gsMap 1.73.4__tar.gz → 1.73.6__tar.gz

gsmap-1.73.6/.dockerignore

@@ -0,0 +1,71 @@
+# Git
+.git
+.gitignore
+
+# Python
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+*.egg-info
+*.egg
+dist
+build
+eggs
+.eggs
+parts
+bin
+var
+sdist
+wheels
+pip-wheel-metadata
+*.manifest
+*.spec
+
+# Testing
+.pytest_cache
+.coverage
+htmlcov
+.tox
+.nox
+coverage.xml
+*.cover
+.hypothesis
+
+# Jupyter
+*.ipynb_checkpoints
+
+# Documentation
+docs/
+visualization_web_docs/
+
+# IDE
+.vscode
+.idea
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Logs
+logs/
+*.log
+
+# Node
+node_modules/
+
+# Cache
+.ruff_cache/
+.claude/
+
+# Other
+*.png
+*.jpg
+*.jpeg
+*.gif
+*.bmp
+*.svg

gsmap-1.73.6/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,34 @@
+---
+name: Bug report
+about: Create a report to help us improve gsMap
+title: ""
+labels: bug
+assignees: ""
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+
+```bash
+# Paste your gsmap script here
+```
+
+**Error messages/logs**
+
+```
+Paste the error messages or logs here
+```
+
+**Environment (please complete the following information):**
+ - Python version: [output of python --version]
+ - gsMap version: [output of gsmap --version]
+ - OS: [e.g. Ubuntu 22.04, macOS 13]
+
+**Input data information (if applicable):**
+- ST data description: [e.g. 10x Visium, Stero-seq, etc.]
+- Data dimensions: [e.g. 10,000 spots × 20,000 genes]
+
+**Additional context**
+Add any other context about the problem here.

gsmap-1.73.6/.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,26 @@
+---
+name: Feature request
+about: Suggest an idea for gsMap
+title: '[FEATURE] '
+labels: 'enhancement'
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Use case**
+Describe the use case for this feature. How would it benefit users of gsMap?
+
+**Relevant literature or methods**
+If applicable, provide references to relevant papers, methods, or algorithms that support this feature.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

gsmap-1.73.6/.github/workflows/build.yml

@@ -0,0 +1,44 @@
+name: Build and Test
+
+# CI workflow that builds and validates the Python package on every push/PR
+# This ensures the package is always in a buildable state
+# For actual releases, use the release.yml workflow triggered by tags
+on: 
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          flit
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: |
+          flit build
+          ls -lh dist
+      - name: Verify the built packages
+        run: |
+          python3 -m pip install --upgrade pip
+          python3 -m pip install twine
+          twine check dist/*
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/

gsmap-1.73.6/.github/workflows/docker-publish.yml

@@ -0,0 +1,72 @@
+name: Build Docker Image (Manual)
+
+# This workflow is for manual Docker builds only
+# For automatic releases, the release.yml workflow handles everything when you push a tag
+on:
+  workflow_dispatch:  # Manual trigger only
+    inputs:
+      tag:
+        description: 'Docker image tag (e.g., dev, test, custom-tag)'
+        required: false
+        default: 'manual'
+      push:
+        description: 'Push to registry (true/false)'
+        required: false
+        default: 'false'
+
+env:
+  REGISTRY: ghcr.io
+  # Convert repository name to lowercase for Docker compatibility
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push:
+    name: Build Docker Image (Manual)
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      
+      - name: Convert repository name to lowercase
+        id: repo
+        run: echo "name=$(echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]')" >> $GITHUB_OUTPUT
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Container Registry
+        if: ${{ github.event.inputs.push == 'true' }}
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: ${{ github.event.inputs.push == 'true' }}
+          tags: ${{ env.REGISTRY }}/${{ steps.repo.outputs.name }}:${{ github.event.inputs.tag }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Output instructions
+        run: |
+          if [ "${{ github.event.inputs.push }}" == "true" ]; then
+            echo "✅ Docker image pushed to: ${{ env.REGISTRY }}/${{ steps.repo.outputs.name }}:${{ github.event.inputs.tag }}"
+            echo ""
+            echo "Pull with:"
+            echo "  docker pull ${{ env.REGISTRY }}/${{ steps.repo.outputs.name }}:${{ github.event.inputs.tag }}"
+          else
+            echo "✅ Docker image built locally (not pushed)"
+            echo ""
+            echo "To push manually, re-run workflow with push=true"
+          fi

