gsMap 1.71.2__tar.gz → 1.73.0__tar.gz

gsmap-1.73.0/.coveragerc

@@ -0,0 +1,41 @@
+[run]
+source = src/gsMap
+omit =
+    # Exclude the files you mentioned
+    src/gsMap/utils/jackknife.py
+    src/gsMap/format_sumstats.py
+    # Other files you might want to exclude
+    */tests/*
+    */__init__.py
+    src/gsMap/templates/*
+    # Additional excludes
+    src/gsMap/__main__.py
+    src/gsMap/setup.py
+
+[report]
+exclude_lines =
+    # Have to re-enable the standard pragma
+    pragma: no cover
+
+    # Don't complain about missing debug-only code
+    def __repr__
+    if self\.debug
+
+    # Don't complain if tests don't hit defensive assertion code
+    raise NotImplementedError
+    raise ValueError
+    except ImportError
+    except Exception
+    except:
+
+    # Don't complain if non-runnable code isn't run
+    if 0:
+    if __name__ == .__main__.:
+    if False:
+
+    # Skip pass statements
+    pass
+
+[paths]
+source =
+    src/gsMap

gsmap-1.73.0/.github/workflows/docs.yml

@@ -0,0 +1,55 @@
+name: docs
+
+on:
+  push:
+    paths:
+      - "docs/**"
+      - "visualization_web_docs/**"
+
+jobs:
+  deploy_docs:
+    runs-on: self-hosted
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+
+      # --- Build 'docs' documentation ---
+      - name: Install 'docs' dependencies
+        run: |
+          python -m pip install '.[doc]'
+
+      - name: Build 'docs' documentation
+        working-directory: ./docs
+        run: |
+          make html
+
+      - name: Deploy 'docs' to website_docs
+        run: |
+          DOCS_OUTPUT_DIR="/mnt/website_docs/gsmap"  # Adjust if you want a different subfolder
+          mkdir -p "$DOCS_OUTPUT_DIR"
+          rsync -avz ./docs/build/html/ "$DOCS_OUTPUT_DIR/"
+          echo "Documentation for 'docs' deployed to: $DOCS_OUTPUT_DIR"
+
+#      # --- Build 'visualization_web_docs' documentation ---
+#      - name: Install 'visualization_web_docs' dependencies
+#        working-directory: ./visualization_web_docs
+#        run: |
+#          python -m pip install -r requirements.txt
+#
+#      - name: Build 'visualization_web_docs' documentation
+#        working-directory: ./visualization_web_docs
+#        run: |
+#          make html
+#
+#      - name: Deploy 'visualization_web_docs' to website_docs
+#        run: |
+#          DOCS_OUTPUT_DIR="/mnt/website_docs/visualization_web_docs" # Deploy to a separate folder
+#          mkdir -p "$DOCS_OUTPUT_DIR"
+#          rsync -avz ./visualization_web_docs/build/html/ "$DOCS_OUTPUT_DIR/"
+#          echo "Documentation for 'visualization_web_docs' deployed to: $DOCS_OUTPUT_DIR"

gsmap-1.73.0/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,97 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+on: push
+
+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: Store the distribution packages
+        if: startsWith(github.ref, 'refs/tags/') # store only on tag pushes
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
+    needs:
+      - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/gsMap
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+      - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write # IMPORTANT: mandatory for sigstore
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.tar.gz
+            ./dist/*.whl
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          '${{ github.ref_name }}'
+          --repo '${{ github.repository }}'
+          --notes ""
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        run: >-
+          gh release upload
+          '${{ github.ref_name }}' dist/**
+          --repo '${{ github.repository }}'

