diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 537d85647..fbfde58d3 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -68,3 +68,23 @@ jobs: run: | coverage combine coverage*/.coverage* coverage report --show-missing + + docs: + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + + - uses: actions/setup-python@v4 + with: + python-version: "3.9" + cache: pip + cache-dependency-path: pyproject.toml + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install .[docs,strict] + + - name: Build + run: sphinx-build -W docs _build \ No newline at end of file diff --git a/README.md b/README.md index 24178e89f..d3b282ac4 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,7 @@ Contributions are welcome. Please raise a pull request for contributions first. - please ensure high coverage of the code based on the tests # Commit guidelines -1. `pip install pre-commit` +1. `pip install pre-commit`. 2. Next, run `pre-commit install` (this will install all the hooks from pre-commit-config.yaml) 3. Step 1 and 2, needs to be done only once in the local repository 4. 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The original can be found at + ``sphinx/ext/autosummary/templates/autosummary/module.rst``. #} + +{% block attributes %} +{% if attributes %} + .. rubric:: Module Attributes + + .. autosummary:: + :toctree: + :nosignatures: + {% for item in attributes %} + {{ item }} + {%- endfor %} +{% endif %} +{% endblock %} + +{% block functions %} +{% if functions %} + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + {% for item in functions %} + {{ item }} + {%- endfor %} +{% endif %} +{% endblock %} + +{% block classes %} + +{% set types = [] %} +{% for item in members %} + {% if not item.startswith('_') and not (item in functions or item in attributes or item in exceptions) %} + {% set _ = types.append(item) %} + {% endif %} +{%- endfor %} + +{% if types %} + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + {% for item in types %} + {{ item }} + {%- endfor %} + +{% endif %} +{% endblock %} diff --git a/docs/about/changelog.md b/docs/about/changelog.md new file mode 100644 index 000000000..3139cd42b --- /dev/null +++ b/docs/about/changelog.md @@ -0,0 +1,2 @@ +```{include} ../../CHANGELOG.md +``` diff --git a/docs/about/contributing.md b/docs/about/contributing.md new file mode 100644 index 000000000..ef6daa82a --- /dev/null +++ b/docs/about/contributing.md @@ -0,0 +1,2 @@ +```{include} ../../CONTRIBUTING.md +``` diff --git a/docs/about/contributors.md b/docs/about/contributors.md new file mode 100644 index 000000000..760298a4b --- /dev/null +++ b/docs/about/contributors.md @@ -0,0 +1,29 @@ +# Contributors + +[gh]: https://cdnjs.cloudflare.com/ajax/libs/octicons/8.5.0/svg/mark-github.svg +[orc]: ../_static/orcid.svg + + +**Janine George** [![gh]][JaGeo] [![orc]][0000-0001-8907-0336] \ +Junior Group Leader \ +Federal Institute for Materials Research and Testing (Berlin) \ +Friedrich Schiller University Jena + +[JaGeo]: https://github.com/JaGeo +[0000-0001-8907-0336]: https://orcid.org/0000-0001-8907-0336 + +**Christina Ertural** [![gh]][QuantumChemist] [![orc]][0000-0002-7696-5824] \ +Postdoctoral Researcher \ +Federal Institute for Materials Research and Testing (Berlin) + +[QuantumChemist]: https://github.com/QuantumChemist +[0000-0002-7696-5824]: https://orcid.org/0000-0002-7696-5824 + + +**Aakash Ashok Naik** [![gh]][naik-aakash] [![orc]][0000-0002-6071-6786] \ +PhD student \ +Federal Institute for Materials Research and Testing (Berlin) \ +Friedrich Schiller University Jena + +[naik-aakash]: https://github.com/naik-aakash +[0000-0002-6071-6786]: https://orcid.org/0000-0002-6071-6786 diff --git a/docs/about/license.md b/docs/about/license.md new file mode 100644 index 000000000..6e7701bd9 --- /dev/null +++ b/docs/about/license.md @@ -0,0 +1,33 @@ +License +======= + +`autoplex` is developed under a modified BSD License, reproduced below: + +``` +Copyright (c) 2023, autoplex development team. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +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. +``` diff --git a/docs/conf.py b/docs/conf.py new file mode 100644 index 000000000..a6a354b9e --- /dev/null +++ b/docs/conf.py @@ -0,0 +1,171 @@ +# ruff: noqa: E501 + +"""Sphinx configuration file.""" + +# -- 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 + +from atomate2 import __version__ + +sys.path.insert(0, os.path.abspath("../../")) + +# -- Project information ----------------------------------------------------- + +project = "autoplex" +copyright = "2023, autoplex development team" # noqa: A001 +author = "Christina Ertural" + +# The short X.Y version +version = __version__ +# The full version, including alpha/beta/rc tags +release = __version__ + +# -- General configuration --------------------------------------------------- + +# 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.napoleon", + "sphinx.ext.intersphinx", + "sphinx.ext.viewcode", + "sphinx.ext.autosummary", + "myst_parser", + "sphinxcontrib.autodoc_pydantic", + "numpydoc", + "sphinx_design", + "sphinx_copybutton", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = ["Thumbs.db", ".DS_Store", "test*.py"] + +myst_heading_anchors = 2 # enable headings as link targets +myst_enable_extensions = [ + "amsmath", + "colon_fence", + "dollarmath", + "html_admonition", + "html_image", +] + +# use type hints +autodoc_typehints = "description" +# autoclass_content = "both" +# autodoc_member_order = "bysource" + +# better napoleon support +napoleon_use_param = True +napoleon_use_rtype = True +napoleon_use_ivar = True + +# The suffix(es) of source filenames. +source_suffix = [".rst", ".md"] + +mathjax3_config = { + "tex": { + "macros": { + "N": "\\mathbb{N}", + "floor": ["\\lfloor#1\\rfloor", 1], + "bmat": ["\\left[\\begin{array}"], + "emat": ["\\end{array}\\right]"], + } + } +} +latex_elements = { + "preamble": r"""\newcommand\N{\mathbb{N}} +\newcommand\floor[1]{\lfloor#1\rfloor} +\newcommand{\bmat}{\left[\begin{array}} +\newcommand{\emat}{\end{array}\right]} +""" +} +language = "en" +html_extra_path = ["images/badge.svg"] +html_static_path = ["_static"] +html_css_files = ["custom.css", "github.css"] +suppress_warnings = "etoc.toctree" + +# autodoc options +autosummary_imported_members = False +autodoc_preserve_defaults = True +autoclass_content = "class" +autodoc_member_order = "bysource" + +python_use_unqualified_type_names = True + +# don't overwrite summary but generate them if they don't exist +autosummary_generate = True +autosummary_generate_overwrite = True + +# numpydoc options +numpydoc_class_members_toctree = False +numpydoc_show_class_members = False +numpydoc_show_inherited_class_members = False +numpydoc_attributes_as_param_list = False +numpydoc_xref_param_type = True + +# sphinx-panels shouldn't add bootstrap css as the pydata-sphinx-theme already loads it +panels_add_bootstrap_css = False + +# control pydantic model docs +autodoc_pydantic_model_show_json = False +autodoc_pydantic_model_show_field_summary = False +autodoc_pydantic_model_show_config = False +autodoc_pydantic_model_show_config_summary = False +autodoc_pydantic_model_show_validator_members = False +autodoc_pydantic_model_member_order = "bysource" +autodoc_pydantic_settings_show_json = False +autodoc_pydantic_settings_show_field_summary = False +autodoc_pydantic_settings_show_config = False +autodoc_pydantic_settings_show_config_summary = False +autodoc_pydantic_settings_show_validator_members = False +autodoc_pydantic_settings_member_order = "bysource" +autodoc_pydantic_field_list_validators = False +autodoc_pydantic_field_show_constraints = False + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +html_theme = "sphinx_book_theme" +html_theme_options = { + "repository_provider": "github", + "repository_url": "https://github.com/JaGeo/autoplex", + "use_repository_button": True, + "use_issues_button": True, +} + + +#html_static_path = ["_static"] + +html_css_files = ['custom.css'] + +# hide sphinx footer +html_show_sphinx = False +html_show_sourcelink = False + +# downgrad mathjax +mathjax_path = 'https://cdn.jsdelivr.net/npm/mathjax@2/MathJax.js?config=TeX-AMS-MML_HTMLorMML' +mathjax2_config = { + 'tex2jax': { + 'inlineMath': [['$', '$'], ['\\(', '\\)']], + 'processEscapes': True, + 'ignoreClass': 'document', + 'processClass': 'math|output_area', + } +} +html_title = "autoplex" diff --git a/docs/dev/dev_install.md b/docs/dev/dev_install.md new file mode 100644 index 000000000..1d3cd7a4b --- /dev/null +++ b/docs/dev/dev_install.md @@ -0,0 +1,52 @@ +# Developer Installation + +Install autoplex from source, by cloning the repository via [github](https://github.com/JaGeo/autoplex.git) + +```bash +git clone https://github.com/JaGeo/autoplex.git +cd autoplex +pip install -e .