Merge pull request #18 from AurelienBesnier/namespace

Namespace

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

@@ -2,66 +2,17 @@ name: build_publish_anaconda
 
 on:
   push:
-    branches: [ master ]
+    branches:
+      - '**'
+    tags:
+      - 'v*'
   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            
+    branches:
+      - '**'
+
 
-    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
+jobs:
+  build:
+    uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main
+    secrets:
+      anaconda_token: ${{ secrets.ANACONDA_TOKEN }}

setup.py

@@ -16,16 +16,12 @@
 """
 """
 # ==============================================================================
-from setuptools import setup, find_packages, Extension, Command
+from setuptools import setup, find_namespace_packages
+
 # ==============================================================================
 
 pkg_root_dir = 'src'
-packages = find_packages(pkg_root_dir)
-top_pkgs = [pkg for pkg in packages if len(pkg.split('.')) <= 2]
-package_dir = dict([('', pkg_root_dir)] +
-                   [(pkg, pkg_root_dir + "/" + pkg.replace('.', '/'))
-                    for pkg in top_pkgs])
-
+packages = find_namespace_packages(where='src', include=['openalea.*'])
 name = "agroservices"
 
 _version = {}
@@ -41,9 +37,9 @@
 This package is intended to be close to the webservice. 
 Therefore the requests will have the same API that each web service. 
 '''
-author= 'Christian Fournier, Marc Labadie, Christophe Pradal'
-url='https://github.com/H2020-IPM-openalea/agroservices'
-license="GPL-v3"
+author = 'Christian Fournier, Marc Labadie, Christophe Pradal'
+url = 'https://github.com/H2020-IPM-openalea/agroservices'
+license = "CeCILL-C"
 
 setup(
     name=name,
@@ -59,9 +55,9 @@
 
     # package installation
     packages=packages,
-    package_dir=package_dir,
+    package_dir={'': 'src'},
     zip_safe=False,
 
     # See MANIFEST.in
     include_package_data=True,
-    )
+)

src/agroservices/ipm/ipm.py

@@ -11,27 +11,32 @@
 ################## Interface Python IPM using Bioservice ########################################################
 
 import json
-from jsf import JSF
-from typing import Union
 from pathlib import Path
-from agroservices.services import REST
-from agroservices.ipm.datadir import datadir
+from typing import Union
+
 import agroservices.ipm.fakers as fakers
 import agroservices.ipm.fixes as fixes
+from agroservices.ipm.datadir import datadir
+from agroservices.services import REST
 
 __all__ = ["IPM"]
 
+
 def load_model(dssid, model):
     model = fixes.fix_prior_load_model(dssid, model)
     if 'input_schema' in model['execution']:
-        model['execution']['input_schema'] = json.loads(model['execution']['input_schema'])
+        model['execution']['input_schema'] = json.loads(
+            model['execution']['input_schema'])
     model = fixes.fix_load_model(dssid, model)
     return model
 
+
 def read_dss(dss):
-    dss['models'] = {model["id"]: load_model(dss['id'], model) for model in dss["models"]}
+    dss['models'] = {model["id"]: load_model(dss['id'], model) for model in
+                     dss["models"]}
     return dss
 
+
 class IPM(REST):
     """
     Interface to the IPM  https://ipmdecisions.nibio.no/
@@ -79,7 +84,8 @@ class IPM(REST):
         >>> ipm.post_schema_dss_yaml_validate() 
     """
 
-    def __init__(self, name='IPM', url="https://platform.ipmdecisions.net", callback=None, *args, **kwargs):
+    def __init__(self, name='IPM', url="https://platform.ipmdecisions.net",
+                 callback=None, *args, **kwargs):
         """Constructor
 
