pylluminator 0.1__tar.gz

pylluminator-0.1/.github/workflows/run_test.yml

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+name: Run Unit Test via Pytest
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |  
+          python -m pip install --upgrade pip  
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi  
+      - name: Test with pytest
+        run: |  
+          coverage run -m pytest  -v -s
+      - name: Generate Coverage Report
+        run: |  
+          coverage xml
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

pylluminator-0.1/.gitignore

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+# development
+.idea
+__pycache__
+drafts/
+stub.py
+data/
+.ipynb_checkpoints/
+.gitattributes
+build
+notebooks/
+
+# tests
+.coverage
+coverage.xml
+htmlcov
+tests/*.png
+
+# tutorial files that are not ipynb (saved models)
+docs/tutorials/*
+!docs/tutorials/*.ipynb
+
+# data
+*.gz
+
+# documentations
+_build/
+generated/
+_autosummary/
+
+# packaging
+*.egg
+eggs/
+.eggs
+*.egg-info/
+wheels/
+dist/
+build/

pylluminator-0.1/.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+   os: ubuntu-22.04
+   tools:
+     python: "3.12"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+python:
+   install:
+      - requirements: docs/requirements.txt  # to install sphinx, nbsphinx..
+      - requirements: requirements.txt  # package requirements (needed to build the python notebooks)
+      - method: pip
+        path: . # install the package locally

pylluminator-0.1/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 eliopato
+
+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.

