Docker tweaks

.github/workflows/test.yml

@@ -34,9 +34,23 @@ jobs:
           pip install -q -U pip
           pip install --progress-bar=off -r requirements.txt
 
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
       - name: Docker build
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          load: true
+          tags: covid19:latest
+
+      - name: Check docker image
         run: |
-          docker build -t covid19 .
+          echo "######## DOCKER IMAGES ########"
+          docker images
+          # ensure image is actually present before moving on
+          docker image inspect covid19:latest && echo "--- image built and loaded"
+          echo "######## DOCKER IMAGES ########"
 
       - name: Run lint checks & tests
         run: |

Dockerfile

@@ -34,15 +34,10 @@ ENV PATH=$PATH:/opt/miniconda3/bin/
 
 # install environment's dependencies
 COPY environment.yml /opt/
-RUN conda env create -f /opt/environment.yml
-
-# install artic into conda environment "artic"
-RUN git clone https://github.com/artic-network/fieldbioinformatics.git \
-        && cd fieldbioinformatics \
-        && git checkout 1.2.1 \
-      	&& conda env create -f environment.yml \
-        && conda run -n artic python setup.py install \
-        && conda clean -a
+RUN conda env create --solver libmamba --file /opt/environment.yml
+
+RUN conda create -n artic
+RUN conda install --name artic --solver libmamba -c bioconda -c conda-forge -c defaults artic==1.2.3
 
 # install snpeff
 RUN curl -k -L https://sourceforge.net/projects/snpeff/files/snpEff_v4_5covid19_core.zip/download --output snpEff_v4_5covid19_core.zip\