed002a.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed002a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed002b.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed002b.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed002b.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed002b.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed002c.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed002c.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed002c.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed002c.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed003.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed003.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed003.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed003.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed004.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed004.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed004.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed004.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed005.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed005.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed005.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed005.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed005a.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed005a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed005a.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed005a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed005b.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed005b.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed005b.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed005b.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed006.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed006.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed006.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed006.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed007.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed007.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed007.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed007.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed007a.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed007a.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed007a.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed007a.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed008.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed008.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed008.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed008.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed009.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed009.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed009.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed009.fepout.bz2 diff --git a/src/alchemtest/namd/restarted_reversed/restarted_reversed010.fepout.bz2 b/alchemtest/namd/restarted_reversed/restarted_reversed010.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/restarted_reversed/restarted_reversed010.fepout.bz2 rename to alchemtest/namd/restarted_reversed/restarted_reversed010.fepout.bz2 diff --git a/src/alchemtest/namd/tyr2ala/descr.rst b/alchemtest/namd/tyr2ala/descr.rst similarity index 100% rename from src/alchemtest/namd/tyr2ala/descr.rst rename to alchemtest/namd/tyr2ala/descr.rst diff --git a/src/alchemtest/namd/tyr2ala/in-aqua/backward/backward-on.fepout.bz2 b/alchemtest/namd/tyr2ala/in-aqua/backward/backward-on.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/tyr2ala/in-aqua/backward/backward-on.fepout.bz2 rename to alchemtest/namd/tyr2ala/in-aqua/backward/backward-on.fepout.bz2 diff --git a/src/alchemtest/namd/tyr2ala/in-aqua/forward/forward-on.fepout.bz2 b/alchemtest/namd/tyr2ala/in-aqua/forward/forward-on.fepout.bz2 similarity index 100% rename from src/alchemtest/namd/tyr2ala/in-aqua/forward/forward-on.fepout.bz2 rename to alchemtest/namd/tyr2ala/in-aqua/forward/forward-on.fepout.bz2 diff --git a/alchemtest/py.typed b/alchemtest/py.typed new file mode 100644 index 0000000..6e3cdd2 --- /dev/null +++ b/alchemtest/py.typed @@ -0,0 +1 @@ +# PEP 561 marker file. See https://peps.python.org/pep-0561/ diff --git a/src/alchemtest/tests/__init__.py b/alchemtest/tests/__init__.py similarity index 100% rename from src/alchemtest/tests/__init__.py rename to alchemtest/tests/__init__.py diff --git a/src/alchemtest/tests/test_amber.py b/alchemtest/tests/test_amber.py similarity index 100% rename from src/alchemtest/tests/test_amber.py rename to alchemtest/tests/test_amber.py diff --git a/src/alchemtest/tests/test_generic.py b/alchemtest/tests/test_generic.py similarity index 100% rename from src/alchemtest/tests/test_generic.py rename to alchemtest/tests/test_generic.py