Merge pull request openalea-incubator#31 from pradal/conda

Conda
pradal · May 12, 2022 · 31523c0 · 31523c0
2 parents abe05ef + 8519516
commit 31523c0
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diff --git a/.github/workflows/conda-package-build.yml b/.github/workflows/conda-package-build.yml
@@ -0,0 +1,67 @@
+name: build_publish_anaconda
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build-and-publish:
+    name: ${{ matrix.os }}, Python 3.${{ matrix.python-minor-version }} for conda deployment
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      max-parallel: 3
+      matrix:
+        os: [ ubuntu-latest]
+        python-minor-version: [9]
+        isMaster:
+          - ${{ github.ref == 'refs/heads/master' || startsWith(github.ref, 'refs/heads/dev') }}
+        exclude:
+          - isMaster: false
+            os: ubuntu-latest
+            python-minor-version: 7
+          - isMaster: false
+            os: ubuntu-latest
+            python-minor-version: 8
+          - isMaster: false
+            os: macos-latest
+            python-minor-version: 7
+          - isMaster: false
+            os: macos-latest
+            python-minor-version: 8
+          - isMaster: false
+            os: macos-latest
+            python-minor-version: 9
+          - isMaster: false
+            os: windows-latest
+            python-minor-version: 7
+          - isMaster: false
+            os: windows-latest
+            python-minor-version: 8
+          - isMaster: false
+            os: windows-latest
+            python-minor-version: 9            
+
+    steps:
+    - name: Chekout
+      uses: actions/checkout@v3
+    - name: Determine publish
+      uses: haya14busa/action-cond@v1
+      id: publish
+      with:
+        cond: ${{ contains(github.ref, 'master') || startsWith(github.ref, 'refs/heads/v') }}
+        if_true: 'true'
+        if_false: 'false'
+    - name: Build and Publish
+      uses: openalea/[email protected]
+      with:
+        conda: conda
+        mamba: true
+        python: ${{ matrix.python-minor-version }}
+        numpy: '20.0'
+        channels: openalea3, conda-forge
+        token: ${{ secrets.ANACONDA_TOKEN }}
+        publish: ${{ steps.publish.outputs.value }}
+        label: main
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -0,0 +1,45 @@
+{% set data = load_setup_py_data() %}
+
+package:
+  name: alinea.adel
+  version: {{ data.get('version') }}
+
+source:
+  path: ..
+
+build:
+  noarch: python
+  preserve_egg_dir: True
+  number: 0
+  script: {{PYTHON}} setup.py install 
+
+requirements:
+  build:
+    - python {{PY_VER}}
+    - setuptools
+    - openalea.deploy
+  run:
+    - python >=3.6
+    - openalea.mtg
+    - scipy
+    - rpy2
+    - alinea.caribu
+    - alinea.astk
+
+test:
+  requires:
+    - pytest
+  imports:
+    - alinea.adel
+  source_files:
+    - test/**
+    - test/data/**
+  commands:
+    - cd test
+    - pytest -v --ignore=test_povray.py
+
+about:
+  home: {{ data.get('url') }}
+  license: {{ data.get('license') }}
+  summary: {{ data.get('description') }}
+
diff --git a/setup.cfg b/setup.cfg
diff --git a/setup.py b/setup.py
@@ -1,26 +1,22 @@
 #!/usr/bin/env python
 # -*- coding: iso-8859-15 -*-
 
-
 import os, sys 
 from setuptools import setup, find_packages
-from openalea.deploy.metainfo import read_metainfo
+#from openalea.deploy.metainfo import read_metainfo
 pj = os.path.join
 
+version = '2.0.0-dev'
+name = 'alinea.adel'
 
-# Reads the metainfo file
-metadata = read_metainfo('metainfo.ini', verbose=True)
-for key,value in metadata.items():
-    exec("%s = '%s'" % (key, value))
+description= '3D plant simulation of graminae crops'
+long_description= 'The Adel package characterise 3D plant development for graminae crops.'
 
