Release2025

.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

@@ -1,5 +1,4 @@
 # MetaFSPM
-(Not yet)
 [![Docs](https://readthedocs.org/projects/mtg/badge/?version=latest)](https://metafspm.readthedocs.io/)
 (Not yet)
 [![Build Status](https://github.com/openalea/mtg/actions/workflows/conda-package-build.yml/badge.svg?branch=master)](https://github.com/openalea/mtg/actions/workflows/conda-package-build.yml?query=branch%3Amaster)

conda/environment.yml

@@ -0,0 +1,15 @@
+name: metafspm
+channels:
+  - openalea3
+  - conda-forge
+dependencies:
+  - python
+  - pyyaml
+  - numpy
+  - numba
+  - openalea.mtg
+  - pandas
+  - pip
+  # let pip install the rest using pyproject.toml (if you are okay with conda/pip mix)
+  - pip:
+      - -e .."[doc]"

conda/meta.yaml

@@ -1,13 +1,13 @@
 {% set pyproject = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
 {% set name = pyproject.get('project').get('name') %}
 {% set description = pyproject.get('project').get('description') %}
-{% set version = GIT_DESCRIBE_TAG | replace("v", "") %}
+{% set version = environ.get('SETUPTOOLS_SCM_PRETEND_VERSION', "0.0.0.dev") %}
 {% set license = pyproject.get('project').get('license') %}
 {% set home = pyproject.get('project', {}).get('urls', {}).get('Homepage', '') %}
 {% set build_deps = pyproject.get("build-system", {}).get("requires", []) %}
 {% set deps = pyproject.get('project', {}).get('dependencies', []) %}
-{% set conda_deps = pyproject.get('tool', {}).get('conda-environment', {}).get('dependencies',[]) %}
-
+{% set conda_deps = pyproject.get('tool', {}).get('conda', {}).get('environment', {}).get('dependencies',[]) %}
+{% set test_deps = pyproject.get('project', {}).get('optional-dependencies', {}).get('test',[]) %}
 
 package:
   name: {{ name }}
@@ -18,15 +18,17 @@ source:
 
 build:
   noarch: python
+  number: 0
   preserve_egg_dir: True
+  string: py{{ PY_VER }}
   # pip install options mainly ensure that dependencies are handled by conda (and not pip)
   # --no-deps ensure pip will not install deps not declared in meta.yaml (but declared in pyproject.toml)
   # --no-build-isolation ensure pip will not replace build deps declared in meta.yaml (and declared in pyproject.toml)
   # --ignore-installed ensure that compiled files (accidentally present in sources or uncleaned locally) will be overwritten
   script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
 
 requirements:
-  host:
+  build:
     - python
     {% for dep in build_deps %}
     - {{ dep }}
@@ -38,20 +40,30 @@ requirements:
     - {{ dep }}
     {% endfor %}
 
+
 test:
   requires:
-    - pytest
-    - nbmake
+    {% for dep in test_deps %}
+    - {{ dep }}
+    {% endfor %}
+
   imports:
-    - {{ name }}
+    - {{ pyproject["project"]["name"] }}
+
   source_files:
-    - test/test_*.py
-    - doc/notebooks/*.ipynb
+    - test/**
+
+
   commands:
-   - pytest -v
-   - pytest --nbmake
+    - cd test
+    - pytest -v
 
 about:
   home: {{ home }}
+  summary: {{ description }}
   license: {{ license }}
-  summary: {{ description }}
+
+extra:
+  recipe-maintainers:
+    - GeraultTr
+    - pradal

doc/conf.py

@@ -119,7 +119,7 @@
 html_context = {
     # "github_url": "https://github.com", # or your GitHub Enterprise site
     "github_user": "openalea",
-    "github_repo": "my_pkg",
+    "github_repo": "metafspm",
     "github_version": "main",
     "doc_path": "doc",
 }
@@ -128,8 +128,8 @@
 latex_elements = {
 }
 latex_documents = [
-    (master_doc, 'pkg_name.tex', u'pkg_name Documentation',
-     u'INRA / INRIA / CIRAD', 'manual'),
+    (master_doc, 'metafspm.tex', u'metafspm Documentation',
+     u'INRAE / inria / CIRAD', 'manual'),
 ]
 
 # -- Options for manual page output ---------------------------------------

pyproject.toml

@@ -19,16 +19,16 @@ include-package-data = false # force explicit declaration of data (disable autom
 name = "openalea.metafspm"
 authors = [
   { name = "Tristan Gérault", email = "tristan.gerault@inrae.fr" },
-  { name = "Christophe Pradal", email = "christophe.pradal@fnria.fr" }
+  { name = "Christophe Pradal", email = "christophe.pradal@cirad.fr" }
 ]
-description = "FSPM modelling toolkit for OpenAlea"
+description = "Generic Management of FSPM dynamic processes and scheduling for OpenAlea"
 readme = "README.md"
 license = "CECILL-C"
 license-files = ["LICEN[CS]E*"]
 requires-python = ">=3.8"
 dynamic = ["version"]
 classifiers = [
-  "Development Status :: 1 - Planning",
+  "Development Status :: 3 - Alpha Copy",
   "Intended Audience :: Science/Research",
   "Intended Audience :: Developers",
   #"License :: OSI Approved :: CeCILL-C License",
@@ -41,6 +41,7 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Topic :: Scientific/Engineering",
   "Framework :: OpenAlea",
 ]
@@ -50,17 +51,20 @@ classifiers = [
 dependencies = []
 
 # section specific to conda-only distributed package (not used by pip yet)
-[tool.conda-environment]
-
+[tool.conda.environment]
 
 dependencies = [
-    "pyyaml"
+    "pyyaml",
+    "numpy",
+    "numba"
 ]
 
 [project.optional-dependencies]
 test = [
   "pytest",
-  "nbmake"
+  "nbmake",
+  "pandas",
+  "openalea.mtg",
 ]
 dev = [
   "pytest >=6",
@@ -78,6 +82,9 @@ doc = [
 
 [project.urls]
 Repository = "https://github.com/openalea/metafpsm"
+Homepage = "https://metafspm.readthedocs.io/"
+"Bug Tracker" = "https://github.com/openalea/metafspm/issues"
+Discussions = "https://github.com/openalea/metafspm/discussions"
 
 [project.entry-points."wralea"]
-"my_pkg" = "openalea.metafspm_wralea"
+"metafspm" = "openalea.metafspm_wralea"