Merge branch 'openalea:master' into master

AurelienBesnier · Feb 7, 2024 · 79a5e32 · 79a5e32
2 parents d504e97 + a6d767b
commit 79a5e32
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diff --git a/.github/workflows/conda-package-build.yml b/.github/workflows/conda-package-build.yml
@@ -14,4 +14,4 @@ jobs:
   build:
     uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main
     secrets:
-      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
+      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,8 +1,9 @@
-conda:
-  file: doc/environment.yml
+version: 2
 
 build:
-  image: latest
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
 
-python:
-  setup_py_install: false
+conda:
+  environment: doc/environment.yml
diff --git a/README.md b/README.md
@@ -1,10 +1,9 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1436634.svg)](https://doi.org/10.5281/zenodo.1436634)
 [![Licence](https://anaconda.org/openalea/openalea.phenomenal/badges/license.svg)](https://cecill.info/licences/Licence_CeCILL_V1.1-US.txt)
-[![Platform](https://anaconda.org/openalea/openalea.phenomenal/badges/platforms.svg)](https://anaconda.org/openalea/openalea.phenomenal)
-[![Last version](https://anaconda.org/openalea/openalea.phenomenal/badges/version.svg)](https://anaconda.org/OpenAlea/openalea.phenomenal/files)
-[![Build Status](https://travis-ci.org/openalea/phenomenal.svg?branch=master)](https://travis-ci.org/openalea/phenomenal)
-[![Build status](https://ci.appveyor.com/api/projects/status/k7up7iy2ur2wmipx/branch/master?svg=true)](https://ci.appveyor.com/project/artzet-s/phenomenal/branch/master)
+[![Platform](https://anaconda.org/openalea3/openalea.phenomenal/badges/platforms.svg)](https://anaconda.org/openalea3/openalea.phenomenal)
+[![Last version](https://anaconda.org/openalea3/openalea.phenomenal/badges/version.svg)](https://anaconda.org/OpenAlea3/openalea.phenomenal/files)
+[![GitHub CI](https://github.com/openalea/phenomenal/actions/workflows/conda-package-build.yml/badge.svg)](https://github.com/openalea/phenomenal/actions/workflows/conda-package-build.yml)
 [![Documentation Status](https://readthedocs.org/projects/phenomenal/badge/?version=latest)](https://phenomenal.readthedocs.io/en/latest/?badge=latest)
 [![aunch interactive phenomenal notebook with myBinder service](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/openalea/phenomenal/master?filepath=examples)
 

diff --git a/binder/environment.yml b/binder/environment.yml
@@ -1,7 +1,7 @@
 name: phenomenal
 channels:
   - conda-forge
-  - openalea
+  - openalea3
 
 dependencies:
   - openalea.phenomenal

diff --git a/conda/conda_build_config.yml b/conda/conda_build_config.yml
@@ -0,0 +1,21 @@
+# from conda-forge-pinning
+c_compiler:
+  - gcc                        # [linux]
+  - clang                      # [osx]
+  - vs2019                     # [win and x86_64]
+  - vs2022                     # [win and arm64]
+c_compiler_version:            # [unix]
+  - 12                         # [linux]
+  - 16                         # [osx]
+  - 10                         # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux]
+  - 11                         # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux]
+cxx_compiler:
+  - gxx                        # [linux]
+  - clangxx                    # [osx]
+  - vs2019                     # [win and x86_64]
+  - vs2022                     # [win and arm64]
+cxx_compiler_version:          # [unix]
+  - 12                         # [linux]
+  - 16                         # [osx]
+  - 10                         # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux]
+  - 11                         # [os.environ.get("CF_CUDA_ENABLED", "False") == "True" and linux]
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -9,40 +9,40 @@ build:
   number: 0
   preserve_egg_dir: True
   string: phenomenal
-  script:
-    - {{ PYTHON }} setup.py install #--single-version-externally-managed --record record.txt
+  script: 
+    - {{PYTHON}} setup.py build_ext -j{{ CPU_COUNT }}
+    - {{ PYTHON }} -m pip install . -vv
 
 requirements:
-
-  build:
-    - {{ compiler('c') }}
-    - {{ compiler("cxx") }}
-    - python 
-    - setuptools
-    - numpy
+  host:
+    - python
+    - numpy 
+    - scipy
     - cython
 
-  host:
+  build:
+    - {{ compiler('c') }} 
+    - {{ compiler("cxx") }} 
     - python
     - setuptools
-    - cython    
     - numpy
     - scipy
+    - cython
 
   run:
-    - python
-    - numpy
+    - python x.x
+    - numpy x.x
     - cython
     - numba
     - scipy
     - scikit-image
     - scikit-learn
     - networkx
     - opencv [win or linux]
-    - opencv!=4.1.2 [osx]
+    - opencv >4.1.2 [osx]
     - matplotlib
     - vtk
-    - skan=0.10
+    - skan>=0.10
     - pywin32 [win]
 
 test:

diff --git a/doc/environment.yml b/doc/environment.yml
@@ -1,8 +1,9 @@
 name: phenomenal
 channels:
   - conda-forge
-  - openalea
+  - openalea3
 
 dependencies:
   - python
-  - openalea.phenomenal
+  - sphinx_rtd_theme
+  - openalea.phenomenal
diff --git a/setup.py b/setup.py
@@ -68,12 +68,12 @@
     packages=packages,
     package_dir={'': 'src'},
     zip_safe=False,
-    ext_modules=cythonize(extentions),
+    ext_modules=cythonize(extentions, language_level = "3"),
 
     entry_points={
         "wralea": ["openalea.phenomenal = openalea.phenomenal_wralea", ],
     },
 
     # See MANIFEST.in
     include_package_data=True,
-    )
+    )