pylluminator-0.1/PKG-INFO

@@ -0,0 +1,210 @@
+Metadata-Version: 2.4
+Name: pylluminator
+Version: 0.1
+Summary: Tool to preprocess, analyze and visualize DNA methylation data from Illumina micro-arrays
+Author-email: Elio <elio.fanchon@univ-amu.fr>
+Maintainer-email: Elio <elio.fanchon@univ-amu.fr>
+License-Expression: MIT
+Project-URL: Homepage, https://pylluminator.readthedocs.io/
+Project-URL: Documentation, https://pylluminator.readthedocs.io/
+Project-URL: Repository, https://github.com/eliopato/pylluminator
+Project-URL: Issues, https://github.com/eliopato/pylluminator/issues
+Keywords: dna-methylation,epigenetics,illumina,bioinformatics,microarray,methylation,DMR
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.12
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: pandas
+Requires-Dist: numpy
+Requires-Dist: scikit-learn
+Requires-Dist: statsmodels
+Requires-Dist: scipy
+Requires-Dist: pyranges1
+Requires-Dist: linear_segment
+Requires-Dist: patsy
+Requires-Dist: ailist
+Requires-Dist: notebook
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: inmoose
+Dynamic: license-file
+
+|logo| Welcome to pylluminator
+==============================
+
+.. image:: https://img.shields.io/github/last-commit/eliopato/pylluminator.svg
+   :target: https://github.com/eliopato/pylluminator/commits/master
+   :alt: Last commit
+
+.. image:: https://img.shields.io/github/actions/workflow/status/eliopato/pylluminator/run_test.yml?branch=main
+   :target: https://github.com/eliopato/pylluminator/actions
+   :alt: Test Status
+
+.. image:: https://img.shields.io/codecov/c/github/eliopato/pylluminator
+   :target: https://codecov.io/gh/eliopato/pylluminator
+   :alt: Code coverage
+
+.. image:: https://readthedocs.org/projects/pylluminator/badge/?version=latest
+   :target: https://pylluminator.readthedocs.io/en/latest/
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/badge/License-MIT-blue.svg
+   :target: ./LICENSE
+   :alt: MIT License
+
+Pylluminator is a Python package designed to provide an efficient workflow for processing and analyzing DNA
+methylation data, mirroring the functionalities of the popular R package `SeSAMe <https://bioconductor.org/packages/release/bioc/html/sesame.html>`_.
+
+It supports the following Illumina's Infinium array versions :
+
+* human : 27k, 450k, MSA, EPIC, EPIC+, EPICv2
+* mouse : MM285
+* mammalian: Mammal40
+
+.. |logo| image:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/logo.png
+    :width: 100px
+
+.. note::
+
+   **This project is under active development.**
+
+
+Main functionalities
+--------------------
+
+* idat files parsing
+
+* data preprocessing
+
+  * background correction
+  * normalization
+  * dye bias correction
+  * pOOBAH
+  * batch effect correction with ComBat
+
+* data analysis and visualisation
+
+  * beta values (density, PCA, MDS, dendrogram...)
+  * DMP and DMR, accounting for replicates / random effects
+  * CNV
+
+* quality control
+
+Visualization examples:
+
+.. list-table::
+
+    * - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_1_-_Read_data_and_get_betas_16_0.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_1_-_Read_data_and_get_betas_16_0.png
+
+            Fig 1. Beta values
+
+      - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_15_0.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_15_0.png
+
+            Fig 2. Differentially methylated regions (DMRs)
+
+    * - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_17_1.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_17_1.png
+
+            Fig 3. Gene visualization
+
+      - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_4_-_Copy_Number_Variation_9_0.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_4_-_Copy_Number_Variation_9_0.png
+
+            Fig 4. Copy number variations (CNVs)
+
+
+Installation
+------------
+
+With pip
+~~~~~~~~
+
+You can install Pylluminator directly with:
+
+.. code-block:: shell
+
+    pip install pylluminator
+
+From source
+~~~~~~~~~~~
+
+We recommend using a virtual environment with Python 3.12 to build pylluminator from source. Here is an example using Conda.
+
+Setup the virtual environment (optional)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you don't have Conda installed yet, here are the instructions depending on your OS : `Windows <https://docs.conda.io/projects/conda/en/latest/user-guide/install/windows.html>`_ | `Linux <https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html>`_ | `MacOS <https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html>`_.
+After installing it, make sure you have Pip installed by running the following command in the terminal:
+
+.. code-block:: shell
+
+    conda install anaconda::pip
+
+Now you can create a Conda environment named "pylluminator" and activate it. You can change the name to your liking ;)
+
+.. code-block:: shell
+
+    conda create -n pylluminator python=3.12
+    conda activate pylluminator
+
+
+Install pylluminator
+^^^^^^^^^^^^^^^^^^^^^
+
+You can download the latest source from github, or clone the repository with this command:
+
+.. code-block:: shell
+
+    git clone https://github.com/eliopato/pylluminator.git
+
+Your are now ready to install the dependencies and the package :
+
+.. code-block:: shell
+
+    cd pylluminator
+    pip install .
+
+
+Usage
+-----
+
+Refer to https://pylluminator.readthedocs.io/ for step-by-step tutorials and detailed documentation.
+
+Contributing
+------------
+We welcome contributions! If you'd like to help improve the package, please follow these steps:
+
+1. Fork the repository.
+2. Create a new branch for your feature or bugfix.
+3. Make your changes and test them.
+4. Submit a pull request describing your changes.
+
+Bug reports / new features suggestion
+-------------------------------------
+
+If you encounter any bugs, have questions, or feel like the package is missing a very important feature, please open an issue on the `GitHub Issues <https://github.com/eliopato/pylluminator/issues>`_ page.
+
+When opening an issue, please provide as much detail as possible, including:
+
+- Steps to reproduce the issue
+- The version of the package you are using
+- Any relevant code snippets or error messages
+
+License
+-------
+
+This project is licensed under the MIT License - see the `LICENSE <./LICENSE>`_ file for details.
+
+Acknowledgements
+----------------
+
+This package is strongly inspired from `SeSAMe <https://bioconductor.org/packages/release/bioc/html/sesame.html>`_ and
+includes code from `methylprep <https://github.com/FoxoTech/methylprep>`_ for .idat files parsing.
+

