Push Apptainer Image to GHCR + Build Installer & Docker Image using C…

…onda-Forge Package (#353)

* see if this can push to ghcr

* fix URI

* don't push docker image

* don't push docker image

* see if this lets us login to ghcr

* we can push to github's container registry directly

* now when we trigger a build, we build the latest version we can discover from the tags

* forgot to remove bit where we install package from source

* use docker ignore to make sure we keep the context as small as we can

* make it explicit we don't push before we test, and make sure we have the same build args for when we do push

* add juypterlab and notebook to docker image

* Apply suggestions from code review

.dockerignore

@@ -0,0 +1,5 @@
+# Ignore everything
+*
+
+# Only allow
+!production/environment.yml

.github/workflows/docker.yaml

@@ -59,11 +59,6 @@ jobs:
       - name: Print FQIRP
         run: echo ${{ steps.fqirp.outputs.FQIRP  }}
 
-      - name: Build package at the latest tag
-        run: |
-          python3 -m pip install --upgrade build
-          python3 -m build
-
       - name: Log in to the Container registry
         uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
         with:
@@ -92,8 +87,11 @@ jobs:
           context: .
           file: production/Dockerfile
           load: true
+          push: false
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            VERSION=${{ steps.latest-version.outputs.VERSION }}
 
       - name: Test image
         run: |
@@ -111,6 +109,8 @@ jobs:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            VERSION=${{ steps.latest-version.outputs.VERSION }}
 
       - name: Setup Apptainer
         uses: eWaterCycle/setup-apptainer@v2
@@ -120,16 +120,12 @@ jobs:
       - name: Build Apptainer Image
         run: singularity build openfe_${{ steps.latest-version.outputs.VERSION }}.sif docker-daemon:${{ steps.fqirp.outputs.FQIRP }}
 
-      - name: Test Apptainer Image
+      - name: Test & Push Apptainer Image
         run: |
           mkdir test_apptainer
           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_${{ steps.latest-version.outputs.VERSION }}.sif pytest --pyargs openfecli --pyargs openfe -v -n auto
-          cd ../
-
-      - uses: actions/upload-artifact@v3
-        with:
-          name: openfe_${{ steps.latest-version.outputs.VERSION }}.sif
-          path: openfe_${{ steps.latest-version.outputs.VERSION }}.sif
+          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

devtools/installer/construct.yaml

@@ -12,11 +12,13 @@ transmute_file_type: .conda
 
 specs:
   - conda
-  - gufe=={{ environ["VERSION"] }}
+  - jupyterlab
   - mamba
+  - notebook
   - openfe=={{ environ["VERSION"] }}
   - pip
   - pytest
+  - pytest-xdist
   - python 3.9.*
 
 # Not building an .exe for windows or a .pkg for macOS

production/Dockerfile

@@ -3,17 +3,17 @@ FROM mambaorg/micromamba:1.4.1
 LABEL org.opencontainers.image.source=https://github.com/OpenFreeEnergy/openfe
 LABEL org.opencontainers.image.description="A Python package for executing alchemical free energy calculations."
 LABEL org.opencontainers.image.licenses=MIT
+# OpenFE Version we want to build
+ARG VERSION
 
 # Don't buffer stdout & stderr streams, so if there is a crash no partial buffer output is lost
 # https://docs.python.org/3/using/cmdline.html#cmdoption-u
 ENV PYTHONUNBUFFERED=1
 
 COPY --chown=$MAMBA_USER:$MAMBA_USER production/environment.yml /tmp/env.yaml
-COPY --chown=$MAMBA_USER:$MAMBA_USER dist/*py3-none-any.whl /tmp
-RUN micromamba install -y -n base git -f /tmp/env.yaml && \
+RUN micromamba install -y -n base git "openfe==$VERSION" -f /tmp/env.yaml && \
     micromamba clean --all --yes
 
 # Ensure that conda environment is automatically activated
 # https://github.com/mamba-org/micromamba-docker#running-commands-in-dockerfile-within-the-conda-environment
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
-RUN python -m pip install --no-deps *py3-none-any.whl

production/environment.yml

@@ -2,32 +2,13 @@ name: openfe
 channels:
   - conda-forge
 dependencies:
-  - click
   # Issues with 11.8 on    lilac
   - cudatoolkit==11.7
-  - gufe==0.7.*
-  - libnetcdf<4.9
-  - lomap2>=2.1.0
-  - networkx
-  - numpy<1.24
-  - openff-models>=0.0.4
-  - openff-toolkit>=0.12.0
-  - openff-units>=0.2.0
-  - openmmforcefields>=0.11.2
-  - openmmtools==0.21.5
+  - jupyterlab
+  - notebook
+  - openfe
   - pip
-  - plugcli
   - py3dmol
-  - pydantic
   - pytest
   - pytest-xdist
   - python==3.9
-  - rdkit
-  - typing-extensions
-  # build time dep
-  - versioningit
-  # docs
-  - myst-parser
-  - sphinx-click
-  - pydata-sphinx-theme
-  - autodoc-pydantic