3 files changed, 113 insertions, 0 deletions
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
new file mode 100644
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+++ b/.github/workflows/codeql-analysis.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: '27 17 * * 5'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python' ]
+        # Learn more:
+        # https://docs.github.com/en/free-pro-team@latest/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#changing-the-languages-that-are-analyzed
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # 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.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+    
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
diff --git a/.github/workflows/linter.yml b/.github/workflows/linter.yml
new file mode 100644
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+++ b/.github/workflows/linter.yml
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+name: Lint Code Base
+
+#
+# Documentation:
+# https://help.github.com/en/articles/workflow-syntax-for-github-actions
+#
+
+on: [push]
+
+jobs:
+  build:
+    name: Lint Code Base
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v4
+      - name: Lint Code Base
+        uses: docker://github/super-linter:v2.1.0
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          VALIDATE_PYTHON: false
+          VALIDATE_BASH: true
diff --git a/.github/workflows/testpy.yml b/.github/workflows/testpy.yml
new file mode 100644
index 0000000..9ca33ac
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+++ b/.github/workflows/testpy.yml
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+name: build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+        include:
+        - os: macos-latest
+          python-version: '3.10'
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install coverage pytest-cov flake8
+        pip install -r requirements.txt
+    - name: Test
+      run: |
+        pytest --cov=modelcif --cov-branch --cov-report=xml --cov-append -v .
+        flake8 --ignore E402,W503,W504
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}