pylluminator-0.1/README.rst

@@ -0,0 +1,174 @@
+|logo| Welcome to pylluminator
+==============================
+
+.. image:: https://img.shields.io/github/last-commit/eliopato/pylluminator.svg
+   :target: https://github.com/eliopato/pylluminator/commits/master
+   :alt: Last commit
+
+.. image:: https://img.shields.io/github/actions/workflow/status/eliopato/pylluminator/run_test.yml?branch=main
+   :target: https://github.com/eliopato/pylluminator/actions
+   :alt: Test Status
+
+.. image:: https://img.shields.io/codecov/c/github/eliopato/pylluminator
+   :target: https://codecov.io/gh/eliopato/pylluminator
+   :alt: Code coverage
+
+.. image:: https://readthedocs.org/projects/pylluminator/badge/?version=latest
+   :target: https://pylluminator.readthedocs.io/en/latest/
+   :alt: Documentation Status
+
+.. image:: https://img.shields.io/badge/License-MIT-blue.svg
+   :target: ./LICENSE
+   :alt: MIT License
+
+Pylluminator is a Python package designed to provide an efficient workflow for processing and analyzing DNA
+methylation data, mirroring the functionalities of the popular R package `SeSAMe <https://bioconductor.org/packages/release/bioc/html/sesame.html>`_.
+
+It supports the following Illumina's Infinium array versions :
+
+* human : 27k, 450k, MSA, EPIC, EPIC+, EPICv2
+* mouse : MM285
+* mammalian: Mammal40
+
+.. |logo| image:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/logo.png
+    :width: 100px
+
+.. note::
+
+   **This project is under active development.**
+
+
+Main functionalities
+--------------------
+
+* idat files parsing
+
+* data preprocessing
+
+  * background correction
+  * normalization
+  * dye bias correction
+  * pOOBAH
+  * batch effect correction with ComBat
+
+* data analysis and visualisation
+
+  * beta values (density, PCA, MDS, dendrogram...)
+  * DMP and DMR, accounting for replicates / random effects
+  * CNV
+
+* quality control
+
+Visualization examples:
+
+.. list-table::
+
+    * - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_1_-_Read_data_and_get_betas_16_0.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_1_-_Read_data_and_get_betas_16_0.png
+
+            Fig 1. Beta values
+
+      - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_15_0.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_15_0.png
+
+            Fig 2. Differentially methylated regions (DMRs)
+
+    * - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_17_1.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_3_-_Calculate_DMP_and_DMR_17_1.png
+
+            Fig 3. Gene visualization
+
+      - .. figure:: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_4_-_Copy_Number_Variation_9_0.png
+            :target: https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/tutorials_4_-_Copy_Number_Variation_9_0.png
+
+            Fig 4. Copy number variations (CNVs)
+
+
+Installation
+------------
+
+With pip
+~~~~~~~~
+
+You can install Pylluminator directly with:
+
+.. code-block:: shell
+
+    pip install pylluminator
+
+From source
+~~~~~~~~~~~
+
+We recommend using a virtual environment with Python 3.12 to build pylluminator from source. Here is an example using Conda.
+
+Setup the virtual environment (optional)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If you don't have Conda installed yet, here are the instructions depending on your OS : `Windows <https://docs.conda.io/projects/conda/en/latest/user-guide/install/windows.html>`_ | `Linux <https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html>`_ | `MacOS <https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html>`_.
+After installing it, make sure you have Pip installed by running the following command in the terminal:
+
+.. code-block:: shell
+
+    conda install anaconda::pip
+
+Now you can create a Conda environment named "pylluminator" and activate it. You can change the name to your liking ;)
+
+.. code-block:: shell
+
+    conda create -n pylluminator python=3.12
+    conda activate pylluminator
+
+
+Install pylluminator
+^^^^^^^^^^^^^^^^^^^^^
+
+You can download the latest source from github, or clone the repository with this command:
+
+.. code-block:: shell
+
+    git clone https://github.com/eliopato/pylluminator.git
+
+Your are now ready to install the dependencies and the package :
+
+.. code-block:: shell
+
+    cd pylluminator
+    pip install .
+
+
+Usage
+-----
+
+Refer to https://pylluminator.readthedocs.io/ for step-by-step tutorials and detailed documentation.
+
+Contributing
+------------
+We welcome contributions! If you'd like to help improve the package, please follow these steps:
+
+1. Fork the repository.
+2. Create a new branch for your feature or bugfix.
+3. Make your changes and test them.
+4. Submit a pull request describing your changes.
+
+Bug reports / new features suggestion
+-------------------------------------
+
+If you encounter any bugs, have questions, or feel like the package is missing a very important feature, please open an issue on the `GitHub Issues <https://github.com/eliopato/pylluminator/issues>`_ page.
+
+When opening an issue, please provide as much detail as possible, including:
+
+- Steps to reproduce the issue
+- The version of the package you are using
+- Any relevant code snippets or error messages
+
+License
+-------
+
+This project is licensed under the MIT License - see the `LICENSE <./LICENSE>`_ file for details.
+
+Acknowledgements
+----------------
+
+This package is strongly inspired from `SeSAMe <https://bioconductor.org/packages/release/bioc/html/sesame.html>`_ and
+includes code from `methylprep <https://github.com/FoxoTech/methylprep>`_ for .idat files parsing.
+

