cellme 1.0.0__tar.gz

cellme-1.0.0/.github/CODEOWNERS

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+* @clintval

cellme-1.0.0/.github/dependabot.yml

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+version: 2
+updates:
+  # GitHub Actions — every workflow action is pinned to a commit SHA.
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # Quarantine fresh releases so a compromised publish has time to be caught.
+    cooldown:
+      default-days: 7
+    # Batch all action bumps into a single PR to reduce noise.
+    groups:
+      github-actions:
+        patterns:
+          - "*"
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+
+  # Python dependencies (uv) — reads pyproject.toml + uv.lock.
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    # Same one-week quarantine as the actions ecosystem above.
+    cooldown:
+      default-days: 7
+    versioning-strategy: "increase-if-necessary"
+    groups:
+      python-runtime:
+        dependency-type: "production"
+        patterns:
+          - "*"
+      python-dev:
+        dependency-type: "development"
+        patterns:
+          - "*"
+    commit-message:
+      prefix: "chore"
+      include: "scope"

cellme-1.0.0/.github/workflows/publish_cellme.yml

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+name: publish
+
+on:
+  push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+
+concurrency:
+  group: publish-${{ github.ref }}
+  cancel-in-progress: false
+
+env:
+  UV_VERSION: 0.12.0
+
+permissions:
+  contents: read
+
+jobs:
+  on-main-branch-check:
+    runs-on: ubuntu-latest
+    outputs:
+      on_main: ${{ steps.contains_tag.outputs.retval }}
+    steps:
+      # TODO: remove this when the following PR is merged and released:
+      #   https://github.com/rickstaa/action-contains-tag/pull/18
+      - name: git config --global remote.origin.followRemoteHEAD never
+        run: git config --global remote.origin.followRemoteHEAD never
+
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - uses: rickstaa/action-contains-tag@a9ff27d505ba2bf074a2ebb48b208e76d35ff308  # v1.2.10
+        id: contains_tag
+        with:
+          reference: "main"
+          tag: "${{ github.ref_name }}"
+
+  tests:
+    name: tests
+    needs: on-main-branch-check
+    if: ${{ needs.on-main-branch-check.outputs.on_main == 'true' }}
+    uses: "./.github/workflows/python_package.yml"
+
+  build:
+    name: build package
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9  # v9.0.0
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: 3.12
+          # This is a release build, so resolve against upstream rather than a
+          # warm cache that a less-trusted ref could have poisoned.
+          enable-cache: 'false'
+
+      # cellme is pure Python, so a single build produces the sdist and one
+      # universal py3-none-any wheel. No per-Python or per-platform matrix.
+      - name: Build sdist and wheel
+        run: uv build --sdist --wheel
+
+      - name: Verify package metadata
+        run: uv run --with twine twine check --strict dist/*
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: dist
+          path: dist/
+          if-no-files-found: error
+
+  publish-to-pypi:
+    runs-on: ubuntu-latest
+    needs: build
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c  # v8.0.1
+        with:
+          name: dist
+          path: dist/
+
+      - uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33  # v1.14.2
+        with:
+          skip-existing: true
+          print-hash: true
+          verbose: true
+
+  make-changelog:
+    runs-on: ubuntu-latest
+    needs: publish-to-pypi
+    outputs:
+      release_body: ${{ steps.git-cliff.outputs.content }}
+    steps:
+      - name: Checkout the Repository at the Tagged Commit
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          fetch-depth: 0
+          ref: ${{ github.ref_name }}
+          persist-credentials: false
+
+      - name: Generate a Changelog
+        uses: orhun/git-cliff-action@f50e11560dce63f7c33227798f90b924471a88b5  # v4.8.0
+        id: git-cliff
+        with:
+          config: pyproject.toml
+          args: --latest --verbose
+        env:
+          GITHUB_REPO: ${{ github.repository }}
+
+  make-github-release:
+    runs-on: ubuntu-latest
+    needs: make-changelog
+    permissions:
+      contents: write
+    steps:
+      - name: Download the built distributions
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c  # v8.0.1
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        id: create_release
+        uses: softprops/action-gh-release@3d0d9888cb7fd7b750713d6e236d1fcb99157228  # v3.0.2
+        with:
+          name: ${{ github.ref_name }}
+          body: ${{ needs.make-changelog.outputs.release_body }}
+          draft: false
+          prerelease: false
+          files: "dist/*"

cellme-1.0.0/.github/workflows/python_package.yml

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+name: Code checks
+
+on:
+  push:
+  workflow_call:
+
+env:
+  UV_VERSION: 0.12.0
+
+permissions:
+  contents: read
+
+jobs:
+  Tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.12", "3.13", "3.14"]
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9  # v9.0.0
+        with:
+          version: ${{ env.UV_VERSION }}
+          python-version: ${{ matrix.PYTHON_VERSION }}
+          enable-cache: 'true'
+          cache-suffix: ${{ matrix.PYTHON_VERSION }}
+
+      - name: Test the library
+        run: |
+          uv run --locked poe check-all
+

cellme-1.0.0/.gitignore

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+.vscode/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+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
+
+# 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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# 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
+.venv
+venv/
+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/

