switch tests to build in conda env

.github/workflows/test_build.yml

@@ -24,10 +24,32 @@ jobs:
     steps:
     - name: Checkout repo
       uses: actions/checkout@v4
-    - name: Build msyd
-      uses: schneebergerlab/msyd@main
+      # use old install manually
+      # since switching to conda no longer supports different python version
+      #    - name: Build msyd
+      #      uses: schneebergerlab/msyd@main
+      #      #      with:
+      #      #        python-version: ${{ matrix.python-version }}
+    - name: Set up Python ${{ inputs.python-version }}
+      uses: actions/setup-python@v5
       with:
-        python-version: ${{ matrix.python-version }}
+        python-version: ${{ inputs.python-version }}
+        cache: pip
+    - name: Update pip
+      run: python -m pip install --upgrade pip setuptools
+      shell: bash
+    - name: Install SyRI manually
+      run: |
+        # manually install syris dependencies
+        # the python version spoofing requires the --no-deps flag, so this is necessary
+        pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
+        # manually use pip to install syri from github, as it isn't on pypi
+        # spoof python version to get around bounds check
+        pip install 'git+https://github.com/schneebergerlab/syri.git' --python-version '3.10' --no-deps --no-warn-conflicts --target $(python -m site --user-site)
+      shell: bash
+    - name: Install other dependencies
+      run: pip install -r requirements.txt
+      shell: bash
     - name: Test installation
       run: |
         msyd --version

.github/workflows/test_example.yml

@@ -19,13 +19,13 @@ jobs:
     steps:
     - name: Build msyd
       uses: schneebergerlab/msyd@main
-      with:
-        python-version: "3.12"
-    - name: Install minimap2 manually # conda doesn't seem to work
-      run: |
-        curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf -
-        mv minimap2-2.28_x64-linux\/minimap2 ./
-        ./minimap2 -h # test it worked & is callable
+      #      with:
+      #        python-version: "3.12"
+      #    - name: Install minimap2 manually # conda doesn't seem to work
+      #      run: |
+      #        curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf -
+      #        mv minimap2-2.28_x64-linux\/minimap2 ./
+      #        ./minimap2 -h # test it worked & is callable
     - name: Test example_run.sh
       run: ./.github/workflows/run_test_example.sh
       shell: bash

action.yml

@@ -3,37 +3,42 @@
 name: Build msyd
 description: "Checks out, installs dependencies and builds the msyd package. Formulated as a composite action to reduce code duplication in testing. Composite workflows cannot perserve state."
 
-inputs:
-  python-version:
-    description: 'Python version to use'
-    required: true
-    default: '3.12'
+#inputs:
+#  python-version:
+#    description: 'Python version to use'
+#    required: true
+#    default: '3.12'
 
 runs:
   using: composite
   steps:
   - name: Checkout repo
     uses: actions/checkout@v4
-  - name: Set up Python ${{ inputs.python-version }}
-    uses: actions/setup-python@v5
-    with:
-      python-version: ${{ inputs.python-version }}
-      cache: pip
-  - name: Update pip
-    run: python -m pip install --upgrade pip setuptools
-    shell: bash
-  - name: Install SyRI manually
+    #  - name: Set up Python ${{ inputs.python-version }}
+    #    uses: actions/setup-python@v5
+    #    with:
+    #      python-version: ${{ inputs.python-version }}
+    #      cache: pip
+    #  - name: Update pip
+    #    run: python -m pip install --upgrade pip setuptools
+    #    shell: bash
+    #  - name: Install SyRI manually
+    #    run: |
+    #      # manually install syris dependencies
+    #      # the python version spoofing requires the --no-deps flag, so this is necessary
+    #      pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
+    #      # manually use pip to install syri from github, as it isn't on pypi
+    #      # spoof python version to get around bounds check
+    #      pip install 'git+https://github.com/schneebergerlab/syri.git' --python-version '3.10' --no-deps --no-warn-conflicts --target $(python -m site --user-site)
+    #    shell: bash
+    #  - name: Install other dependencies
+    #    run: pip install -r requirements.txt
+    #    shell: bash
+  - name: Setup conda env
     run: |
-      # manually install syris dependencies
-      # the python version spoofing requires the --no-deps flag, so this is necessary
-      pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
-      # manually use pip to install syri from github, as it isn't on pypi
-      # spoof python version to get around bounds check
-      pip install 'git+https://github.com/schneebergerlab/syri.git' --python-version '3.10' --no-deps --no-warn-conflicts --target $(python -m site --user-site)
-    shell: bash
-  - name: Install other dependencies
-    run: pip install -r requirements.txt
-    shell: bash
+      $CONDA/bin/conda env create -n msyd --file ./environment.yml
+      $CONDA/bin/conda activate msyd
+    # python -m pip install mappy
   - name: Build msyd
     run: pip install .
     shell: bash