Merge remote-tracking branch 'origin/master' into Haploflow-test1

Dockerfile

@@ -68,13 +68,17 @@ RUN apt-get update && \
 RUN apt-get install -q -y libcairo2-dev
 RUN pip install --upgrade pip
 
-COPY . /opt/micall/
-
+## Install just the dependencies of MiCall (for faster build times in development).
+COPY pyproject.toml README.md /opt/micall/
 RUN pip install /opt/micall[denovo,basespace]
-RUN micall make_blast_db
 
 ## Trigger matplotlib to build its font cache
 RUN python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
 
+COPY . /opt/micall/
+
+RUN pip install /opt/micall[denovo,basespace]
+RUN micall make_blast_db
+
 WORKDIR /data
 ENTRYPOINT ["micall", "micall_docker"]

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "pyvdrm @ git+https://github.com/cfe-lab/[email protected]",
     "numpy==2.1.3",
     "scipy==1.14.1",
-    "matplotlib==3.9.2",
+    "matplotlib==3.9.3",
     "cutadapt==4.9",
     "python-Levenshtein==0.26.1",
     "PyYAML==6.0.2",
@@ -44,8 +44,8 @@ dependencies = [
 [project.optional-dependencies]
 test = [
     # Dependencies required for running the test suite
-    "pytest==8.3.3",
-    "coverage==7.6.4",
+    "pytest==8.3.4",
+    "coverage==7.6.8",
     "pandas==2.2.3",
     "seaborn==0.13.2",
     "ete3",
@@ -58,7 +58,7 @@ test = [
 ]
 dev = [
     # Dependencies required for development (linting, type checking, etc.)
-    "ruff==0.7.2",
+    "ruff==0.8.1",
     "mypy==1.13.0",
     "mypy-extensions==1.0.0",
     "gprof2dot==2024.6.6",