Merge pull request #16 from openalea/release2025

[WIP] Release2025

Author: baugetfa

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

@@ -2,16 +2,19 @@ name: build_publish_anaconda
 
 on:
   push:
-    branches: 
+    branches:
       - '**'
     tags:
       - 'v*'
   pull_request:
-    branches: 
+    branches:
       - '**'
 
 jobs:
   build:
     uses: openalea/github-action-conda-build/.github/workflows/conda-package-build.yml@main
-    secrets: 
+    secrets:
       anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
+    with:
+      python-minor-version: '[10]'
+      label: latest

README.md

@@ -24,16 +24,17 @@ The **rsml** python package provides:
 
 #### Conda 
 
-The **rsml** package is an openalea package that can be installed using conda. After installing conda, enter the following command on your conda environment::
+The **rsml** package is an openalea package that can be installed using conda or mamba:
 
-    conda install rsml -c openalea/label/unstable -c openalea
+    mamba create -n rsml -c conda-forge -c openalea3 rsml
+    mamba activate rsml
 
 
 #### From the source
 
-The **rsml** package is an openalea package and thus requires openalea.deploy to be installed. To install it, go to the rsml folder and enter the following command::
+To install it, go to the rsml folder and enter the following command::
 
-    python setup.py install
+    pip install .
 
 
 ### Use
@@ -59,30 +60,3 @@ 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.

conda/meta.yaml

@@ -1,46 +1,52 @@
-{% set data = load_setup_py_data() %}
+{% set pyproject = load_file_data('../pyproject.toml', from_recipe_dir=True) %}
+{% set name = pyproject.get('project').get('name') %}
+#{% set version = GIT_DESCRIBE_TAG | replace("v", "") %}
+{% set version = "1.4.0" %}
 
 package:
-  name: rsml
-  version: {{ data.get('version') }}
+  name: {{ name }}
+  version: {{ version }}
 
 source:
   path: ..
 
 build:
   noarch: python
-  preserve_egg_dir: True
   number: 0
-  script: {{PYTHON}} setup.py install #--single-version-externally-managed --record=record.txt
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{version}}
+  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
 
 requirements:
   build:
-    - python  {{PY_VER}}
-    - openalea.deploy
+    - python {{ pyproject["project"]["requires-python"] }}
+    {% for dep in pyproject["build-system"]["requires"] %}
+    - {{ dep.lower() }}
+    {% endfor %}
+
   run:
-    - python >=3.6
-    - openalea.mtg
-    - matplotlib
-    - pandas
-    - xlsxwriter
-    - path
-    - numpy
+    - python {{ pyproject["project"]["requires-python"] }}
+    {% for dep in pyproject["project"]["dependencies"] %}
+    - {{ dep.lower() }}
+    {% endfor %}
+    {% for dep in pyproject["tool"]["conda"]["environment"]["dependencies"] %}
+    - {{ dep.lower() }}
+    {% endfor %}
 
 test:
   requires:
-    - pytest 
-    - openalea.deploy
+    - pytest
   imports:
     - rsml
   source_files:
-    - share/data/**
     - test/**
+    - test/data/**
   commands:
     - cd test
     - pytest -v 
 
 about:
-  home: http://github.com/openalea/RSML
-  license: Cecill-c License
-  summary: RSML - The language of root architecture
+  summary: {{ pyproject["project"]["description"] }}
+  license: {{ pyproject["project"]["license"] }}
+  home: {{ pyproject["project"]["urls"]["Homepage"] }}
 

doc/_static/openalea_web.svg

@@ -1,18 +1,16 @@
-from openalea.deploy.shared_data import shared_data
 
 import rsml
 from rsml import misc
 from rsml import measurements
+from rsml.data import data_dir as rsml_dir
 
 import numpy as np
 from matplotlib import pyplot as plt
 from glob import glob
 import os
 
 # load rsml
-rsml_dir = shared_data(rsml.__path__)#,'AR570/2012_11_25_09h00_chl110_1_1.rsml')
-rsml_files = sorted(glob(rsml_dir/"AR570/*.rsml"))
-# rsml_file = "/home/fabrice/Documents/RSML/example/data/arabidopsis-simple.rsml"
+rsml_files = sorted(rsml_dir.glob("AR570/*.rsml"))
 def plot(x,y, label):
     l = plt.plot(x,y, '+')[0]
 
@@ -62,14 +60,7 @@ def plot_from_file(rsml_file, ax, split_plant, label=""):
 
 plt.ion()
 plt.clf()
-                                       
 
-# plot last time step, for each plant
-#ax = plt.subplot(1,1,1) 
-#filename = os.path.split(rsml_files[-1])[-1]
-#plot_from_file(rsml_files[-1], ax, split_plant=True)
-#ax.set_title("Individual plants at day 12")    
-    
 # plot for each time step, no plant distinction 
 ax = plt.subplot(1,1,1)#, sharex=ax, sharey=ax)
 days = [6,7,8,10,11,12]

example/RSML tutorial in Python.ipynb

@@ -9,7 +9,7 @@
 import rsml
 from rsml.continuous import *
 from openalea.mtg import MTG, traversal
-from shared_functions import *
+
 
 def my_toporder(g, scale):
   # F. Bauget 2020-03-18 : testing RSML continuous from rsml2mtg()  to hydroroot disctrete copied from rsml.continuous

example/RSML_tutorial_in_Python.ipynb

@@ -0,0 +1,77 @@
+[build-system]
+requires = ["setuptools",
+    "setuptools_scm",
+  ]
+build-backend = "setuptools.build_meta"
+
+# enable dynamic versioning based on git tags
+[tool.setuptools_scm]
+
+[project]
+name = "rsml"
+dynamic = ["version"]
+description = "RootSystemML (RSML) is a file format to represent root architectural data. This package is an openalea pckage to manage it, import/export between .rsml files and MTG, etc."
+readme = "README.md"
+authors = [
+    { name = "Christophe Pradal", email = "christophe.pradal@cirad.fr" }
+]
+license = "CECILL-C"
+license-files = ["LICEN[CS]E*"]
+keywords = ["OpenAlea", "RSML", "Plant Architecture"]
+requires-python = ">=3.9"
+classifiers = [
+  "Intended Audience :: Science/Research",
+  "Intended Audience :: Developers",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering",
+]
+
+dependencies = [
+    "matplotlib",
+    "pandas",
+    "xlsxwriter",
+    "path",
+    "numpy",
+]
+
+[project.urls]
+Homepage = "http://github.com/openalea/rsml"
+"Bug Tracker" = "https://github.com/openalea/rsml/issues"
+Discussions = "https://github.com/openalea/rsml/discussions"
+
+[project.entry-points."wralea"]
+mtg = "rsml_wralea"
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+]
+doc = [
+  "sphinx-favicon",
+  "sphinx-rtd-theme",
+  "pydata-sphinx-theme",
+  "myst-parser",
+  "sphinx-favicon",
+  "nbsphinx",
+]
+
+# section specific to conda-only distributed package (not used by pip yet)
+# based on astk, used in hydroroot with a meta.yaml that only use metadata from
+# pyproject => only pyproject.toml must be modified
+[tool.conda.environment]
+channels = [
+  "openalea3",
+  "conda-forge"
+]
+dependencies = [
+    "openalea.mtg",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+namespaces = true
+