Merge remote-tracking branch 'upstream/main' into next

.github/workflows/CI.yml

@@ -10,6 +10,10 @@ on:
   schedule:
     - cron: "0 0 * * *"
 
+defaults:
+  run:
+    shell: bash -l {0}
+
 jobs:
   test:
 
@@ -21,8 +25,6 @@ jobs:
       matrix:
         python-version:
           - 3.7
-          # - 3.8
-          # - 3.9
         cfg:
           - os: ubuntu-latest
             conda-env: basic
@@ -40,43 +42,32 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Setup Conda Environment
-        uses: conda-incubator/[email protected]
+        uses: mamba-org/provision-with-micromamba@main
+
         with:
-          python-version: ${{ matrix.python-version }}
           environment-file: devtools/conda-envs/${{ matrix.cfg.conda-env }}.yaml
-
-          channels: openeye,conda-forge,defaults
-
-          activate-environment: test
-          auto-update-conda: true
-          auto-activate-base: false
-          show-channel-urls: true
-          mamba-version: "*"
-          miniforge-version: latest
-          miniforge-variant: Mambaforge
-          use-mamba: true
+          extra-specs: |
+            python=${{ matrix.python-version }}
+          channel-priority: "flexible"
 
       - name: License OpenEye
-        shell: bash -l {0}
+
         run: |
           echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}
           python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
         env:
           SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
 
       - name: Install Package
-        shell: bash -l {0}
         run: |
           python setup.py develop --no-deps
 
       - name: Conda Environment Information
-        shell: bash -l {0}
         run: |
           conda info
           conda list
 
       - name: Run Tests
-        shell: bash -l {0}
         run: |
           pytest -v --cov=openff --cov-config=setup.cfg openff/qcsubmit/tests/ --cov-report=xml
 

.gitignore

@@ -64,6 +64,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/api/generated
 
 # PyBuilder
 target/

.readthedocs.yml

@@ -11,4 +11,4 @@ formats:
     - pdf
 
 conda:
-  environment: docs/environment.yml
+  environment: devtools/conda-envs/docs.yaml

devtools/conda-envs/basic.yaml

@@ -25,7 +25,7 @@ dependencies:
 
   ### Core dependencies.
 
-  - openff-toolkit-base
+  - openff-toolkit-base =0.10.6
   - rdkit
   - pydantic
   - pyyaml

docs/environment.yml → devtools/conda-envs/docs.yaml

@@ -14,19 +14,22 @@ dependencies:
   - nbsphinx-link
   - sphinx_rtd_theme
   - sphinxcontrib-bibtex
+  - sphinx-notfound-page
+  - myst-parser
   - pandoc
   - ipython
 
     # Standard dependencies
-  - openff-toolkit-base
+  - openff-toolkit-base =0.10.6
 #  - rdkit                MOCKED
   - pydantic
   - pyyaml
-  - qcportal
+  - qcportal >=0.15
   - torsiondrive
   - basis_set_exchange
   - typing-extensions
   - cachetools
 
   - pip:
       - autodoc_pydantic
+      - git+https://github.com/openforcefield/openff-sphinx-theme.git@main

devtools/conda-envs/psi4.yaml

@@ -1,9 +1,9 @@
 name: test
 
 channels:
+  - psi4
   - openeye
   - conda-forge
-  - psi4/label/dev
   - defaults
 
 dependencies:
@@ -25,11 +25,17 @@ dependencies:
   - psi4 =1.4a2.dev1058+670a850
   - gau2grid =2.0.3
 
+  # Psi4 dependencies
+  - psi4 =1.5
+  - libint2=*=hc9558a2_9
+  - intel-openmp!=2019.5
+  - gau2grid >=2.0
+
   - openeye-toolkits
 
   ### Core dependencies.
 
-  - openff-toolkit-base
+  - openff-toolkit-base =0.10.6
   - rdkit
   - pydantic
   - pyyaml

docs/api.rst

@@ -1,9 +1,9 @@
 API
 ===
 
-Below is an outline of the API for ``openff-qcsubmit`` See the examples for details on how to use these objects.
+Below is an outline of the API for ``openff-qcsubmit``. See the examples for details on how to use these objects.
 
-.. warning:: The ``openff-qcsubmit`` package is still pre-alpha so the API is still in flux.
+.. warning:: The ``openff-qcsubmit`` package is still pre-alpha, so the API is still in flux.
 
 Datasets
 --------