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Alberto NogalesAlberto Nogales
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ci: add GitHub Actions, tests, Sphinx docs; fix packaging
- .github/workflows/tests.yml: CI on Python 3.10 & 3.11 (pytest) - .github/workflows/docs.yml: build Sphinx docs → GitHub Pages - tests/test_gema.py: 51 unit tests covering Map, Classification, all normalizations, weight inits, save/load round-trip - docs/: Sphinx + ReadTheDocs config (sphinx_rtd_theme, autodoc) - .readthedocs.yaml: ReadTheDocs v2 build config - setup.py: fix author/url, add extras_require [test]/[docs], python_requires>=3.9 - README.md: replace missing CI badge with GitHub Actions badge
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‎.github/workflows/docs.yml‎

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name: Docs
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on:
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push:
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branches: [master]
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: pages
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Install dependencies
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run: |
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pip install -e .
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pip install -r docs/requirements.txt
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- name: Build Sphinx docs
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run: sphinx-build -b html docs/ docs/_build/html
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- name: Upload Pages artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: docs/_build/html
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deploy:
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needs: build
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runs-on: ubuntu-latest
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/tests.yml‎

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name: Tests
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on:
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push:
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branches: [master, main]
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pull_request:
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branches: [master, main]
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.11"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: pip install -e ".[test]"
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- name: Run tests
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run: python -m pytest tests/ -v --tb=short

‎.readthedocs.yaml‎

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version: 2
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build:
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os: ubuntu-22.04
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tools:
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python: "3.11"
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sphinx:
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configuration: docs/conf.py
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python:
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install:
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- requirements: docs/requirements.txt
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- method: pip
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path: .

‎README.md‎

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# GEMA — Self-Organizing Maps in Python
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[![Tests](https://github.com/ufvceiec/GEMA/actions/workflows/tests.yml/badge.svg)](https://github.com/ufvceiec/GEMA/actions/workflows/tests.yml)
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[![Python](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11-blue.svg)](https://www.python.org/downloads/)
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[![PyPI](https://img.shields.io/pypi/v/GEMA?color=blue)](https://pypi.org/project/GEMA/)
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[![License](https://img.shields.io/github/license/ufvceiec/GEMA.svg)](LICENSE)
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**GEMA** (*GEnerador de Mapas Autoasociativos*) is an open-source Python library for building, training, and analysing Self-Organizing Maps (SOMs / Kohonen maps). It covers the full workflow: data normalisation → training → classification → quality metrics → interactive visualisation.
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> **Cite as:**

‎docs/api.rst‎

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API Reference
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=============
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GEMA.map
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--------
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.. automodule:: GEMA.map
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:members:
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:undoc-members:
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:show-inheritance:
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GEMA.classification
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-------------------
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.. automodule:: GEMA.classification
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:members:
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:undoc-members:
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:show-inheritance:
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GEMA.visualization
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------------------
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.. automodule:: GEMA.visualization
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:members:
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:undoc-members:
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:show-inheritance:
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GEMA.iterativesom
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-----------------
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.. automodule:: GEMA.iterativesom
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:members:
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:undoc-members:
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:show-inheritance:

‎docs/conf.py‎

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import os
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import sys
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sys.path.insert(0, os.path.abspath(".."))
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project = "GEMA"
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author = "Alberto Nogales, Álvaro José García-Tejedor"
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release = "0.4.3"
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version = "0.4.3"
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copyright = f"2024, {author}"
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extensions = [
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"sphinx.ext.autodoc",
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"sphinx.ext.napoleon",
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"sphinx.ext.viewcode",
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]
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templates_path = ["_templates"]
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exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
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html_theme = "sphinx_rtd_theme"
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html_static_path = ["_static"]

‎docs/index.rst‎

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GEMA — Self-Organizing Maps
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===========================
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.. toctree::
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:maxdepth: 2
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:caption: Contents:
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installation
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api
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Indices and tables
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==================
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* :ref:`genindex`
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* :ref:`modindex`
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* :ref:`search`

‎docs/installation.rst‎

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Installation
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============
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Requirements
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------------
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GEMA requires Python 3.9 or later. All runtime dependencies are listed in
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``requirements.txt`` and are installed automatically when you install the
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package via pip.
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Install from PyPI
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-----------------
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.. code-block:: bash
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pip install GEMA
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Install from source
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-------------------
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.. code-block:: bash
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git clone https://github.com/ufvceiec/GEMA.git
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cd GEMA
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pip install -e .
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Running the tests
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-----------------
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.. code-block:: bash
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pip install -e ".[test]"
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python -m pytest tests/ -v

‎docs/requirements.txt‎

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sphinx>=7.0
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sphinx-rtd-theme>=1.3
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sphinx-autodoc-typehints>=1.24

‎setup.py‎

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setuptools.setup(
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name="GEMA",
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version="0.4.3",
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author="UFV CEIEC",
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author_email="ceiec.info@ceiec.es",
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author="Alberto Nogales, Álvaro José García-Tejedor",
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author_email="alberto.nogales@uah.es",
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description="A library to build and study Self-Organizing-Maps",
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long_description=long_description,
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long_description_content_type="text/markdown",
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url="https://github.com/ufvceiec/GEMA",
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packages=setuptools.find_packages(),
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python_requires=">=3.7",
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python_requires=">=3.9",
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install_requires=[
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"numpy",
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"tqdm",
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"scikit-learn",
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"scipy",
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],
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extras_require={
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'test': ['pytest>=7.0', 'pytest-cov>=4.0'],
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},
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classifiers=[
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.7",

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