diff --git a/src/alchemtest/tests/test_gmx.py b/alchemtest/tests/test_gmx.py similarity index 100% rename from src/alchemtest/tests/test_gmx.py rename to alchemtest/tests/test_gmx.py diff --git a/src/alchemtest/tests/test_gomc.py b/alchemtest/tests/test_gomc.py similarity index 100% rename from src/alchemtest/tests/test_gomc.py rename to alchemtest/tests/test_gomc.py diff --git a/src/alchemtest/tests/test_namd.py b/alchemtest/tests/test_namd.py similarity index 100% rename from src/alchemtest/tests/test_namd.py rename to alchemtest/tests/test_namd.py diff --git a/src/alchemtest/tests/test_utils.py b/alchemtest/tests/test_utils.py similarity index 100% rename from src/alchemtest/tests/test_utils.py rename to alchemtest/tests/test_utils.py diff --git a/devtools/README.md b/devtools/README.md new file mode 100644 index 0000000..1fe1009 --- /dev/null +++ b/devtools/README.md @@ -0,0 +1,56 @@ +# Development, testing, and deployment tools + +This directory contains a collection of tools for running Continuous Integration (CI) tests, +conda installation, and other development tools not directly related to the coding process. + + +## Manifest + +### Continuous Integration + +You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and +Windows testing if you only plan to deploy on specific platforms. These are just to help you get started. + +### Conda Environment: + +This directory contains the files to setup the Conda environment for testing purposes + +* `conda-envs`: directory containing the YAML file(s) which fully describe Conda Environments, their dependencies, and those dependency provenance's + * `test_env.yaml`: Simple test environment file with base dependencies. Channels are not specified here and therefore respect global Conda configuration + +### Additional Scripts: + +This directory contains OS agnostic helper scripts which don't fall in any of the previous categories +* `scripts` + * `create_conda_env.py`: Helper program for spinning up new conda environments based on a starter file with Python Version and Env. Name command-line options + + +## How to contribute changes +- Clone the repository if you have write access to the main repo, fork the repository if you are a collaborator. +- Make a new branch with `git checkout -b {your branch name}` +- Make changes and test your code +- Ensure that the test environment dependencies (`conda-envs`) line up with the build and deploy dependencies (`conda-recipe/meta.yaml`) +- Push the branch to the repo (either the main or your fork) with `git push -u origin {your branch name}` + * Note that `origin` is the default name assigned to the remote, yours may be different +- Make a PR on GitHub with your changes +- We'll review the changes and get your code into the repo after lively discussion! + + +## Checklist for updates +- [ ] Make sure there is an/are issue(s) opened for your specific update +- [ ] Create the PR, referencing the issue +- [ ] Debug the PR as needed until tests pass +- [ ] Tag the final, debugged version + * `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags` +- [ ] Get the PR merged in + +## Versioningit Auto-version +[versioningit](https://pypi.org/project/versioningit) will automatically infer what version +is installed by looking at the `git` tags and how many commits ahead this version is. The format follows +[PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of: +```regexp +\d+.\d+.\d+(?\+\d+-[a-z0-9]+) +``` +If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, +e.g. `alchemtest-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits +ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash. diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml index c79a37b..2911bdb 100644 --- a/devtools/conda-envs/test_env.yaml +++ b/devtools/conda-envs/test_env.yaml @@ -14,7 +14,8 @@ dependencies: - pytest-cov - codecov - # Pip-only installs - #- pip: - # - codecov + - wheel + - pytest-pep8 + - build + diff --git a/devtools/scripts/create_conda_env.py b/devtools/scripts/create_conda_env.py new file mode 100644 index 0000000..9ece84a --- /dev/null +++ b/devtools/scripts/create_conda_env.py @@ -0,0 +1,95 @@ +import argparse +import os +import re +import glob +import shutil +import subprocess as sp +from tempfile import TemporaryDirectory +from contextlib import contextmanager +# YAML imports +try: + import yaml # PyYAML + loader = yaml.safe_load +except ImportError: + try: + import ruamel_yaml as yaml # Ruamel YAML + except ImportError: + try: + # Load Ruamel YAML from the base conda environment + from importlib import util as import_util + CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE']) + ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..', + 'lib', 'python*.