Conda packaging

.github/workflows/conda-package-build.yml

@@ -1,18 +1,23 @@
-name: Building Package
+name: OpenAlea CI
 
 on:
   push:
     branches:
-      - '**'
+      - main
+      - master
     tags:
       - 'v*'
   pull_request:
-    branches:
-      - '**'
-
+    types:
+      - opened
+      - synchronize
+      - reopened
+  release:
+    types:
+      - published
 
 jobs:
   build:
-    uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main
+    uses: openalea/action-build-publish-anaconda/.github/workflows/openalea_ci.yml@main
     secrets:
-      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
+      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}

conda/environment.yml

@@ -4,11 +4,8 @@ channels:
 dependencies:
   - openalea.mtg
   - openalea.plantgl
-  - alinea.caribu
-  - alinea.astk
-  - numpy
-  - scipy
-  - sympy
-  - pandas
-  - jsonschema
-  - pvlib-python
+  - openalea.caribu
+  - openalea.astk
+  - pip
+  - pip:
+      - ..[test,doc]

conda/meta.yaml

@@ -1,35 +1,60 @@
-package:
-  name: hydroshoot
-  version: "5.2.2"
+{% 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 = 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', {}).get('environment', {}).get('dependencies',[]) %}
+{% set test_deps = pyproject.get('project', {}).get('optional-dependencies', {}).get('test',[]) %}
 
+package:
+  name: {{ name }}
+  version: {{ version }}
 
 source:
-  git_url: ../
+  path: ..
 
 build:
-  noarch: python
+  string: py{{ PY_VER }}
+  number: 0
   preserve_egg_dir: True
-  script: {{PYTHON}} -m pip install .
+  script:
+    - {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
 
 requirements:
-  build:
-    - python {{PY_VER}}
-    - setuptools
+  host:
+    - python
+    - setuptools_scm
+    {% for dep in build_deps %}
+    - {{ dep }}
+    {% endfor  %}
 
   run:
     - python
-    - numpy
-    - scipy
-    - sympy
-    - pandas
-    - jsonschema
-    - pvlib-python
-    - openalea.mtg
-    - openalea.plantgl
-    - alinea.caribu
-    - alinea.astk
+    {% for dep in deps + conda_deps %}
+    - {{ dep }}
+    {% endfor %}
+
+
+test:
+  imports:
+    - {{ name }}
+  requires:
+    - pytest
+  source_files:
+    - test/
+  commands:
+    - pytest -v
 
 about:
-  summary: "HydroShoot is an FSPM model to simulate gas-exchange on vine"
-  license: "cecill-c"
-  license_file: LICENSE
+  home: {{ home }}
+  summary: {{ description }}
+  license: {{ license }}
+
+extra:
+  recipe-maintainers:
+    - artzet-s
+    - pradal
+    - fournier

doc/environment.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
   - openalea.mtg
   - openalea.plantgl
-  - alinea.caribu
+  - openalea.caribu
   - alinea.astk
   - numpy
   - scipy

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -11,21 +11,17 @@ authors = [
   { name = "Eric Lebon"},
 ]
 description = "A functional-structural plant model (FSPM) to simulate gas and energy exchange of grapevine"
-license = {file = "LICENSE"}
-requires-python = ">=3.8"
+license = "CECILL-C"
+license-files = ["LICEN[CS]E*"]
+requires-python = ">=3.9"
 classifiers = [
   "Intended Audience :: Science/Research",
   "Intended Audience :: Developers",
-  "License :: OSI Approved :: CeCILL-C License",
   "Operating System :: OS Independent",
+  "Framework :: OpenAlea",
   "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",
 ]
 
@@ -55,11 +51,31 @@ Discussions = "https://github.com/openalea/hydroshoot/discussions"
 Changelog = "https://github.com/openalea/hydroshoot/releases"
 
 [tool.setuptools.dynamic]
-version = {attr = "hydroshoot.version.__version__"}
 readme = {file = ["README.rst"]}
 
+# enable dynamic version based on git tags
+[tool.setuptools_scm]
+# Format version to ease alignment with conda/meta.yaml tag-based versioning
+fallback_version = "5.2.2.dev0"
+version_scheme = "guess-next-dev"
+local_scheme = "no-local-version"
+
 [tool.setuptools.packages.find]
 where = ["src"]
 
 [tool.setuptools.package-data]
 "hydroshoot_data" = ["*"]
+
+# not used yet by pip, but by meta.yaml
+[tool.conda.environment]
+channels = [
+  "openalea3",
+  "conda-forge",
+]
+# deps not available in pip with conda name
+dependencies = [
+  "openalea.mtg",
+  "openalea.plantgl",
+  "openalea.caribu",
+  "openalea.astk",
+]

src/hydroshoot/__init__.py

@@ -1,7 +1,7 @@
-# {# pkglts, base
+from importlib.metadata import version, PackageNotFoundError
 
-from . import version
-
-__version__ = version.__version__
-
-# #}
+try:
+    __version__ = version("hydroshoot")
+except PackageNotFoundError:
+    # package is not installed
+    pass

src/hydroshoot/energy.py

@@ -10,10 +10,10 @@
 
 from math import pi
 
-import alinea.astk.icosphere as ico
+import openalea.astk.icosphere as ico
 import openalea.plantgl.all as pgl
-from alinea.caribu.CaribuScene import CaribuScene
-from alinea.caribu.sky_tools import turtle
+from openalea.caribu.CaribuScene import CaribuScene
+from openalea.caribu.sky_tools import turtle
 from openalea.mtg.mtg import MTG
 from scipy import optimize
 from sympy import Symbol

src/hydroshoot/irradiance.py

@@ -6,10 +6,10 @@
 TODO: plug to the standard interface of Caribu module.
 """
 
-import alinea.astk.icosphere as ico
-from alinea.caribu.CaribuScene import CaribuScene
-from alinea.caribu.sky_tools import turtle, Gensun, GetLightsSun
-from alinea.caribu.sky_tools.spitters_horaire import RdRsH
+import openalea.astk.icosphere as ico
+from openalea.caribu.CaribuScene import CaribuScene
+from openalea.caribu.sky_tools import turtle, Gensun, GetLightsSun
+from openalea.caribu.sky_tools.spitters_horaire import RdRsH
 from numpy import array, deg2rad
 from openalea.plantgl.all import Translated, Sphere, Shape, Material, Color3, Viewer
 from pandas import date_range