gsmap-1.73.6/.github/workflows/release.yml

@@ -0,0 +1,176 @@
+name: Release Pipeline
+
+# This is the main release workflow that handles everything when you push a version tag
+# It builds Python packages, Docker images, publishes to PyPI and ghcr.io, and creates GitHub releases
+on:
+  push:
+    tags:
+      - 'v*'  # Trigger ONLY on version tags
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag to release (e.g., v1.0.0)'
+        required: true
+        type: string
+
+jobs:
+  build-python:
+    name: Build Python distribution 📦
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flit
+      - name: Build package
+        run: |
+          flit build
+          ls -lh dist
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-pypi:
+    name: Publish to PyPI 🐍
+    needs: build-python
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gsMap
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  build-docker:
+    name: Build Docker images 🐳
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      
+      - name: Convert repository name to lowercase
+        id: repo
+        run: echo "name=$(echo ${{ github.repository }} | tr '[:upper:]' '[:lower:]')" >> $GITHUB_OUTPUT
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ steps.repo.outputs.name }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=raw,value=latest
+
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-name: ghcr.io/${{ steps.repo.outputs.name }}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true
+
+  create-release:
+    name: Create GitHub Release 📝
+    needs: [publish-pypi, build-docker]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      id-token: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        
+      - name: Download Python distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Sign distributions with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+
+      - name: Generate Release Notes
+        id: release_notes
+        run: |
+          VERSION="${GITHUB_REF#refs/tags/}"
+          echo "# gsMap ${VERSION}" > release_notes.md
+          echo "" >> release_notes.md
+          echo "## 📦 Installation" >> release_notes.md
+          echo "" >> release_notes.md
+          echo "### PyPI" >> release_notes.md
+          echo '```bash' >> release_notes.md
+          echo "pip install gsMap==${VERSION#v}" >> release_notes.md
+          echo '```' >> release_notes.md
+          echo "" >> release_notes.md
+          echo "### Docker" >> release_notes.md
+          echo '```bash' >> release_notes.md
+          echo "docker pull ghcr.io/${{ github.repository }}:${VERSION#v}" >> release_notes.md
+          echo '```' >> release_notes.md
+          echo "" >> release_notes.md
+          echo "## 📋 What's Changed" >> release_notes.md
+          echo "" >> release_notes.md
+          echo "See [full changelog](https://github.com/${{ github.repository }}/compare/$(git describe --tags --abbrev=0 ${GITHUB_REF}^)...${VERSION})" >> release_notes.md
+
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          gh release create \
+            '${{ github.ref_name }}' \
+            --repo '${{ github.repository }}' \
+            --title "gsMap ${{ github.ref_name }}" \
+            --notes-file release_notes.md
+
+      - name: Upload artifacts to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          gh release upload \
+            '${{ github.ref_name }}' dist/** \
+            --repo '${{ github.repository }}'

{gsmap-1.73.4 → gsmap-1.73.6}/.gitignore

@@ -245,3 +245,6 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
+
+# vscode
+.vscode