gsmap-1.73.0/.github/workflows/test_linux.yml

@@ -0,0 +1,88 @@
+name: test
+
+on:
+  push:
+    branches: [main, "[0-9]+.[0-9]+.x"]
+  pull_request:
+  schedule:
+    - cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: [self-hosted, cpu]
+
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.10", "3.13"]
+
+    name: Python ${{ matrix.python }} integration
+
+    env:
+      PYTHON: ${{ matrix.python }}
+      RUNNER_WORKDIR: ${{ vars.RUNNER_WORKDIR_BASE || '/mnt/workdir' }}/${{ github.repository }}/${{ github.workflow }}-${{ github.run_number }}-${{ matrix.python }}
+      TEST_DATA_DIR: /gsmap_test_data
+
+    steps:
+      - name: Create unique workdir
+        run: |
+          mkdir -p $RUNNER_WORKDIR
+          echo "Created workdir: $RUNNER_WORKDIR"
+
+      - uses: actions/checkout@v4
+        # Remove the custom path to let the runner use its default location
+
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip wheel uv
+          python -m uv pip install -e "gsMap[tests] @ ."
+
+      - name: Run pytest
+        env:
+          MPLBACKEND: agg
+          DISPLAY: :42
+          COLUMNS: 120
+        run: |
+          python -m pytest --cov=src \
+              --cov-report=term-missing \
+              --cov-report=xml \
+              --cov-report=html \
+              --cov-config=.coveragerc \
+              -v -s --color=yes \
+              --run-real-data \
+              --work-dir=${{ env.RUNNER_WORKDIR }} \
+              --test-data=${{ env.TEST_DATA_DIR }}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false
+
+      - name: Retain test results
+        if: always()
+        run: |
+          cp -r coverage.xml coverage-html/ .coverage $RUNNER_WORKDIR/ || true
+          echo "Test results are stored in $RUNNER_WORKDIR"
+          # Create a summary file with metadata
+          echo "Test run completed at $(date)" > $RUNNER_WORKDIR/test-summary.txt
+          echo "Workflow: ${{ github.workflow }}" >> $RUNNER_WORKDIR/test-summary.txt
+          echo "Run ID: ${{ github.run_id }}" >> $RUNNER_WORKDIR/test-summary.txt
+          echo "Run Number: ${{ github.run_number }}" >> $RUNNER_WORKDIR/test-summary.txt
+          echo "Python Version: ${{ matrix.python }}" >> $RUNNER_WORKDIR/test-summary.txt
+          echo "Repository: ${{ github.repository }}" >> $RUNNER_WORKDIR/test-summary.txt
+          echo "Ref: ${{ github.ref }}" >> $RUNNER_WORKDIR/test-summary.txt

{gsmap-1.71.2 → gsmap-1.73.0}/.gitignore

@@ -245,13 +245,3 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
-
-test/
-# 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/
-
-!/test/GPS-snakemake-workflow.smk

gsmap-1.73.0/.markdownlint.yaml

@@ -0,0 +1,20 @@
+# default to true for all rules
+default: true
+
+# MD007/unordered-list-indent
+MD007:
+  indent: 4
+
+# MD033/no-inline-html
+MD033: false
+
+# MD041/first-line-h1
+MD041: false
+
+# MD013/line-length
+MD013: false
+
+# MD024/no-duplicate-heading
+MD024:
+  # Allow when nested under different parents e.g. CHANGELOG.md
+  siblings_only: true

gsmap-1.73.0/.pre-commit-config.yaml

@@ -0,0 +1,66 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - pre-commit
+  - pre-push
+minimum_pre_commit_version: 2.16.0
+repos:
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.19.1
+    hooks:
+      - id: blacken-docs
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+        types: [yaml]
+
+  - repo: https://github.com/executablebooks/mdformat
+    rev: 0.7.21
+    hooks:
+      - id: mdformat
+        additional_dependencies:
+          - mdformat-mkdocs
+        exclude: |
+          (?x)^(
+            \.github/.*\.md
+          )$
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.43.0
+    hooks:
+      - id: markdownlint-fix
+        exclude: |
+          (?x)^(
+            \.github/.*\.md
+          )$
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.2
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

{gsmap-1.71.2 → gsmap-1.73.0}/LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2023 liyang
+Copyright (c) 2025 JianYang-Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ 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 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.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

