revert to python 3.9 in containers

Author: rjchallis

.github/workflows/changes.yml

@@ -1,8 +1,8 @@
 name: detect-changes
 
 env:
-  DEFAULT_PYTHON: '["3.10"]'
-  #MATRIX_PYTHON: '["3.10"]'
+  DEFAULT_PYTHON: '["3.9"]'
+  #MATRIX_PYTHON: '["3.9"]'
   MATRIX_PYTHON: '["3.9","3.10","3.11","3.12","3.13"]'
   DEFAULT_PLATFORM: '["linux"]'
   MATRIX_PLATFORM: '["linux", "macos"]'

.github/workflows/package-pipeline.yml

@@ -16,8 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
-        with:
-          python-version: ${{ inputs.python-version }}
+        with: ${{ inputs.python-version }}
       - name: Install dependencies
         run: |
           python3 -m pip install --upgrade pip

.github/workflows/update-dependencies.yml

@@ -17,19 +17,19 @@ jobs:
       - package-api
     uses: ./.github/workflows/package-host.yml
     with:
-      python-version: 3.10
+      python-version: 3.9
       platform: linux
 
   package-pipeline:
     uses: ./.github/workflows/package-pipeline.yml
     with:
-      python-version: 3.10
+      python-version: 3.9
       platform: linux
 
   package-blobtools:
     uses: ./.github/workflows/package-blobtools.yml
     with:
-      python-version: 3.10
+      python-version: 3.9
       platform: linux
 
   update-docker-image:

src/docker/blobtools/Dockerfile

@@ -64,7 +64,7 @@ ENV CONDA_DEFAULT_ENV $CONDA_DIR/envs/btk_env
 
 ENV PATH $CONDA_DEFAULT_ENV/bin:$PATH
 
-ENV PYTHONPATH $CONDA_DEFAULT_ENV/lib/python3.10/site-packages:$PYTHONPATH
+ENV PYTHONPATH $CONDA_DEFAULT_ENV/lib/python3.9/site-packages:$PYTHONPATH
 
 WORKDIR /blobtoolkit
 

src/docker/blobtools/env.yaml

@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   - pip==24.2
-  - python==3.10.15
+  - python==3.9.20
   - seqtk==1.4
   - pip:
       - blobtoolkit[full]==blobtoolkit==4.3.12

src/docker/dependencies/Dockerfile

@@ -91,7 +91,7 @@ ENV CONDA_DEFAULT_ENV $CONDA_DIR/envs/btk_env
 
 ENV PATH /blobtoolkit:$CONDA_DEFAULT_ENV/bin:$PATH
 
-ENV PYTHONPATH $CONDA_DEFAULT_ENV/lib/python3.10/site-packages:$PYTHONPATH
+ENV PYTHONPATH $CONDA_DEFAULT_ENV/lib/python3.9/site-packages:$PYTHONPATH
 
 COPY startup.sh /blobtoolkit
 

src/docker/dependencies/env.yaml

@@ -12,7 +12,7 @@ dependencies:
   - minimap2==2.24
   - blobtk==0.5.3
   - pip==24.2
-  - python==3.10.15
+  - python==3.9.20
   - samtools==1.15.1
   - seqtk==1.4
   - pip:

src/docker/env.yaml

@@ -12,7 +12,7 @@ dependencies:
   - minimap2==2.24
   - blobtk==0.5.3
   - pip==24.2
-  - python==3.12
+  - python==3.9.20
   - samtools==1.15.1
   - seqtk==1.4
   - pip: