seqwin 0.3.1__tar.gz

seqwin-0.3.1/.github/workflows/main.yml

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+name: Build and Test
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  smoke:
+    name: ${{ matrix.runner }} / py${{ matrix.python-version }}
+    runs-on: ${{ matrix.runner }}
+    timeout-minutes: 45
+
+    strategy:
+      fail-fast: false
+      matrix:
+        runner: [ubuntu-24.04, macos-15, windows-2025]
+        python-version: ["3.10", "3.13"]
+        include:
+          - runner: ubuntu-24.04
+            arch: x64
+          - runner: macos-15
+            arch: arm64
+          - runner: windows-2025
+            arch: x64
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: ${{ matrix.arch }}
+          cache: pip
+
+      - name: Build and install package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install --prefer-binary . -v
+
+      - name: Smoke tests
+        run: |
+          seqwin --help
+          python -c "import seqwin; print(seqwin.__version__)"
+          python -c "from seqwin.btllib import indexlr; print(indexlr.__name__)"
+          python -m pip check
+
+      - name: Run integration test
+        if: matrix.python-version == '3.10'
+        run: |
+          python test/run_test.py

seqwin-0.3.1/.github/workflows/publish.yml

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+name: Build and publish to PyPI
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  check_version:
+    name: Check version matches tag
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Verify version
+        # skip unless this run is on a v* tag ref
+        if: startsWith(github.ref, 'refs/tags/v')
+        shell: bash
+        run: |
+          # Extract tag name and strip the 'v' prefix
+          TAG_VERSION=${GITHUB_REF#refs/tags/v}
+          echo "Triggered by tag: v$TAG_VERSION"
+
+          # Safely extract the __version__ string from _version.py without executing it
+          FILE_VERSION=$(python3 -c "
+          import re
+          with open('src/seqwin/_version.py', 'r') as f:
+              match = re.search(r'__version__\s*=\s*[\'\"]([^\'\"]+)[\'\"]', f.read())
+              if match:
+                  print(match.group(1))
+              else:
+                  print('NOT_FOUND')
+          ")
+
+          echo "Version in src/seqwin/_version.py: $FILE_VERSION"
+          
+          if [ "$FILE_VERSION" = "NOT_FOUND" ]; then
+            echo "::error::Could not find __version__ in src/seqwin/_version.py"
+            exit 1
+          fi
+
+          if [ "$TAG_VERSION" != "$FILE_VERSION" ]; then
+            echo "::error::Tag version ($TAG_VERSION) does not match file version ($FILE_VERSION)"
+            exit 1
+          fi
+
+          echo "Success: Versions match!"
+
+  build_sdist:
+    name: Build sdist
+    needs: [check_version]
+    runs-on: ubuntu-24.04
+    timeout-minutes: 30
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+          cache: pip
+
+      - name: Build source distribution
+        run: |
+          python -m pip install --upgrade pip build twine
+          python -m build --sdist --outdir dist
+          twine check dist/*
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+          if-no-files-found: error
+
+  build_wheels:
+    name: Build wheels / ${{ matrix.name }}
+    needs: [check_version]
+    runs-on: ${{ matrix.runner }}
+    timeout-minutes: 90
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: linux-x64
+            runner: ubuntu-24.04
+          - name: linux-arm64
+            runner: ubuntu-24.04-arm
+          - name: macos-x64
+            runner: macos-15-intel
+          - name: macos-arm64
+            runner: macos-15
+          - name: windows-x64
+            runner: windows-2025
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+          cache: pip
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.4.1
+        env:
+          CIBW_BUILD: 'cp310-* cp311-* cp312-* cp313-*'
+          CIBW_SKIP: 'pp* cp3??t-* *-musllinux_*'
+          CIBW_ARCHS_WINDOWS: AMD64
+          CIBW_ENVIRONMENT_MACOS: MACOSX_DEPLOYMENT_TARGET=10.15
+          CIBW_TEST_ENVIRONMENT_MACOS: PIP_PREFER_BINARY=1
+          CIBW_TEST_COMMAND: >
+            seqwin --help &&
+            python -c "import seqwin; print(seqwin.__version__)" &&
+            python -c "from seqwin.btllib import indexlr; print(indexlr.__name__)" &&
+            python {project}/test/run_test.py &&
+            python -m pip check
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.name }}
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish to PyPI
+    needs: [build_sdist, build_wheels]
+    if: startsWith(github.ref, 'refs/tags/v')
+    runs-on: ubuntu-24.04
+    environment:
+      name: pypi
+      url: https://pypi.org/p/seqwin
+    permissions:
+      contents: read
+      id-token: write
+
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          path: dist
+          merge-multiple: true
+
+      - name: Download sdist
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.13'
+
+      - name: Verify distributions
+        run: |
+          python -m pip install --upgrade pip twine
+          twine check dist/*
+          ls -lh dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

seqwin-0.3.1/.gitignore

@@ -0,0 +1,216 @@
+# For test data
+test/assemblies.tar
+test/assemblies/
+test/seqwin-out/
+*.tmp
+
+# For macOS
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#  For a library or package, you might want to ignore these files since the code is
+#  intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#  According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#  However, in case of collaboration, if having platform-specific dependencies or dependencies
+#  having no cross-platform support, pipenv may install dependencies that don't work, or not
+#  install all needed dependencies.
+# Pipfile.lock
+
+# UV
+#  Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#  This is especially recommended for binary packages to ensure reproducibility, and is more
+#  commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#  Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#  This is especially recommended for binary packages to ensure reproducibility, and is more
+#  commonly ignored for libraries.
+#  https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#  Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#  pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#  https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#  Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#  Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#  in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
+# Abstra
+#  Abstra is an AI-powered process automation framework.
+#  Ignore directories containing user credentials, local state, and settings.
+#  Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+.vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/