initial commit

Author: tony-kuo

.github/workflows/docker.yaml

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+# Build docker container and push to GitHub registry
+name: Docker
+on:
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN
+permissions:
+  contents: read
+  packages: write
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# Build and push
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: type=raw,value=latest,enable={{is_default_branch}}
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: ./docker
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/pages.yaml

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+# Build and deploy Sphinx docs to GitHub Pages
+name: Pages
+on:
+  push:
+    branches: ['main']
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build job
+  build:
+    runs-on: ubuntu-latest
+    container:
+      image: ghcr.io/genentech/signature:latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Install dependencies
+        run: |
+          pip install -r docs/requirements.txt
+      - name: Setup Pages
+        id: pages
+        uses: actions/configure-pages@v3
+      - name: Sphinx build
+        run: |
+          sphinx-build -b html docs _build
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./_build
+  # Deployment job
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.github/workflows/pypi-publish.yaml

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+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Publish to PyPI
+
+on:
+  workflow_dispatch
+#  push:
+#    tags: '^[0-9]+.[0-9]+.[0-9]+'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install system dependencies
+        run: |
+          sudo apt install pandoc
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest tox
+
+      - name: Build package
+        run: |
+          python -m tox -e clean,build
+
+      - name: Publish package
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/pypi-test.yaml

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+ # This workflow will install Python dependencies, run tests and lint with a single version of Python
+ # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Test the library
+
+on:
+  workflow_dispatch
+#   push:
+#     branches: [main]
+#   pull_request:
+#     branches: [main]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    name: Python ${{ matrix.python-version }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest tox
+
+      # - name: Lint with flake8
+      #   run: |
+      #     # stop the build if there are Python syntax errors or undefined names
+      #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+      #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+      #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Test with tox
+        run: |
+          tox

.gitignore

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+# Temporary and binary files
+*~
+*.py[cod]
+*.so
+*.cfg
+!.isort.cfg
+!setup.cfg
+*.orig
+*.log
+*.pot
+__pycache__/*
+.cache/*
+.*.swp
+*/.ipynb_checkpoints/*
+.DS_Store
+
+# Project files
+.ropeproject
+.project
+.pydevproject
+.settings
+.idea
+.vscode
+tags
+
+# Package files
+*.egg
+*.eggs/
+.installed.cfg
+*.egg-info
+
+# Unittest and coverage
+htmlcov/*
+.coverage
+.coverage.*
+.tox
+junit*.xml
+coverage.xml
+.pytest_cache/
+
+# Build and docs folder/files
+build/*
+dist/*
+sdist/*
+docs/_rst/*
+docs/_build/*
+cover/*
+MANIFEST
+
+# Per-project virtualenvs
+.venv*/
+.conda*/
+.python-version

LICENSE

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+Copyright Genentech, Inc., 2025. 
+
+Licensed under the Genentech Non-Commercial Software License Version 1.0, September 2022 (the "License"); you may not use the associated software except in compliance with the License. 
+
+Note the Genentech Non-Commercial Software License reuses most of the text of the Apache License, Version 2.0, except that it includes a restriction against commercial use. The full text of the Apache License, Version 2.0 can be found at https://www.apache.org/licenses/LICENSE-2.0.
+
+Genentech Non-Commercial Software License Version 1.0, September 2022
+
+Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+"License" shall mean the terms and conditions for use, reproduction, and distribution as defined by Sections 1 through 9 of this document.
+
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+
+"You" (or "Your") shall mean an individual or Legal Entity exercising permissions granted by this License.
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+"Source" form shall mean the preferred form for making modifications, including but not limited to software source code, documentation source, and configuration files.
+
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+"Work" shall mean the work of authorship, whether in Source or Object form, made available under the License, as indicated by a copyright notice that is included in or attached to the work.
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+END OF TERMS AND CONDITIONS

MANIFEST.in

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+exclude .gitignore
+recursive-exclude .github *
+recursive-exclude docker *

NEWS.rst

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+Release Notes
+========================================================================
+
+Version 0.1.0:  October 3, 2024
+------------------------------------------------------------------------
+
++ Initial public release.

README.rst

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+SIGnature: Scoring the Importance of Genes
+================================================================================
+
+**SIGnature** is a python package that enables the efficient generation and collection of gene attributions.
+
+Attribution scores can be used for rapid gene signature scoring across database of 22 million single cell transcriptomes.
+
+See the notebooks folder for tutorials on querying and generating attributions.