-
-# #retrieving packages
-# pkg_root_dir = '.'
-# pkgs = [ pkg for pkg in find_packages(pkg_root_dir) if namespace not in pkg]
-# top_pkgs = [pkg for pkg in pkgs if  len(pkg.split('.')) < 2]
-# packages = [ namespace + "." + pkg for pkg in pkgs]
-# package_dir = dict( [('',pkg_root_dir)] + [(namespace + "." + pkg, pkg_root_dir + "/" + pkg) for pkg in top_pkgs] )
-# wralea_entry_points = ['%s = %s'%(pkg,namespace + '.' + pkg) for pkg in top_pkgs]
+authors= 'Christian Fournier, Christophe Pradal'
+authors_email = 'christian fournier at inrae fr'
+
+url = 'https://github.com/openalea-incubator/adel'
+license = 'Cecill-C'
 
 # Main setup
 setup(
@@ -37,27 +33,24 @@
     packages= find_packages('src'),
     # python packages directory
     package_dir= {'': 'src'},
-    namespace_packages=['alinea'],
+    #namespace_packages=['alinea'],
 
 
     # Namespace packages creation by deploy
     # Add package platform libraries if any
     include_package_data=True,
     package_data = {'' : ['*.RData', '*.R', '*.8', '*.h', '*.str','*.txt', '*.l', '*.map', '*.csv', '*.png'],},
-    share_dirs = {os.path.join(*('alinea', 'adel', 'data')): os.path.join(*('src', 'alinea','adel', 'data')),
-                  os.path.join(*('alinea', 'adel', 'echap_leaf_data')): os.path.join(*('src', 'alinea','adel', 'echap_leaf_data'))},
+    share_dirs = {pj(*('alinea', 'adel', 'data')): pj(*('src', 'alinea','adel', 'data')),
+                  pj(*('alinea', 'adel', 'echap_leaf_data')): pj(*('src', 'alinea','adel', 'echap_leaf_data'))},
 
     # Add package platform libraries if any
     zip_safe = False,
 
-
     # Scripts
     entry_points = { 'wralea': [ 'adel= alinea.adel',] },
 
     # Dependencies (other are listed in doc to avoid setputools/pip/conda possible conflicts in automatic installs)
     setup_requires = ['openalea.deploy'],
-    install_requires = [],
-    dependency_links = [],
    )
 
 

