Merge pull request #5190 from prckent/doxygencleanup

Improve doxygen docs + cleanup
QMCPACK · Sep 26, 2024 · 0a1b901 · 0a1b901
2 parents 92746e6 + 427f5a4
commit 0a1b901
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Showing 118 changed files with 9 additions and 3 deletions.
diff --git a/docs/external_tools.rst b/docs/external_tools.rst
@@ -25,6 +25,12 @@ In general:
 
 These set the basic flags required to build with either of these sanitizer libraries which are mutually exclusive. Depending on your system and linker, these may be incompatible with the "Release" build, so set ``-DCMAKE_BUILD_TYPE=Debug`` or ``-DCMAKE_BUILD_TYPE=RelWithDebInfo``. They are tested on GitHub Actions CI using deterministic tests ``ctest -L deterministic`` (currently ubsan). See the following links for additional information on use, run time, and build options of the sanitizers: https://clang.llvm.org/docs/AddressSanitizer.html & https://clang.llvm.org/docs/MemorySanitizer.html.
 
+Doxygen source documentation
+----------------------------
+
+If doxygen and optionally dot from graphviz are detected by CMake, a qmcpack_doxygen target will be defined. ``make qmcpack_doxygen`` will then generate html-based
+documentation in the build directory. This target is not enabled by default because generation of the documentation may take several minutes. This automatically
+generated documentation includes class diagrams and browsable and searchable lists of all functions, classes, and files. 
 
 Intel VTune
 -----------

diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt
@@ -1,9 +1,9 @@
 find_package(Doxygen)
 if(NOT DOXYGEN_FOUND)
-    message(STATUS "The qmcpack_doxygen target for the QMCPACK developer/API "
-        "documentation requires doxygen and (optionally) dot from graphviz."
-    )
+    message(STATUS "doxygen not found. Source code documentation via qmcpack_doxygen target requires doxygen and (optionally) dot from graphviz.")
     return()
+else()
+    message(STATUS "doxygen found. For source code documentation build the qmcpack_doxygen target.")
 endif()
 
 set(DOXYGEN_PROJECT_NAME QMCPACK)

