Refactoring namespace

README.md

@@ -26,7 +26,7 @@ The **rsml** python package provides:
 
 The **rsml** package is an openalea package that can be installed using conda or mamba:
 
-    mamba create -n rsml -c conda-forge -c openalea3 rsml
+    mamba create -n rsml -c conda-forge -c openalea3 openalea.rsml
     mamba activate rsml
 
 
@@ -40,7 +40,7 @@ To install it, go to the rsml folder and enter the following command::
 ### Use
 
 ```python
-    import rsml
+    import openalea.rsml as rsml
 
     # load rsml
     g = rsml.rsml2mtg( filename )
@@ -53,7 +53,7 @@ To install it, go to the rsml folder and enter the following command::
     rsml.mtg2rsml(g, filename)
 
     # export mesurements to tabular file
-    from rsml import measurements
+    from openalea.rsml import measurements
     measurements.export(g, filename[:-5]+'.csv')
 ```    
 

conda/environment.yml

@@ -1,13 +1,11 @@
 name: rsml_dev
 channels:
-  - conda-forge
+  - openalea3/label/dev
+  - openalea3/label/rc
   - openalea3
+  - conda-forge
 dependencies:
   - matplotlib-base
-  - pandas
-  - xlsxwriter
-  - path
-  - numpy
   - openalea.mtg
   # let pip install the rest using pyproject.toml (if you are okay with conda/pip mix)
   - pip:

conda/meta.yaml

@@ -20,7 +20,6 @@ build:
   noarch: python
   number: 0
   preserve_egg_dir: True
-  string: py{{ PY_VER }}
   script:
     - {{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-build-isolation -vv
 
@@ -45,7 +44,7 @@ test:
     {% endfor %}
 
   imports:
-    - rsml
+    - openalea.rsml
 
   source_files:
     - test/**

doc/conf.py

@@ -4,15 +4,22 @@
 
 import pydata_sphinx_theme # Pydata theme: https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html
 
+from importlib.metadata import metadata
+project='rsml'
+meta = metadata('openalea.' + project)
+release = meta.get("version")
+# for example take major/minor
+version = ".".join(release.split('.')[:3])
+# author = meta['Author-email'].split(' <')[0]
+desc = meta['Summary']
+urls = {k:v for k,v in [item.split(',') for item in meta.get_all('Project-URL')]}
+author = u'Christophe Pradal'
 
-# Get the project root dir, which is the parent dir of this
-cwd = os.getcwd()
-project_root = os.path.dirname(cwd)
-
-# Insert the project root dir as the first element in the PYTHONPATH.
-# This lets us ensure that the source package is imported, and that its
-# version is used.
-sys.path.insert(0, os.path.join(project_root, 'src'))
+# 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
@@ -30,13 +37,14 @@
     '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', '_templates']
+exclude_patterns = ['build', '_build', '_templates']
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 source_suffix = {
@@ -46,22 +54,7 @@
 # The master toctree document.
 master_doc = 'index'
 # General information about the project.
-project = u'rsml'
 copyright = u'Cecill-C INRAE / INRIA / CIRAD'
-author = u'Christophe Pradal'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-pkgver={}
-with open("../src/rsml/version.py") as fp:
-    exec(fp.read(), pkgver)
-# The short X.Y version.
-version = str(pkgver["MAJOR"])+'.'+str(pkgver["MINOR"])
-# The full version, including alpha/beta/rc tags.
-release = pkgver["__version__"]
-
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
@@ -81,15 +74,17 @@
 # further.  For a list of options available for each theme, see the
 # documentation.
 html_theme_options = {
+  "show_nav_level": 4,
   "header_links_before_dropdown": 6,
   "sidebarwidth": 200,
+  "show_nav_level": 2,
   "sticky_navigation": "false",
   "collapse_navigation": "false",
   "display_version": "true",
   "icon_links": [
     {
         "name": "GitHub",
-        "url": "https://github.com/openalea/openalea.rtfd.io",
+        "url": "https://github.com/openalea/rsml",
         "icon": "fa-brands fa-github",
     },
     ],
@@ -100,6 +95,7 @@
         "**/*": ["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,
@@ -120,21 +116,30 @@
 # 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 = 'rsml_documentation'
+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": "rsml",
+    "github_version": "main",
+    "doc_path": "doc",
+}
 
 # -- Options for LaTeX output ---------------------------------------------
 latex_elements = {
 }
 latex_documents = [
     (master_doc, 'rsml.tex', u'rsml Documentation',
-     u'INRAE / inria / CIRAD', 'manual'),
+     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, 'rsml', u'rsml Documentation',
+    (master_doc, project, project + ' Documentation',
      [author], 1)
 ]
 
@@ -143,9 +148,9 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'rsml', u'rsml Documentation',
-     author, 'rsml', 'RootSystemML (RSML) is a file format to represent root architectural data.',
+    (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)}
+intersphinx_mapping = {'python': ('https://docs.python.org/', None)}

pyproject.toml

@@ -12,7 +12,7 @@ version_scheme = "guess-next-dev"
 local_scheme = "no-local-version"
 
