bacpop-145 Make gha PopPUNK installation match dockerfile

.github/workflows/pytest.yml

@@ -33,16 +33,21 @@ jobs:
       working-directory: ./main
       run: |
         ./scripts/download_db --small storage
+
+    - name: Install Linux packages
+      run: |
+        sudo apt-get update -q 
+        sudo apt-get install -q -y --no-install-recommends bzip2 ca-certificates git libglib2.0-0 libsm6 libxext6 libxrender1 mercurial openssh-client procps subversion wget
 
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v2
       with:
-        python-version: "3.9"
+        python-version: "3.10"
 
     - name: Setup Miniconda
       uses: conda-incubator/[email protected]
       with:
-        python-version: 3.9
+        python-version: "3.10"
         activate-environment: beebop_py
         channels: bioconda, conda-forge
 
@@ -51,45 +56,25 @@ jobs:
       run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
       shell: bash
 
-    - name: Restore Conda env from cache
-      uses: actions/cache@v2
-      with:
-        path: /usr/share/miniconda/envs/beebop_py
-        key:
-          # Refresh cache each day
-          conda-${{ runner.os }}--${{ runner.arch }}--${{
-          steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER}}
-      env:
-        # Increment this value to manually reset cache.
-        CACHE_NUMBER: 0
-      id: cache-conda
-
-#    - name: Install poppunk
-#      run: conda install poppunk
-#  currently the latest poppunk release is missing some functions required for beebop. For now installing from source:
-
-    - name: Get poppunk source code
-      uses: actions/checkout@v3
-      with:
-        repository:  bacpop/PopPUNK 
-        ref: fix-json-serialisation
-        path: poppunk
-
-    - name: install poppunk & dependencies
-      working-directory: ./poppunk
+    #- name: Restore Conda env from cache
+    #  uses: actions/cache@v2
+    #  with:
+    #    path: /usr/share/miniconda/envs/beebop_py
+    #    key:
+    #      # Refresh cache each day
+    #      conda-${{ runner.os }}--${{ runner.arch }}--${{
+    #      steps.get-date.outputs.today }}-${{ env.CACHE_NUMBER}}
+    #  env:
+    #    # Increment this value to manually reset cache.
+    #    CACHE_NUMBER: 0
+    #  id: cache-conda
+
+    - name: Install poppunk dependencies
       run: |
-        source $CONDA/etc/profile.d/conda.sh
-        conda activate beebop_py
-        conda install graph-tool
-        conda install mandrake
-        conda install rapidnj
-        sudo apt-get update
-        sudo apt-get install libeigen3-dev libegl1
-        sudo apt-get install libopenblas-dev
-        sudo apt-get install -y '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev libxkbcommon-x11-dev
-        pip install joblib==1.1.0
-        conda install -c bioconda pp-sketchlib=2.0.0
-        pip3 install git+https://github.com/bacpop/PopPUNK
+          conda install python=3.10
+
+    - name: Install poppunk
+      run: conda install poppunk
 
     - name: Install Poetry
       uses: snok/install-poetry@v1