[docs,strict,dev] +``` +This will install autoplex will all dependencies for tests, pre-commit and docs building. + +## Running unit tests + +Unit tests can be run from the source folder using `pytest`. + +```bash +pytest +``` +This will run all the tests. + +To get a detailed report of test coverage you can use following command +```bash +pytest --cov=autoplex --cov-report term-missing --cov-append +``` + +If you feel test execution takes too long locally, you can speedup the execution using [pytest-xdist](https://pypi.org/project/pytest-xdist/). Install this in library in your environment using + +```bash +pip install pytest-xdist +``` + +Once installed, you can now use multiple processors to run your tests. For example, if you want to use 8 processors to run tests in parallel, run + +```bash +pytest -n 8 +``` + +We rely on pytest-split to run tests in parallel on github workflow, thus it is necessary to update the test-durations files in the repository, incase you add new tests. To generate this file, use + +```bash +pytest --cov=autoplex --cov-append --splits 1 --group 1 --durations-path ./tests/test_data/.pytest-split-durations --store-durations +``` + +## Building the documentation locally + +The autoplex documentation can be built using the sphinx package. + +The docs can be built to the `_build` directory: + +```bash +sphinx-build -W docs _build +``` diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 000000000..eacde2967 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,80 @@ +```{toctree} +:caption: User Guide +:hidden: +user/index +user/tutorials +``` + +```{toctree} +:caption: Reference +:hidden: +reference/index +``` + +```{toctree} +:caption: Developer Guide +:hidden: +dev/dev_install +``` + +```{toctree} +:caption: About +:hidden: +about/changelog +about/contributors +about/contributing +about/license +``` + +# autoplex documentation + +**Date**: {sub-ref}`today` + +**Useful links**: +[Source Repository](https://github.com/JaGeo/autoplex) | +[Issues & Ideas](https://github.com/JaGeo/autoplex/issues) | + +Autoplex is a library for automated fitting and benchmarking of ML potentials.. + +::::{grid} 1 1 2 2 +:class-container: text-center +:gutter: 3 + +:::{grid-item-card} +:link: user/index +:link-type: doc +:class-header: bg-light +**User Guide** +^^^ +The user guide provides information for getting started with *autoplex*. +::: + +:::{grid-item-card} +:link: user/tutorials +:link-type: doc +:class-header: bg-light +**Tutorials** +^^^ +Tutorials for using autoplex. +::: + +:::{grid-item-card} +:link: reference/index +:link-type: doc +:class-header: bg-light +**API reference** +^^^ +The reference guide contains a detailed description of the *atomate2* API. It +assumes that you have an understanding of the key concepts. +::: + +:::{grid-item-card} +:link: dev/dev_install +:link-type: doc +:class-header: bg-light +**Developer guide** +^^^ +Do you want to develop your own workflows or improve existing functionalities? +Check out the developer guide. +::: +:::: diff --git a/docs/reference/autoplex.auto.flows.CompleteDFTvsMLBenchmarkWorkflow.rst b/docs/reference/autoplex.auto.flows.CompleteDFTvsMLBenchmarkWorkflow.rst new file mode 100644 index 000000000..72ae79012 --- /dev/null +++ b/docs/reference/autoplex.auto.flows.CompleteDFTvsMLBenchmarkWorkflow.rst @@ -0,0 +1,8 @@ +CompleteDFTvsMLBenchmarkWorkflow +================================ + +.. currentmodule:: autoplex.auto.flows + +.. autoclass:: CompleteDFTvsMLBenchmarkWorkflow + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.auto.flows.DFTDataGenerationFlow.rst b/docs/reference/autoplex.auto.flows.DFTDataGenerationFlow.rst new file mode 100644 index 000000000..bf1060ce6 --- /dev/null +++ b/docs/reference/autoplex.auto.flows.DFTDataGenerationFlow.rst @@ -0,0 +1,8 @@ +DFTDataGenerationFlow +===================== + +.. currentmodule:: autoplex.auto.flows + +.. autoclass:: DFTDataGenerationFlow + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.auto.flows.PhononDFTMLBenchmarkFlow.rst b/docs/reference/autoplex.auto.flows.PhononDFTMLBenchmarkFlow.rst new file mode 100644 index 000000000..ad5b0f9bc --- /dev/null +++ b/docs/reference/autoplex.auto.flows.PhononDFTMLBenchmarkFlow.rst @@ -0,0 +1,8 @@ +PhononDFTMLBenchmarkFlow +======================== + +.. currentmodule:: autoplex.auto.flows + +.. autoclass:: PhononDFTMLBenchmarkFlow + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.auto.flows.PhononDFTMLFitFlow.rst b/docs/reference/autoplex.auto.flows.PhononDFTMLFitFlow.rst new file mode 100644 index 000000000..bbe45013a --- /dev/null +++ b/docs/reference/autoplex.auto.flows.PhononDFTMLFitFlow.rst @@ -0,0 +1,8 @@ +PhononDFTMLFitFlow +================== + +.. currentmodule:: autoplex.auto.flows + +.. autoclass:: PhononDFTMLFitFlow + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.auto.flows.TYPE_CHECKING.rst b/docs/reference/autoplex.auto.flows.TYPE_CHECKING.rst new file mode 100644 index 000000000..17bed117a --- /dev/null +++ b/docs/reference/autoplex.auto.flows.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.auto.flows + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.auto.flows.rst b/docs/reference/autoplex.auto.flows.rst new file mode 100644 index 000000000..7816f267b --- /dev/null +++ b/docs/reference/autoplex.auto.flows.rst @@ -0,0 +1,62 @@ +autoplex.auto.flows +=================== + +.. automodule:: autoplex.auto.flows + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + CompleteDFTvsMLBenchmarkWorkflow + DFTDataGenerationFlow + PhononDFTMLBenchmarkFlow + PhononDFTMLFitFlow + TYPE_CHECKING + + + + + + + + + + diff --git a/docs/reference/autoplex.auto.jobs.MLPhononMaker.rst b/docs/reference/autoplex.auto.jobs.MLPhononMaker.rst new file mode 100644 index 000000000..0369803a8 --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.MLPhononMaker.rst @@ -0,0 +1,8 @@ +MLPhononMaker +============= + +.. currentmodule:: autoplex.auto.jobs + +.. autoclass:: MLPhononMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.auto.jobs.TYPE_CHECKING.rst b/docs/reference/autoplex.auto.jobs.TYPE_CHECKING.rst new file mode 100644 index 000000000..00f44d153 --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.auto.jobs + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.auto.jobs.dft_phonopy_gen_data.rst b/docs/reference/autoplex.auto.jobs.dft_phonopy_gen_data.rst new file mode 100644 index 000000000..7ca2dd2a0 --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.dft_phonopy_gen_data.rst @@ -0,0 +1,6 @@ +dft\_phonopy\_gen\_data +======================= + +.. currentmodule:: autoplex.auto.jobs + +.. autofunction:: dft_phonopy_gen_data \ No newline at end of file diff --git a/docs/reference/autoplex.auto.jobs.dft_random_gen_data.rst b/docs/reference/autoplex.auto.jobs.dft_random_gen_data.rst new file mode 100644 index 000000000..f0ce3071b --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.dft_random_gen_data.rst @@ -0,0 +1,6 @@ +dft\_random\_gen\_data +====================== + +.. currentmodule:: autoplex.auto.jobs + +.. autofunction:: dft_random_gen_data \ No newline at end of file diff --git a/docs/reference/autoplex.auto.jobs.get_iso_atom.rst b/docs/reference/autoplex.auto.jobs.get_iso_atom.rst new file mode 100644 index 000000000..ae9fb154e --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.get_iso_atom.rst @@ -0,0 +1,6 @@ +get\_iso\_atom +============== + +.. currentmodule:: autoplex.auto.jobs + +.. autofunction:: get_iso_atom \ No newline at end of file diff --git a/docs/reference/autoplex.auto.jobs.get_phonon_ml_calculation_jobs.rst b/docs/reference/autoplex.auto.jobs.get_phonon_ml_calculation_jobs.rst new file mode 100644 index 000000000..3f9256185 --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.get_phonon_ml_calculation_jobs.rst @@ -0,0 +1,6 @@ +get\_phonon\_ml\_calculation\_jobs +================================== + +.. currentmodule:: autoplex.auto.jobs + +.. autofunction:: get_phonon_ml_calculation_jobs \ No newline at end of file diff --git a/docs/reference/autoplex.auto.jobs.rst b/docs/reference/autoplex.auto.jobs.rst new file mode 100644 index 000000000..4b093d351 --- /dev/null +++ b/docs/reference/autoplex.auto.jobs.rst @@ -0,0 +1,64 @@ +autoplex.auto.jobs +================== + +.. automodule:: autoplex.auto.jobs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + + dft_phonopy_gen_data + dft_random_gen_data + get_iso_atom + get_phonon_ml_calculation_jobs + + + + + + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + MLPhononMaker + TYPE_CHECKING + + + + + + + + + + diff --git a/docs/reference/autoplex.auto.rst b/docs/reference/autoplex.auto.rst new