Merge branch 'main' into stable

.github/workflows/build.yml

@@ -208,7 +208,7 @@ jobs:
           files: ${{ needs.BuildPip.outputs.asset }}
 
   Docker:
-    needs: [BuildPip]
+    needs: [Tag, BuildPip]
     runs-on: ubuntu-latest
     permissions:
       packages: write
@@ -242,12 +242,8 @@ jobs:
           echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
       - name: 'Push image'
         run: |
-          IMAGE_ID=ghcr.io/${{ github.repository_owner }}/${{ env.image_name }}
-          # Change all uppercase to lowercase
-          IMAGE_ID=$(echo "$IMAGE_ID" | tr '[:upper:]' '[:lower:]')
-          # Strip git ref prefix from version
-          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
-
+          IMAGE_ID=$(echo ghcr.io/${{ github.repository_owner }}/${{ env.image_name }} | tr '[:upper:]' '[:lower:]')
+          VERSION=${{ needs.Tag.outputs.tag }}
           echo "IMAGE_ID=$IMAGE_ID | VERSION=$VERSION"
           docker tag ${{ env.image_name }} "${IMAGE_ID}:${VERSION}"
           docker push "${IMAGE_ID}:${VERSION}"

Dockerfile

@@ -1,6 +1,6 @@
-FROM python:3
+FROM python:3.9
 
 COPY *whl /opt/
 RUN pip install --no-cache-dir /opt/*whl
 
-CMD ["python", "-m", "rpfa"]
+ENTRYPOINT ["python", "-m", "rpfa"]

README.md

@@ -36,6 +36,21 @@ python -m rpfa \
     [output file]
     --output-file <CSV file>
 ```
+Or with docker:  
+```sh
+docker run \
+    -it \
+    --rm \
+    -v $PWD:/data \
+    rpfbaanalysis:latest \
+    --input-model /data/<SBML file> \
+    --input-pathway-file /data/<SBML file> \
+    --input-medium-file /data/<CSV file> \
+    --biomass-rxn-id <id reaction, str> \
+    --target-rxn-id <id reaction, str> \
+    --substrate-rxn-id <id reaction, str>
+    --output-file /data/<CSV file>
+```
 
 ## Tests
 *pytest* is installed with this package.