Merge pull request #1 from Multiomics-Analytics-Group/mk_pkg

Author: enryH

.github/workflows/cdci.yml

@@ -0,0 +1,77 @@
+name: Python package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+    
+jobs:
+  # format:
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - uses: psf/black@stable 
+  # lint:
+  #   name: Lint with ruff
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version: "3.11"
+  #     - name: Install ruff
+  #       run: | 
+  #         pip install ruff
+  #     - name: Lint with ruff  
+  #       run: |
+  #         # stop the build if there are Python syntax errors or undefined names
+  #         ruff check .
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: '**/pyproject.toml'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          pip install -e .
+      # - name: Run tests
+      #   run: python -m pytest tests
+  
+
+
+  publish:
+    name: Publish package
+    if: startsWith(github.ref, 'refs/tags')
+    permissions:
+      id-token: write
+    needs:
+      - test
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+  
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install twine and build
+        run: python -m pip install --upgrade twine build
+      - name: Build
+        run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

pyproject.toml

@@ -0,0 +1,68 @@
+[project]
+authors = [{ name = "Alberto Santos Delgado", email = "[email protected]" },
+           { name = "Henry Webel", email = "[email protected]"}]
+name = "vuecore"
+dynamic = ["version"]
+description = "A Python package for plotting related to multimodal molecular data. Works with acore."
+license = { text = "GNU General Public License v3" }
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+]
+
+dependencies = [
+    "numpy",
+    "pandas",
+    # "dsp-pandas", # has only pandas related dependencies
+    "scipy",
+    "plotly",
+    # "biopython",
+    "beautifulsoup4",
+    "requests",
+    "dash", # from dash import html
+    # "networkx",
+    "matplotlib",
+    # "cy-jupyterlab",
+    # "nltk",
+    # "webweb"
+    # "acore",
+]
+
+[project.optional-dependencies]
+docs = [
+  "sphinx",
+  "sphinx-book-theme",
+  "myst-nb",
+  "ipywidgets",
+  "sphinx-new-tab-link!=0.2.2",
+  "jupytext",
+]
+dev = [
+  "black",
+  "flake8",
+  "ruff",
+  "isort",
+  "pytest",
+  "pytest-cov",
+  "twine",
+  "wheel",
+  "jupytext",
+  "ipykernel",
+]
+
+[project.urls]
+Homepage = "https://github.com/Multiomics-Analytics-Group/vuecore"
+Issues = "https://github.com/Multiomics-Analytics-Group/vuecore/issues"
+Documentation = "https://analytics-core.readthedocs.io/"
+
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

setup.cfg

@@ -0,0 +1,10 @@
+[flake8]
+exclude = docs
+max-line-length = 90
+aggressive = 2
+
+[tool:pytest]
+addopts = --ignore=setup.py
+
+[isort]
+profile=black

setup.py

@@ -1,54 +1,5 @@
-# builtin
-import setuptools
+from setuptools import setup
 
-def get_long_description():
-    with open("README.md", "r") as readme_file:
-        long_description = readme_file.read()
-    return long_description
-
-
-def get_requirements():
-    with open('requirements.txt') as f:
-        required = f.read().splitlines()
-    return required
-    
-
-def create_pip_wheel():
-    requirements = get_requirements()
-    setuptools.setup(
-        name="acore",
-        version="0.1.0",
-        license="MIT",
-        description="An open-source Python package for Statistical Analysis of Omics datasets",
-        long_description=get_long_description(),
-        long_description_content_type="text/markdown",
-        author="Multi-omics Network Analytics lab",
-        author_email="[email protected]",
-        url="",
-        project_urls={
-            "Multi-omics Network Analytics": "",
-            "GitHub": "",
-            "ReadTheDocs": "",
-            "PyPi": "",
-            "Scientific paper": "https://www.nature.com/articles/s41587-021-01145-6",
-        },
-        keywords=["statistics", "bioinformatics", "multi-omics",],
-        classifiers=[
-            "Intended Audience :: Science/Research",
-            "License :: OSI Approved :: MIT License",
-            "Operating System :: OS Independent",
-            "Programming Language :: Python :: 3",
-            "Topic :: Scientific :: Bioinformatics",
-        ],
-        packages=[
-            "acore",
-        ],
-        include_package_data=True,
-        entry_points={},
-        install_requires=requirements,
-        python_requires=">=3.9,<4",
-    )
-
-
-if __name__ == "__main__":
-    create_pip_wheel()
+setup(
+    zip_safe=False,
+)

vcore/Dendrogram.py src/vuecore/Dendrogram.py

@@ -0,0 +1,3 @@
+from importlib import metadata
+
+__version__ = metadata.version("vuecore")