Update doc

.readthedocs.yml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
+conda:
+  environment: doc/environment.yml
+
+sphinx:
+  # Path to your Sphinx configuration file.
+  configuration: doc/conf.py

README.md

@@ -1,6 +1,6 @@
-## Deepberry : segmentation and time-lapse tracking of grapevine berries
+# Deepberry : segmentation and time-lapse tracking of grapevine berries
 
-### Installation from source
+## Installation from source
 
     # for prediction
     mamba create -n grapevine -c conda-forge python=3.12 (3.9>=version<3.13) 
@@ -20,7 +20,7 @@
     # (optional) for model validation metrics:
     pip install .[validation]
 
-### Maintainers
+## Maintainers
 
 * Benoit Daviet ([email protected])
 * Fournier Christian ([email protected])

doc/conf.py

@@ -2,6 +2,14 @@
 import os
 import sys
 
+from importlib.metadata import metadata
+
+pkg_name='deepberry'
+meta = metadata('openalea.' + pkg_name)
+release = meta.get("version")
+# for example take major/minor
+version = ".".join(release.split('.')[:3])
+
 # 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.
@@ -24,6 +32,7 @@
     "sphinx.ext.todo",  # support for todo items
     "sphinx.ext.napoleon",  # support for numpy and google style docstrings
     "sphinx_favicon",  # support for favicon
+    "sphinx_copybutton",
     "nbsphinx",  # for integrating jupyter notebooks
     "myst_parser",  # for parsing .md files
 ]
@@ -32,7 +41,7 @@
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 autosummary_generate = True
-exclude_patterns = ["_build", "_templates"]
+exclude_patterns = ["build", "_templates"]
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 source_suffix = {
@@ -49,14 +58,6 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-# find version number in /src/$pkg_pth/version.py
-pkgver = {}
-with open("../src/openalea/deepberry/version.py") as fp:
-    exec(fp.read(), pkgver)
-# The short X.Y version.
-version = pkgver["__version__"]
-# The full version, including alpha/beta/rc tags.
-release = pkgver["__version__"]
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
@@ -81,9 +82,9 @@
     "collapse_navigation": "false",
     "icon_links": [
         {
-            "name": "GitLab",
-            "url": "https://forgemia.inra.fr/phenome/deepberry",
-            "icon": "fa-brands fa-gitlab",
+            "name": "GitHub",
+            "url": "https://github.com/openalea/deepberry",
+            "icon": "fa-brands fa-github",
         },
     ],
     "show_version_warning_banner": True,

doc/environment.yml

@@ -1,4 +1,4 @@
-name: phenomenal
+name: deepberry
 channels:
   - conda-forge
 dependencies:

pyproject.toml

@@ -44,8 +44,8 @@ doc = [
   "pydata-sphinx-theme",
   "myst-parser",
   "sphinx-favicon",
+  "sphinx-copybutton",
   "ipykernel",
-  "ipyvolume",
   "ipython_genutils",
   "nbsphinx",
 ]