*', 'site-packages', + 'ruamel_yaml', '__init__.py'))[0] + # Based on importlib example, but only needs to load_module since its the whole package, not just + # a module + spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path) + yaml = spec.loader.load_module() + except (KeyError, ImportError, IndexError): + raise ImportError("No YAML parser could be found in this or the conda environment. " + "Could not find PyYAML or Ruamel YAML in the current environment, " + "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. " + "Environment not created!") + loader = yaml.YAML(typ="safe").load # typ="safe" avoids odd typing on output + + +@contextmanager +def temp_cd(): + """Temporary CD Helper""" + cwd = os.getcwd() + with TemporaryDirectory() as td: + try: + os.chdir(td) + yield + finally: + os.chdir(cwd) + + +# Args +parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.') +parser.add_argument('-n', '--name', type=str, + help='The name of the created Python environment') +parser.add_argument('-p', '--python', type=str, + help='The version of the created Python environment') +parser.add_argument('conda_file', + help='The file for the created Python environment') + +args = parser.parse_args() + +# Open the base file +with open(args.conda_file, "r") as handle: + yaml_script = loader(handle.read()) + +python_replacement_string = "python {}*".format(args.python) + +try: + for dep_index, dep_value in enumerate(yaml_script['dependencies']): + if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value): # Match explicitly 'python' and its formats + yaml_script['dependencies'].pop(dep_index) + break # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse +except (KeyError, TypeError): + # Case of no dependencies key, or dependencies: None + yaml_script['dependencies'] = [] +finally: + # Ensure the python version is added in. Even if the code does not need it, we assume the env does + yaml_script['dependencies'].insert(0, python_replacement_string) + +# Figure out conda path +if "CONDA_EXE" in os.environ: + conda_path = os.environ["CONDA_EXE"] +else: + conda_path = shutil.which("conda") +if conda_path is None: + raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path") + +print("CONDA ENV NAME {}".format(args.name)) +print("PYTHON VERSION {}".format(args.python)) +print("CONDA FILE NAME {}".format(args.conda_file)) +print("CONDA PATH {}".format(conda_path)) + +# Write to a temp directory which will always be cleaned up +with temp_cd(): + temp_file_name = "temp_script.yaml" + with open(temp_file_name, 'w') as f: + f.write(yaml.dump(yaml_script)) + sp.call("{} env create -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True) diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 0000000..d397790 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,24 @@ +# Compiling alchemtest's Documentation + +The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/). +To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed. + + +```bash +conda install sphinx sphinx_rtd_theme +``` + + +Once installed, you can use the `Makefile` in this directory to compile static HTML pages by +```bash +make html +``` + +The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself +be inside a directory called `html/` depending on what version of Sphinx is installed). + + +A configuration file for [Read The Docs](https://readthedocs.org/) (readthedocs.yaml) is included in the top level of the repository. To use Read the Docs to host your documentation, go to https://readthedocs.org/ and connect this repository. You may need to change your default branch to `main` under Advanced Settings for the project. + +If you would like to use Read The Docs with `autodoc` (included automatically) and your package has dependencies, you will need to include those dependencies in your documentation yaml file (`docs/requirements.yaml`). + diff --git a/docs/amber.rst b/docs/amber.rst index e1839b1..d84f026 100644 --- a/docs/amber.rst +++ b/docs/amber.rst @@ -24,34 +24,34 @@ They can be accessed using the following accessor functions: .. _amber_bace_improper: -.. include:: ../src/alchemtest/amber/bace_improper/descr.rst +.. include:: ../alchemtest/amber/bace_improper/descr.rst .. autofunction:: alchemtest.amber.load_bace_improper .. _amber_bace_example: -.. include:: ../src/alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst +.. include:: ../alchemtest/amber/bace_CAT-13d~CAT-17a/descr.rst .. autofunction:: alchemtest.amber.load_bace_example .. _amber_simplesolvated: -.. include:: ../src/alchemtest/amber/simplesolvated/descr.rst +.. include:: ../alchemtest/amber/simplesolvated/descr.rst .. autofunction:: alchemtest.amber.load_simplesolvated .. _amber_invalidfiles: -.. include:: ../src/alchemtest/amber/testfiles/descr_invalid.rst +.. include:: ../alchemtest/amber/testfiles/descr_invalid.rst .. autofunction:: alchemtest.amber.load_invalidfiles .. _load_testfiles: -.. include:: ../src/alchemtest/amber/testfiles/descr.rst +.. include:: ../alchemtest/amber/testfiles/descr.rst .. autofunction:: alchemtest.amber.load_testfiles diff --git a/docs/conf.py b/docs/conf.py index ffe035a..936c703 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -1,27 +1,37 @@ # -*- coding: utf-8 -*- # -# alchemtest documentation build configuration file, created by -# sphinx-quickstart on Fri Mar 24 12:44:43 2017. +# Configuration file for the Sphinx documentation builder. # -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. +# This file does only contain a selection of the most common options. For a +# full list see the documentation: +# http://www.sphinx-doc.org/en/stable/config + +# -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) +# Incase the project was not installed +import os +import sys +sys.path.insert(0, os.path.abspath('..')) -# -- General configuration ------------------------------------------------ +import alchemtest + + +# -- Project information ----------------------------------------------------- + +project = 'alchemtest' +copyright = ("2017-2024, The Alchemtest Authors.") +author = 'The Alchemtest Authors' + +from alchemtest._version import __version__ +release = __version__ +version = release + + +# -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # @@ -30,11 +40,20 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ['sphinx.ext.autodoc', - 'sphinx.ext.intersphinx', - 'sphinx.ext.mathjax', +extensions = [ 'sphinx.ext.autosummary', - 'sphinx.ext.napoleon'] + 'sphinx.ext.autodoc', + 'sphinx.ext.mathjax', + 'sphinx.ext.viewcode', + 'sphinx.ext.napoleon', + 'sphinx.ext.intersphinx', + 'sphinx.ext.extlinks', +] + +autosummary_generate = True +napoleon_google_docstring = False +napoleon_use_param = False +napoleon_use_ivar = True # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] @@ -48,29 +67,6 @@ # The master toctree document. master_doc = 'index' -# General information about the project. -project = u'alchemtest' -author = u'David Dotson and contributors' -copyright = u'2017-2019, ' + author - - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# automatically get the version information (requires that -# alchemtest is installed) -# We always display the full release string; if something else is -# desired, see the commented out code - -from alchemtest._version import get_versions -release = get_versions()['version'] -del get_versions - -version = release -#version = release.split("+")[0] # only major.minor.patch -#version = "."join(release.split(".")[:2]) # only major.minor - # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # @@ -80,25 +76,20 @@ # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path +# This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = 'default' -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - -# -- Options for HTML output ---------------------------------------------- +# -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' -html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. @@ -110,14 +101,24 @@ # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] +# Custom sidebar templates, must be a dictionary that maps document names +# to template names. +# +# The default sidebars (for documents that don't match any pattern) are +# defined by theme itself. Builtin themes are using these templates by +# default: ``['localtoc.html', 'relations.html', 'sourcelink.html', +# 'searchbox.html']``. +# +# html_sidebars = {} + -# -- Options for HTMLHelp output ------------------------------------------ +# -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'alchemtestdoc' -# -- Options for LaTeX output --------------------------------------------- +# -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). @@ -141,34 +142,33 @@ # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (master_doc, 'alchemtest.tex', u'alchemtest Documentation', - u'David Dotson', 'manual'), + (master_doc, 'alchemtest.tex', 'alchemtest Documentation', + author, 'manual'), ] -# -- Options for manual page output --------------------------------------- +# -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'alchemtest', u'alchemtest Documentation', + (master_doc, 'alchemtest', 'alchemtest Documentation', [author], 1) ] -# -- Options for Texinfo output ------------------------------------------- +# -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'alchemtest', u'alchemtest Documentation', - author, 'alchemtest', 'One line description of project.', + (master_doc, 'alchemtest', 'alchemtest Documentation', + author, 'alchemtest', 'The simple alchemistry test set.', 'Miscellaneous'), ] - -# Example configuration for intersphinx: refer to the Python standard library. +# -- Extension configuration ------------------------------------------------- intersphinx_mapping = {'https://docs.python.org/': None, - 'alchemlyb': ('https://alchemlyb.readthedocs.io/en/latest/', None)} + 