diff --git a/src/alinea/adel/Tutorials/__wralea__.py b/src/alinea/adel/Tutorials/__wralea__.py
@@ -38,7 +38,7 @@
    10: ('alinea.adel.data', 'phenTCa0N.csv'),
    11: ('alinea.adel.wheat.data', 'SRSo.RData'),
    12: ('openalea.data structure', 'int'),
-   13: ('vplants.plantgl.visualization', 'plot3D'),
+   13: ('openalea.plantgl.visualization', 'plot3D'),
    14: ('alinea.adel.wheat.data', 'So99.RData'),
    15: ('openalea.python method', 'getattr'),
    16: ('openalea.data structure', 'int'),
@@ -1889,17 +1889,17 @@
    8: ('alinea.adel.geometry', 'leaf to mesh'),
    9: ('openalea.data structure', 'int'),
    10: ('openalea.data structure', 'int'),
-   11: ('vplants.plantgl.visualization', 'plot3D'),
+   11: ('openalea.plantgl.visualization', 'plot3D'),
    12: ('openalea.data structure', 'int'),
    13: ('alinea.adel.data', 'leaves.db'),
    14: ('openalea.data structure', 'int'),
    15: ('openalea.flow control', 'annotation'),
    16: ('openalea.flow control', 'annotation'),
    17: ('alinea.adel.geometry', 'leaf element'),
-   18: ('vplants.plantgl.visualization', 'plot3D'),
-   19: ('vplants.plantgl.objects', 'Scene'),
-   20: ('vplants.plantgl.objects', 'Shape'),
-   21: ('vplants.plantgl.objects', 'Material'),
+   18: ('openalea.plantgl.visualization', 'plot3D'),
+   19: ('openalea.plantgl.objects', 'Scene'),
+   20: ('openalea.plantgl.objects', 'Shape'),
+   21: ('openalea.plantgl.objects', 'Material'),
    22: ('openalea.color', 'color')},
                              elt_connections={  31307220: (8, 0, 18, 0),
    31307232: (19, 0, 11, 0),
@@ -2998,7 +2998,7 @@
    67: ('alinea.adel.macro', 'calculate_LAI_TC_ViaCaribu'),
    68: ('alinea.adel.macro', 'constructPlantGLScene'),
    69: ('alinea.adel.macro', 'colors'),
-   70: ('vplants.plantgl.visualization', 'plot3D'),
+   70: ('openalea.plantgl.visualization', 'plot3D'),
    71: ('alinea.adel.macro', 'getFieldPlotDescription'),
    72: ('alinea.adel.macro', 'calculateTCViaPovray')},
                              elt_connections={  37677512: (48, 0, 72, 2),
@@ -3602,8 +3602,8 @@
    24: ('openalea.data structure', 'float'),
    25: ('openalea.data structure.tuple', 'tuple'),
    26: ('openalea.data structure.tuple', 'tuple'),
-   27: ('vplants.l-py', 'LSystem'),
-   28: ('vplants.l-py', 'run'),
+   27: ('openalea.l-py', 'LSystem'),
+   28: ('openalea.l-py', 'run'),
    29: ('openalea.file', 'read'),
    30: ('openalea.data structure.tuple', 'tuple'),
    32: ('openalea.data structure.string', 'string')},
@@ -6060,10 +6060,10 @@
                              doc='',
                              inputs=[],
                              outputs=[],
-                             elt_factory={  2: ('vplants.l-py', 'LSystem'),
+                             elt_factory={  2: ('openalea.l-py', 'LSystem'),
    3: ('openalea.file', 'read'),
-   4: ('vplants.l-py', 'run'),
-   5: ('vplants.l-py', 'plot'),
+   4: ('openalea.l-py', 'run'),
+   5: ('openalea.l-py', 'plot'),
    6: ('alinea.adel.data', 'Adel2.lpy'),
    7: ('alinea.adel.stand', 'CanMTGPlanter'),
    8: ('openalea.flow control', 'iter'),
@@ -8895,7 +8895,7 @@
    18: ('alinea.caribu', 'Caribu'),
    19: ('alinea.adel.io', 'to_plantgl'),
    20: ('alinea.adel.povray', 'povray'),
-   21: ('vplants.plantgl.visualization', 'plot3D'),
+   21: ('openalea.plantgl.visualization', 'plot3D'),
    22: ('alinea.adel.io', 'apply_property'),
    23: ('openalea.data structure', 'int'),
    24: ('alinea.adel.povray', 'col_item'),
@@ -12142,7 +12142,7 @@
    42: ('alinea.adel.io', 'to_plantgl'),
    43: ('openalea.data structure', 'int'),
    44: ('alinea.adel.povray', 'povray'),
-   45: ('vplants.plantgl.visualization', 'plot3D'),
+   45: ('openalea.plantgl.visualization', 'plot3D'),
    46: ('openalea.function operator', 'map'),
    48: ('alinea.adel.io', 'apply_property'),
    49: ('openalea.data structure', 'int'),
@@ -14475,7 +14475,7 @@
    22: ('alinea.caribu', 'Caribu'),
    23: ('alinea.adel.io', 'to_plantgl'),
    24: ('alinea.adel.povray', 'povray'),
-   25: ('vplants.plantgl.visualization', 'plot3D'),
+   25: ('openalea.plantgl.visualization', 'plot3D'),
    26: ('alinea.adel.io', 'apply_property'),
    27: ('openalea.data structure', 'int'),
    28: ('alinea.adel.povray', 'col_item'),
@@ -18515,7 +18515,7 @@
    41: ('alinea.adel.io', 'to_plantgl'),
    42: ('openalea.file', 'filename'),
    43: ('alinea.adel.povray', 'povray'),
-   44: ('vplants.plantgl.visualization', 'plot3D'),
+   44: ('openalea.plantgl.visualization', 'plot3D'),
    45: ('openalea.function operator', 'map'),
    46: ('alinea.adel.macro', 'LAIg'),
    47: ('alinea.adel.io', 'apply_property'),
@@ -18524,7 +18524,7 @@
    51: ('openalea.file', 'start'),
    53: ('alinea.adel.macro', 'genMTG_3out'),
    54: ('alinea.adel.macro', 'genFilepath'),
-   55: ('vplants.plantgl.visualization', 'plot3D'),
+   55: ('openalea.plantgl.visualization', 'plot3D'),
    56: ('openalea.file', 'start'),
    57: ('alinea.adel.stand', 'post_processing'),
    58: ('alinea.adel.macro', 'genFilepath'),
@@ -21779,7 +21779,7 @@
    41: ('alinea.adel.io', 'to_plantgl'),
    42: ('openalea.data structure', 'int'),
    43: ('alinea.adel.povray', 'povray'),
-   44: ('vplants.plantgl.visualization', 'plot3D'),
+   44: ('openalea.plantgl.visualization', 'plot3D'),
    45: ('openalea.function operator', 'map'),
    46: ('openalea.flow control', 'annotation'),
    47: ('alinea.adel.io', 'apply_property'),
@@ -23131,7 +23131,7 @@
    50: ('alinea.adel.simulation', 'AdelRunOptions'),
    51: ('alinea.adel.povray', 'povray'),
    52: ('openalea.color', 'color'),
-   53: ('vplants.plantgl.visualization', 'plot3D'),
+   53: ('openalea.plantgl.visualization', 'plot3D'),
    54: ('openalea.file', 'start'),
    55: ('openalea.color', 'color'),
    56: ('alinea.adel.io', 'apply_property'),
@@ -24567,8 +24567,8 @@
    15: ('alinea.caribu', 'MtgToCan'),
    16: ('alinea.adel.io', 'duplicate mtg'),
    17: ('alinea.adel.macro', 'plot'),
-   18: ('vplants.l-py', 'run'),
-   19: ('vplants.l-py', 'LSystem')},
+   18: ('openalea.l-py', 'run'),
+   19: ('openalea.l-py', 'LSystem')},
                              elt_connections={  35910096: (3, 1, 9, 0),
    35910120: (3, 0, 8, 0),
    35910144: (5, 1, 3, 0),
@@ -25005,7 +25005,7 @@
    42: ('alinea.adel.io', 'to_plantgl'),
    43: ('openalea.data structure', 'int'),
    44: ('alinea.adel.povray', 'povray'),
-   45: ('vplants.plantgl.visualization', 'plot3D'),
+   45: ('openalea.plantgl.visualization', 'plot3D'),
    46: ('openalea.function operator', 'map'),
    48: ('alinea.adel.io', 'apply_property'),
    49: ('openalea.data structure', 'int'),

