Build Doc

.readthedocs.yml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: "ubuntu-24.04"
   tools:
-    python: "miniconda3-3.12-24.9"
+    python: "mambaforge-22.9"
 
 conda:
   environment: conda/environment.yml

README.md

@@ -2,14 +2,14 @@
 
 ---
 
-[![Docs](https://readthedocs.org/projects/stat_tool/badge/?version=latest)](https://stat_tool.readthedocs.io/)
+[![Docs](https://readthedocs.org/projects/stat-tool/badge/?version=latest)](https://stat_tool.readthedocs.io/)
 [![Build Status](https://github.com/openalea/stat_tool/actions/workflows/conda-package-build.yml/badge.svg?branch=main)](https://github.com/openalea/stat_tool/actions/workflows/conda-package-build.yml?query=branch%3Amaster)
 [![License](https://img.shields.io/badge/License--CeCILL-C-blue)](https://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html)
 [![Anaconda-Server Badge](https://anaconda.org/openalea3/stat_tool/badges/version.svg)](https://anaconda.org/openalea3/stat_tool)
 
 ---
 
-[Read Latest Documentation](https://stat_tool.readthedocs.io/) - [Browse GitHub Code Repository](https://github.com/openalea/stat_tool/)
+[Read Latest Documentation](https://stat-tool.readthedocs.io/) - [Browse GitHub Code Repository](https://github.com/openalea/stat_tool/)
 
 ---
 
@@ -23,19 +23,6 @@ Thanks to all that ontribute making this package what it is !
   <img src="https://contrib.rocks/image?repo=openalea/stat_tool" />
 </a>
 
-## Note for developers
+## Installation
 
-- Compile and install with
-
-  pip install -e .
-
-after activation of the conda environment depicted in the online documentation.
-
-  * Compilation options for developers such as WITH_TEST, WITH_EFENCE are defined in pyproject.toml. They can be used with
-
-  pip install --no-build-isolation --config-settings=cmake.define.WITH_TEST=TRUE -e .
-  pip install --no-build-isolation --config-settings=cmake.build-type="Debug" -e .
-
-and also combined:
-
-    pip install --no-build-isolation --config-settings=cmake.define.WITH_TEST=TRUE --config-settings=cmake.define.WITH_EFENCE=TRUE --config-settings=cmake.build-type="Debug" -e .
+See instructions on documentation, section [Installation](./installation.md)

TODO

@@ -0,0 +1,6 @@
+- [x] Fix “ContinousParametric” and “ContinousParametricProcess” classes API documentation
+- [x] Move "Usage Example" from "User guide" section (user/index.rst) to "Usage" (usage.md) section
+- [ ] Add docstrings to constants. Simply add "///" instead of "//" ? Find how to transfert comments from doxygen xml to breathe
+- [x] Welcome page: better integrate code lines (`pip install...`). Also move section "Note for developpers" into a more appropriated section ?
+- [ ] Move objects description from "tutorials.rst" into "Usage" section
+- [ ] Ensure that warnings are raise is non-existing keyword arguments are used in functions (e.g. Nbiteration in place of NbIteration)

conda/environment.yml

@@ -4,6 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - scikit-build-core
+  - setuptools_scm
   - cmake
   - boost
   - matplotlib-base

doc/Makefile

@@ -4,6 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS      =
 SPHINXBUILD     = sphinx-build
+DOXYGENBUILD    = doxygen
 SPHINXATUOBUILD = sphinx-autobuild
 PAPER           =
 BUILDDIR        = _build
@@ -49,60 +50,70 @@ help:
 
 .PHONY: clean
 clean:
+	rm -Rf xml
+	rm -Rf html
 	rm -rf $(BUILDDIR)/*
 	rm -rf generated/*
 	rm -rf auto_gallery/
 
+
+.PHONY: doxygen
+doxygen: Doxyfile
+	$(DOXYGENBUILD) 
+	@echo
+	@echo "Doxygen build finished. The HTML pages are in ./html."
+
+
 .PHONY: html
-html:
+html: doxygen
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
 .PHONY: rtdhtml
-rtdhtml:
+rtdhtml: doxygen
 	$(SPHINXBUILD) -T -j auto -E -W --keep-going -b html -d $(BUILDDIR)/doctrees -D language=en . $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
 
