Merge pull request #77 from crosenth/master

Added some unittests

.github/workflows/docker-pipeline.yml

@@ -2,14 +2,19 @@ name: Build and push docker image for pipeline
 
 on:
   push:
-    tags: [ '*.*.*' ]
+    branches:
+      - "*"
+    tags: 
+      - "*.*.*"
+  schedule:
+    - cron: '0 6 15 * *'  # 15th of each month at 6am
 
 env:
   REGISTRY: ghcr.io
   IMAGE_NAME: ${{ github.repository }}
 
 jobs:
-  build_pipeline_image:
+  build_and_test_pipeline_image:
     runs-on: ubuntu-latest
 
     steps:
@@ -29,9 +34,31 @@ jobs:
       with:
         images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
+    - name: Build image
+      uses: docker/build-push-action@v6
+      with:
+        annotations: ${{ steps.meta.outputs.annotations }}
+        build-args: |
+          MEFETCH_EMAIL=${{ secrets.MEFETCH_EMAIL }}
+          MEFETCH_API_KEY=${{ secrets.MEFETCH_API_KEY }}
+          YA16SDB_VERSION=${{ steps.meta.outputs.version }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max
+        labels: ${{ steps.meta.outputs.labels }}
+        load: true
+        push: false
+        tags: |
+          ${{ steps.meta.outputs.tags }}
+          gha_image
+
+    - name: Test run and unnitests
+      run: docker run gha_image /bin/bash -c "scons settings=testfiles/settings.conf;python -m unittest"
+
     - name: Build and push tag
+      if: github.ref_type == 'tag'
       uses: docker/build-push-action@v6
       with:
+        annotations: ${{ steps.meta.outputs.annotations }}
         cache-from: type=gha
         cache-to: type=gha,mode=max
         labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -1,23 +1,20 @@
 FROM python:3.11-bookworm
-
-RUN apt-get update && apt-get upgrade -y && apt-get install --assume-yes --no-install-recommends \
-    ca-certificates git wget
-
-ADD requirements.txt /usr/local/share/ya16sdb/
-ADD bin/bootstrap.sh /usr/local/share/ya16sdb/bin/
-
+ARG MEFETCH_API_KEY MEFETCH_EMAIL YA16SDB_VERSION
+ENV \
+MEFETCH_API_KEY=${MEFETCH_API_KEY} \
+MEFETCH_EMAIL=${MEFETCH_EMAIL} \
+PIP_ROOT_USER_ACTION=ignore \
+SCONSFLAGS="--file /usr/local/share/ya16sdb/SConstruct" \
+YA16SDB_VERSION=${YA16SDB_VERSION}
+RUN apt-get update && apt-get upgrade -y && apt-get install -y ca-certificates wget
 WORKDIR /usr/local/share/ya16sdb/
-RUN ["/bin/bash", "-c", "bin/bootstrap.sh /usr/local/"]
-
-ADD .git/ /usr/local/share/ya16sdb/.git/
-ADD data/ /usr/local/share/ya16sdb/data/
-ADD bin/ /usr/local/share/ya16sdb/bin/
-ADD SConstruct ncbi.conf /usr/local/share/ya16sdb/
-
-RUN find /usr/local/share/ya16sdb/ -type f -exec chmod 644 {} \; && \
-find /usr/local/share/ya16sdb/ -type d -exec chmod 755 {} \; && \
-find /usr/local/share/ya16sdb/bin/ -type f -exec chmod 755 {} \;
-
-ENV SCONSFLAGS="--file /usr/local/share/ya16sdb/SConstruct"
-
+COPY requirements.txt SConstruct ncbi.conf ./
+COPY testfiles/ ./testfiles/
+COPY tests/ ./tests/
+COPY bin/ ./bin/
+COPY data/ ./data/
+RUN bin/bootstrap.sh /usr/local/
+RUN find . -type f -exec chmod 644 {} \; && \
+find . -type d -exec chmod 755 {} \; && \
+find ./bin/ -type f -exec chmod 755 {} \;
 CMD ["scons", "--dry-run"]