pylluminator-0.1/docs/annotations.rst

@@ -0,0 +1,96 @@
+Annotations
+===========
+
+Manifests and other annotation files are built from the `SeSAMe package <https://zwdzwd.github.io/InfiniumAnnotation>`_ and illumina (cf `illumina docs <https://support.illumina.com.cn/downloads/infinium-methylationepic-v2-0-product-files.html>`_)
+
+They are stored and versioned in the `pylluminator-data GitHub repository <https://github.com/eliopato/pylluminator-data/raw/main/>`_
+
+Manifest
+--------
+
+Description of the columns of the `probe_infos.csv` file. If you want to use a custom manifest, you will need to provide this information.
+
+``illumina_id`` : ID that matches probe IDs in .idat files
+
+``probe_id`` : probe ID used in annotation files :
+
+  * First letters : Either ``cg`` (CpG), ``ch`` (CpH), ``mu`` (multi-unique), ``rp`` (repetitive element), ``rs`` (SNP probes), ``ctl`` (control), ``nb`` (somatic mutations found in cancer)
+  * Last 4 characters : top or bottom strand (``T/B``), converted or opposite strand (``C/O``), Infinium probe type (``1/2``), and the number of synthesis for representation of the probe on the array (``1,2,3,…,n``).
+
+``type`` : probe type, Infinium-I or Infinium-II
+
+``probe_type`` : ``cg`` (CpG), ``ch`` (CpH), ``mu`` (multi-unique), ``rp`` (repetitive element), ``rs`` (SNP probes), ``ctl`` (control), ``nb`` (somatic mutations found in cancer)
+
+``channel``: color channel, green (methylated) or red (unmethylated)
+
+``address_[A/B]``: Chip/tango address for A-allele and B-allele. For Infinium type I, allele A is Unmethylated, allele B is Methylated. For type II, address B is not set as there is only one probe. Addresses match the Illumina IDs found in IDat files.
+
+``start``: the start position of the probe sequence
+
+``end``: the end position of the probe sequence. Usually the start position +1 because probes typically span a single CpG site.
+
+``chromosome``: chromosome number/letter
+
+``mask_info``: name of the masks for this probe. Multiple masks are separated by semicolons. (details below)
+
+``genes``: genes encoded by this sequence. Multiple gene names are separated by semicolons.
+
+``transcript_types``: The types of transcripts linked to the probe's genomic location. These indicate whether the region corresponds to protein_coding, nonsense_mediated_decay, retained_intron, or other annotations. Multiple transcript types are separated by semicolons.
+
+Masks
+-----
+
+Common masks
+~~~~~~~~~~~~~
+
+``M_mapping``: unmapped probes, or probes having too low mapping quality (alignment score under 35, either probe for Infinium-I) or Infinium-I probe allele A and B mapped to different locations
+
+``M_nonuniq``: mapped probes but with mapping quality smaller than 10, either probe for Infinium-I
+
+``M_uncorr_titration``: CpGs with titration correlation under 0.9. Functioning probes should have very high correlation with titrated methylation fraction.
+
+Human masks (general and population-specific)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+``M_commonSNP5_5pt``: mapped probes having at least a common SNP with MAF>=5% within 5bp from 3'-extension
+
+``M_commonSNP5_1pt``: mapped probes having at least a common SNP with MAF>=1% within 5bp from 3'-extension
+
+``M_1baseSwitchSNPcommon_1pt``: mapped Infinium-I probes with SNP (MAF>=1%) hitting the extension base and changing the color channel
+
+``M_2extBase_SNPcommon_1pt``: mapped Infinium-II probes with SNP (MAF>=1%) hitting the extension base.
+
+``M_SNP_EAS_1pt``: EAS population-specific mask (MAF>=1%).
+
+``M_1baseSwitchSNP_EAS_1pt``: EAS population-specific mask (MAF>=1%).
+
+``M_2extBase_SNP_EAS_1pt``: EAS population-specific mask (MAF>=1%).
+
+... more populations, e.g., ``EAS``, ``EUR``, ``AFR``, ``AMR``, ``SAS``.
+
+Mouse masks (general and strain-specific)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+``M_PWK_PhJ``: mapped probes having at least a PWK_PhJ strain-specific SNP within 5bp from 3'-extension
+
+``M_1baseSwitchPWK_PhJ``: mapped Infinium-I probes with PWK_PhJ strain-specific SNP hitting the extension base and changing the color channel
+
+``M_2extBase_PWK_PhJ``: mapped Infinium-II probes with PWK_PhJ strain-specific SNP hitting the extension base.
+
+... more strains, e.g., ``AKR_J``, ``A_J``, ``NOD_ShiLtJ``, ``MOLF_EiJ``, ``129P2_OlaHsd`` ...
+
+Genome information
+------------------
+
+``genome_info/gap_info.csv``: contains information on gaps in the genomic sequence. These gaps represent regions
+that are not sequenced or that are known to be problematic in the data, such as areas that may have low coverage or difficult-to-sequence regions.
+
+``genome_info/seq_length.csv``: keys are chromosome identifiers (e.g., 1, 2, ... X, etc.), and values are the corresponding sequence lengths (in base pairs).
+
+``genome_info/transcripts_list.csv``: high-level overview of the transcripts and their boundaries (start and end positions).
+
+``genome_info/transcripts_exons.csv``: information at the level of individual exons within each transcript (type, gene name, gene id...).
+Details on `transcript_types` values can be found in `GRCh37 database <https://grch37.ensembl.org/info/genome/genebuild/biotypes.html>`_
+
+``genome_info/chromosome_regions.csv``: Names, addresses and Giemsa stain pattern of all chromosomes' regions.
+