gsmap-1.73.0/PKG-INFO

@@ -0,0 +1,169 @@
+Metadata-Version: 2.4
+Name: gsMap
+Version: 1.73.0
+Summary: Genetics-informed pathogenic spatial mapping
+Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: POSIX :: Linux
+License-File: LICENSE
+Requires-Dist: numpy < 2.0.0
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: tqdm
+Requires-Dist: pyyaml
+Requires-Dist: torch
+Requires-Dist: torch-geometric
+Requires-Dist: pyranges
+Requires-Dist: pyfiglet
+Requires-Dist: plotly
+Requires-Dist: kaleido
+Requires-Dist: jinja2
+Requires-Dist: scanpy >=1.8.0
+Requires-Dist: zarr>=2,<3
+Requires-Dist: bitarray >=2.9.2, <3.0.0
+Requires-Dist: pyarrow
+Requires-Dist: scikit-misc
+Requires-Dist: sphinx ; extra == "doc"
+Requires-Dist: sphinx-argparse ; extra == "doc"
+Requires-Dist: sphinx-autobuild ; extra == "doc"
+Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
+Requires-Dist: sphinx-basic-ng ; extra == "doc"
+Requires-Dist: sphinx-charts ; extra == "doc"
+Requires-Dist: sphinx-copybutton ; extra == "doc"
+Requires-Dist: sphinx_inline_tabs ; extra == "doc"
+Requires-Dist: sphinx-markdown-tables ; extra == "doc"
+Requires-Dist: sphinx-rtd-theme ; extra == "doc"
+Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
+Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
+Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
+Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
+Requires-Dist: furo ; extra == "doc"
+Requires-Dist: myst-parser ; extra == "doc"
+Requires-Dist: nbsphinx ; extra == "doc"
+Requires-Dist: pytest>=7.0.0 ; extra == "tests"
+Requires-Dist: pytest-cov>=4.0.0 ; extra == "tests"
+Requires-Dist: coverage ; extra == "tests"
+Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
+Project-URL: Home, https://github.com/JianYang-Lab/gsMap
+Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
+Provides-Extra: doc
+Provides-Extra: tests
+
+# gsMap
+
+|               |                                                                                                      |                |                                                                                                    |
+| ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |
+| __Version__   | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url]                        | __Status__     | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |
+| __Activity__  | [![GitHub commits][commits-badge]][commits-url] [![Last Commit][last-commit-badge]][last-commit-url] | __Quality__    | [![codecov][codecov-badge]][codecov-url] [![Ruff][ruff-badge]][ruff-url]                           |
+| __CI/CD__     | [![Docs][docs-badge]][docs-url] [![test][test-badge]][test-url]                                      | __Community__  | [![GitHub stars][stars-badge]][stars-url] [![GitHub forks][forks-badge]][forks-url]                |
+| __Downloads__ | [![Downloads][downloads-badge]][downloads-url]                                                       | __License__    | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url]                         |
+| __Platform__  | [![Linux][linux-badge]][linux-url]                                                                   | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url]                           |
+
+## Introduction
+
+`gsMap` (genetically informed spatial mapping of cells for complex traits)
+integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
+summary statistics to map cells to human complex traits, including diseases,
+in a spatially resolved manner.
+
+## Key Features
+
+- __Spatially-aware High-Resolution Trait Mapping__
+- __Spatial Region Identification__
+- __Putative Causal Genes Identification__
+
+![Model Architecture](schematic.png)
+
+## Installation
+
+Install using pip:
+
+```bash
+conda create -n gsMap python>=3.10
+conda activate gsMap
+pip install gsMap
+```
+
+Install from source:
+
+```bash
+git clone https://github.com/JianYang-Lab/gsMap
+cd gsMap
+pip install -e .
+```
+
+Verify the installation by running the following command:
+
+```bash
+gsmap --help
+```
+
+## Usage
+
+Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
+
+## Online Visualization
+
+To visualize the traits-cell association spatial maps,
+please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
+
+## Citation
+
+Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
+[Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)
+Nature (2025).
+
+Please cite the paper and give us a STAR if you find gsMap useful for your research.
+
+<!-- Badge links -->
+
+[codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU
+[codecov-url]: https://codecov.io/gh/JianYang-Lab/gsMap
+[commits-badge]: https://img.shields.io/github/commit-activity/m/JianYang-Lab/gsMap
+[commits-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[docs-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml/badge.svg
+[docs-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml
+[doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue
+[doi-url]: https://doi.org/10.1038/s41586-025-08757-x
+[downloads-badge]: https://static.pepy.tech/badge/gsMap
+[downloads-url]: https://pepy.tech/project/gsMap
+[forks-badge]: https://img.shields.io/github/forks/JianYang-Lab/gsMap
+[forks-url]: https://github.com/JianYang-Lab/gsMap/network/members
+[issues-badge]: https://img.shields.io/github/issues/JianYang-Lab/gsMap
+[issues-url]: https://github.com/JianYang-Lab/gsMap/issues
+[last-commit-badge]: https://img.shields.io/github/last-commit/JianYang-Lab/gsMap
+[last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main
+[license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
+[license-url]: https://opensource.org/licenses/MIT
+[linux-badge]: https://img.shields.io/badge/Linux-%E2%9C%93-success
+[linux-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+[maintenance-badge]: https://img.shields.io/badge/Maintained%3F-yes-green.svg
+[maintenance-url]: https://github.com/JianYang-Lab/gsMap/graphs/commit-activity
+[pr-badge]: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
+[pr-url]: https://github.com/JianYang-Lab/gsMap/pulls
+[pypi-badge]: https://img.shields.io/pypi/v/gsMap
+[pypi-url]: https://pypi.org/project/gsMap/
+[python-badge]: https://img.shields.io/pypi/pyversions/gsMap
+[python-url]: https://www.python.org
+[ruff-badge]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
+[ruff-url]: https://github.com/astral-sh/ruff
+[stars-badge]: https://img.shields.io/github/stars/JianYang-Lab/gsMap
+[stars-url]: https://github.com/JianYang-Lab/gsMap/stargazers
+[status-badge]: https://www.repostatus.org/badges/latest/active.svg
+[status-url]: https://www.repostatus.org/#active
+[test-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml/badge.svg
+[test-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
+