Merge pull request #13 from pradal/temporal

Temporal

.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/[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 }}

.gitignore

@@ -1,45 +1,103 @@
-# Compiled source #
-###################
-*.com
-*.class
-*.dll
-*.exe
-*.o
+# {# pkglts, github
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# pkglts files
+.pkglts/info.log*
+
+# Packages
+*.egg
+*.egg-info
+.eggs
+.Python
+*.pth
+dist/
+build/
+env/
+downloads/
+eggs/
+parts/
+bin/
+var/
+sdist/
+develop-eggs/
+.installed.cfg
+lib/
+lib64/
+
+# editors
+.idea/
+
+# Vim files
+*.swp
+*.*~
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+.settings
+
+
+# C extensions
 *.so
+*.dll
+*.dylib
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+
+# Compiled Object files
+*.os
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
 
-# Packages #
-############
-# it's better to unpack these files and commit the raw source
-# git has its own built in compression methods
-*.7z
-*.dmg
-*.gz
-*.iso
-*.jar
-*.rar
-*.tar
-*.zip
-
-# Logs and databases #
-######################
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+.amlog
+.sconsign.dblite
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
 *.log
-*.sql
-*.sqlite
 
-# OS generated files #
-######################
+# PyBuilder
+target/
+
+# jupyter notebooks
+.ipynb_checkpoints/
+
+# svn
+.svn
+.cache/
+
+# coverage
+.coverage
+
+# sphinx autogen file
+doc/_dvlpt/
+
+
+# #}
+
+# user custom filters
+
+# Notebook
+.ipynb_checkpoints/
+
+# Mac
 .DS_Store
-.DS_Store?
-._*
-.Spotlight-V100
-.Trashes
-ehthumbs.db
-Thumbs.db
-
-# tmp #
-#######
-*.pyc
-*~
-
-./share/data/rsml
-src/RSML.egg-info
+# VS Code
+.vscode
+*.code-workspace

README.md

@@ -59,3 +59,30 @@ The **rsml** package is an openalea package and thus requires openalea.deploy to
 ### Tutorial
 
 [RSML tutorial in Python](http://nbviewer.ipython.org/github/RootSystemML/RSML-conversion-tools/blob/master/python/rsml/example/RSML%20tutorial%20in%20Python.ipynb)
+
+
+# Limit order 1(primary) order 2 (secondary)
+## 4/5 different array with key : plant
+- Total Length, 
+- nb racine (t absolute) (P1), 
+- primary length
+- nude tip length 
+- frequency vs IBD (P2)
+
+# Axis : time in raw
+## time is known
+
+Plant Lateral lenght
+- Length by root  (t) (question unit?)
+    - time as col
+    - name : Ln nth root along primary from base
+
+Tab Position
+- col : L1 ... Ln
+- position on primary
+
+
+- # root , position lateral (from base , distance)
+
+script : rsmlanalysis rsmls.txt| *.rsml
+TODO: define options to group all the analysis in a same file (csv) or in several files.

setup.py

@@ -6,13 +6,13 @@
 from setuptools import setup, find_packages
 
 # Define metainfo
-version = '1.1.2'
+version = '1.2.0'
 name = 'RSML'
 package = 'RSML'
 description= 'RSML package provide IO functionality between .rsml file and MTG'
 long_description=  'RSML package provide IO functionality between .rsml file and MTG, as well as ploting and standard measurements.' 
 authors= 'C. Pradal, J. Diener'
-authors_email = 'christophe.pradal@inria.fr'
+authors_email = 'christophe.pradal at cirad.fr'
 url = 'https://github.com/openalea/RSML'
 license = 'Cecill-C'
 
@@ -60,5 +60,9 @@
     # Declare scripts and wralea as entry_points (extensions) of your package
     entry_points={
         'wralea': ['rsml = rsml_wralea'],
+        'console_scripts': [
+            'hirros = rsml.hirros:main'  # Define a console script to run your Voilà app
+        ]
+
     },
 )