         Parameters
@@ -90,7 +96,7 @@ def __init__(self, name='IPM', url="https://platform.ipmdecisions.net", callback
             Use cache, by default False
         """
         # hack ipmdecisions.net is down
-        #url = 'https://ipmdecisions.nibio.no'
+        # url = 'https://ipmdecisions.nibio.no'
         super().__init__(
             name=name,
             url=url,
@@ -154,7 +160,8 @@ def get_schema_weatherdata(self) -> dict:
 
         # schema weather data validate
 
-    def post_schema_weatherdata_validate(self, jsonfile: Union[str, Path] = 'weather_data.json') -> dict:
+    def post_schema_weatherdata_validate(self, jsonfile: Union[
+        str, Path] = 'weather_data.json') -> dict:
         """Validates the posted weather data against the Json schema
 
         Parameters
@@ -180,7 +187,8 @@ def post_schema_weatherdata_validate(self, jsonfile: Union[str, Path] = 'weather
 
         ###################### WeatherAdaptaterService #############################
 
-    def get_weatheradapter(self, source: dict, params: dict = None, credentials: dict = None) -> dict:
+    def get_weatheradapter(self, source: dict, params: dict = None,
+                           credentials: dict = None) -> dict:
         """Call weatheradapter service for a given weatherdata source
 
         Parameters
@@ -208,7 +216,8 @@ def get_weatheradapter(self, source: dict, params: dict = None, credentials: dic
         if params is None:
             params = fakers.weather_adapter_params(source)
 
-        endpoint = source['endpoint'].format(WEATHER_API_URL=self._url + '/api/wx')
+        endpoint = source['endpoint'].format(
+            WEATHER_API_URL=self._url + '/api/wx')
 
         if not source['authentication_type'] == 'CREDENTIALS':
             res = self.http_get(endpoint, params=params, frmt='json')
@@ -222,7 +231,8 @@ def get_weatheradapter(self, source: dict, params: dict = None, credentials: dic
 
     # weatherdatasource
 
-    def get_weatherdatasource(self, source_id=None, access_type=None, authentication_type=None) -> list:
+    def get_weatherdatasource(self, source_id=None, access_type=None,
+                              authentication_type=None) -> list:
         """Access a dict of available wetherdata sources, of a source referenced by its id
 
         Parameters
@@ -250,23 +260,27 @@ def get_weatherdatasource(self, source_id=None, access_type=None, authentication
         for r in res:
             if 'geoJSON' in r['spatial']:
                 if r['spatial']['geoJSON'] is not None:
-                    r['spatial']['geoJSON'] = json.loads(r['spatial']['geoJSON'])
+                    r['spatial']['geoJSON'] = json.loads(
+                        r['spatial']['geoJSON'])
 
         sources = {item['id']: item for item in res}
         sources = fixes.fix_get_weatherdatasource(sources)
 
         if source_id is None:
             res = sources
             if access_type is not None:
-                res = {k: v for k, v in res.items() if v['access_type'] == access_type}
+                res = {k: v for k, v in res.items() if
+                       v['access_type'] == access_type}
             if authentication_type is not None:
-                res = {k: v for k, v in res.items() if v['authentication_type'] == authentication_type}
+                res = {k: v for k, v in res.items() if
+                       v['authentication_type'] == authentication_type}
             return res
         elif source_id in sources:
             return sources[source_id]
         else:
             raise ValueError(
-                "datasource error: source_id is not referencing a valid datasource: %s" % (','.join(sources.keys())))
+                "datasource error: source_id is not referencing a valid datasource: %s" % (
+                    ','.join(sources.keys())))
 
     def post_weatherdatasource_location(
             self,
@@ -402,7 +416,8 @@ def get_dss(self, execution_type=None) -> dict:
         if execution_type is not None:
             filtered = {}
             for id, dss in all_dss.items():
-                models = {k:v for k,v in dss['models'].items() if v['execution']['type'] == execution_type}
+                models = {k: v for k, v in dss['models'].items() if
+                          v['execution']['type'] == execution_type}
                 if len(models) > 0:
                     dss['models'] = models
                     filtered[id] = dss