 [project]
-name = "rsml"
+name = "openalea.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"
@@ -47,7 +47,7 @@ Homepage = "http://github.com/openalea/rsml"
 Discussions = "https://github.com/openalea/rsml/discussions"
 
 [project.entry-points."wralea"]
-mtg = "rsml_wralea"
+"rsml" = "openalea.rsml_wralea"
 
 [project.optional-dependencies]
 test = [
@@ -58,7 +58,7 @@ doc = [
   "sphinx-rtd-theme",
   "pydata-sphinx-theme",
   "myst-parser",
-  "sphinx-favicon",
+  "sphinx-copybutton",
   "nbsphinx",
 ]
 

src/openalea/rsml/__init__.py

@@ -0,0 +1,2 @@
+from openalea.rsml.io   import rsml2mtg, mtg2rsml
+from openalea.rsml.plot import plot2d, plot3d

src/rsml/continuous.py → src/openalea/rsml/continuous.py

@@ -34,7 +34,7 @@ def discrete_to_continuous(g, position='position'):
       - convert "discrete" functions (such as diameter)
       - convert continuous functions?
     """
-    from rsml.metadata import add_property_definition
+    from openalea.rsml.metadata import add_property_definition
 
     # accessor of the segment position property
     if isinstance(position, str):

src/rsml/hirros.py → src/openalea/rsml/hirros.py

@@ -10,7 +10,7 @@
 import numpy as np
 import pandas as pd
 
-import rsml
+import openalea.rsml
 
 
 def walk(dir: str, recursive=True):

src/rsml/matching.py → src/openalea/rsml/matching.py

@@ -4,7 +4,7 @@
 
 import numpy as _np
 
-from rsml.misc import plant_vertices
+from openalea.rsml.misc import plant_vertices
 
 def match_plants(t1,t2, max_distance=None):
     """
@@ -114,7 +114,7 @@ def find_match(axes1, axes2):
 
 def _match_root_axes(t1, axes1, t2, axes2, max_distance=None):
     """ return "best" match between axes in `axes1` and in `axes2` """
-    from rsml.misc import hausdorff_distance
+    from openalea.rsml.misc import hausdorff_distance
 
     # construct distance matrix
     geom1 = t1.property('geometry')

src/rsml/metadata.py → src/openalea/rsml/metadata.py

@@ -2,7 +2,7 @@
 Manage rsml metadata attributes
 
 The metadata element in rsml contains some mandatory content and optional ones.
-In the IO operation from rsml file to&from mtg, these metadata are looked for 
+In the IO operation from openalea.rsml file to&from mtg, these metadata are looked for
 in the 'metadata' graph property of the mtg::
 
     mtg.graph_properties()['metadata']

src/rsml/plot.py → src/openalea/rsml/plot.py

@@ -145,7 +145,7 @@ def multiple_plot(files, image=True):
     '''
     from openalea.core.path import path
     from matplotlib import pyplot as plt
-    import rsml
+    import openalea.rsml
     import os
 
     def get_file(f):    

test/test.py

@@ -2,8 +2,8 @@
 N = 2
 
 from time import sleep
-from rsml.data import data_dir
-import rsml
+from openalea.rsml.data import data_dir
+import openalea.rsml as rsml
 
 img_dir = data_dir
 data = data_dir

test/test_discrete_mtg.py

@@ -4,8 +4,8 @@
 import pickle 
 
 def load_discrete():
-    from rsml.data import data_dir
-    import rsml
+    from openalea.rsml.data import data_dir
+    import openalea.rsml as rsml
     filename = data_dir/'discrete.bmtg'
     with open(filename, 'rb') as f:   # F. Bauget 2022-04-12: needs bytes
         g = pickle.load(f, encoding="latin1") # F. Bauget 2022-04-12: Python 2 bytestring data to Python 3
@@ -38,8 +38,8 @@ def simple_tree():
     return g
 
 def test_discrete_to_continuous():
-    from rsml.continuous import discrete_to_continuous
-    from rsml.continuous import continuous_to_discrete
+    from openalea.rsml.continuous import discrete_to_continuous
+    from openalea.rsml.continuous import continuous_to_discrete
 
     def test_tree(g0):
         gc = discrete_to_continuous(g0.copy())

test/test_hirros.py

@@ -1,8 +1,8 @@
 """
 Tests for the measurements module
 """
-import rsml
-from rsml import hirros
+import openalea.rsml as rsml
+from openalea.rsml import hirros
 
 def get_mtg():
     fn = 'data/61_graph_expertized.rsml'

test/test_measurements.py

@@ -19,7 +19,7 @@ def simple_tree():
     return g
 
 def test_length():
-    from rsml.measurements import root_length
+    from openalea.rsml.measurements import root_length
 
     g = simple_tree()
     L = root_length(g)
@@ -28,7 +28,7 @@ def test_length():
     assert sorted(L.values())==[1,3], 'invalid axe length'
 
 def test_RSML_Measurement():
-    from rsml.measurements import RSML_Measurements
+    from openalea.rsml.measurements import RSML_Measurements
 
     g = simple_tree()
     m = RSML_Measurements()