{gsmap-1.73.4 → gsmap-1.73.6}/.pre-commit-config.yaml

@@ -5,6 +5,8 @@ default_stages:
   - pre-commit
   - pre-push
 minimum_pre_commit_version: 2.16.0
+ci:
+  autoupdate_schedule: quarterly
 repos:
   - repo: https://github.com/asottile/blacken-docs
     rev: 1.19.1
@@ -29,7 +31,7 @@ repos:
           )$
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.44.0
+    rev: v0.45.0
     hooks:
       - id: markdownlint-fix
         exclude: |
@@ -38,7 +40,7 @@ repos:
           )$
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.7
+    rev: v0.12.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

gsmap-1.73.6/DOCKER_README.md

@@ -0,0 +1,130 @@
+# Docker Setup for gsMap
+
+This guide explains how to build and run gsMap using Docker for reproducible analysis.
+
+## Quick Start - Using Pre-built Images
+
+The easiest way to use gsMap with Docker is to pull the pre-built image from GitHub Container Registry:
+
+```bash
+# Pull the latest image
+docker pull ghcr.io/jianyang-lab/gsmap:latest
+
+# Or pull a specific version
+docker pull ghcr.io/jianyang-lab/gsmap:v1.0.0
+
+# Run gsMap
+docker run --rm ghcr.io/jianyang-lab/gsmap:latest --help
+```
+
+## Prerequisites
+
+- Docker installed on your system
+- Docker Compose (optional, for easier management)
+
+## Building the Docker Image
+
+### Option 1: Using Docker directly
+
+```bash
+# Build the image
+docker build -t gsmap:latest .
+```
+
+### Option 2: Using Docker Compose
+
+```bash
+# Build the image using docker-compose
+docker-compose build
+```
+
+## Running gsMap in Docker
+
+### Using Docker directly
+
+```bash
+# Show help
+docker run --rm gsmap:latest --help
+
+# Run with mounted data directory
+docker run --rm \
+  -v $(pwd)/data:/data \
+  -v $(pwd)/results:/results \
+  gsmap:latest [subcommand] [options]
+
+# Example: Run a specific gsMap command
+docker run --rm \
+  -v $(pwd)/data:/data \
+  -v $(pwd)/results:/results \
+  gsmap:latest format-sumstats \
+  --sumstats /data/input.txt \
+  --out /results/output
+```
+
+### Using Docker Compose
+
+```bash
+# Show help
+docker-compose run --rm gsmap --help
+
+# Run a specific command
+docker-compose run --rm gsmap [subcommand] [options]
+
+# Example with custom command
+docker-compose run --rm gsmap format-sumstats \
+  --sumstats /data/input.txt \
+  --out /results/output
+```
+
+## Volume Mounts
+
+The Docker setup includes two default volume mounts:
+- `./data:/data` - For input data files
+- `./results:/results` - For output results
+
+Place your input files in the `data/` directory and reference them with `/data/` prefix in commands.
+Results will be saved to the `results/` directory.
+
+## Interactive Shell
+
+To get an interactive shell for debugging:
+
+```bash
+# Using Docker
+docker run --rm -it \
+  -v $(pwd)/data:/data \
+  -v $(pwd)/results:/results \
+  --entrypoint /bin/bash \
+  gsmap:latest
+
+# Using Docker Compose
+docker-compose run --rm --entrypoint /bin/bash gsmap
+```
+
+## Tips for Reproducibility
+
+1. **Pin versions**: Consider updating the Dockerfile to use specific versions of dependencies
+2. **Document data**: Keep track of input data versions and sources
+3. **Tag images**: Use version tags for your Docker images
+   ```bash
+   docker build -t gsmap:v1.0.0 .
+   ```
+4. **Save configurations**: Store your command parameters in scripts or configuration files
+
+## Multi-platform builds (Optional)
+
+For building images that work on different architectures (e.g., AMD64, ARM64):
+
+```bash
+# Setup buildx (one-time)
+docker buildx create --name mybuilder --use
+
+# Build for multiple platforms
+docker buildx build --platform linux/amd64,linux/arm64 -t gsmap:latest --push .
+```
+
+## Troubleshooting
+
+- If you encounter memory issues, increase Docker's memory limit in Docker Desktop settings
+- For permission issues with mounted volumes, ensure the data and results directories have appropriate permissions
+- If builds are slow, consider using a `.dockerignore` file to exclude unnecessary files