file mode 100644 index 000000000..a977988c2 --- /dev/null +++ b/docs/reference/autoplex.auto.rst @@ -0,0 +1,43 @@ +autoplex.auto +============= + +.. automodule:: autoplex.auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + autoplex.auto.flows + autoplex.auto.jobs + diff --git a/docs/reference/autoplex.benchmark.flows.PhononBenchmarkMaker.rst b/docs/reference/autoplex.benchmark.flows.PhononBenchmarkMaker.rst new file mode 100644 index 000000000..c4f59b0ca --- /dev/null +++ b/docs/reference/autoplex.benchmark.flows.PhononBenchmarkMaker.rst @@ -0,0 +1,8 @@ +PhononBenchmarkMaker +==================== + +.. currentmodule:: autoplex.benchmark.flows + +.. autoclass:: PhononBenchmarkMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.flows.TYPE_CHECKING.rst b/docs/reference/autoplex.benchmark.flows.TYPE_CHECKING.rst new file mode 100644 index 000000000..f34c48f53 --- /dev/null +++ b/docs/reference/autoplex.benchmark.flows.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.benchmark.flows + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.flows.rst b/docs/reference/autoplex.benchmark.flows.rst new file mode 100644 index 000000000..fc8131080 --- /dev/null +++ b/docs/reference/autoplex.benchmark.flows.rst @@ -0,0 +1,50 @@ +autoplex.benchmark.flows +======================== + +.. automodule:: autoplex.benchmark.flows + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + PhononBenchmarkMaker + TYPE_CHECKING + + + + + + + + + + diff --git a/docs/reference/autoplex.benchmark.jobs.TYPE_CHECKING.rst b/docs/reference/autoplex.benchmark.jobs.TYPE_CHECKING.rst new file mode 100644 index 000000000..5283da775 --- /dev/null +++ b/docs/reference/autoplex.benchmark.jobs.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.benchmark.jobs + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.jobs.compute_bandstructure_benchmark_metrics.rst b/docs/reference/autoplex.benchmark.jobs.compute_bandstructure_benchmark_metrics.rst new file mode 100644 index 000000000..945ce05b8 --- /dev/null +++ b/docs/reference/autoplex.benchmark.jobs.compute_bandstructure_benchmark_metrics.rst @@ -0,0 +1,6 @@ +compute\_bandstructure\_benchmark\_metrics +========================================== + +.. currentmodule:: autoplex.benchmark.jobs + +.. autofunction:: compute_bandstructure_benchmark_metrics \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.jobs.rst b/docs/reference/autoplex.benchmark.jobs.rst new file mode 100644 index 000000000..45a3ac027 --- /dev/null +++ b/docs/reference/autoplex.benchmark.jobs.rst @@ -0,0 +1,56 @@ +autoplex.benchmark.jobs +======================= + +.. automodule:: autoplex.benchmark.jobs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + + compute_bandstructure_benchmark_metrics + write_benchmark_metrics + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + TYPE_CHECKING + + + + + + + + + + diff --git a/docs/reference/autoplex.benchmark.jobs.write_benchmark_metrics.rst b/docs/reference/autoplex.benchmark.jobs.write_benchmark_metrics.rst new file mode 100644 index 000000000..8629f0c71 --- /dev/null +++ b/docs/reference/autoplex.benchmark.jobs.write_benchmark_metrics.rst @@ -0,0 +1,6 @@ +write\_benchmark\_metrics +========================= + +.. currentmodule:: autoplex.benchmark.jobs + +.. autofunction:: write_benchmark_metrics \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.rst b/docs/reference/autoplex.benchmark.rst new file mode 100644 index 000000000..b095213b6 --- /dev/null +++ b/docs/reference/autoplex.benchmark.rst @@ -0,0 +1,44 @@ +autoplex.benchmark +================== + +.. automodule:: autoplex.benchmark + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + autoplex.benchmark.flows + autoplex.benchmark.jobs + autoplex.benchmark.utils + diff --git a/docs/reference/autoplex.benchmark.utils.compare_plot.rst b/docs/reference/autoplex.benchmark.utils.compare_plot.rst new file mode 100644 index 000000000..688281633 --- /dev/null +++ b/docs/reference/autoplex.benchmark.utils.compare_plot.rst @@ -0,0 +1,6 @@ +compare\_plot +============= + +.. currentmodule:: autoplex.benchmark.utils + +.. autofunction:: compare_plot \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.utils.get_rmse.rst b/docs/reference/autoplex.benchmark.utils.get_rmse.rst new file mode 100644 index 000000000..219d79c4b --- /dev/null +++ b/docs/reference/autoplex.benchmark.utils.get_rmse.rst @@ -0,0 +1,6 @@ +get\_rmse +========= + +.. currentmodule:: autoplex.benchmark.utils + +.. autofunction:: get_rmse \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.utils.rmse_kdep_plot.rst b/docs/reference/autoplex.benchmark.utils.rmse_kdep_plot.rst new file mode 100644 index 000000000..7d65dab38 --- /dev/null +++ b/docs/reference/autoplex.benchmark.utils.rmse_kdep_plot.rst @@ -0,0 +1,6 @@ +rmse\_kdep\_plot +================ + +.. currentmodule:: autoplex.benchmark.utils + +.. autofunction:: rmse_kdep_plot \ No newline at end of file diff --git a/docs/reference/autoplex.benchmark.utils.rst b/docs/reference/autoplex.benchmark.utils.rst new file mode 100644 index 000000000..ce871bf41 --- /dev/null +++ b/docs/reference/autoplex.benchmark.utils.rst @@ -0,0 +1,46 @@ +autoplex.benchmark.utils +======================== + +.. automodule:: autoplex.benchmark.utils + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + + compare_plot + get_rmse + rmse_kdep_plot + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/reference/autoplex.data.flows.DFTPhononMaker.rst b/docs/reference/autoplex.data.flows.DFTPhononMaker.rst new file mode 100644 index 000000000..49e466a07 --- /dev/null +++ b/docs/reference/autoplex.data.flows.DFTPhononMaker.rst @@ -0,0 +1,8 @@ +DFTPhononMaker +============== + +.. currentmodule:: autoplex.data.flows + +.. autoclass:: DFTPhononMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.data.flows.IsoAtomMaker.rst b/docs/reference/autoplex.data.flows.IsoAtomMaker.rst new file mode 100644 index 000000000..de76ee85f --- /dev/null +++ b/docs/reference/autoplex.data.flows.IsoAtomMaker.rst @@ -0,0 +1,8 @@ +IsoAtomMaker +============ + +.. currentmodule:: autoplex.data.flows + +.. autoclass:: IsoAtomMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.data.flows.IsoAtomStaticMaker.rst b/docs/reference/autoplex.data.flows.IsoAtomStaticMaker.rst new file mode 100644 index 000000000..38ba70c02 --- /dev/null +++ b/docs/reference/autoplex.data.flows.IsoAtomStaticMaker.rst @@ -0,0 +1,8 @@ +IsoAtomStaticMaker +================== + +.. currentmodule:: autoplex.data.flows + +.. autoclass:: IsoAtomStaticMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.data.flows.RandomStructuresDataGenerator.rst b/docs/reference/autoplex.data.flows.RandomStructuresDataGenerator.rst new file mode 100644 index 000000000..ec6270e3f --- /dev/null +++ b/docs/reference/autoplex.data.flows.RandomStructuresDataGenerator.rst @@ -0,0 +1,8 @@ +RandomStructuresDataGenerator +============================= + +.. currentmodule:: autoplex.data.flows + +.. autoclass:: RandomStructuresDataGenerator + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.data.flows.TYPE_CHECKING.rst b/docs/reference/autoplex.data.flows.TYPE_CHECKING.rst new file mode 100644 index 000000000..1ee5d579d --- /dev/null +++ b/docs/reference/autoplex.data.flows.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.data.flows + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.data.flows.TightDFTStaticMaker.rst b/docs/reference/autoplex.data.flows.TightDFTStaticMaker.rst new file mode 100644 index 000000000..141bfc2fe --- /dev/null +++ b/docs/reference/autoplex.data.flows.TightDFTStaticMaker.rst @@ -0,0 +1,8 @@ +TightDFTStaticMaker +=================== + +.. currentmodule:: autoplex.data.flows + +.. autoclass:: TightDFTStaticMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.data.flows.rst b/docs/reference/autoplex.data.flows.rst new file mode 100644 index 000000000..05b24871a --- /dev/null +++ b/docs/reference/autoplex.data.flows.rst @@ -0,0 +1,66 @@ +autoplex.data.flows +=================== + +.. automodule:: autoplex.data.flows + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + DFTPhononMaker + IsoAtomMaker + IsoAtomStaticMaker + RandomStructuresDataGenerator + TYPE_CHECKING + TightDFTStaticMaker + + + + + + + + + + diff --git a/docs/reference/autoplex.data.jobs.TYPE_CHECKING.rst b/docs/reference/autoplex.data.jobs.TYPE_CHECKING.rst new file mode 100644 index 000000000..1abf902d2 --- /dev/null +++ b/docs/reference/autoplex.data.jobs.