Merge pull request #1161 from cfe-lab/update-devcontainer

Update devcontainer

.devcontainer/devcontainer.json

@@ -5,7 +5,7 @@
 
   // More info: https://containers.dev/guide/dockerfile
   "build": {
-    "dockerfile": "Dockerfile"
+    "dockerfile": "../Dockerfile"
   },
 
   // Features to add to the dev container. More info: https://containers.dev/features.
@@ -14,8 +14,8 @@
   // Use 'forwardPorts' to make a list of ports inside the container available locally.
   // "forwardPorts": [],
 
-  // Use 'postCreateCommand' to run commands after the container is created.
-  "postCreateCommand": "python -m pip install .[dev]",
+  // Use 'onCreateCommand' to run commands after the container is created, but before anything else starts.
+  "onCreateCommand": "python -m pip install .[dev,test]",
 
   // Configure tool-specific properties.
   "customizations": {

.dockerignore

@@ -2,6 +2,9 @@
 .idea
 bin
 docs
+*cache*
+.github
+Dockerfile
 micall/tests/working
 micall/tests/microtest/scratch
 micall/tests/microtest/micall-results
@@ -12,4 +15,4 @@ venv_micall
 */*.pyc
 */*/*.pyc
 */*/*/*.pyc
-simgs
+simgs

.github/workflows/build-and-test.yml

@@ -76,6 +76,17 @@ jobs:
           python -m pip install codecov
           codecov
 
+  docker-test:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: Build docker image
+        run: docker build --tag micall --file Dockerfile .
+      - name: Run docker image entrypoint
+        run: docker run micall --help
+      - name: Check docker image entrypoint
+        run: docker run micall --help | grep -i -e 'docker'
+
   singularity-test:
     runs-on: ubuntu-20.04
     steps:

Dockerfile

@@ -86,28 +86,14 @@ RUN apt-get install -q -y zlib1g-dev libncurses5-dev libncursesw5-dev && \
 ## Install dependencies for genetracks/drawsvg
 RUN apt-get install -q -y libcairo2-dev
 
-COPY pyproject.toml /opt/micall/
+COPY . /opt/micall/
 
-## Python packages, plus trigger matplotlib to build its font cache
-WORKDIR /opt
-RUN pip install --upgrade pip && \
-  pip install .[basespace] && \
-  python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
+RUN pip install --upgrade pip
+RUN pip install /opt/micall[basespace]
+RUN micall make_blast_db
 
-## MiCall
-COPY micall_docker.py micall_kive.py micall_kive_resistance.py version.tx[t] /opt/micall/
-COPY micall/__init__.py micall/project* /opt/micall/micall/
-
-COPY micall/blast_db/make_blast_db.py    /opt/micall/micall/blast_db/make_blast_db.py
-COPY micall/core    /opt/micall/micall/core/
-COPY micall/data    /opt/micall/micall/data/
-COPY micall/drivers    /opt/micall/micall/drivers/
-COPY micall/g2p     /opt/micall/micall/g2p/
-COPY micall/resistance   /opt/micall/micall/resistance/
-COPY micall/monitor /opt/micall/micall/monitor/
-COPY micall/utils   /opt/micall/micall/utils/
-
-RUN python /opt/micall/micall/blast_db/make_blast_db.py
+## Trigger matplotlib to build its font cache
+RUN python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
 
 WORKDIR /data
-ENTRYPOINT ["python", "/opt/micall/micall_docker.py"]
+ENTRYPOINT ["micall", "micall_docker"]