cellme-1.0.0/CLAUDE.md

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+# CLAUDE.md
+
+## Template Setup
+
+**On first interaction in a new project:** If this section is present, the project
+has not yet been initialized.
+
+Run `/init`, then replace this entire section with its output. Keep the rest of
+this CLAUDE.md intact below it.
+
+## Git Workflow
+
+### Commit Granularity
+
+Commit after completing one of:
+- A single function/method implementation
+- One refactoring step (rename, extract, move)
+- A bug fix with its regression test
+- A documentation update
+
+**Size guidelines:**
+- Per commit: 100–300 lines preferred, 400 max
+- Per PR: No hard limit, but consider splitting if >800 lines or >5 unrelated files
+
+**Good commit scope examples:**
+- `Add FastaIndex.validate() method`
+- `Rename species_map → species_to_ref_fasta_map`
+- `Fix off-by-one in BED coordinate parsing`
+
+### Commit Messages
+
+Use [Conventional Commits](https://www.conventionalcommits.org/) for commit messages and PR
+titles+bodies. Common types: `feat`, `fix`, `chore`, `docs`, `refactor`, `test`.
+
+```
+<type>: <imperative description> (<72 chars total)
+
+Detailed body explaining:
+- What changed
+- Why (link issues with "Closes #123" or "Related to #456")
+- Any non-obvious implementation choices
+```
+
+### Commit Rules
+- Run `uv run poe fix-and-check-all` before each commit; all checks must pass
+- No merge commits
+- Do not rebase without explicit user approval
+- **Never mix formatting and functional changes.** If unavoidable, isolate formatting into separate commits at start or end of branch.
+
+### Branch Hygiene
+- Use `.gitignore` liberally
+- Never commit: IDE files, personal test files, local debug data, commented-out code
+
+## Coding Conventions
+
+### Organization
+- Extract logic into small–medium functions with clear inputs/outputs
+- Scope variables tightly; limit visibility to where needed
+- Use block comments for visual separation when function extraction isn't practical
+
+### Naming
+- Meaningful names, even if long: `species_to_ref_fasta_map` not `species_map`
+- Short names only for tight scope (loop indices, single-line lambdas)
+- Signal behavior in function names: `to_y()`, `is_valid()` → returns value; `update_x()` → side effect
+
+## Testing
+
+### Principles
+- Generate test data programmatically; avoid committing test data files
+- Test behavior, not implementation—tests should survive refactoring
+- Cover: expected behavior, error conditions, boundary cases
+- Scale rigor to code longevity: thorough for shared code, lighter for one-off scripts
+
+### Coverage Expectations
+- New public functions: at least one happy-path test + one error case
+- Bug fixes: add a regression test that would have caught the bug
+- Performance-critical code: include benchmark or explain in PR why not needed
+
+## Documentation Maintenance
+
+When modifying code, update as needed:
+- [ ] Docstrings (if signature or behavior changed)
+- [ ] README.md (if usage patterns changed)
+- [ ] Migration notes (if breaking change)
+
+## Python-Specific
+
+### Pragmatism
+- Balance functional, OOP, and imperative—use what's clearest
+- When in doubt, prefer pure functions and immutable data
+- Know your utility libraries; contribute upstream rather than writing one-offs
+
+### Style
+- Heavier use of classes and type annotations than typical Python
+- Prefer `@dataclass(frozen=True)` and Pydantic models with `frozen=True`
+
+### Functions
+- Functions should have **either** returns **or** side effects, not both
+- Exceptions: logging, caching (where side effect is performance-only)
+
+### Documentation
+- Google-style docstrings with `Args:`, `Returns:`, `Yields:`, and `Raises:` blocks
+- Docstrings are required on all public functions/classes
+- Code comments should explain non-obvious choices and complex logic
+
+### Typing
+- **Required:** Type annotations on all function parameters and returns
+- **Parameters:** Accept the most general type practical (e.g., `Iterable` over `List`)
+- **Returns:** Return the most specific type without exposing implementation details
+- Annotate locals when: they become return values, or called function lacks hints
+- Use type aliases or `NewType` for complex structures
+- Avoid `Any`—prefer type alias or `TypeVar`
+- Avoid `cast()` and `type: ignore`—prefer alternatives, but when unavoidable (e.g., incorrect upstream stubs), document the reason inline.
+

cellme-1.0.0/CONTRIBUTING.md

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+# Development and Testing
+
+## Primary Development Commands
+
+To check and resolve linting issues in the codebase, run:
+
+```console
+uv run ruff check --fix
+```
+
+To check and resolve formatting issues in the codebase, run:
+
+```console
+uv run ruff format
+```
+
+To check the unit tests in the codebase, run:
+
+```console
+uv run pytest
+```
+
+To check the typing in the codebase, run:
+
+```console
+uv run mypy
+```
+
+To generate a code coverage report after testing locally, run:
+
+```console
+uv run coverage html
+```
+
+To check the lock file is up to date:
+
+```console
+uv lock --check
+```
+
+## Shortcut Task Commands
+
+###### For Running Individual Checks
+
+```console
+uv run poe check-format
+uv run poe check-lint
+uv run poe check-tests
+uv run poe check-typing
+```
+
+###### For Running All Checks
+
+```console
+uv run poe check-all
+```
+
+###### For Running Individual Fixes
+
+```console
+uv run poe fix-format
+uv run poe fix-lint
+```
+
+###### For Running All Fixes
+
+```console
+uv run poe fix-all
+```
+
+###### For Running All Fixes and Checks
+
+```console
+uv run poe fix-and-check-all
+```

cellme-1.0.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright © 2026 Fulcrum Genomics LLC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.