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.data.jobs + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.data.jobs.generate_randomized_structures.rst b/docs/reference/autoplex.data.jobs.generate_randomized_structures.rst new file mode 100644 index 000000000..25debc142 --- /dev/null +++ b/docs/reference/autoplex.data.jobs.generate_randomized_structures.rst @@ -0,0 +1,6 @@ +generate\_randomized\_structures +================================ + +.. currentmodule:: autoplex.data.jobs + +.. autofunction:: generate_randomized_structures \ No newline at end of file diff --git a/docs/reference/autoplex.data.jobs.phonon_maker_random_structures.rst b/docs/reference/autoplex.data.jobs.phonon_maker_random_structures.rst new file mode 100644 index 000000000..032c5ed20 --- /dev/null +++ b/docs/reference/autoplex.data.jobs.phonon_maker_random_structures.rst @@ -0,0 +1,6 @@ +phonon\_maker\_random\_structures +================================= + +.. currentmodule:: autoplex.data.jobs + +.. autofunction:: phonon_maker_random_structures \ No newline at end of file diff --git a/docs/reference/autoplex.data.jobs.rst b/docs/reference/autoplex.data.jobs.rst new file mode 100644 index 000000000..22afad80b --- /dev/null +++ b/docs/reference/autoplex.data.jobs.rst @@ -0,0 +1,56 @@ +autoplex.data.jobs +================== + +.. automodule:: autoplex.data.jobs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + + generate_randomized_structures + phonon_maker_random_structures + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + TYPE_CHECKING + + + + + + + + + + diff --git a/docs/reference/autoplex.data.rst b/docs/reference/autoplex.data.rst new file mode 100644 index 000000000..d45c31909 --- /dev/null +++ b/docs/reference/autoplex.data.rst @@ -0,0 +1,44 @@ +autoplex.data +============= + +.. automodule:: autoplex.data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + autoplex.data.flows + autoplex.data.jobs + autoplex.data.utils + diff --git a/docs/reference/autoplex.data.utils.rst b/docs/reference/autoplex.data.utils.rst new file mode 100644 index 000000000..c69a8af44 --- /dev/null +++ b/docs/reference/autoplex.data.utils.rst @@ -0,0 +1,33 @@ +autoplex.data.utils +=================== + +.. automodule:: autoplex.data.utils + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/reference/autoplex.fitting.flows.MLIPFitMaker.rst b/docs/reference/autoplex.fitting.flows.MLIPFitMaker.rst new file mode 100644 index 000000000..45914f829 --- /dev/null +++ b/docs/reference/autoplex.fitting.flows.MLIPFitMaker.rst @@ -0,0 +1,8 @@ +MLIPFitMaker +============ + +.. currentmodule:: autoplex.fitting.flows + +.. autoclass:: MLIPFitMaker + :show-inheritance: + :members: \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.flows.TYPE_CHECKING.rst b/docs/reference/autoplex.fitting.flows.TYPE_CHECKING.rst new file mode 100644 index 000000000..3c5c1016d --- /dev/null +++ b/docs/reference/autoplex.fitting.flows.TYPE_CHECKING.rst @@ -0,0 +1,6 @@ +TYPE\_CHECKING +============== + +.. currentmodule:: autoplex.fitting.flows + +.. autodata:: TYPE_CHECKING \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.flows.rst b/docs/reference/autoplex.fitting.flows.rst new file mode 100644 index 000000000..66b12959e --- /dev/null +++ b/docs/reference/autoplex.fitting.flows.rst @@ -0,0 +1,50 @@ +autoplex.fitting.flows +====================== + +.. automodule:: autoplex.fitting.flows + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. rubric:: Classes + + .. autosummary:: + :toctree: + :nosignatures: + + MLIPFitMaker + TYPE_CHECKING + + + + + + + + + + diff --git a/docs/reference/autoplex.fitting.jobs.gapfit.rst b/docs/reference/autoplex.fitting.jobs.gapfit.rst new file mode 100644 index 000000000..913810e46 --- /dev/null +++ b/docs/reference/autoplex.fitting.jobs.gapfit.rst @@ -0,0 +1,6 @@ +gapfit +====== + +.. currentmodule:: autoplex.fitting.jobs + +.. autofunction:: gapfit \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.jobs.rst b/docs/reference/autoplex.fitting.jobs.rst new file mode 100644 index 000000000..e391eb6bc --- /dev/null +++ b/docs/reference/autoplex.fitting.jobs.rst @@ -0,0 +1,42 @@ +autoplex.fitting.jobs +===================== + +.. automodule:: autoplex.fitting.jobs + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + + gapfit + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/reference/autoplex.fitting.rst b/docs/reference/autoplex.fitting.rst new file mode 100644 index 000000000..5ef371886 --- /dev/null +++ b/docs/reference/autoplex.fitting.rst @@ -0,0 +1,44 @@ +autoplex.fitting +================ + +.. automodule:: autoplex.fitting + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. rubric:: Modules + +.. autosummary:: + :toctree: + :recursive: + + autoplex.fitting.flows + autoplex.fitting.jobs + autoplex.fitting.utils + diff --git a/docs/reference/autoplex.fitting.utils.gap_hyperparameter_constructor.rst b/docs/reference/autoplex.fitting.utils.gap_hyperparameter_constructor.rst new file mode 100644 index 000000000..e301dfd4f --- /dev/null +++ b/docs/reference/autoplex.fitting.utils.gap_hyperparameter_constructor.rst @@ -0,0 +1,6 @@ +gap\_hyperparameter\_constructor +================================ + +.. currentmodule:: autoplex.fitting.utils + +.. autofunction:: gap_hyperparameter_constructor \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.utils.get_list_of_vasp_calc_dirs.rst b/docs/reference/autoplex.fitting.utils.get_list_of_vasp_calc_dirs.rst new file mode 100644 index 000000000..e3cfe8728 --- /dev/null +++ b/docs/reference/autoplex.fitting.utils.get_list_of_vasp_calc_dirs.rst @@ -0,0 +1,6 @@ +get\_list\_of\_vasp\_calc\_dirs +=============================== + +.. currentmodule:: autoplex.fitting.utils + +.. autofunction:: get_list_of_vasp_calc_dirs \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.utils.load_gap_hyperparameter_defaults.rst b/docs/reference/autoplex.fitting.utils.load_gap_hyperparameter_defaults.rst new file mode 100644 index 000000000..79b0eb41e --- /dev/null +++ b/docs/reference/autoplex.fitting.utils.load_gap_hyperparameter_defaults.rst @@ -0,0 +1,6 @@ +load\_gap\_hyperparameter\_defaults +=================================== + +.. currentmodule:: autoplex.fitting.utils + +.. autofunction:: load_gap_hyperparameter_defaults \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.utils.outcar_2_extended_xyz.rst b/docs/reference/autoplex.fitting.utils.outcar_2_extended_xyz.rst new file mode 100644 index 000000000..43edb1979 --- /dev/null +++ b/docs/reference/autoplex.fitting.utils.outcar_2_extended_xyz.rst @@ -0,0 +1,6 @@ +outcar\_2\_extended\_xyz +======================== + +.. currentmodule:: autoplex.fitting.utils + +.. autofunction:: outcar_2_extended_xyz \ No newline at end of file diff --git a/docs/reference/autoplex.fitting.utils.rst b/docs/reference/autoplex.fitting.utils.rst new file mode 100644 index 000000000..f45d166a5 --- /dev/null +++ b/docs/reference/autoplex.fitting.utils.rst @@ -0,0 +1,48 @@ +autoplex.fitting.utils +====================== + +.. automodule:: autoplex.fitting.utils + + + + + + + + .. rubric:: Functions + + .. autosummary:: + :toctree: + :nosignatures: + + gap_hyperparameter_constructor + get_list_of_vasp_calc_dirs + load_gap_hyperparameter_defaults + outcar_2_extended_xyz + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/reference/index.rst b/docs/reference/index.rst new file mode 100644 index 000000000..a4e2055e8 --- /dev/null +++ b/docs/reference/index.rst @@ -0,0 +1,18 @@ +.. _api: + +API reference +------------- + +This section gives an overview of the API for autoplex. + +.. currentmodule:: autoplex + +.. autosummary:: + :recursive: + :toctree: + :nosignatures: + + auto + benchmark + data + fitting diff --git a/docs/user/index.md b/docs/user/index.md new file mode 100644 index 000000000..3c66669b3 --- /dev/null +++ b/docs/user/index.md @@ -0,0 +1,7 @@ +Getting started +================ +```{include} ../../README.md +--- +start-line: 3 +--- +``` diff --git a/docs/user/tutorials.md b/docs/user/tutorials.md new file mode 100644 index 000000000..06110e944 --- /dev/null +++ b/docs/user/tutorials.md @@ -0,0 +1,5 @@ +Tutorials +========== + +`autoplex` tutorials can be added in this file (one can also replace it with juypter notebook if necessary with same name) + diff --git a/pyproject.toml b/pyproject.toml index 9908799d3..409d9211d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -41,17 +41,18 @@ exclude = ["tutorials", "tests"] [project.optional-dependencies] -docs = ["Sphinx==4.5.0", - "jupyter", - "sphinx-argparse", - "sphinx-book-theme==0.3.3", - "m2r2", - "myst-parser", - "docutils", - "mendeleev==0.14.0", - "pymatgen>=2023.9.10", - "sphinx-argparse==0.4.0", - "typing"] +docs = [ + "autodoc_pydantic==2.0.1", + "ipython", + "jsonschema[format]", + "myst_parser==2.0.0", + "numpydoc==1.6.0", + "sphinx-copybutton==0.5.2", + "sphinx==7.2.6", + "sphinx_design==0.5.0", + "myst-nb==1.0.0", + "sphinx-book-theme==1.1.0", +] strict = [ #"pymatgen==2023.9.10",