diff --git a/src/alinea/adel/Tutorials/ssdbm/__wralea__.py b/src/alinea/adel/Tutorials/ssdbm/__wralea__.py
@@ -295,7 +295,7 @@
    7: ('openalea.numpy.creation', 'linspace'),
    8: ('openalea.function operator', 'reduce'),
    11: ('alinea.adel.stand', 'CanMTGPlanter'),
-   12: ('vplants.plantgl.visualization', 'plot3D'),
+   12: ('openalea.plantgl.visualization', 'plot3D'),
    13: ('alinea.adel.stand', 'agronomic plot'),
    17: ('alinea.adel.tutorials.ssdbm.mtg', 'union'),
    18: ('alinea.adel.data', 'leaves.db'),
@@ -792,7 +792,7 @@
    7: ('openalea.numpy.creation', 'linspace'),
    8: ('openalea.function operator', 'reduce'),
    11: ('alinea.adel.stand', 'CanMTGPlanter'),
-   12: ('vplants.plantgl.visualization', 'plot3D'),
+   12: ('openalea.plantgl.visualization', 'plot3D'),
    13: ('alinea.adel.stand', 'agronomic plot'),
    23: ('ssdbm', 'Light Interception')},
                              elt_connections={  140522878453448: (23, 1, 12, 0),
@@ -3175,7 +3175,7 @@
    {  'desc': '', 'interface': None, 'name': 'g'}],
                              elt_factory={  2: ('alinea.adel.geometry', 'MTG Interpreter time'),
    3: ('alinea.adel.stand', 'CanMTGPlanter'),
-   4: ('vplants.plantgl.visualization', 'plot3D'),
+   4: ('openalea.plantgl.visualization', 'plot3D'),
    5: ('alinea.adel.tutorials.ssdbm', 'Light Interception'),
    6: ('openalea.flow control', 'rendez vous'),
    7: ('alinea.adel.data', 'leaves.db'),