 .PHONY: livehtml
-livehtml:
+livehtml: doxygen
 	# @echo "$(SPHINXATUOBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html"
 	$(SPHINXATUOBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 
 .PHONY: dirhtml
-dirhtml:
+dirhtml: doxygen
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
 .PHONY: singlehtml
-singlehtml:
+singlehtml: doxygen
 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 	@echo
 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 
 .PHONY: html-noplot
-html-noplot:
+html-noplot: doxygen
 	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
 .PHONY: pickle
-pickle:
+pickle: doxygen
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
 .PHONY: json
-json:
+json: doxygen
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
 .PHONY: htmlhelp
-htmlhelp:
+htmlhelp: doxygen
 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
 	@echo
 	@echo "Build finished; now you can run HTML Help Workshop with the" \
@@ -128,7 +139,7 @@ applehelp:
 	      "bundle."
 
 .PHONY: devhelp
-devhelp:
+devhelp: doxygen
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
@@ -138,111 +149,111 @@ devhelp:
 	@echo "# devhelp"
 
 .PHONY: epub
-epub:
+epub: doxygen
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
 .PHONY: epub3
-epub3:
+epub3: doxygen
 	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
 	@echo
 	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
 
 .PHONY: latex
-latex:
+latex: doxygen
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo
 	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
 	@echo "Run \`make' in that directory to run these through (pdf)latex" \
 	      "(use \`make latexpdf' here to do that automatically)."
 
 .PHONY: latexpdf
-latexpdf:
+latexpdf: doxygen
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through pdflatex..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf
 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
 
 .PHONY: latexpdfja
-latexpdfja:
+latexpdfja: doxygen
 	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
 	@echo "Running LaTeX files through platex and dvipdfmx..."
 	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
 	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
 
 .PHONY: text
-text:
+text: doxygen
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
 	@echo
 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
 
 .PHONY: man
-man:
+man: doxygen
 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
 	@echo
 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
 
 .PHONY: texinfo
-texinfo:
+texinfo: doxygen
 	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
 	@echo
 	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
 	@echo "Run \`make' in that directory to run these through makeinfo" \
 	      "(use \`make info' here to do that automatically)."
 
 .PHONY: info
-info:
+info: doxygen
 	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
 	@echo "Running Texinfo files through makeinfo..."
 	make -C $(BUILDDIR)/texinfo info
 	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
 
 .PHONY: gettext
-gettext:
+gettext: doxygen
 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
 	@echo
 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
 
 .PHONY: changes
-changes:
+changes: doxygen
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
 .PHONY: linkcheck
-linkcheck:
+linkcheck: doxygen
 	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
 	@echo
 	@echo "Link check complete; look for any errors in the above output " \
 	      "or in $(BUILDDIR)/linkcheck/output.txt."
 
 .PHONY: doctest
-doctest:
+doctest: doxygen
 	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
 	@echo "Testing of doctests in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/doctest/output.txt."
 
 .PHONY: coverage
-coverage:
+coverage: doxygen
 	$(SPHINXBUILD) -b coverage $(ALLSPHINXOPTS) $(BUILDDIR)/coverage
 	@echo "Testing of coverage in the sources finished, look at the " \
 	      "results in $(BUILDDIR)/coverage/python.txt."
 
 .PHONY: xml
-xml:
+xml: doxygen
 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
 	@echo
 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
 .PHONY: pseudoxml
-pseudoxml:
+pseudoxml: doxygen
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
 
 .PHONY: dummy
-dummy:
+dummy: 
 	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
 	@echo
 	@echo "Build finished. Dummy builder generates no files."

doc/api/classes.rst

@@ -15,9 +15,9 @@ Classes
    :members:
 .. doxygenclass:: stat_tool::CompoundData
    :members:
-.. doxygenclass:: ContinousParametric
+.. doxygenclass:: stat_tool::ContinuousParametric
    :members:
-.. doxygenclass:: ContinousParametricProcess
+.. doxygenclass:: stat_tool::ContinuousParametricProcess
    :members:
 .. doxygenclass:: stat_tool::Convolution
    :members:

doc/api/index.rst

@@ -2,23 +2,23 @@ API Reference
 =============
 
 .. toctree::
-   :maxdepth: 4
+   :maxdepth: 2
+   :caption: AML API:
 
    ../user/list.rst
-   python
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Python API:
+
+   ../user/autosum.rst
 
 
 .. toctree::
-   :maxdepth: 4
-   :hidden:
+   :maxdepth: 2
    :caption: C++ API:
 
    classes
    enums
    constants
 
-
-
-    .. functions
-    .. doxygenindex::
-