'alchemlyb': ('https://alchemlyb.readthedocs.io/en/latest/', None)} \ No newline at end of file diff --git a/docs/contributing.rst b/docs/contributing.rst index 899d91b..f88009c 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -21,7 +21,7 @@ directory layout in `alchemtest/gmx/benzene`_) but you should provide files that are typical of how the specific code is run. .. _`alchemtest/gmx/benzene`: - https://github.com/alchemistry/alchemtest/tree/master/src/alchemtest/gmx/benzene + https://github.com/alchemistry/alchemtest/tree/master/alchemtest/gmx/benzene Data set description -------------------- @@ -91,7 +91,7 @@ Process .. code-block:: bash - recursive-include src/alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out *.xvg + recursive-include alchemtest *.gz *.bz2 *.zip *.rst *.txt *.out *.xvg will include your files into the package: If your filename extension(s) are not matched, add them. @@ -143,7 +143,7 @@ Process 5. Create a `Pull Request`_ with your new code and files. 6. Add a *test* that checks that your files can be found. Look in the - :file:`src/alchemtest/tests` directory and follow the examples that + :file:`alchemtest/tests` directory and follow the examples that are already there. We are also happy to help you with this step — just ask. @@ -164,10 +164,10 @@ Process https://docs.github.com/en/github/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork .. _`alchemtest/gmx`: - https://github.com/alchemistry/alchemtest/tree/master/src/alchemtest/gmx + https://github.com/alchemistry/alchemtest/tree/master/alchemtest/gmx .. _`alchemtest/namd`: - https://github.com/alchemistry/alchemtest/tree/master/src/alchemtest/namd + https://github.com/alchemistry/alchemtest/tree/master/alchemtest/namd .. _`restructured text (reST)`: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html diff --git a/docs/generic.rst b/docs/generic.rst index e53291a..b6e00bf 100644 --- a/docs/generic.rst +++ b/docs/generic.rst @@ -44,6 +44,6 @@ Which will give the :class:`pymbar.utils.ParameterError` :: Which will work. -.. include:: ../src/alchemtest/generic/BFGS/descr.rst +.. include:: ../alchemtest/generic/BFGS/descr.rst .. autofunction:: alchemtest.generic.load_MBAR_BGFS \ No newline at end of file diff --git a/docs/gmx.rst b/docs/gmx.rst index d61eb48..f7a80e2 100644 --- a/docs/gmx.rst +++ b/docs/gmx.rst @@ -34,7 +34,7 @@ were run independently. .. _gmx_benzene: -.. include:: ../src/alchemtest/gmx/benzene/descr.rst +.. include:: ../alchemtest/gmx/benzene/descr.rst .. autofunction:: alchemtest.gmx.load_benzene @@ -47,17 +47,17 @@ Data for *extended ensemble* simulations; case 1 and case 2 are extended ensembles in the alchemical parameters, case 3 includes replica exchange (REX). -.. include:: ../src/alchemtest/gmx/expanded_ensemble/case_1/descr.rst +.. include:: ../alchemtest/gmx/expanded_ensemble/case_1/descr.rst .. autofunction:: alchemtest.gmx.load_expanded_ensemble_case_1 -.. include:: ../src/alchemtest/gmx/expanded_ensemble/case_2/descr.rst +.. include:: ../alchemtest/gmx/expanded_ensemble/case_2/descr.rst .. autofunction:: alchemtest.gmx.load_expanded_ensemble_case_2 -.. include:: ../src/alchemtest/gmx/expanded_ensemble/case_3/descr.rst +.. include:: ../alchemtest/gmx/expanded_ensemble/case_3/descr.rst .. autofunction:: alchemtest.gmx.load_expanded_ensemble_case_3 @@ -72,7 +72,7 @@ contains a total energy column, one contains a potential energy column and one does not contain a energy column. .. _gmx_water_particle: -.. include:: ../src/alchemtest/gmx/water_particle/descr.rst +.. include:: ../alchemtest/gmx/water_particle/descr.rst .. autofunction:: alchemtest.gmx.load_water_particle_with_total_energy .. autofunction:: alchemtest.gmx.load_water_particle_with_potential_energy @@ -90,6 +90,6 @@ In the ligand leg, only the coulombic and Van der Waals interactions are decoupled. -.. include:: ../src/alchemtest/gmx/ABFE/descr.rst +.. include:: ../alchemtest/gmx/ABFE/descr.rst .. autofunction:: alchemtest.gmx.load_ABFE diff --git a/docs/gomc.rst b/docs/gomc.rst index fda74c7..f996668 100644 --- a/docs/gomc.rst +++ b/docs/gomc.rst @@ -27,6 +27,6 @@ were run independently. .. _gomc_benzene: -.. include:: ../src/alchemtest/gomc/benzene/descr.rst +.. include:: ../alchemtest/gomc/benzene/descr.rst .. autofunction:: alchemtest.gomc.load_benzene diff --git a/docs/index.rst b/docs/index.rst index b646560..b8fe37c 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -50,7 +50,7 @@ suite it may contain bugs. Please raise any issues or questions in the .. _`Open Definition 2.1`: http://opendefinition.org/od/2.1/en/ .. _`alchemistry/alchemtest`: https://github.com/alchemistry/alchemtest -.. _`semantic versioning`: https://semver.org +.. _`semantic versioning`: https://semver.org .. _`Issue Tracker`: https://github.com/alchemistry/alchemtest/issues .. _`NEP 29`: https://numpy.org/neps/nep-0029-deprecation_policy.html @@ -74,4 +74,4 @@ suite it may contain bugs. Please raise any issues or questions in the namd gomc generic - + diff --git a/docs/make.bat b/docs/make.bat index 0722060..161ae33 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -1,36 +1,36 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build -set SPHINXPROJ=alchemtest - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% - -:end -popd +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build +set SPHINXPROJ=alchemtest + +if "%1" == "" goto help + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.http://sphinx-doc.org/ + exit /b 1 +) + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% + +:end +popd diff --git a/docs/namd.rst b/docs/namd.rst index 32ae3c7..7575cf9 100644 --- a/docs/namd.rst +++ b/docs/namd.rst @@ -19,25 +19,25 @@ engine. They can be accessed using the following accessor functions: .. _namd_tyr2ala: -.. include:: ../src/alchemtest/namd/tyr2ala/descr.rst +.. include:: ../alchemtest/namd/tyr2ala/descr.rst .. autofunction:: alchemtest.namd.load_tyr2ala .. _namd_idws: -.. include:: ../src/alchemtest/namd/idws/descr.rst +.. include:: ../alchemtest/namd/idws/descr.rst .. autofunction:: alchemtest.namd.load_idws .. _namd_restarted: -.. include:: ../src/alchemtest/namd/restarted/descr.rst +.. include:: ../alchemtest/namd/restarted/descr.rst .. autofunction:: alchemtest.namd.load_restarted .. _namd_restarted_reversed: -.. include:: ../src/alchemtest/namd/restarted_reversed/descr.rst +.. include:: ../alchemtest/namd/restarted_reversed/descr.rst .. autofunction:: alchemtest.namd.load_restarted_reversed diff --git a/docs/requirements.yaml b/docs/requirements.yaml new file mode 100644 index 0000000..f65a963 --- /dev/null +++ b/docs/requirements.yaml @@ -0,0 +1,9 @@ +name: docs +channels: +dependencies: + # Base depends + - python + - pip + # Doc + - sphinx + - sphinx_rtd_theme diff --git a/environment.yml b/environment.yml deleted file mode 100644 index d4fde97..0000000 --- a/environment.yml +++ /dev/null @@ -1,4 +0,0 @@ -name: alchemtest -dependencies: -- python=3.5 -- sphinx diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..1d5912f --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,100 @@ +[build-system] +requires = ["setuptools>=61.0", "versioningit~=2.0"] +build-backend = "setuptools.build_meta" + +# Self-descriptive entries which should always be present +# https://packaging.python.org/en/latest/specifications/declaring-project-metadata/ +[project] +name = "alchemtest" +description = "The simple alchemistry test set." +dynamic = ["version"] +readme = "README.md" +authors = [ + { name = "David Dotson", email = "dotsdl@gmail.com" }, + { name = "Oliver Beckstein", email = "orbeckst@gmail.com" }, + { name = "Zhiyi Wu", email = "william@zhiyiwu.me" } +] +license = { text = "BSD-3-Clause" } +# See https://pypi.org/classifiers/ +classifiers = [ + 'Development Status :: 4 - Beta', + 'Intended Audience :: Science/Research', + 'License :: OSI Approved :: BSD License', + 'Operating System :: POSIX', + 'Operating System :: MacOS :: MacOS X', + 'Operating System :: Microsoft :: Windows ', + 'Programming Language :: Python', + 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3.10', + 'Programming Language :: Python :: 3.11', + 'Programming Language :: Python :: 3.12', + 'Topic :: Scientific/Engineering', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + 'Topic :: Scientific/Engineering :: Chemistry', +] +requires-python = ">=3.9" +# Declare any run-time dependencies that should be installed with the package. +#dependencies = [ +# "importlib-resources;python_version<'3.10'", +#] + +# Update the urls once the hosting is set up. +[project.urls] +"Source" = "https://github.com/alchemistry/alchemtest/" +"Documentation" = "https://alchemtest.readthedocs.io/" + +[project.optional-dependencies] +test = [ + "pytest>=6.1.2", + "pytest-runner" +] +doc = ["sphinx", "sphinx_rtd_theme"] + +[tool.setuptools] +# This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details +# +# As of version 0.971, mypy does not support type checking of installed zipped +# packages (because it does not actually import the Python packages). +# We declare the package not-zip-safe so that our type hints are also available +# when checking client code that uses our (installed) package. +# Ref: +# https://mypy.readthedocs.io/en/stable/installed_packages.html?highlight=zip#using-installed-packages-with-mypy-pep-561 +zip-safe = false +# Let setuptools discover the package in the current directory, +# but be explicit about non-Python files. +# See also: +# https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html#setuptools-specific-configuration +# Note that behavior is currently evolving with respect to how to interpret the +# "data" and "tests" subdirectories. As of setuptools 63, both are automatically +# included if namespaces is true (default), even if the package is named explicitly +# (instead of using 'find'). With 'find', the 'tests' subpackage is discovered +# recursively because of its __init__.py file, but the data subdirectory is excluded +# with include-package-data = false and namespaces = false. +include-package-data = true +[tool.setuptools.packages.find] +namespaces = false +where = ["."] + +# Ref https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data +[tool.setuptools.package-data] +alchemtest = [ + "py.typed" +] + +[tool.versioningit] +default-version = "1+unknown" + +[tool.versioningit.format] +distance = "{base_version}+{distance}.