alphavx 0.0.5__tar.gz

alphavx-0.0.5/.env.example

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+# ============================================
+# AlphaVX Environment Configuration
+# ============================================
+# Copy this file to .env.alphavx and fill in your values:
+#   cp .env.example .env.alphavx
+#
+# We use ".env.alphavx" instead of ".env" because anndata
+# (an alphagenome dependency) auto-reads ".env" and crashes
+# on unknown keys.
+#
+# NEVER commit .env.alphavx to git — it contains your API key.
+# ============================================
+
+# Required: Your AlphaGenome API key
+# Sign up at: https://deepmind.google.com/science/alphagenome/
+ALPHAVX_API_KEY=your-alphagenome-api-key-here
+
+# Optional: Override default settings
+# ALPHAVX_MAX_RETRIES=3
+# ALPHAVX_RETRY_DELAY=5.0
+# ALPHAVX_SEQUENCE_LENGTH=1048576
+# ALPHAVX_QUANTILE_THRESHOLD=0.995

alphavx-0.0.5/.gitattributes

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+* text=auto
+*.py text eol=lf
+*.yaml text eol=lf
+*.yml text eol=lf
+*.md text eol=lf
+*.toml text eol=lf
+*.vcf text eol=lf
+*.sh text eol=lf

alphavx-0.0.5/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, dev]
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Test (Python ${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    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
+          # Install CI deps (excludes alphagenome which needs Google auth).
+          # Tests mock alphagenome via conftest.py.
+          pip install ".[ci]" --no-deps
+          pip install -e . --no-deps
+
+      - name: Lint with ruff
+        run: |
+          ruff check src/ tests/
+          ruff format --check src/ tests/
+
+      - name: Run tests
+        run: |
+          pytest tests/ -v --tb=short

alphavx-0.0.5/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  push:
+    tags: ['v*']
+
+permissions:
+  contents: read
+
+jobs:
+  publish:
+    name: Build & Publish
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: twine upload dist/*

alphavx-0.0.5/.github/workflows/release.yml

@@ -0,0 +1,55 @@
+name: Release
+
+on:
+  push:
+    tags: ['v*']
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    name: Create GitHub Release
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Full history for changelog
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Generate changelog
+        id: changelog
+        run: |
+          # Get previous tag
+          PREV_TAG=$(git tag --sort=-creatordate | head -n 2 | tail -n 1)
+          if [ -z "$PREV_TAG" ] || [ "$PREV_TAG" = "${{ github.ref_name }}" ]; then
+            echo "body=Initial release" >> $GITHUB_OUTPUT
+          else
+            CHANGES=$(git log ${PREV_TAG}..${{ github.ref_name }} --pretty=format:"- %s (%h)" --no-merges)
+            # Write multi-line output
+            echo "body<<EOF" >> $GITHUB_OUTPUT
+            echo "## Changes since ${PREV_TAG}" >> $GITHUB_OUTPUT
+            echo "" >> $GITHUB_OUTPUT
+            echo "$CHANGES" >> $GITHUB_OUTPUT
+            echo "EOF" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          body: ${{ steps.changelog.outputs.body }}
+          files: dist/*
+          generate_release_notes: true

alphavx-0.0.5/.gitignore

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+# ========================
+# OS
+# ========================
+.DS_Store
+.AppleDouble
+.LSOverride
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+$RECYCLE.BIN/
+
+# ========================
+# Editors & IDEs
+# ========================
+.vscode/
+.idea/
+.cursor/
+*.swp
+*.swo
+*~
+
+# ========================
+# Python
+# ========================
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+*.egg
+*.egg-info/
+.eggs/
+MANIFEST
+.Python
+.python-version
+.installed.cfg
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Distribution / packaging
+build/
+dist/
+develop-eggs/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+pip-wheel-metadata/
+
+# PyInstaller
+*.manifest
+*.spec
+
+# ========================
+# Virtual Environments
+# ========================
+.venv
+venv/
+env/
+ENV/
+venv.bak/
+env.bak/
+__pypackages__/
+
+# ========================
+# Environment & Secrets
+# ========================
+.env
+.env.alphavx
+.env.local
+.env.prod
+.env.dev
+.env.*.local
+*.pem
+*.key
+
+# ========================
+# Testing & Coverage
+# ========================
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache/
+.hypothesis/
+.pytest_cache/
+htmlcov/
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+
+# ========================
+# Type Checkers & Linters
+# ========================
+.mypy_cache/
+.dmypy.json
+dmypy.json
+.pyre/
+
+# ========================
+# Frameworks
+# ========================
+
+# Django
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask
+instance/
+.webassets-cache
+flask_session/
+
+# Scrapy
+.scrapy
+
+# Celery
+celerybeat-schedule
+celerybeat.pid
+
+# ========================
+# Docs & Notebooks
+# ========================
+docs/_build/
+.ipynb_checkpoints
+profile_default/
+ipython_config.py
+/site
+
+# ========================
+# Databases
+# ========================
+*.db
+*.sqlite
+
+# ========================
+# Logs & Temp
+# ========================
+*.log
+*.tmp
+*.temp
+
+# ========================
+# Node (occasional use)
+# ========================
+node_modules/
+
+# ========================
+# Misc
+# ========================
+target/
+.ropeproject
+.spyderproject
+.spyproject
+Trash/
+
+# ========================
+# AlphaVX specific
+# ========================
+results/
+cache/
+*.db
+alphavx_cache.db
+*.vcf.gz
+clinvar*.vcf*

alphavx-0.0.5/LICENSE

@@ -0,0 +1,190 @@
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