Merge branch 'main' into visualize-fixes

openforcefield · Dec 20, 2023 · a57a88d · a57a88d
2 parents 584a039 + 524a0e6
commit a57a88d
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -164,7 +164,7 @@ jobs:
       - name: Run notebooks in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
         run: |
-          pytest -v --no-cov --nbval --ignore docs/_build/ docs/
+          pytest -v --no-cov --durations=5 --nbval --ignore docs/_build/ docs/
 
       - name: Run examples in docstrings
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}

diff --git a/.github/workflows/installer.yml b/.github/workflows/installer.yml
@@ -68,7 +68,7 @@ jobs:
         ls build
 
     - name: Upload installer as artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: ${{ matrix.os }}_py${{ matrix.python-version }}.sh
         path: toolkit-installer-constructor/build/openff-toolkit*/openff-toolkit*.sh

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -26,7 +26,7 @@ repos:
   hooks:
     - id: nbqa-pyupgrade
       args:
-        - --py37-plus
+        - --py39-plus
     - id: nbqa-isort
     - id: nbqa-flake8
       args:

diff --git a/docs/index.md b/docs/index.md
@@ -23,6 +23,7 @@ maxdepth: 1
 
 users/concepts
 users/molecule_cookbook
+users/pdb_cookbook/index
 users/smirnoff
 users/virtualsites
 users/developing

diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -23,6 +23,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Improved documentation and warnings
 
+- [PR #1732](https://github.com/openforcefield/openff-toolkit/pull/1732): Add documentation describing the use of PDB files with the toolkit.
+
 ## 0.14.5
 
 ### Bugfixes

diff --git a/docs/users/molecule_cookbook.ipynb b/docs/users/molecule_cookbook.ipynb
diff --git a/docs/users/pdb_cookbook/6hvi_prepared.pdb b/docs/users/pdb_cookbook/6hvi_prepared.pdb
diff --git a/docs/users/pdb_cookbook/RAMP1_solv_box_ions.pdb b/docs/users/pdb_cookbook/RAMP1_solv_box_ions.pdb
diff --git a/docs/users/pdb_cookbook/gromacs_solv_complex.pdb b/docs/users/pdb_cookbook/gromacs_solv_complex.pdb