+
+
+ 
+
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+ 
+
+Optimize force field parameters against reference data
+ + + +--- The `descent` framework aims to offer a modern API for training classical force field parameters (either from a traditional format such as SMIRNOFF or from some ML model) against reference data using `pytorch`. @@ -32,39 +44,6 @@ mamba install -c conda-forge jupyter To get started, see the [examples](examples). -## Development - -A development conda environment can be created and activated by running: - -```shell -make env -conda activate descent -``` - -The environment will include all example and development dependencies, including linters and testing apparatus. - -Unit / example tests can be run using: - -```shell -make test -``` - -The codebase can be formatted by running: - -```shell -make format -``` - -or checked for lint with: - -```shell -make lint -``` - -## License - -The main package is release under the [MIT license](LICENSE). - ## Copyright Copyright (c) 2023, Simon Boothroyd diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml index 87355e7..7cf0eba 100644 --- a/devtools/envs/base.yaml +++ b/devtools/envs/base.yaml @@ -52,3 +52,14 @@ dependencies: - pytest-mock - codecov + + # Docs + - mkdocs + - mkdocs-material + - mkdocs-gen-files + - mkdocs-literate-nav + - mkdocs-jupyter + - mkdocstrings + - mkdocstrings-python + - black + - mike diff --git a/docs/development.md b/docs/development.md new file mode 100644 index 0000000..8bba810 --- /dev/null +++ b/docs/development.md @@ -0,0 +1,28 @@ +# Development + +To create a development environment, you must have [`mamba` installed](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html). + +A development conda environment can be created and activated with: + +```shell +make env +conda activate descent +``` + +To format the codebase: + +```shell +make format +``` + +To run the unit tests: + +```shell +make test +``` + +To serve the documentation locally: + +```shell +mkdocs serve +``` diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..612c7a5 --- /dev/null +++ b/docs/index.md @@ -0,0 +1 @@ +--8<-- "README.md" diff --git a/docs/javascripts/mathjax.js b/docs/javascripts/mathjax.js new file mode 100644 index 0000000..06dbf38 --- /dev/null +++ b/docs/javascripts/mathjax.js @@ -0,0 +1,16 @@ +window.MathJax = { + tex: { + inlineMath: [["\\(", "\\)"]], + displayMath: [["\\[", "\\]"]], + processEscapes: true, + processEnvironments: true + }, + options: { + ignoreHtmlClass: ".*|", + processHtmlClass: "arithmatex" + } +}; + +document$.subscribe(() => { + MathJax.typesetPromise() +}) diff --git a/docs/scripts/gen_ref_pages.py b/docs/scripts/gen_ref_pages.py new file mode 100644 index 0000000..2e0e803 --- /dev/null +++ b/docs/scripts/gen_ref_pages.py @@ -0,0 +1,39 @@ +"""Generate the code reference pages and navigation.""" + +import pathlib + +import mkdocs_gen_files + +nav = mkdocs_gen_files.Nav() +src = pathlib.Path(__file__).parent.parent.parent / "descent" + +mod_symbol = '