Merge pull request #70 from openalea/release2025

Add tutorials originaly in openalea.rtfd

Author: thomasarsouze

doc/conf.py

@@ -1,90 +1,87 @@
 # -*- coding: utf-8 -*-
-import sys
 import os
-
-import pydata_sphinx_theme # Pydata theme: https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html
-
+import sys
 from importlib.metadata import metadata
-project='visualea'
-meta = metadata('openalea.' + project)
+
+project = "visualea"
+meta = metadata("openalea." + project)
 release = meta.get("version")
 # for example take major/minor
-version = ".".join(release.split('.')[:3])
-author = meta['Author'].split(' <')[0]
-desc = meta['Summary']
-urls = {k:v for k,v in [item.split(',') for item in meta.get_all('Project-URL')]}
+version = ".".join(release.split(".")[:3])
+author = meta["Author"].split(" <")[0]
+desc = meta["Summary"]
+urls = {k: v for k, v in [item.split(",") for item in meta.get_all("Project-URL")]}
 
 
 # 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.
 # sys.path.insert(0, os.path.abspath('.'))
-sys.path.insert(0, os.path.abspath('..')) # to include the root of the package
+sys.path.insert(0, os.path.abspath(".."))  # to include the root of the package
 
 # -- 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',  # support for automatic inclusion of docstring
-    'sphinx.ext.autosummary',  # generates autodoc summaries
-    'sphinx.ext.doctest',  # inclusion and testing of doctest code snippets
-    'sphinx.ext.intersphinx', # support for linking to other projects
-    'sphinx.ext.mathjax',  # support for math equations
-    'sphinx.ext.ifconfig',  # support for conditional content
-    'sphinx.ext.viewcode',  # support for links to source code
-    'sphinx.ext.coverage',  # includes doc coverage stats in the documentation
-    'sphinx.ext.todo',      # support for todo items
-    'sphinx.ext.napoleon',  # support for numpy and google style docstrings
-    "sphinx_favicon",      # support for favicon
-    "sphinx_copybutton",      # support for copybutton in code blocks
-    "nbsphinx",     # for integrating jupyter notebooks
-    "myst_parser"   # for parsing .md files
+    "sphinx.ext.autodoc",  # support for automatic inclusion of docstring
+    "sphinx.ext.autosummary",  # generates autodoc summaries
+    "sphinx.ext.doctest",  # inclusion and testing of doctest code snippets
+    "sphinx.ext.intersphinx",  # support for linking to other projects
+    "sphinx.ext.mathjax",  # support for math equations
+    "sphinx.ext.ifconfig",  # support for conditional content
+    "sphinx.ext.viewcode",  # support for links to source code
+    "sphinx.ext.coverage",  # includes doc coverage stats in the documentation
+    "sphinx.ext.todo",  # support for todo items
+    "sphinx.ext.napoleon",  # support for numpy and google style docstrings
+    "sphinx_favicon",  # support for favicon
+    "sphinx_copybutton",  # support for copybutton in code blocks
+    "nbsphinx",  # for integrating jupyter notebooks
+    "myst_parser",  # for parsing .md files
 ]
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 autosummary_generate = True
-exclude_patterns = ['build', '_build', '_templates']
+exclude_patterns = ["build", "_build", "_templates"]
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 source_suffix = {
-    '.rst': 'restructuredtext',
-    '.md': 'markdown',
+    ".rst": "restructuredtext",
+    ".md": "markdown",
 }
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 # General information about the project.
-copyright = u'Cecill-C INRAE / INRIA / CIRAD'
+copyright = "Cecill-C INRAE / INRIA / CIRAD"
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
 language = "en"
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
 # -- 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 = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
-  "header_links_before_dropdown": 6,
-  "sidebarwidth": 200,
-  "sticky_navigation": "false",
-  "collapse_navigation": "false",
-  "display_version": "true",
-  "icon_links": [
-    {
-        "name": "GitHub",
-        "url": "https://github.com/openalea/visualea", # do not want urls['Repository']
-        "icon": "fa-brands fa-github",
-    },
+    "header_links_before_dropdown": 6,
+    "sidebarwidth": 200,
+    "navbar_end": ["version-switcher", "navbar-icon-links"],
+    "collapse_navigation": "false",
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/openalea/visualea",  # do not want urls['Repository']
+            "icon": "fa-brands fa-github",
+        },
     ],
     "show_version_warning_banner": True,
     "footer_start": ["copyright"],
@@ -94,11 +91,11 @@
         "examples/no-sidebar": [],
     },
     "use_edit_page_button": True,
-  }
+}
 # 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']
+html_static_path = ["_static"]
 html_logo = "_static/openalea_web.svg"
 html_favicon = "_static/openalea_web.svg"
 # If false, no module index is generated.
@@ -114,7 +111,7 @@
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
 html_show_copyright = True
 # Output file base name for HTML help builder.
-htmlhelp_basename = project + '_documentation'
+htmlhelp_basename = project + "_documentation"
 # Add infomation about github repository
 html_context = {
     # "github_url": "https://github.com", # or your GitHub Enterprise site
@@ -125,29 +122,37 @@
 }
 
 # -- Options for LaTeX output ---------------------------------------------
-latex_elements = {
-}
+latex_elements = {}
 latex_documents = [
-    (master_doc, 'visualea.tex', u'visualea Documentation',
-     u'INRA / INRIA / CIRAD', 'manual'),
+    (
+        master_doc,
+        "visualea.tex",
+        "visualea Documentation",
+        "INRA / INRIA / CIRAD",
+        "manual",
+    ),
 ]
 
 # -- Options for manual page output ---------------------------------------
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, project, project + ' Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, project, project + " Documentation", [author], 1)]
 
 # -- Options for Texinfo output -------------------------------------------
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, project, project + ' Documentation',
-     author, project, desc,
-     'Miscellaneous'),
+    (
+        master_doc,
+        project,
+        project + " Documentation",
+        author,
+        project,
+        desc,
+        "Miscellaneous",
+    ),
 ]
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'python': ('https://docs.python.org/', None)}
+intersphinx_mapping = {"python": ("https://docs.python.org/", None)}
+

doc/index.rst

@@ -23,7 +23,7 @@ Documentation
     :maxdepth: 1
     :caption: Contents:
 
-    user/manual.rst
+    user/tutorials.rst
     user/autosum.rst
     user/references.rst