Stdlib release25

image/setup.py

@@ -61,7 +61,7 @@
     # tell setup not to create a zip file but install the egg as a directory (recomended to be set to False)
     zip_safe=False,
     # Dependencies
-    setup_requires=['openalea.deploy'],
+    #setup_requires=['openalea.deploy'],
     #install_requires=[],
     #dependency_links=['http://openalea.gforge.inria.fr/pi'],
 

pylab/src/openalea/oapylab/tools.py

@@ -552,7 +552,8 @@ def get_axes(self):
             axes = [axes]
             for axe in axes:
                 import matplotlib
-                assert axe.__module__ in [matplotlib.axes._axes.__name__,matplotlib.axes._subplots.__name__,matplotlib.projections.polar.__name__], 'input must be a valid axes from matplotlib.axes %s given for %s' % (type(axes), axes)
+                print('DEBUG : ', axe.__module__)
+                assert axe.__module__ in [matplotlib.axes._axes.__name__,matplotlib.projections.polar.__name__], 'input must be a valid axes from matplotlib.axes %s given for %s' % (type(axes), axes)
             return axes
 
 

pylab/src/openalea/pylab_decorators_wralea/py_pylab.py

@@ -957,7 +957,7 @@ def __init__(self):
         CustomizeAxes.__init__(self)
 
         self.add_input(name='axes')
-        self.add_input(name='b', interface=IBool, value=True)
+        #self.add_input(name='b', interface=IBool, value=True)
         self.add_input(name='which', interface=IEnumStr(list(tools.which.keys())), value='major')
         self.add_input(name='linestyle', interface=IEnumStr(list(tools.linestyles.keys())),   value='dotted')
         self.add_input(name='color', interface=IEnumStr(list(tools.colors.keys())),   value='black')
@@ -973,7 +973,7 @@ def __call__(self, inputs):
         kwds['linestyle']=tools.linestyles[self.get_input("linestyle")]
         kwds['color']=tools.colors[self.get_input("color")]
         kwds['linewidth']=self.get_input("linewidth")
-        kwds['b']=self.get_input("b")
+        #kwds['b']=self.get_input("b")
         kwds['which']=self.get_input("which")
 
         axes = self.get_axes()

pylab/src/openalea/pylab_plotting_wralea/py_pylab.py

@@ -276,7 +276,10 @@ def call(self, plottype, kwds):
                     print('warning more x inputs than y inputs. correct the connectors')
                 for x,y in zip(xinputs, yinputs):
                     try:
-                        output = plot(x, y, **kwds)
+                        linestyle=kwds.get('linestyle', '-')
+                        if 'linestyle' in kwds:
+                            del kwds['linestyle']
+                        output = plot(x, y, linestyle=linestyle, **kwds)
                     except:
                         #print kwds
                         raise ValueError("plot failed")

stdlib/conda/meta.yaml

@@ -1,44 +1,59 @@
-{% 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 description = pyproject.get('project').get('description') %}
+{% set version = environ.get('SETUPTOOLS_SCM_PRETEND_VERSION', "0.0.0.dev") %}
+{% set license = pyproject.get('project').get('license') %}
+{% set home = pyproject.get('project', {}).get('urls', {}).get('Homepage', '') %}
+{% set build_deps = pyproject.get("build-system", {}).get("requires", []) %}
+{% set deps = pyproject.get('project', {}).get('dependencies', []) %}
+{% set conda_deps = pyproject.get('tool', {}).get('conda', {}).get('environment', {}).get('dependencies',[]) %}
+
 
 package:
-  name: openalea.stdlib
-  version: {{ data.get('version') }}
+  name: {{ name }}
+  version: {{ version }}
 
 source:
   path: ..
 
 build:
   noarch: python
+  string: py{{ PY_VER }}
   preserve_egg_dir: True
-  number: 0
-  script: {{PYTHON}} setup.py install 
+  # pip install options mainly ensure that dependencies are handled by conda (and not pip)
+  # --no-deps ensure pip will not install deps not declared in meta.yaml (but declared in pyproject.toml)
+  # --no-build-isolation ensure pip will not replace build deps declared in meta.yaml (and declared in pyproject.toml)
+  # --ignore-installed ensure that compiled files (accidentally present in sources or uncleaned locally) will be overwritten
+  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
 
 requirements:
-  build:
-    - python {{PY_VER}}
-    - setuptools
-    - openalea.deploy
+  host:
+    - python
+    {% for dep in build_deps %}
+    - {{ dep }}
+    {% endfor  %}
+
   run:
-    - python  <3.11
-    - ipykernel
-    - configobj
-    - openalea.core
+    - python
+    {% for dep in deps + conda_deps %}
+    - {{ dep }}
+    {% endfor %}
 
 test:
-  imports:
-    - openalea.core
   requires:
     - pytest
+    - nbmake
+    - setuptools
+  imports:
+    - openalea.core
+    - {{ name }}
   source_files:
-    - test/
-    - test/*.py
-
+    - test/test_*.py
   commands:
-    - cd test
-    - pytest -v test_*.py
+   - pytest -v
+   - pytest --nbmake
 
 about:
-  home: {{ data.get('url') }}
-  license: Cecill-c License
-  summary: {{ data.get('description') }}
-
+  home: {{ home }}
+  license: {{ license }}
+  summary: {{ description }}

stdlib/doc/conf.py

@@ -1,16 +1,153 @@
-import os,sys
+# -*- coding: utf-8 -*-
+import sys
+import os
 