pylluminator-0.1/docs/api.rst

@@ -0,0 +1,20 @@
+API
+===
+
+.. autosummary::
+    :toctree: _autosummary 
+    :template: custom-module-template.rst
+    :recursive: 
+
+    pylluminator.annotations
+    pylluminator.cnv
+    pylluminator.dm
+    pylluminator.mask
+    pylluminator.quality_control
+    pylluminator.read_idat
+    pylluminator.sample_sheet
+    pylluminator.samples
+    pylluminator.stats
+    pylluminator.utils
+    pylluminator.visualizations
+

pylluminator-0.1/docs/conf.py

@@ -0,0 +1,65 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+# -- Project information -----------------------------------------------------
+
+project = "pylluminator"
+copyright = "2025"
+author = "MMG"
+
+# -- General configuration ---------------------------------------------------
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "nbsphinx"
+]
+
+intersphinx_mapping = {
+    "rtd": ("https://docs.readthedocs.com/platform/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+    "pyranges": ("https://pyranges1.readthedocs.io/en/latest/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None)
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["templates"]
+
+autosummary_generate = True  # Enable autosummary to generate pages
+autodoc_default_flags = ['members']  # Automatically document class members
+
+# -- Options for EPUB output
+epub_show_urls = "footnote"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = []
+
+html_logo = " https://raw.githubusercontent.com/eliopato/pylluminator/refs/heads/main/docs/images/logo.png"