✨ basic docs (#32)

* ✨ basic docs

- file content organization still to fix

* ✨ link images in README using relative docs parameter

- unfortunately does not work with href links as it seems

* 🎨🐛 fix and improve type anntoations

* 🐛 remove non existing attribute

* 🐛 fix imports after merge

* 🚚 move examples to docs, update documentation, relat. paths in config...

- sphinx: easier to integrate notebook example into documentation
- 🐛 fixed one filepath: example_data/MicW2Graph/2_Microbial_Association_Networks/2_Network_visualization2/1_man_example_edgelist.csv  ("_edgelist" was missing)

* ✨ add optional dependencies using poetry syntax

this should now work:
pip install "-e[docs]"

* ✨ add quatro-cli python package and try testing build of docs

* 🐛 misstyped quarto (again...)

* 🐛 add parquet as dependency for pandas

* 🐛 don't fail on warnings (especially with nitpicky mode enabled)

Author: enryH

.github/workflows/docs.yml

@@ -0,0 +1,42 @@
+name: Test documentation building (until it's moved to ReadTheDocs)
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+    
+jobs:
+  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: ${{ matrix.python-version }}
+          cache: 'pip' # caching pip dependencies
+          cache-dependency-path: '**/pyproject.toml'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[docs,quarto]
+      - name: Build references
+        run: |
+            cd docs
+            sphinx-apidoc --force --implicit-namespaces --module-first -o reference ../vuegen
+      - name: Build documentation
+        run: |
+            cd docs
+            sphinx-build -n --keep-going -b html ./ ./_build/
+      - name: save artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: Sphinx_${{ matrix.python-version }}
+          path: docs/_build/

README.md

@@ -1,9 +1,8 @@
-<div align="center">
-  <img width="300px" src="docs/images/vuegen_logo.svg">
-</div>
-
+<!-- <div align="center">
+  <img width="300px" src="images/vuegen_logo.svg">
+</div> -->
+![VueGen Logo](docs/images/vuegen_logo.svg)
 -----------------
-
 <p align="center">
    VueGen is a Python library that automates the creation of scientific reports.
 </p>
@@ -19,19 +18,22 @@ VueGen automates the creation of scientific reports based on a YAML configuratio
 
 An overview of the VueGen workflow is shown in the figure below:
 
-<p align="center">
+<!-- <p align="center">
 <figure>
-  <img width="650px" src="docs/images/vuegen_graph_abstract.png" alt="VueGen overview"/>
+  <img width="650px" src="images/vuegen_graph_abstract.png" alt="VueGen overview"/>
 </figure>
-</p>
+</p> -->
+![VueGen Abstract](docs/images/vuegen_graph_abstract.png)
 
 Also, the class diagram for the project is presented below to illustrate the architecture and relationships between classes:
 
-<p align="center">
+<!-- <p align="center">
 <figure>
-  <img width="650px" src="docs/images/vuegen_classdiagram_noattmeth.png" alt="VueGen class diagram"/>
+  <img width="650px" src="images/vuegen_classdiagram_noattmeth.png" alt="VueGen class diagram"/>
 </figure>
-</p>
+</p> -->
+
+![VueGen Class Diagram](docs/images/vuegen_classdiagram_noattmeth.png)
 
 ## Installation
 
@@ -67,6 +69,7 @@ quarto check
 ## Execution
 
 ```bash
+cd docs
 python vuegen/main.py --config example_data/MicW2Graph/report_config_micw2graph.yaml --report_type streamlit
 ```
 

docs/.gitignore

@@ -0,0 +1,7 @@
+# apidocs
+reference
+# builds
+_build
+quarto_report
+logs
+jupyter_execute

docs/README.md

@@ -0,0 +1,39 @@
+# 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 ../vuegen
+# 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

@@ -0,0 +1,153 @@
+# 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 = "mockup"
+copyright = "2024, Multiomics-Analytics-Group"
+author = "Multiomics-Analytics-Group, Sebastián Ayala Ruano, Henry Webel, Alberto Santos"
+PACKAGE_VERSION = metadata.version("vuegen")
+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
+
+# 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),
+}
+
+# -- 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/vuegen",
+    "repository_url": "https://github.com/Multiomics-Analytics-Group/vuegen",
+    "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 / "vuegen"
+
+    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)