diff --git a/doxygen/Doxyfile → doxygen/attic/Doxyfile b/doxygen/Doxyfile → doxygen/attic/Doxyfile
diff --git a/doxygen/Doxyfile.ug → doxygen/attic/Doxyfile.ug b/doxygen/Doxyfile.ug → doxygen/attic/Doxyfile.ug
diff --git a/doxygen/DoxygenLayout.xml → doxygen/attic/DoxygenLayout.xml b/doxygen/DoxygenLayout.xml → doxygen/attic/DoxygenLayout.xml
diff --git a/doxygen/Makefile → doxygen/attic/Makefile b/doxygen/Makefile → doxygen/attic/Makefile
diff --git a/doxygen/OrbitalOptimization.tex → doxygen/attic/OrbitalOptimization.tex b/doxygen/OrbitalOptimization.tex → doxygen/attic/OrbitalOptimization.tex
diff --git a/doxygen/README → doxygen/attic/README b/doxygen/README → doxygen/attic/README
diff --git a/doxygen/config.h → doxygen/attic/config.h b/doxygen/config.h → doxygen/attic/config.h
diff --git a/doxygen/conversion.tex → doxygen/attic/conversion.tex b/doxygen/conversion.tex → doxygen/attic/conversion.tex
diff --git a/doxygen/dev.cfg → doxygen/attic/dev.cfg b/doxygen/dev.cfg → doxygen/attic/dev.cfg
diff --git a/doxygen/dev.tag → doxygen/attic/dev.tag b/doxygen/dev.tag → doxygen/attic/dev.tag
diff --git a/doxygen/dev/basic.dox → doxygen/attic/dev/basic.dox b/doxygen/dev/basic.dox → doxygen/attic/dev/basic.dox
diff --git a/doxygen/dev/design.dox → doxygen/attic/dev/design.dox b/doxygen/dev/design.dox → doxygen/attic/dev/design.dox
diff --git a/doxygen/dev/einspline.dox → doxygen/attic/dev/einspline.dox b/doxygen/dev/einspline.dox → doxygen/attic/dev/einspline.dox
diff --git a/doxygen/dev/index.dox → doxygen/attic/dev/index.dox b/doxygen/dev/index.dox → doxygen/attic/dev/index.dox
diff --git a/doxygen/dev/jastrow.dox → doxygen/attic/dev/jastrow.dox b/doxygen/dev/jastrow.dox → doxygen/attic/dev/jastrow.dox
diff --git a/doxygen/dev/psi.dox → doxygen/attic/dev/psi.dox b/doxygen/dev/psi.dox → doxygen/attic/dev/psi.dox
diff --git a/doxygen/dev/todo.dox → doxygen/attic/dev/todo.dox b/doxygen/dev/todo.dox → doxygen/attic/dev/todo.dox
diff --git a/doxygen/dev/update.dox → doxygen/attic/dev/update.dox b/doxygen/dev/update.dox → doxygen/attic/dev/update.dox
diff --git a/doxygen/dev/validation.dox → doxygen/attic/dev/validation.dox b/doxygen/dev/validation.dox → doxygen/attic/dev/validation.dox
diff --git a/doxygen/dev_layout.xml → doxygen/attic/dev_layout.xml b/doxygen/dev_layout.xml → doxygen/attic/dev_layout.xml
diff --git a/doxygen/dot/einsplineset_0.graffle → doxygen/attic/dot/einsplineset_0.graffle b/doxygen/dot/einsplineset_0.graffle → doxygen/attic/dot/einsplineset_0.graffle
diff --git a/doxygen/dot/einsplineset_0.pdf → doxygen/attic/dot/einsplineset_0.pdf b/doxygen/dot/einsplineset_0.pdf → doxygen/attic/dot/einsplineset_0.pdf
diff --git a/doxygen/dot/hamiltonian.dot → doxygen/attic/dot/hamiltonian.dot b/doxygen/dot/hamiltonian.dot → doxygen/attic/dot/hamiltonian.dot
diff --git a/doxygen/dot/lcorbitalset.graffle → doxygen/attic/dot/lcorbitalset.graffle b/doxygen/dot/lcorbitalset.graffle → doxygen/attic/dot/lcorbitalset.graffle
diff --git a/doxygen/dot/particleset.dot → doxygen/attic/dot/particleset.dot b/doxygen/dot/particleset.dot → doxygen/attic/dot/particleset.dot
diff --git a/doxygen/dot/particleset.graffle → doxygen/attic/dot/particleset.graffle b/doxygen/dot/particleset.graffle → doxygen/attic/dot/particleset.graffle
diff --git a/doxygen/dot/psi_factory.dot → doxygen/attic/dot/psi_factory.dot b/doxygen/dot/psi_factory.dot → doxygen/attic/dot/psi_factory.dot
diff --git a/doxygen/dot/qmcsys.dot → doxygen/attic/dot/qmcsys.dot b/doxygen/dot/qmcsys.dot → doxygen/attic/dot/qmcsys.dot
diff --git a/doxygen/dot/simulation.dot → doxygen/attic/dot/simulation.dot b/doxygen/dot/simulation.dot → doxygen/attic/dot/simulation.dot
diff --git a/doxygen/dot/wfs.dot → doxygen/attic/dot/wfs.dot b/doxygen/dot/wfs.dot → doxygen/attic/dot/wfs.dot
diff --git a/doxygen/dot/wfs_factory.dot → doxygen/attic/dot/wfs_factory.dot b/doxygen/dot/wfs_factory.dot → doxygen/attic/dot/wfs_factory.dot
