Merge pull request #26 from pradal/namespace

Move alinea to namespace package

Author: pradal

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

@@ -2,66 +2,16 @@ 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/action-build-publish-anaconda@v0.1.3
-      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

@@ -8,7 +8,7 @@
 from os.path import abspath, normpath
 from os.path import join as pj
 
-from setuptools import setup, find_packages
+from setuptools import setup, find_namespace_packages
 
 
 short_descr = "The Alinea.astk package provides utilities for simulation of FSPM models builds under alinea standards"
@@ -62,7 +62,7 @@ def data_rel_pth(pth):
     license='cecill-c',
     zip_safe=False,
 
-    packages=find_packages('src'),
+    packages=find_namespace_packages(where='src', include=['alinea', 'alinea.*', 'astk_data']),
     package_dir={'': 'src'},
 
     include_package_data=True,
@@ -71,7 +71,6 @@ def data_rel_pth(pth):
     #tests_require=parse_requirements("dvlpt_requirements.txt"),
     entry_points={},
     keywords='',
-    test_suite='nose.collector',
 )
 # #}
 # change setup_kwds below before the next pkglts tag

src/alinea/__init__.py

@@ -20,28 +20,17 @@
 def septo3d_reader(data_file, sep):
     """ reader for septo3D meteo files """
 
-    def parse(yr, doy, hr):
-        """ Convert the 'An', 'Jour' and 'hhmm' variables of the
-        meteo dataframe in a datetime object (%Y-%m-%d %H:%M:%S format)
-        """
-        an, jour, heure = [int(x) for x in [yr, doy, int(hr) / 100]]
-        dt = datetime(an - 1, 12, 31)
-        delta = timedelta(days=jour, hours=heure)
-        return dt + delta
-
-    data = pandas.read_csv(data_file,
-                           parse_dates={'date': ['An', 'Jour', 'hhmm']},
-                           date_parser=parse, sep=sep)
+    data = pandas.read_csv(data_file, sep=sep)
     # ,
     # usecols=['An','Jour','hhmm','PAR','Tair','HR','Vent','Pluie'])
 
+    data['date'] = pandas.to_datetime(data['An'] * 1000 + data['Jour'], format='%Y%j')+pandas.to_timedelta(data.hhmm/100, unit='H')
     data.index = data.date
     data = data.rename(columns={'PAR': 'PPFD', 'Tair': 'temperature_air',
                                 'HR': 'relative_humidity', 'Vent': 'wind_speed',
                                 'Pluie': 'rain'})
     return data
 
-
 def PPFD_to_global(data):
     """ Convert the PAR (ppfd in micromol.m-2.sec-1)
     in global radiation (J.m-2.s-1, ie W/m2)
@@ -86,7 +75,7 @@ def linear_degree_days(data, start_date=None, base_temp=0., max_temp=35.):
     return dd - dd[df.index.searchsorted(start_date)]
 
 
-class Weather(object):
+class Weather:
     """ Class compliying echap local_microclimate model protocol (meteo_reader).
         expected variables of the data_file are:
             - 'An'

src/alinea/astk/Weather.py

@@ -2,8 +2,8 @@
 #  -*- coding: utf-8 -*-
 
 major = 2
-minor = 3
-post = 2
+minor = 4
+post = 0
 
 __version__ = ".".join([str(s) for s in (major, minor, post)])
 # #}