✨ first rudementary API documentation

.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 OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+  # apt_packages:
+  #  - some-package
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - method: pip
+     path: .
+     extra_requirements:
+      - docs

README.md

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-# vcore
-Visualization library for omics data
+# Visualization Core (vuecore) library
+
+Visualization library for omics data.
+
+See also acore and vuegen.
+
+## Installation
+
+### Latest stable release from PyPI
+
+```bash
+pip install vuecore
+```
+
+### Latest development version from GitHub
+
+Clone this repository and then install using pip the development version in
+editable mode:
+
+```bash
+# git clone https://github.com/Multiomics-Analytics-Group/vuecore.git
+# cd vuecore
+pip install -e '.[dev]'
+```

docs/.gitignore

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+# apidocs
+reference
+# builds
+_build
+jupyter_execute

docs/README.md

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+# Docs creation
+
+In order to build the docs you need to
+
+1. install sphinx and additional support packages
+2. build the package reference files
+3. run sphinx to create a local html version
+
+The documentation is build using readthedocs automatically.
+
+Install the docs dependencies of the package (as speciefied in toml):
+
+```bash
+# in main folder
+# pip install ".[docs]"
+poetry install --with docs
+```
+
+## Build docs using Sphinx command line tools
+
+Command to be run from `path/to/docs`, i.e. from within the `docs` package folder:
+
+Options:
+
+- `--separate` to build separate pages for each (sub-)module
+
+```bash
+# pwd: docs
+# apidoc
+sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../src/vuecore
+# build docs
+sphinx-build -n -W --keep-going -b html ./ ./_build/
+```
+
+## Include repo README.md into docs
+
+Relative links are used in the main README, which need to be resolved when building. It's
+possible to include the a `relative-docs` option if one uses `index.md` ([see docs](https://myst-parser.readthedocs.io/en/latest/faq/index.html#include-a-file-from-outside-the-docs-folder-like-readme-md)). This does not work
+with `href` links, only native markdown links.

docs/conf.py

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+# 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.
+#
+import os
+from importlib import metadata
+
+# -- Project information -----------------------------------------------------
+
+project = "vuecore"
+copyright = "2024, Multiomics-Analytics-Group"
+author = (
+    "Multiomics-Analytics-Group, Sebastián Ayala Ruano, Henry Webel, Alberto Santos"
+)
+PACKAGE_VERSION = metadata.version("vuecore")
+version = PACKAGE_VERSION
+release = PACKAGE_VERSION
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autodoc.typehints",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx_new_tab_link",
+    "myst_nb",
+]
+
+#  https://myst-nb.readthedocs.io/en/latest/computation/execute.html
+nb_execution_mode = "auto"
+
+myst_enable_extensions = ["dollarmath", "amsmath"]
+
+# Plolty support through require javascript library
+# https://myst-nb.readthedocs.io/en/latest/render/interactive.html#plotly
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+]
+
+# https://myst-nb.readthedocs.io/en/latest/configuration.html
+# Execution
+nb_execution_raise_on_error = True
+# Rendering
+nb_merge_streams = True
+# maximum execution time per cell in seconds
+nb_execution_timeout = 120
+
+# https://myst-nb.readthedocs.io/en/latest/authoring/custom-formats.html#write-custom-formats
+# ! if you use it, then you cannot directly execute the notebook in the browser in colab
+# (the file needs to be fetched from the repository)
+# just keep both syncing it using papermill
+# nb_custom_formats = {".py": ["jupytext.reads", {"fmt": "py:percent"}]}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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",
+    "jupyter_execute",
+    "conf.py",
+]
+
+
+# Intersphinx options
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "networkx": ("https://networkx.org/documentation/stable/", None),
+    "pyvis": ("https://pyvis.readthedocs.io/en/stable/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
+    # "scikit-learn": ("https://scikit-learn.org/stable/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+}
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+# See:
+# https://github.com/executablebooks/MyST-NB/blob/master/docs/conf.py
+# html_title = ""
+html_theme = "sphinx_book_theme"
+# html_logo = "_static/logo-wide.svg"
+# html_favicon = "_static/logo-square.svg"
+html_theme_options = {
+    "github_url": "https://github.com/Multiomics-Analytics-Group/vuecore",
+    "repository_url": "https://github.com/Multiomics-Analytics-Group/vuecore",
+    "repository_branch": "main",
+    "home_page_in_toc": True,
+    "path_to_docs": "docs",
+    "show_navbar_depth": 1,
+    "use_edit_page_button": True,
+    "use_repository_button": True,
+    "use_download_button": True,
+    "launch_buttons": {
+        "colab_url": "https://colab.research.google.com"
+        #     "binderhub_url": "https://mybinder.org",
+        #     "notebook_interface": "jupyterlab",
+    },
+    "navigation_with_keys": False,
+}
+
+# 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 = ["_static"]
+
+
+# -- Setup for sphinx-apidoc -------------------------------------------------
+
+# Read the Docs doesn't support running arbitrary commands like tox.
+# sphinx-apidoc needs to be called manually if Sphinx is running there.
+# https://github.com/readthedocs/readthedocs.org/issues/1139
+
+if os.environ.get("READTHEDOCS") == "True":
+    from pathlib import Path
+
+    PROJECT_ROOT = Path(__file__).parent.parent
+    PACKAGE_ROOT = PROJECT_ROOT / "src" / "vuecore"
+
+    def run_apidoc(_):
+        from sphinx.ext import apidoc
+
+        apidoc.main(
+            [
+                "--force",
+                "--implicit-namespaces",
+                "--module-first",
+                "--separate",
+                "-o",
+                str(PROJECT_ROOT / "docs" / "reference"),
+                str(PACKAGE_ROOT),
+                str(PACKAGE_ROOT / "*.c"),
+                str(PACKAGE_ROOT / "*.so"),
+            ]
+        )
+
+    def setup(app):
+        app.connect("builder-inited", run_apidoc)

docs/index.md

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+<!-- https://myst-parser.readthedocs.io/en/latest/faq/index.html
+#include-a-file-from-outside-the-docs-folder-like-readme-md -->
+
+```{include} ../README.md
+:start-line: 0
+:relative-docs: docs
+:relative-images:
+```
+
+```{toctree}
+:maxdepth: 2
+:caption: Modules
+:hidden:
+
+reference/vuecore
+```
+
+```{toctree}
+:maxdepth: 1
+:caption: MISC:
+:hidden:
+
+README.md
+```