Merge branch 'main' into small-opt-tests

.github/workflows/ci.yaml

@@ -25,7 +25,7 @@ concurrency:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0}
 
 jobs:
   tests:

.github/workflows/docker-cron.yaml

@@ -6,13 +6,13 @@ on:
       - main
   schedule:
     # nightly tests
-    - cron: "0 7 * * *"
+    - cron: "0 14 * * 0"
 
   workflow_dispatch:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0}
 
 env:
   REGISTRY: ghcr.io
@@ -48,11 +48,6 @@ jobs:
       - name: Print FQIRP
         run: echo ${{ steps.fqirp.outputs.FQIRP  }}
 
-      - name: Build package
-        run: |
-          python3 -m pip install --upgrade build
-          python3 -m build
-
       - name: Log in to the Container registry
         uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
         with:
@@ -88,6 +83,6 @@ jobs:
         run: |
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} openfe --help
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} openfe --version
-          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import gufe; print(gufe.__version__)"
+          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import gufe; print(f'{gufe.__version__=}')"
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs gufe -v
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs openfe -v

.github/workflows/docker.yaml

@@ -7,14 +7,15 @@
 # To get a newer version, you will need to update the SHA.
 # You can also reference a tag or branch, but the action may change without warning.
 
+# Workflow to automate docker image building during the openfe release process.
 name: Create and publish a Docker image
 
 on:
   workflow_dispatch:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0}
 
 env:
   REGISTRY: ghcr.io
@@ -94,9 +95,9 @@ jobs:
         run: |
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} openfe --help
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} openfe --version
-          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import gufe; print(gufe.__version__)"
+          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} python -c "import gufe; print(f'{gufe.__version__=}')"
           docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs gufe -v
-          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs openfe -v
+          docker run --rm ${{ steps.fqirp.outputs.FQIRP }} pytest --pyargs openfe openfecli -v
 
       - name: Push Docker image
         uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
@@ -123,7 +124,7 @@ jobs:
           cd test_apptainer
           singularity run ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif --help
           singularity run ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif --version
-          singularity run ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif pytest --pyargs openfe -v -n auto
+          singularity run ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif pytest --pyargs openfe openfecli -v -n auto
           echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
           singularity push ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}-apptainer
           singularity push ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest-apptainer

.github/workflows/installer.yaml

@@ -67,7 +67,7 @@ jobs:
         # Inspired by https://github.com/conda-forge/miniforge/blob/main/.github/workflows/ci.yml
         cp ${{ steps.file-name.outputs.FILE_NAME }} $(echo ${{ steps.file-name.outputs.FILE_NAME }} | sed -e 's/-[^-]*//')
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: ${{ steps.file-name.outputs.FILE_NAME }}
         path: OpenFEforge*

.github/workflows/mypy.yaml

@@ -13,7 +13,7 @@ concurrency:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0}
 
 jobs:
   mypy:
@@ -44,7 +44,7 @@ jobs:
         run: |
           python -m pip install --no-deps git+https://github.com/OpenFreeEnergy/gufe@main
           python -m pip install mypy
-          python -m pip install types-pkg_resources
+          python -m pip install types-setuptools
           python -m pip install --no-deps -e .
 
       - name: "Environment Information"

.github/workflows/package-tests.yaml

@@ -17,9 +17,13 @@ on:
     # At 07:00 UTC on Monday and Thursday.
     - cron: "0 7 * * *"
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0}
 
 jobs:
   package-tests:

.gitignore

@@ -78,6 +78,7 @@ instance/
 # Sphinx documentation
 docs/_build/
 docs/reference/api/generated
+docs/tutorials/*.png
 
 # PyBuilder
 .pybuilder/

MANIFEST.in

@@ -7,7 +7,6 @@ recursive-include openfe/tests/data/ *.edge
 recursive-include openfe/tests/data/ *.dat
 recursive-include openfe/tests/data/ *json.gz
 recursive-include openfe/tests/data/ *json_results.gz
-include openfe/tests/data/cdk8.zip
 include openfecli/tests/data/*.json
 include openfecli/tests/data/*.tar.gz
 recursive-include openfecli/tests/ *.sdf

docs/environment.yaml

@@ -3,29 +3,28 @@ channels:
 - https://conda.anaconda.org/jaimergp/label/unsupported-cudatoolkit-shim
 - https://conda.anaconda.org/conda-forge
 dependencies:
-- autodoc-pydantic<2.0
-- lomap2>=3.0.0
-- kartograf>=1.0.0
-- openff-models>=0.0.5
+- autodoc-pydantic <2.0
+- gitpython
+- kartograf >=1.0.0
+- libsass
+- lomap2 >=3.0.0
+- myst-parser
+- nbsphinx
+- nbsphinx-link
+- openff-models >=0.0.5
 - openff-toolkit >=0.13.0
 - openff-units
 - openmm
 - packaging
 - plugcli
 - python=3.10
-- sphinx<7
+- sphinx <7.3
 - sphinx-click
-- gitpython
-- tqdm
-- libsass
-- nbsphinx
-- nbsphinx-link
-- myst-parser
+- sphinx-design
+- sphinx-toolbox
 - threadpoolctl
+- tqdm
 - pip:
-  - sphinx-design
-  - sphinx-toolbox
-  - sphinx<7
   - git+https://github.com/OpenFreeEnergy/gufe@main
   - git+https://github.com/OpenFreeEnergy/[email protected]