CF-Random PyPi Package

.github/workflows/tests.yml

@@ -0,0 +1,76 @@
+name: CI
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    permissions:
+      pull-requests: write
+      contents: write
+      checks: write
+
+    defaults:
+      run:
+        shell: bash -el {0}
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: latest
+          activate-environment: cf-random
+          python-version: '3.12'
+          auto-activate-base: false
+
+      - name: Cache conda environment
+        uses: actions/cache@v4
+        id: conda-cache
+        with:
+          path: ${{ env.CONDA }}/envs/cf-random
+          key: conda-${{ runner.os }}-${{ hashFiles('install.sh') }}
+
+      - name: Install dependencies
+        if: steps.conda-cache.outputs.cache-hit != 'true'
+        run: |
+          chmod +x install.sh
+          ./install.sh
+
+      - name: Install dev dependencies
+        run: pip install -e ".[dev]"
+
+      - name: Run tests with coverage
+        run: |
+          pytest tests/ --cov=cf_random --cov-report=xml:coverage.xml --cov-report=term-missing | tee pytest-coverage.txt
+
+      - name: Upload coverage report
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-report
+          path: |
+            coverage.xml
+            pytest-coverage.txt
+
+      - name: Build package
+        run: python -m build
+
+      - name: Upload to Test PyPI
+        if: github.event_name == 'pull_request'
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        run: twine upload --repository testpypi dist/*
+
+      - name: Upload to PyPI
+        if: github.ref == 'refs/heads/main' && github.event_name == 'push'
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: twine upload dist/*

.gitignore

@@ -0,0 +1,86 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+# Project specific
+examples/*/results/
+blind_prediction/
+successful_predictions/
+failed_predictions/
+multimer_prediction/
+test_data/
+msa_folder/
+structures_all.csv
+
+# Foldseek
+pdb*
+pdb_*
+tmp/
+
+
+params/
+msa_folder/
+range_fs_pairs_all.txt
+*.pdb
+*.a3m
+2oug_C-search

MANIFEST.in

@@ -0,0 +1,4 @@
+include README.md
+include LICENSE.md
+recursive-include cf_random/data *
+recursive-include examples *