{vcs}{rev}" +dirty = "{base_version}+{distance}.{vcs}{rev}.dirty" +distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty" + +[tool.versioningit.vcs] +# The method key: +method = "git" # <- The method name +# Parameters to pass to the method: +match = ["*"] +default-tag = "1.0.0" + +[tool.versioningit.write] +file = "alchemtest/_version.py" diff --git a/readthedocs.yml b/readthedocs.yml index db0ddf1..4c77a2b 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -7,11 +7,15 @@ sphinx: formats: - pdf +build: + os: "ubuntu-20.04" + tools: + python: "mambaforge-4.10" + +conda: + environment: docs/requirements.yaml + python: - version: 3.7 install: - method: pip - path: . - -conda: - environment: environment.yml + path: . \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 53b4e64..de5e39c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,11 +1,22 @@ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -VCS = git -style = pep440 -versionfile_source = src/alchemtest/_version.py -versionfile_build = alchemtest/_version.py -tag_prefix = -parentdir_prefix = alchemtest- +# Helper file to handle all configs + +[coverage:run] +# .coveragerc to control coverage.py and pytest-cov +omit = + # Omit the tests + */tests/* + # Omit generated versioneer + alchemtest/_version.py + +[yapf] +# YAPF, in .style.yapf files this shows up as "[style]" header +COLUMN_LIMIT = 119 +INDENT_WIDTH = 4 +USE_TABS = False + +[flake8] +# Flake8, PyFlakes, etc +max-line-length = 119 + +[aliases] +test = pytest diff --git a/setup.py b/setup.py deleted file mode 100755 index 92e4d10..0000000 --- a/setup.py +++ /dev/null @@ -1,44 +0,0 @@ -#! /usr/bin/python -"""Setuptools-based setup script for alchemtest. - -For a basic installation just type the command:: - - python setup.py install - -""" - -from setuptools import setup, find_packages - -import versioneer - -setup(name='alchemtest', - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - description='the simple alchemistry test set', - author='David Dotson', - author_email='dotsdl@gmail.com', - maintainer='Oliver Beckstein', - maintainer_email='orbeckst@gmail.com', - classifiers=[ - 'Development Status :: 4 - Beta', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Operating System :: POSIX', - 'Operating System :: MacOS :: MacOS X', - 'Operating System :: Microsoft :: Windows ', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3.8', - 'Programming Language :: Python :: 3.9', - 'Programming Language :: Python :: 3.10', - 'Programming Language :: Python :: 3.11', - 'Topic :: Scientific/Engineering', - 'Topic :: Scientific/Engineering :: Bio-Informatics', - 'Topic :: Scientific/Engineering :: Chemistry', - ], - packages=find_packages('src'), - package_dir={'': 'src'}, - license='BSD', - long_description=open('README.rst').read(), - long_description_content_type = 'text/x-rst', - include_package_data=True, -) diff --git a/src/alchemtest/_version.py b/src/alchemtest/_version.py deleted file mode 100644 index f5bba23..0000000 --- a/src/alchemtest/_version.py +++ /dev/null @@ -1,520 +0,0 @@ - -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "" - cfg.parentdir_prefix = "alchemtest-" - cfg.versionfile_source = "src/alchemtest/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} diff --git a/versioneer.py b/versioneer.py deleted file mode 100644 index 64fea1c..0000000 --- a/versioneer.py +++ /dev/null @@ -1,1822 +0,0 @@ - -# Version: 0.18 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/warner/python-versioneer -* Brian Warner -* License: Public Domain -* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy -* [![Latest Version] -(https://pypip.in/version/versioneer/badge.svg?style=flat) -](https://pypi.python.org/pypi/versioneer/) -* [![Build Status] -(https://travis-ci.org/warner/python-versioneer.png?branch=master) -](https://travis-ci.org/warner/python-versioneer) - -This is a tool for managing a recorded version number in distutils-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -* `pip install versioneer` to somewhere to your $PATH -* add a `[versioneer]` section to your setup.cfg (see below) -* run `versioneer