Merge branch 'main' of https://github.com/metagentools/ConDiGA

.github/workflows/codeql.yml

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+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ "main" ]
+  schedule:
+    - cron: '19 14 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners
+    # Consider using larger runners for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby', 'swift' ]
+        # Use only 'java' to analyze code written in Java, Kotlin or both
+        # Use only 'javascript' to analyze code written in JavaScript, TypeScript or both
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages (C/C++, C#, Go, Java, or Swift).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #     echo "Run, Build Application using script"
+    #     ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/testing.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+
+jobs:
+  tests:
+    name: "Python ${{ matrix.python-version }}"
+    runs-on: ${{ matrix.os }}
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: "actions/checkout@v3"
+        with:
+          fetch-depth: 0
+
+      # Setup env
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: condiga
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
+
+      - name: "Setup Phables on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          python -m pip install --upgrade pip
+          pip install .
+      
+      - name: "Generate coverage report on ${{ matrix.os }} for Python ${{ matrix.python-version }}"
+        run: |
+          pip install pytest pytest-cov
+          pytest --cov=./ --cov-report xml --cov-report lcov --cov-append
+          
+      - name: Coveralls Parallel
+        uses: coverallsapp/github-action@master
+        with:
+          parallel: true
+          github-token: ${{ secrets.github_token }}
+          flag-name: run-${{ matrix.test_number }}
+          path-to-lcov: "coverage.lcov"
+
+  finish:
+    needs: tests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+    steps:
+    - name: Coveralls Finished
+      uses: coverallsapp/github-action@master
+      with:
+        github-token: ${{ secrets.github_token }}
+        parallel-finished: true