diff --git a/doxygen/dot/xmlsymbols.dot → doxygen/attic/dot/xmlsymbols.dot b/doxygen/dot/xmlsymbols.dot → doxygen/attic/dot/xmlsymbols.dot
diff --git a/doxygen/doxygen.sty → doxygen/attic/doxygen.sty b/doxygen/doxygen.sty → doxygen/attic/doxygen.sty
diff --git a/doxygen/eshdf.dot → doxygen/attic/eshdf.dot b/doxygen/eshdf.dot → doxygen/attic/eshdf.dot
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diff --git a/doxygen/features.doc → doxygen/attic/features.doc b/doxygen/features.doc → doxygen/attic/features.doc
diff --git a/doxygen/footer.tex → doxygen/attic/footer.tex b/doxygen/footer.tex → doxygen/attic/footer.tex
diff --git a/doxygen/header.tex → doxygen/attic/header.tex b/doxygen/header.tex → doxygen/attic/header.tex
diff --git a/doxygen/images/DMC-startcalc.eps → doxygen/attic/images/DMC-startcalc.eps b/doxygen/images/DMC-startcalc.eps → doxygen/attic/images/DMC-startcalc.eps
diff --git a/doxygen/images/DMC-startcalc.png → doxygen/attic/images/DMC-startcalc.png b/doxygen/images/DMC-startcalc.png → doxygen/attic/images/DMC-startcalc.png
diff --git a/doxygen/images/DMCTstepConv.eps → doxygen/attic/images/DMCTstepConv.eps b/doxygen/images/DMCTstepConv.eps → doxygen/attic/images/DMCTstepConv.eps
diff --git a/doxygen/images/DMCTstepConv.png → doxygen/attic/images/DMCTstepConv.png b/doxygen/images/DMCTstepConv.png → doxygen/attic/images/DMCTstepConv.png
diff --git a/doxygen/images/FSU-tutorial-0.png → doxygen/attic/images/FSU-tutorial-0.png b/doxygen/images/FSU-tutorial-0.png → doxygen/attic/images/FSU-tutorial-0.png
diff --git a/doxygen/images/FSU-tutorial-1.png → doxygen/attic/images/FSU-tutorial-1.png b/doxygen/images/FSU-tutorial-1.png → doxygen/attic/images/FSU-tutorial-1.png
diff --git a/doxygen/images/FSU-tutorial-2.png → doxygen/attic/images/FSU-tutorial-2.png b/doxygen/images/FSU-tutorial-2.png → doxygen/attic/images/FSU-tutorial-2.png
diff --git a/doxygen/images/FSU-tutorial-3.png → doxygen/attic/images/FSU-tutorial-3.png b/doxygen/images/FSU-tutorial-3.png → doxygen/attic/images/FSU-tutorial-3.png
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diff --git a/doxygen/images/FSU-tutorial-9.png → doxygen/attic/images/FSU-tutorial-9.png b/doxygen/images/FSU-tutorial-9.png → doxygen/attic/images/FSU-tutorial-9.png
diff --git a/doxygen/images/FeO_variance_ratio.png → doxygen/attic/images/FeO_variance_ratio.png b/doxygen/images/FeO_variance_ratio.png → doxygen/attic/images/FeO_variance_ratio.png
diff --git a/doxygen/images/FullDMCPlot.eps → doxygen/attic/images/FullDMCPlot.eps b/doxygen/images/FullDMCPlot.eps → doxygen/attic/images/FullDMCPlot.eps
diff --git a/doxygen/images/FullDMCPlot.png → doxygen/attic/images/FullDMCPlot.png b/doxygen/images/FullDMCPlot.png → doxygen/attic/images/FullDMCPlot.png
diff --git a/doxygen/images/SplineConv.eps → doxygen/attic/images/SplineConv.eps b/doxygen/images/SplineConv.eps → doxygen/attic/images/SplineConv.eps
diff --git a/doxygen/images/SplineConv.png → doxygen/attic/images/SplineConv.png b/doxygen/images/SplineConv.png → doxygen/attic/images/SplineConv.png
diff --git a/doxygen/images/bconds.png → doxygen/attic/images/bconds.png b/doxygen/images/bconds.png → doxygen/attic/images/bconds.png
diff --git a/doxygen/images/compose_figures.pptx → doxygen/attic/images/compose_figures.pptx b/doxygen/images/compose_figures.pptx → doxygen/attic/images/compose_figures.pptx
diff --git a/doxygen/images/core.png → doxygen/attic/images/core.png b/doxygen/images/core.png → doxygen/attic/images/core.png
diff --git a/doxygen/images/dmc_algo.png → doxygen/attic/images/dmc_algo.png b/doxygen/images/dmc_algo.png → doxygen/attic/images/dmc_algo.png
diff --git a/doxygen/images/driver_class.png → doxygen/attic/images/driver_class.png b/doxygen/images/driver_class.png → doxygen/attic/images/driver_class.png
diff --git a/doxygen/images/e_block.eps → doxygen/attic/images/e_block.eps b/doxygen/images/e_block.eps → doxygen/attic/images/e_block.eps
