Update doc + fixes and extensions

.gitignore

@@ -1,7 +1,7 @@
 .vscode/
 .cache/
 build/
-doc/
+doc/_build
 .idea/
 .DS_Store
 CMakeLists.txt.user

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "externals/tinyobjloader"]
-	path = externals/tinyobjloader
-	url = https://github.com/tinyobjloader/tinyobjloader.git

CITATION.cff

@@ -31,7 +31,7 @@ authors:
     family-names: Boudon
     affiliation: CIRAD
     orcid: 'https://orcid.org/0000-0001-9636-3102'
-repository-code: 'https://github.com/openalea-incubator/spice'
+repository-code: 'https://github.com/openalea/spice'
 keywords:
   - photon mapping
   - light simulation

CMakeLists.txt

@@ -1,11 +1,13 @@
 cmake_minimum_required(VERSION 3.20)
 project(photon_mapping LANGUAGES CXX)
 
-set(CMAKE_CXX_STANDARD 23)
+set(CMAKE_CXX_STANDARD 26)
 
 option(BUILD_TESTS "build c++ tests" OFF)
 option(BUILD_CXX_EXAMPLE "build c++ example" OFF)
 
+option(HIP "GPU support with HIP" OFF)
+
 # --- Build setup
 find_package(TBB CONFIG REQUIRED)
 find_package(Threads REQUIRED)
@@ -18,6 +20,7 @@ endif()
 # apple newer C++ features with old SDK
 if(APPLE)
     set(CMAKE_CXX_FLAGS "${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY")
+    set(CMAKE_OSX_DEPLOYMENT_TARGET "10.13")
 endif()
 
 # Embree4
@@ -29,9 +32,31 @@ else()
   message(FATAL_ERROR "Could not find Embree")
 endif()
 
+# find tinyobjloader & tinygltf
+include(FetchContent)
+
+set(TINYOBJLOADER_BUILD_TEST_LOADER OFF CACHE INTERNAL "") 
+
+FetchContent_Declare(
+    tinyobjloader
+    GIT_REPOSITORY https://github.com/tinyobjloader/tinyobjloader.git
+    GIT_TAG        release 
+)
+
+set(TINYGLTF_BUILD_EXAMPLES OFF CACHE INTERNAL "") 
 
-# externals
-add_subdirectory("externals")
+FetchContent_Declare(
+    tinygltf
+    GIT_REPOSITORY https://github.com/syoyo/tinygltf.git
+    GIT_TAG        release 
+)
+
+# Bring both packages into the build tree
+FetchContent_MakeAvailable(tinyobjloader tinygltf)
+
+if(HIP)
+    find_package(hiprt CONFIG REQUIRED)
+endif()
 
 add_subdirectory("src/cpp/include")
 
@@ -41,13 +66,13 @@ add_library(pm INTERFACE src/python/ext_photonmapping_nano.cpp)
 
 set_target_properties(pm
         PROPERTIES
-        CXX_STANDARD 23
+        CXX_STANDARD 26
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS YES
         )
 
 
-target_link_libraries(pm INTERFACE TBB::tbb OpenMP::OpenMP_CXX tinyobjloader embree Threads::Threads photon_map primitive triangle image)
+target_link_libraries(pm INTERFACE TBB::tbb OpenMP::OpenMP_CXX embree Threads::Threads photon_map primitive triangle image)
 
 # wrapper
 add_subdirectory("src/python/")

conda/environment.yml

@@ -6,9 +6,11 @@ dependencies:
   - openalea.lpy
   - openalea.plantgl
   - openalea.widgets
+  - tinyobjloader
   - embree
   - make
   - cxx-compiler
+  - tinygltf
   - cmake
   - tbb
   - tbb-devel

doc/Makefile

@@ -1,17 +1,12 @@
-# {# pkglts, sphinx
 # Makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
-SPHINXBUILD   = sphinx-build
-PAPER         =
-BUILDDIR      = build
-
-# User-friendly check for sphinx-build
-ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
-endif
+SPHINXOPTS      =
+SPHINXBUILD     = sphinx-build
+SPHINXATUOBUILD = sphinx-autobuild
+PAPER           =
+BUILDDIR        = _build
 
