Merge pull request #1187 from cfe-lab/split-denovo-dependencies

Split denovo dependencies

.devcontainer/devcontainer.json

@@ -15,7 +15,7 @@
   // "forwardPorts": [],
 
   // Use 'onCreateCommand' to run commands after the container is created, but before anything else starts.
-  "onCreateCommand": "python -m pip install .[dev,test]",
+  "onCreateCommand": "python -m pip install .[denovo,watcher,dev,test]",
 
   // Configure tool-specific properties.
   "customizations": {

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

@@ -53,11 +53,9 @@ jobs:
           echo "/opt/bowtie2" >> $GITHUB_PATH
 
       - name: Install MiCall's Python dependencies
-        # Have to clean up alignment build files. Otherwise, they'll get reused
-        # in Singularity build with the wrong GLIBC libraries.
         run: |
           python -m pip install --upgrade pip
-          pip install .[dev,test]
+          pip install .[denovo,watcher,dev,test]
 
       - name: Run type checker
         run: |
@@ -73,7 +71,6 @@ jobs:
       - name: Report code coverage
         run: |
           rm -rf micall/tests/microtest/scratch
-          python -m pip install codecov
           codecov
 
   docker-test:

Dockerfile

@@ -89,7 +89,7 @@ RUN pip install --upgrade pip
 
 COPY . /opt/micall/
 
-RUN pip install /opt/micall[basespace]
+RUN pip install /opt/micall[denovo,basespace]
 RUN micall make_blast_db
 
 ## Trigger matplotlib to build its font cache

Singularity

@@ -96,7 +96,7 @@ From: python:3.11
     apt-get install -q -y libcairo2-dev
     # Install micall main executable.
     pip install --upgrade pip
-    pip install /opt/micall
+    pip install /opt/micall[denovo]
     micall make_blast_db
     # Also trigger matplotlib to build its font cache.
     python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'

pyproject.toml

@@ -24,7 +24,6 @@ classifiers = [
 dependencies = [
     # Requirements for running the bare pipeline under Kive.
     "pytz==2024.2",
-    "iva @ git+https://github.com/cfe-lab/[email protected]",
     "biopython==1.84",
     "gotoh @ git+https://github.com/cfe-lab/[email protected]#egg=gotoh&subdirectory=alignment/gotoh",
     "pyvdrm @ git+https://github.com/cfe-lab/[email protected]",
@@ -64,6 +63,11 @@ dev = [
     "mypy==1.13.0",
     "mypy-extensions==1.0.0",
     "gprof2dot==2024.6.6",
+    "codecov==2.1.13",  # For reporting the code coverage.
+]
+denovo = [
+    # Requirements for running De-Novo pipeline (only problematic ones).
+    "iva @ git+https://github.com/cfe-lab/[email protected]",
 ]
 watcher = [
     # Requirements for running the MISEQ_MONITOR.py script