diff --git a/doxygen/images/e_block.pdf → doxygen/attic/images/e_block.pdf b/doxygen/images/e_block.pdf → doxygen/attic/images/e_block.pdf
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diff --git a/doxygen/images/e_trace.pdf → doxygen/attic/images/e_trace.pdf b/doxygen/images/e_trace.pdf → doxygen/attic/images/e_trace.pdf
diff --git a/doxygen/images/e_trace.png → doxygen/attic/images/e_trace.png b/doxygen/images/e_trace.png → doxygen/attic/images/e_trace.png
diff --git a/doxygen/images/eclipse_build_panel.png → doxygen/attic/images/eclipse_build_panel.png b/doxygen/images/eclipse_build_panel.png → doxygen/attic/images/eclipse_build_panel.png
diff --git a/...en/images/eclipse_build_panel_comment.png → ...ic/images/eclipse_build_panel_comment.png b/...en/images/eclipse_build_panel_comment.png → ...ic/images/eclipse_build_panel_comment.png
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diff --git a/doxygen/images/finite-size-scaling.eps → doxygen/attic/images/finite-size-scaling.eps b/doxygen/images/finite-size-scaling.eps → doxygen/attic/images/finite-size-scaling.eps
diff --git a/doxygen/images/finite-size-scaling.png → doxygen/attic/images/finite-size-scaling.png b/doxygen/images/finite-size-scaling.png → doxygen/attic/images/finite-size-scaling.png
diff --git a/doxygen/images/h_calltree.png → doxygen/attic/images/h_calltree.png b/doxygen/images/h_calltree.png → doxygen/attic/images/h_calltree.png
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diff --git a/doxygen/images/ham_xml.png → doxygen/attic/images/ham_xml.png b/doxygen/images/ham_xml.png → doxygen/attic/images/ham_xml.png
diff --git a/doxygen/images/mcconfig.png → doxygen/attic/images/mcconfig.png b/doxygen/images/mcconfig.png → doxygen/attic/images/mcconfig.png
diff --git a/doxygen/images/mpi_openmp_objects.pdf → doxygen/attic/images/mpi_openmp_objects.pdf b/doxygen/images/mpi_openmp_objects.pdf → doxygen/attic/images/mpi_openmp_objects.pdf
diff --git a/doxygen/images/mpi_openmp_objects.png → doxygen/attic/images/mpi_openmp_objects.png b/doxygen/images/mpi_openmp_objects.png → doxygen/attic/images/mpi_openmp_objects.png
diff --git a/doxygen/images/opt-conv.eps → doxygen/attic/images/opt-conv.eps b/doxygen/images/opt-conv.eps → doxygen/attic/images/opt-conv.eps
diff --git a/doxygen/images/opt-conv.png → doxygen/attic/images/opt-conv.png b/doxygen/images/opt-conv.png → doxygen/attic/images/opt-conv.png
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diff --git a/doxygen/images/qmc_workflow.png → doxygen/attic/images/qmc_workflow.png b/doxygen/images/qmc_workflow.png → doxygen/attic/images/qmc_workflow.png
diff --git a/doxygen/images/qmcdrivers.png → doxygen/attic/images/qmcdrivers.png b/doxygen/images/qmcdrivers.png → doxygen/attic/images/qmcdrivers.png
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diff --git a/doxygen/images/sampleinput.pdf → doxygen/attic/images/sampleinput.pdf b/doxygen/images/sampleinput.pdf → doxygen/attic/images/sampleinput.pdf
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diff --git a/doxygen/input_opt.tex → doxygen/attic/input_opt.tex b/doxygen/input_opt.tex → doxygen/attic/input_opt.tex
diff --git a/doxygen/input_qmc.tex → doxygen/attic/input_qmc.tex b/doxygen/input_qmc.tex → doxygen/attic/input_qmc.tex
diff --git a/doxygen/intro.tex → doxygen/attic/intro.tex b/doxygen/intro.tex → doxygen/attic/intro.tex
diff --git a/doxygen/intro_advanced.tex → doxygen/attic/intro_advanced.tex b/doxygen/intro_advanced.tex → doxygen/attic/intro_advanced.tex
diff --git a/doxygen/intro_io.tex → doxygen/attic/intro_io.tex b/doxygen/intro_io.tex → doxygen/attic/intro_io.tex
diff --git a/doxygen/myfooter.html → doxygen/attic/myfooter.html b/doxygen/myfooter.html → doxygen/attic/myfooter.html
diff --git a/doxygen/myheader.html → doxygen/attic/myheader.html b/doxygen/myheader.html → doxygen/attic/myheader.html
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