mgnify-methods 0.1.0__tar.gz

mgnify_methods-0.1.0/.github/FUNDING.yml

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+# These are supported funding model platforms
+
+github: [palec87]
+patreon: # Replace with a single Patreon username
+open_collective: # Replace with a single Open Collective username
+ko_fi: # Replace with a single Ko-fi username
+tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
+community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
+liberapay: # Replace with a single Liberapay username
+issuehunt: # Replace with a single IssueHunt username
+lfx_crowdfunding: # Replace with a single LFX Crowdfunding project-name e.g., cloud-foundry
+polar: # Replace with a single Polar username
+buy_me_a_coffee: # Replace with a single Buy Me a Coffee username
+thanks_dev: # Replace with a single thanks.dev username
+custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

mgnify_methods-0.1.0/.github/ISSUE_TEMPLATE//360/237/220/233-bug-report.md

@@ -0,0 +1,30 @@
+---
+name: "\U0001F41B Bug report"
+about: Create a report to help us improve
+title: "[BUG]"
+labels: ''
+assignees: ''
+
+---
+
+✏️ **Describe the bug**
+A clear and concise description of what the bug is.
+
+👯 **To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. run command '...'
+3. function error '...'
+
+🌈 **Expected behavior**
+Description of what you expected to happen.
+
+📸 **Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+ℹ️ **System information:**
+ - OS: [e.g. iOS]
+ - python version: [e.g. 3.12]
+
+➕ **Additional context**
+Add any other context about the problem here.

mgnify_methods-0.1.0/.github/ISSUE_TEMPLATE//360/237/222/241-feature-request.md

@@ -0,0 +1,21 @@
+---
+name: "\U0001F4A1 Feature request"
+about: Suggest an idea for this project
+title: "[Feature]"
+labels: ''
+assignees: ''
+
+---
+
+❓ **Is your feature request related to a problem?**
+What the problem is. Ex. I'm always frustrated when [...]
+Link to an open issue: [...]
+
+❗ **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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

mgnify_methods-0.1.0/.github/workflows/test-deploy.yml

@@ -0,0 +1,104 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: tests
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} py${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        platform: [ubuntu-latest, windows-latest, macos-latest]  # is not tested atm
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Install dependencies
+        run: |
+          uv sync --extra dev
+          uv pip install git+https://github.com/fair-ease/py-udal-mgo.git
+
+      # this runs the platform-specific tests declared in tox.ini
+      - name: Test with pytest
+        uses: aganders3/headless-gui@v2
+        with:
+          run: uv run pytest -v --color=yes --cov=src --cov-report=xml
+        env:
+          PLATFORM: ${{ matrix.platform }}
+          MPLBACKEND: Agg
+
+    #   - name: Codecov
+    #     uses: codecov/codecov-action@v5.4.2
+    #     with:
+    #       token: ${{ secrets.CODECOV_TOKEN }}
+
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+    needs:
+    - test
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        persist-credentials: false
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      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/project/mgnify-methods/  # 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@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

mgnify_methods-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# 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
+.envrc
+.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/
+
+# 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/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+.vscode/
+.venv/
+notebooks/analysis_*/
+notebooks/MGYS00006680/
+outputs/
+paper/
+
+.history/

mgnify_methods-0.1.0/.python-version

@@ -0,0 +1 @@
+3.12

mgnify_methods-0.1.0/.readthedocs.yaml

@@ -0,0 +1,23 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  jobs:
+    post_install:
+      - uv sync --extra docs
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

mgnify_methods-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 David Paleček
+
+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.

mgnify_methods-0.1.0/Makefile

@@ -0,0 +1,50 @@
+.PHONY: help install dev-install test coverage lint format clean docs build
+
+help:  ## Show this help message
+	@echo 'Usage: make [target]'
+	@echo ''
+	@echo 'Available targets:'
+	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "  %-20s %s\n", $$1, $$2}' $(MAKEFILE_LIST)
+
+install:  ## Install the package
+	uv sync && \
+	uv pip install git+https://github.com/fair-ease/py-udal-mgo.git
+
+dev-install:  ## Install the package with development dependencies
+	uv sync --extra dev --extra docs && \
+	uv pip install git+https://github.com/fair-ease/py-udal-mgo.git && \
+	uv run python -m ipykernel install --user --name mgnify-methods --display-name "mgnify-methods"
+
+test:  ## Run tests
+	uv run pytest tests/
+
+coverage:  ## Run tests with coverage report
+	uv run pytest --cov=src --cov-report=html --cov-report=term tests/
+
+lint:  ## Run linters (ruff and mypy)
+	uv run ruff check src tests
+	uv run mypy src
+
+format:  ## Format code with ruff
+	uv run ruff format src tests
+	uv run ruff check --fix src tests
+
+clean:  ## Clean build artifacts and cache files
+	rm -rf build/
+	rm -rf dist/
+	rm -rf *.egg-info
+	rm -rf .pytest_cache/
+	rm -rf .mypy_cache/
+	rm -rf .ruff_cache/
+	rm -rf htmlcov/
+	rm -rf .coverage
+	find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
+	find . -type f -name "*.pyc" -delete
+
+docs:  ## Build documentation
+	cd docs && uv run sphinx-build -b html source _build/html
+
+build:  ## Build the package
+	uv build
+
+.DEFAULT_GOAL := help

