using the latest cookiecutter to make maintenance easier (#93)

* use the MolSSI cookiecutter for project structure
  - remove src directory and put alchemtest under the top level
  - update our CI with cookiecutter CI
* fix #92 (support Python 3.12)
* replace versioneer with versioningit
* fix rtd
* add CONTRIBUTING.md and preliminary CODE_OF_CONDUCT.md

NOTE: This commit touched almost every file (mostly due to move) so when running `git blame`,  **exclude this commit from git blame**.

.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

.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 =

.gitattributes

@@ -1 +1 @@
-src/alchemtest/_version.py export-subst
+alchemtest/_version.py export-subst

.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)

.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

.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)

.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/')

.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/

.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