gsMap 1.60__tar.gz

gsmap-1.60/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,120 @@
+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
+      uses: actions/upload-artifact@v3
+      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/<package-name>  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      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@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v1.2.3
+      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 }}'
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/<package-name>
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/

gsmap-1.60/.github/workflows/sphinx.yml

@@ -0,0 +1,24 @@
+name: "Sphinx: Render docs"
+
+on: push
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+    - uses: actions/checkout@v4
+    - name: Build HTML
+      uses: ammaraskar/sphinx-action@master
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: html-docs
+        path: docs/build/html/
+    - name: Deploy
+      uses: peaceiris/actions-gh-pages@v3
+      if: github.ref == 'refs/heads/main'
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: docs/build/html

gsmap-1.60/.gitignore

@@ -0,0 +1,257 @@
+### JetBrains+all template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### JupyterNotebooks template
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Remove previous ipynb_checkpoints
+#   git rm -r .ipynb_checkpoints/
+
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+
+# 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
+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/
+
+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-1.60/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2023 liyang
+
+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.

gsmap-1.60/PKG-INFO

@@ -0,0 +1,124 @@
+Metadata-Version: 2.1
+Name: gsMap
+Version: 1.60
+Summary: Genetics-informed pathogenic spatial mapping
+Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Operating System :: POSIX :: Linux
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: scikit-learn
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: tqdm
+Requires-Dist: progress
+Requires-Dist: pyyaml
+Requires-Dist: torch
+Requires-Dist: torch-geometric
+Requires-Dist: pyranges
+Requires-Dist: pyfiglet
+Requires-Dist: plotly
+Requires-Dist: kaleido
+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"
+Project-URL: Documentation, https://...
+Project-URL: Home, https://github.com/LeonSong1995/gsMap
+Project-URL: Website, https://...
+Provides-Extra: doc
+
+# gsMap (genetically informed spatial mapping of cells for complex traits)
+[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/MeDuSA?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+
+## Features
+
+....
+
+## Installation
+
+install use pip:
+
+```bash
+pip install gsMap-mapping
+```
+
+install from source:
+
+```bash
+git clone
+cd gsMap-mapping
+pip install -e .
+```
+
+## Usage
+
+To use gsMap, navigate to the command line and enter `gsMap` followed by the subcommand that corresponds to the desired operation. Each subcommand may require specific arguments to run.
+
+### Basic Command Structure
+
+```bash
+gsMap subcommand [arguments...]
+```
+
+- `subcommand`: The specific operation you wish to perform.
+- `arguments`: The arguments and options required for the subcommand.
+
+### Available Subcommands
+
+(Provide a list and brief description of each available subcommand. For example:)
+
+- `run_find_latent_representations`: Finds latent representations using a GNN-VAE model.
+- `run_latent_to_gene`: Maps latent representations to gene markers.
+- `run_generate_ldscore`: Generates LD scores for genomic spots.
+- `run_spatial_ldsc`: Conducts spatial LDSC analysis.
+- `run_cauchy_combination`: Performs Cauchy combination tests for annotations.
+- `run_all_mode`: Executes a comprehensive pipeline covering all steps.
+
+### Examples
+
+To run a specific functionality, you need to provide the appropriate subcommand and arguments. For example:
+### Running Requirement
+
+
+```bash
+gsMap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
+```
+
+This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.
+
+## Contributing
+
+...
+
+## License
+
+....
+
+---
+

gsmap-1.60/README.md

@@ -0,0 +1,70 @@
+# gsMap (genetically informed spatial mapping of cells for complex traits)
+[![stars-badge](https://img.shields.io/github/stars/LeonSong1995/MeDuSA?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
+[![license-badge](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+
+## Features
+
+....
+
+## Installation
+
+install use pip:
+
+```bash
+pip install gsMap-mapping
+```
+
+install from source:
+
+```bash
+git clone
+cd gsMap-mapping
+pip install -e .
+```
+
+## Usage
+
+To use gsMap, navigate to the command line and enter `gsMap` followed by the subcommand that corresponds to the desired operation. Each subcommand may require specific arguments to run.
+
+### Basic Command Structure
+
+```bash
+gsMap subcommand [arguments...]
+```
+
+- `subcommand`: The specific operation you wish to perform.
+- `arguments`: The arguments and options required for the subcommand.
+
+### Available Subcommands
+
+(Provide a list and brief description of each available subcommand. For example:)
+
+- `run_find_latent_representations`: Finds latent representations using a GNN-VAE model.
+- `run_latent_to_gene`: Maps latent representations to gene markers.
+- `run_generate_ldscore`: Generates LD scores for genomic spots.
+- `run_spatial_ldsc`: Conducts spatial LDSC analysis.
+- `run_cauchy_combination`: Performs Cauchy combination tests for annotations.
+- `run_all_mode`: Executes a comprehensive pipeline covering all steps.
+
+### Examples
+
+To run a specific functionality, you need to provide the appropriate subcommand and arguments. For example:
+### Running Requirement
+
+
+```bash
+gsMap run_find_latent_representations --input_hdf5_path <path> --output_hdf5_path <path> --sample_name <name>
+```
+
+This command initiates the process of finding latent representations based on the given HDF5 input and output paths and sample name.
+
+## Contributing
+
+...
+
+## License
+
+....
+
+---

gsmap-1.60/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

gsmap-1.60/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

gsmap-1.60/docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx==6
+gsMap[doc]