Merge remote-tracking branch 'upstream/main' into better-zstandard-ba…

…ndaid

.github/workflows/CI.yml

@@ -76,9 +76,14 @@ jobs:
       - name: Install environment with ${{ env.JOBNAME }}
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: devtools/conda-envs/${{ env.ENVFILE }}.yaml
           create-args: >-
             python=${{ matrix.python-version }}
+          # default - will pull down 2.0 which we don't want!
+          # micromamba-version: latest
+          # pin to latest 1.x release
+          micromamba-version: "1.5.10-0"
 
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:

.github/workflows/beta_rc.yaml

@@ -34,16 +34,23 @@ jobs:
       - name: Install environment with ${{ env.JOBNAME }}
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: devtools/conda-envs/test_env.yaml
           condarc: |
             channels:
               - conda-forge/label/openmm_rc
               - conda-forge/label/mdtraj_rc
+              - conda-forge/label/openff-toolkit_rc
+              - conda-forge/label/openff-interchange_rc
               - openeye/label/rc
               - openeye
               - conda-forge
           create-args: >-
             python=${{ matrix.python-version }}
+          # default - will pull down 2.0 which we don't want!
+          # micromamba-version: latest
+          # pin to latest 1.x release
+          micromamba-version: "1.5.10-0"
 
       - name: Make oe_license.txt file from GH org secret "OE_LICENSE"
         env:

.github/workflows/conda.yml

@@ -38,16 +38,22 @@ jobs:
         uses: mamba-org/setup-micromamba@v1
         if: ${{ matrix.openeye == 'false' }}
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: devtools/conda-envs/conda.yaml
           create-args: >-
             python=${{ matrix.python-version }}
       - name: Install from conda with OpenEye
         uses: mamba-org/setup-micromamba@v1
         if: ${{ matrix.openeye == 'true' }}
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: devtools/conda-envs/conda_oe.yaml
           create-args: >-
             python=${{ matrix.python-version }}
+          # default - will pull down 2.0 which we don't want!
+          # micromamba-version: latest
+          # pin to latest 1.x release
+          micromamba-version: "1.5.10-0"
 
       - name: Additional info about the build
         run: |
@@ -126,4 +132,4 @@ jobs:
 
       - name: Run example notebooks
         run: |
-          python -m pytest -r fE -v -x --tb=short --nbval-lax --ignore=examples/deprecated examples
+          python -m pytest -r fE -v -x --tb=short --nbval-lax --ignore=examples/deprecated examples

.github/workflows/examples.yml

@@ -62,9 +62,14 @@ jobs:
       - name: Install conda environment with ${{ env.ENVFILE }}
         uses: mamba-org/setup-micromamba@v1
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: devtools/conda-envs/${{env.ENVFILE}}-examples.yaml
           create-args: >-
             python=${{ matrix.python-version }}
+          # default - will pull down 2.0 which we don't want!
+          # micromamba-version: latest
+          # pin to latest 1.x release
+          micromamba-version: "1.5.10-0"
 
       - name: Additional info about the build
         run: |

.github/workflows/installer.yml

@@ -25,6 +25,7 @@ jobs:
     - name: Install conda environment
       uses: mamba-org/setup-micromamba@v1
       with:
+        micromamba-version: '1.5.10-0'
         environment-file: devtools/conda-envs/installer.yaml
         create-args: >-
           python=${{ matrix.python-version }}
@@ -108,4 +109,3 @@ jobs:
         # This should work if run directly at release time, but a safer approach would be
         # to `git checkout` the corresponding tag of the release, see PR #577
         pytest $PYTEST_ARGS ../
-

docs/index.md

@@ -12,7 +12,7 @@ maxdepth: 1
 installation
 examples
 releasehistory
-faq
+Frequently Asked Questions (FAQ) <https://docs.openforcefield.org/faq>
 :::
 
 :::{toctree}

docs/users/molecule_cookbook.ipynb

@@ -391,7 +391,7 @@
    "id": "821c4687",
    "metadata": {},
    "source": [
-    "We can downgrade this error to a warning with the `allow_undefined_stereo` argument. This will create a molecule with undefined stereochemistry, which might lead to incorrect parametrization or surprising conformer generation. See the [FAQ](../faq.md#im-getting-stereochemistry-errors-when-loading-a-molecule-from-a-smiles-string) for more details."
+    "We can downgrade this error to a warning with the `allow_undefined_stereo` argument. This will create a molecule with undefined stereochemistry, which might lead to incorrect parametrization or surprising conformer generation. See the [FAQ](inv:openff.docs#faq-stereochemistry-errors-from-smiles) for more details."
    ]
   },
   {