mgnify_methods-0.1.0/PKG-INFO

@@ -0,0 +1,116 @@
+Metadata-Version: 2.4
+Name: mgnify-methods
+Version: 0.1.0
+Summary: Support methods and classes for the Biodiversity studies on Mgnify metagenomes
+Author-email: palec87 <palec87@users.noreply.github.com>
+License-File: LICENSE
+Requires-Python: >=3.12
+Requires-Dist: biopython>=1.81.0
+Requires-Dist: ipykernel>=6.0.0
+Requires-Dist: jsonapi-client>=0.9.9
+Requires-Dist: jupyterlab>=4.0.0
+Requires-Dist: marine-omics>=0.1.17
+Requires-Dist: matplotlib-venn>=1.1.2
+Requires-Dist: matplotlib>=3.8.0
+Requires-Dist: numpy>=1.25.0
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pydantic>=2.12.0
+Requires-Dist: pydeseq2>=0.5.4
+Requires-Dist: requests>=2.31.0
+Requires-Dist: scikit-learn>=1.4.0
+Requires-Dist: scipy>=1.11.0
+Requires-Dist: seaborn>=0.13.0
+Requires-Dist: setuptools<81.0.0,>=68.0.0
+Requires-Dist: tqdm>=4.66.0
+Provides-Extra: dev
+Requires-Dist: ipykernel>=6.0.0; extra == 'dev'
+Requires-Dist: jupyterlab>=4.0.0; extra == 'dev'
+Requires-Dist: mypy>=1.8.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.1.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: myst-parser>=2.0.0; extra == 'docs'
+Requires-Dist: sphinx-autodoc-typehints>=1.25.0; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme>=2.0.0; extra == 'docs'
+Requires-Dist: sphinx>=7.0.0; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# mgnify-methods
+
+Support methods and classes for the Biodiversity studies on Mgnify metagenomes
+
+## Installation
+
+### Using uv (recommended)
+
+```bash
+uv add mgnify-methods
+```
+
+### Using pip
+
+```bash
+pip install mgnify-methods
+```
+
+### From source
+
+```bash
+git clone https://github.com/palec87/mgnify-methods.git
+cd mgnify-methods
+uv sync
+```
+
+## Development
+
+This project uses `uv` for dependency management and has a `Makefile` for common development tasks.
+
+### Setup development environment
+
+```bash
+make dev-install
+```
+
+### Run tests
+
+```bash
+make test
+```
+
+### Run linters
+
+```bash
+make lint
+```
+
+### Format code
+
+```bash
+make format
+```
+
+### Build documentation
+
+```bash
+make docs
+```
+
+### Build package
+
+```bash
+make build
+```
+
+### Available Make targets
+
+Run `make help` to see all available targets.
+
+## Documentation
+
+Documentation is available at [ReadTheDocs](https://mgnify-methods.readthedocs.io/) (once deployed).
+
+## License
+
+See [LICENSE](LICENSE) file for details.
+

mgnify_methods-0.1.0/README.md

@@ -0,0 +1,78 @@
+# mgnify-methods
+
+Support methods and classes for the Biodiversity studies on Mgnify metagenomes
+
+## Installation
+
+### Using uv (recommended)
+
+```bash
+uv add mgnify-methods
+```
+
+### Using pip
+
+```bash
+pip install mgnify-methods
+```
+
+### From source
+
+```bash
+git clone https://github.com/palec87/mgnify-methods.git
+cd mgnify-methods
+uv sync
+```
+
+## Development
+
+This project uses `uv` for dependency management and has a `Makefile` for common development tasks.
+
+### Setup development environment
+
+```bash
+make dev-install
+```
+
+### Run tests
+
+```bash
+make test
+```
+
+### Run linters
+
+```bash
+make lint
+```
+
+### Format code
+
+```bash
+make format
+```
+
+### Build documentation
+
+```bash
+make docs
+```
+
+### Build package
+
+```bash
+make build
+```
+
+### Available Make targets
+
+Run `make help` to see all available targets.
+
+## Documentation
+
+Documentation is available at [ReadTheDocs](https://mgnify-methods.readthedocs.io/) (once deployed).
+
+## License
+
+See [LICENSE](LICENSE) file for details.
+