diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index 925aae96..74957c81 100644 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -23,7 +23,7 @@ jobs: use-mamba: true - name: Install dependencies run: | - mamba env update -f environments/posebench_environment.yaml && pip install -e . && pip install -r docs/.docs.requirements + mamba install -c conda-forge -y openff-amber-ff-ports openff-forcefields openff-interchange openff-interchange-base openff-models openff-toolkit openff-toolkit-base openff-units openff-utilities openmm openmmforcefields && pip install -e . && pip install -r docs/.docs.requirements - name: Sphinx build run: | rm -rf docs/build/ && sphinx-build docs/source/ docs/build/ diff --git a/docs/.docs.requirements b/docs/.docs.requirements index 172e1712..3d9232bb 100644 --- a/docs/.docs.requirements +++ b/docs/.docs.requirements @@ -1,3 +1,6 @@ +beartype +biopandas +biopython docutils==0.20.1 # NOTE: currently required due to an `m2r2` bug: https://github.com/CrossNox/m2r2/issues/68 furo ipython @@ -7,8 +10,16 @@ matplotlib nbsphinx nbsphinx-link nbstripout +pandas pandoc +pdb4amber +posebusters +prody pydocstyle +pypdb +rdkit +rdkit-pypi +rootutils sphinx sphinx-copybutton sphinx-inline-tabs @@ -17,4 +28,6 @@ sphinxext-opengraph sphinxcontrib-gtagjs sphinxcontrib-jquery sphinx_codeautolink +timeout_decorator +tqdm watermark diff --git a/environments/posebench_environment.yaml b/environments/posebench_environment.yaml index 5d8c4053..ae4d2325 100644 --- a/environments/posebench_environment.yaml +++ b/environments/posebench_environment.yaml @@ -10,7 +10,7 @@ channels: dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=2_kmp_llvm - - ambertools + - ambertools=23.3=py39h7fa913e_6 - antlr-python-runtime=4.9.3=pyhd8ed1ab_1 - argon2-cffi=23.1.0=pyhd8ed1ab_0 - argon2-cffi-bindings=21.2.0=py39hd1e30aa_4 @@ -37,7 +37,7 @@ dependencies: - bson=0.5.9=py_0 - bzip2=1.0.8=h7f98852_4 - c-ares=1.25.0=hd590300_0 - - c-blosc2 + - c-blosc2=2.13.2=hb4ffafa_0 - ca-certificates=2024.2.2=hbcca054_0 - cachecontrol=0.13.1=pyhd8ed1ab_0 - cachecontrol-with-filecache=0.13.1=pyhd8ed1ab_0 @@ -242,7 +242,7 @@ dependencies: - openh264=2.1.1=h780b84a_0 - openjpeg=2.4.0=hb52868f_1 - openmm=8.1.0=py39he81762f_1 - - openmmforcefields + - openmmforcefields=0.11.2=pyhd8ed1ab_1 - openssl=3.3.0=hd590300_0 - ordered-set=4.1.0=py39h06a4308_0 - orjson=3.8.8=py39h52d8a92_0 @@ -285,7 +285,7 @@ dependencies: - pyproject_hooks=1.0.0=py39h06a4308_0 - pyrsistent=0.18.0=py39heee7806_0 - pysocks=1.7.1=pyha2e5f31_6 - - pytables + - pytables=3.9.2=py39hfbd31a7_1 - pytest=7.4.0=py39h06a4308_0 - python=3.9.17=h0755675_0_cpython - python-build=0.10.0=py39h06a4308_0