install` in your source tree, commit the results - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes. - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/warner/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other langauges) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - -### Unicode version strings - -While Versioneer works (and is continually tested) with both Python 2 and -Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. -Newer releases probably generate unicode version strings on py2. It's not -clear that this is wrong, but it may be surprising for applications when then -write these strings to a network connection or include them in bytes-oriented -APIs like cryptographic checksums. - -[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates -this question. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -""" - -from __future__ import print_function -try: - import configparser -except ImportError: - import ConfigParser as configparser -import errno -import json -import os -import re -import subprocess -import sys - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ("Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND').") - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: - print("Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py)) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: - parser.readfp(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None - cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): - cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -LONG_VERSION_PY['git'] = ''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%%d" %% pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %s" % r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%s*" % tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%s'" - % describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = ("tag '%s' doesn't start with prefix '%s'" - % (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(manifest_in, versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] - if ipy: - files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: - pass - if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %s but none started with prefix %s" % - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.18) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except EnvironmentError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", - contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, - indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, \ - "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, "error": "unable to compute version", - "date": None} - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(): - """Get the custom setuptools/distutils subclasses used by Versioneer.""" - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/warner/python-versioneer/issues/52 - - cmds = {} - - # we add "version" to both distutils and setuptools - from distutils.core import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - cmds["version"] = cmd_version - - # we override "build_py" in both distutils and setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # we override different "build_py" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py - else: - from distutils.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, - cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - cmds["build_py"] = cmd_build_py - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if 'py2exe' in sys.modules: # py2exe enabled? - try: - from py2exe.distutils_buildexe import py2exe as _py2exe # py3 - except ImportError: - from py2exe.build_exe import py2exe as _py2exe # py2 - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % - {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - cmds["py2exe"] = cmd_py2exe - - # we override different "sdist" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist - else: - from distutils.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, - self._versioneer_generated_versions) - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -INIT_PY_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - - -def do_setup(): - """Main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (EnvironmentError, configparser.NoSectionError, - configparser.NoOptionError) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", - file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write(LONG % {"DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - }) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), - "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except EnvironmentError: - old = "" - if INIT_PY_SNIPPET not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print(" appending versionfile_source ('%s') to MANIFEST.in" % - cfg.versionfile_source) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1)