Build only needed packages for docs

BioinfoMachineLearning · May 24, 2024 · 1eee695 · 1eee695
1 parent 10c81ef
commit 1eee695
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Showing 3 changed files with 18 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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