 # Internal variables.
 PAPEROPT_a4     = -D latex_paper_size=a4
@@ -20,19 +15,22 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
+.PHONY: help
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       to make standalone HTML files"
+	@echo "  rtdhtml    Build html using same settings used on ReadtheDocs"
+	@echo "  livehtml   Make standalone HTML files and rebuild the documentation when a change is detected. Also includes a livereload enabled web server"
 	@echo "  dirhtml    to make HTML files named index.html in directories"
 	@echo "  singlehtml to make a single large HTML file"
 	@echo "  pickle     to make pickle files"
 	@echo "  json       to make JSON files"
 	@echo "  htmlhelp   to make HTML files and a HTML help project"
 	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  applehelp  to make an Apple Help Book"
 	@echo "  devhelp    to make HTML files and a Devhelp project"
 	@echo "  epub       to make an epub"
+	@echo "  epub3      to make an epub3"
 	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
 	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
 	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
@@ -46,135 +44,205 @@ help:
 	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
 	@echo "  linkcheck  to check all external links for integrity"
 	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+	@echo "  coverage   to run coverage check of the documentation (if enabled)"
+	@echo "  dummy      to check syntax errors of document sources"
 
+.PHONY: clean
 clean:
 	rm -rf $(BUILDDIR)/*
+	rm -rf generated/*
+	rm -rf auto_gallery/
 
+.PHONY: html
 html:
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 
+.PHONY: rtdhtml
+rtdhtml:
+	$(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 $(BUILDDIR)/html."
+
+
+.PHONY: livehtml
+livehtml:
+	# @echo "$(SPHINXATUOBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html"
+	$(SPHINXATUOBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+
+.PHONY: dirhtml
 dirhtml:
 	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
 
+.PHONY: singlehtml
 singlehtml:
 	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
 	@echo
 	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
 
+.PHONY: html-noplot
+html-noplot:
+	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+.PHONY: pickle
 pickle:
 	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
 	@echo
 	@echo "Build finished; now you can process the pickle files."
 
+.PHONY: json
 json:
 	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
 	@echo
 	@echo "Build finished; now you can process the JSON files."
 
+.PHONY: htmlhelp
 htmlhelp:
 	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
 	@echo
 	@echo "Build finished; now you can run HTML Help Workshop with the" \
 	      ".hhp project file in $(BUILDDIR)/htmlhelp."
 
+.PHONY: qthelp
 qthelp:
 	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
 	@echo
 	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
 	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
-	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pkglts.qhcp"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/xarray.qhcp"
 	@echo "To view the help file:"
-	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pkglts.qhc"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/xarray.qhc"
+
+.PHONY: applehelp
+applehelp:
+	$(SPHINXBUILD) -b applehelp $(ALLSPHINXOPTS) $(BUILDDIR)/applehelp
+	@echo
+	@echo "Build finished. The help book is in $(BUILDDIR)/applehelp."
+	@echo "N.B. You won't be able to view it unless you put it in" \
+	      "~/Library/Documentation/Help or install it in your application" \
+	      "bundle."
 
+.PHONY: devhelp
 devhelp:
 	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
 	@echo
 	@echo "Build finished."
 	@echo "To view the help file:"
-	@echo "# mkdir -p $$HOME/.local/share/devhelp/pkglts"
-	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pkglts"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/xarray"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/xarray"
 	@echo "# devhelp"
 
+.PHONY: epub
 epub:
 	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
 	@echo
 	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
 
+.PHONY: epub3
+epub3:
+	$(SPHINXBUILD) -b epub3 $(ALLSPHINXOPTS) $(BUILDDIR)/epub3
+	@echo
+	@echo "Build finished. The epub3 file is in $(BUILDDIR)/epub3."
+
+.PHONY: latex
 latex:
 	$(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:
 	$(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:
 	$(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:
 	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
 	@echo
 	@echo "Build finished. The text files are in $(BUILDDIR)/text."
 
+.PHONY: man
 man:
 	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
 	@echo
 	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
 
+.PHONY: texinfo
 texinfo:
 	$(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:
 	$(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:
 	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
 	@echo
 	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
 
+.PHONY: changes
 changes:
 	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
 	@echo
 	@echo "The overview file is in $(BUILDDIR)/changes."
 
+.PHONY: linkcheck
 linkcheck:
 	$(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:
 	$(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:
+	$(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:
 	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
 	@echo
 	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
 
+.PHONY: pseudoxml
 pseudoxml:
 	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
 	@echo
 	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
 
-# #}
+.PHONY: dummy
+dummy:
+	$(SPHINXBUILD) -b dummy $(ALLSPHINXOPTS) $(BUILDDIR)/dummy
+	@echo
+	@echo "Build finished. Dummy builder generates no files."

doc/index.rst

@@ -15,6 +15,7 @@ Openalea Spice documentation
    guide.rst
    code_example.rst
    notebook_examples.rst
+   references.rst
 
 
 .. include:: ../README.md