-# read sphinx conf.py file
-from openalea.misc.sphinx_configuration import *
-from openalea.misc.sphinx_tools import sphinx_check_version
-from openalea.deploy.metainfo import read_metainfo
+import pydata_sphinx_theme # Pydata theme: https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html
 
-sphinx_check_version()                      # check that sphinx version is recent
-metadata = read_metainfo('../metainfo.ini') # read metainfo from common file with setup.py
-for key in ['version','project','release','authors', 'name', 'package']:
-    exec("%s = '%s'" % (key, metadata[key]))
+from importlib.metadata import metadata
+project='stdlib'
+meta = metadata('openalea.' + project)
+release = meta.get("version")
+# for example take major/minor
+version = ".".join(release.split('.')[:3])
+author = meta['Author'].split(' <')[0]
+desc = meta['Summary']
+urls = {k:v for k,v in [item.split(',') for item in meta.get_all('Project-URL')]}
 
-# by product that need to be updated:
-latex_documents = [('contents', 'main.tex', project + ' documentation', authors, 'manual')]
 
-project = project + '.' + package
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+# sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('..')) # to include the root of the package
+
+# -- General configuration ------------------------------------------------
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',  # support for automatic inclusion of docstring
+    'sphinx.ext.autosummary',  # generates autodoc summaries
+    'sphinx.ext.doctest',  # inclusion and testing of doctest code snippets
+    'sphinx.ext.intersphinx', # support for linking to other projects
+    'sphinx.ext.mathjax',  # support for math equations
+    'sphinx.ext.ifconfig',  # support for conditional content
+    'sphinx.ext.viewcode',  # support for links to source code
+    'sphinx.ext.coverage',  # includes doc coverage stats in the documentation
+    'sphinx.ext.todo',      # support for todo items
+    'sphinx.ext.napoleon',  # support for numpy and google style docstrings
+    "sphinx_favicon",      # support for favicon
+    "sphinx_copybutton",      # support for copybutton in code blocks
+    "nbsphinx",     # for integrating jupyter notebooks
+    "myst_parser"   # for parsing .md files
+]
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+autosummary_generate = True
+exclude_patterns = ['build', '_build', '_templates']
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+source_suffix = {
+    '.rst': 'restructuredtext',
+    '.md': 'markdown',
+}
+# The master toctree document.
+master_doc = 'index'
+# General information about the project.
+copyright = u'Cecill-C INRAE / INRIA / CIRAD'
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+# -- Options for HTML output ----------------------------------------------
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'pydata_sphinx_theme'
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+  "header_links_before_dropdown": 6,
+  "sidebarwidth": 200,
+  "sticky_navigation": "false",
+  "collapse_navigation": "false",
+  "display_version": "true",
+  "icon_links": [
+    {
+        "name": "GitHub",
+        "url": urls['Repository'],
+        "icon": "fa-brands fa-github",
+    },
+    ],
+    "show_version_warning_banner": True,
+    "footer_start": ["copyright"],
+    "footer_center": ["sphinx-version"],
+    "secondary_sidebar_items": {
+        "**/*": ["page-toc", "edit-this-page", "sourcelink"],
+        "examples/no-sidebar": [],
+    },
+    "use_edit_page_button": True,
+  }
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+html_logo = "_static/openalea_web.svg"
+html_favicon = "_static/openalea_web.svg"
+# If false, no module index is generated.
+html_domain_indices = True
+# If false, no index is generated.
+html_use_index = True
+# If true, the index is split into individual pages for each letter.
+html_split_index = False
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = True
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+html_show_sphinx = True
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+html_show_copyright = True
+# Output file base name for HTML help builder.
+htmlhelp_basename = project + '_documentation'
+# Add infomation about github repository
+html_context = {
+    # "github_url": "https://github.com", # or your GitHub Enterprise site
+    "github_user": "openalea",
+    "github_repo": "openalea-components",
+    "github_version": "main",
+    "doc_path": "doc",
+}
+
+# -- Options for LaTeX output ---------------------------------------------
+latex_elements = {
+}
+latex_documents = [
+    (master_doc, 'stdlib.tex', u'stdlib Documentation',
+     u'INRA / INRIA / CIRAD', 'manual'),
+]
+
+# -- Options for manual page output ---------------------------------------
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, project, project + ' Documentation',
+     [author], 1)
+]
+
+# -- Options for Texinfo output -------------------------------------------
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, project, project + ' Documentation',
+     author, project, desc,
+     'Miscellaneous'),
+]
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'python': ('https://docs.python.org/', None)}