Add additional channels for doc environment

.readthedocs.yml

@@ -6,7 +6,7 @@ build:
     python: "mambaforge-22.9"
 
 conda:
-  environment: doc/environment.yml
+  environment: conda/environment.yml
 
 sphinx:
   # Path to your Sphinx configuration file.

README.md

@@ -35,48 +35,19 @@ gramineaous plants(Fournier & Pradal, unpublished), the Adel-Maize
 together with the wheat parameterization model of Abichou et al. (2013)
 and the plastic leaf model of Fournier & Pradal (2012)
 
-## Requirements
 
--   OpenAlea.mtg
--   OpenAlea.plantgl
--   OpenAlea.caribu
--   Openalea.astk
--   NumPy
--   Scipy
--   MatplotLib-base
--   Pandas
--   Rpy2
+## Installation
 
-## Installation with mamba
+### Users
 
-Create an environment:
+```bash
+mamba env create -n adel -c openalea3 -c conda-forge openalea.adel 
+``` 
 
-> mamba create -n adel -c conda-forge -c openalea3 openalea.adel -y
+### Developers
 
-Activate the environment:
-
-> mamba activate adel
-
-Locate RHOME:
-
-> R RHOME
-
-Set R_HOME to the R HOME dir returned above:
-
-> mamba env config vars set R_HOME=r_home_dir_returned_by_rhome
-
-## Installation from source
-
-Create an environment
-
-> mamba env create -n adel -f conda/environment.yml
-
-Set R_HOME (see above)
-
-Install adel
-
-``` console
-git clone https://github.com/openalea/adel.git 
-cd adel
-pip install -e .
+```bash
+git clone 'https://github.com/openalea/adel.git'
+cd caribu
+mamba env create -n adel_dev -f ./conda/environment.yml
 ```

conda/environment.yml

@@ -7,12 +7,14 @@ channels:
 dependencies:
   # list here manually conda-only deps (listed in [tool.conda.environment] section of pyproject)
   - python
-  - pip
+  - pandoc
   - openalea.mtg
   - openalea.plantgl
   - openalea.caribu
   - openalea.astk
-  - rpy2
+  - matplotlib-base
+  - openalea.widgets
+  - pip
   # let pip install the rest using pyproject.toml (if you are okay with conda/pip mix)
   - pip:
-      - -e .."[doc, test]"
+      - -e ..[doc, test]

conda/meta.yaml

@@ -18,7 +18,6 @@ source:
 
 build:
   noarch: python
-  preserve_egg_dir: True
   number: 0
   script: {{PYTHON}} -m pip install --no-deps  --no-build-isolation . -vv
 

pyproject.toml

@@ -2,6 +2,19 @@
 requires = ["setuptools", "setuptools_scm"]
 build-backend = "setuptools.build_meta"
 
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+readme = {file = ["README.md"]}
+
+# enable dynamic version based on git tags
+[tool.setuptools_scm]
+# Configure to align with the one of meta.yaml
+fallback_version = "0.0.0.dev0"
+version_scheme = "guess-next-dev"
+local_scheme = "no-local-version"
+
 [project]
 name = "openalea.adel"
 authors = [
@@ -10,21 +23,17 @@ authors = [
   { name = "Bruno Andrieu" },
 ]
 description = "3D plant simulation of graminae crops"
-license = {file = "LICENSE.txt"}
-requires-python = ">=3.8"
+license = "CECILL-C"
+license-files = ["LICEN[CS]E*"]
+requires-python = ">=3.10"
+keywords = ["openalea", "FSPM", "cereals"]
 classifiers = [
   "Intended Audience :: Science/Research",
   "Intended Audience :: Developers",
-  "License :: OSI Approved :: CeCILL-C License",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering",
 ]
 dynamic = ["readme","version"]
@@ -38,6 +47,16 @@ dependencies = [
 
 [project.optional-dependencies]
 test = ["pytest"]
+doc = [
+  "pydata-sphinx-theme",
+  "myst-parser",
+  "sphinx-favicon",
+  "nbsphinx",
+  "nbsphinx-link",
+  "ipykernel",
+  "sphinx-copybutton",
+  "ipython_genutils",
+]
 notebook = ["jupyter"]
 
 [project.urls]
@@ -60,18 +79,10 @@ dependencies = [
     "openalea.plantgl",
     "openalea.caribu",
     "openalea.astk",
+    "openalea.core",
     "matplotlib-base"
 ]
-[tool.setuptools.dynamic]
-readme = {file = ["README.md"]}
 
-[tool.setuptools.packages.find]
-where = ["src"]
-include = ["openalea.*"]
 
 [tool.setuptools.package-data]
 "*" = ['*.RData', '*.R', '*.8', '*.h', '*.str','*.txt', '*.l', '*.map', '*.csv', '*.json', '*.png']
-
-# enable dynamic versioning based on git tags
-[tool.setuptools_scm]
-# can be empty if no extra settings are needed, presence enables setuptools-scm

src/alinea/adel/__init__.py

@@ -0,0 +1 @@
+raise ImportError("alinea.adel has been deprecated; Use openalea.adel instead")