From 7bc71b5c34acd5abba6b3e46d3f5bf129b137400 Mon Sep 17 00:00:00 2001 From: Jon Rood Date: Tue, 24 Sep 2024 12:22:07 -0600 Subject: [PATCH] Move docs to gh-pages (#1307) --- .github/problem-matchers/gcc.json | 18 + .github/problem-matchers/sphinx.json | 40 ++ .github/workflows/docs.yml | 57 +++ CMakeLists.txt | 6 - docs/CMakeLists.txt | 62 --- docs/Doxyfile.breathe.in | 39 -- docs/_static/.blank | 1 - docs/conf.py | 237 ------------ docs/{Doxyfile.in => doxygen/Doxyfile} | 319 ++++++++++------ docs/requirements.txt | 6 - docs/sphinx/conf.py | 356 ++++++++++++++++++ docs/{ => sphinx}/index.rst | 0 docs/{ => sphinx}/naluLowMach.jpg | Bin docs/{ => sphinx}/references/references.bib | 0 .../developer/apidocs/actuatorsources.rst | 0 .../source/developer/apidocs/eqsystems.rst | 0 .../source/developer/apidocs/linsys.rst | 0 .../source/developer/apidocs/masterelem.rst | 0 .../source/developer/apidocs/postprocess.rst | 0 .../source/developer/apidocs/realms.rst | 0 .../source/developer/apidocs/userfunc.rst | 0 .../source/developer/build_doc.rst | 0 docs/{ => sphinx}/source/developer/code.rst | 0 .../{ => sphinx}/source/developer/contrib.rst | 0 .../source/developer/dox_example/example.h | 0 .../dox_example/xml/class_example_class.xml | 0 .../developer/dox_example/xml/combine.xslt | 0 .../developer/dox_example/xml/compound.xsd | 0 .../developer/dox_example/xml/example_8h.xml | 0 .../developer/dox_example/xml/index.xml | 0 .../developer/dox_example/xml/index.xsd | 0 .../dox_example/xml/namespacestd.xml | 0 docs/{ => sphinx}/source/developer/index.rst | 0 docs/{ => sphinx}/source/developer/infra.rst | 0 .../source/developer/mainpage.dox | 0 docs/{ => sphinx}/source/developer/style.rst | 0 .../{ => sphinx}/source/developer/testing.rst | 0 .../source/developer/workflow.rst | 0 .../source/developer/write_developer_doc.rst | 0 .../source/developer/write_user_doc.rst | 0 .../{ => sphinx}/source/theory/adaptivity.rst | 0 .../source/theory/advectionStabilization.rst | 0 .../source/theory/amsAbl_ransBelowKs.yaml | 0 .../source/theory/boundaryConditions.rst | 0 .../source/theory/codeAbstractions.rst | 0 .../source/theory/couplingApproach.rst | 0 .../source/theory/discretizationApproach.rst | 0 .../source/theory/images/actuatorDisk.png | Bin .../theory/images/contactSearchAndEval.pdf | Bin .../source/theory/images/cvfem_conv.png | Bin .../source/theory/images/cvfem_nodes.png | Bin .../source/theory/images/cvfem_onecv.png | Bin .../source/theory/images/cylinder_overset.png | Bin .../source/theory/images/dgHex8Tet4Duct.png | Bin .../source/theory/images/dgQuad4Quad9MMS.png | Bin .../source/theory/images/hadapt.pdf | Bin .../source/theory/images/hadapt2.pdf | Bin .../source/theory/images/hadapt3.pdf | Bin .../{ => sphinx}/source/theory/images/hex.pdf | Bin .../source/theory/images/ordinate.pdf | Bin .../theory/images/oversetBlockOneTwo.png | Bin .../theory/images/oversetBlockOneTwoCut.png | Bin .../source/theory/images/oversetHC.png | Bin .../source/theory/images/oversetNodes.png | Bin .../source/theory/images/oversetSphere.png | Bin .../source/theory/images/pecletFactor.pdf | Bin .../source/theory/images/quadel.pdf | Bin .../source/theory/images/rotbox_overset.png | Bin .../theory/images/tioga_cyl_velocity.png | Bin .../theory/images/tioga_cyl_vorticity.png | Bin .../source/theory/images/twoBlockDiag.pdf | Bin .../source/theory/images/we_cvfem_p1.png | Bin docs/{ => sphinx}/source/theory/index.rst | 0 .../source/theory/lowMachNumberDerivation.rst | 0 .../source/theory/multiPhysics.rst | 0 docs/{ => sphinx}/source/theory/nso.rst | 0 docs/{ => sphinx}/source/theory/overset.rst | 0 .../source/theory/pressureStabilization.rst | 0 .../source/theory/propertyEvaluation.rst | 0 .../source/theory/ransAbl_momentum.yaml | 0 .../source/theory/ransAbl_wallUserData.yaml | 0 .../source/theory/rteStabilization.rst | 0 .../source/theory/supportedEquationSet.rst | 0 docs/{ => sphinx}/source/theory/symmetry.yaml | 0 .../source/theory/timeDiscretization.rst | 0 .../source/theory/topologicalSupport.rst | 0 .../source/theory/turbulenceModeling.rst | 0 .../{ => sphinx}/source/theory/windEnergy.rst | 0 .../source/user/build_manually.rst | 0 docs/{ => sphinx}/source/user/build_spack.rst | 0 docs/{ => sphinx}/source/user/building.rst | 0 .../source/user/do-config-nalu-wind.sh | 0 .../source/user/do-config-trilinos.sh | 0 docs/{ => sphinx}/source/user/index.rst | 0 .../user/nalu_run/McAlisterLessonsLearned.rst | 0 .../source/user/nalu_run/abl_forcing.rst | 0 .../source/user/nalu_run/figures/ramp.png | Bin .../nalu_run/grid07_conformal10_surf_tip.png | Bin .../grid07_conformal10_surf_tip_close.png | Bin docs/{ => sphinx}/source/user/nalu_run/nalu.i | 0 .../source/user/nalu_run/nalu_inp.rst | 0 .../source/user/nalu_run/nalu_mesh.rst | 0 .../source/user/nalu_run/nalux.rst | 0 .../source/user/nalu_run/turbine_modeling.rst | 0 docs/{ => sphinx}/source/user/running.rst | 0 .../source/user/verify_installation.rst | 0 .../source/verification/figures/T_123.png | Bin .../verification/figures/T_linear_gradBC.png | Bin .../figures/T_parabolic_gradBC.png | Bin .../figures/U_x_CTV_subsequent_L2.pdf | Bin .../verification/figures/U_x_precursor.pdf | Bin .../source/verification/figures/Ux_123.png | Bin .../source/verification/figures/Ux_23.png | Bin .../source/verification/figures/Uz_L2_dp.pdf | Bin .../figures/abl_sub_check_one_two.png | Bin .../verification/figures/abl_sub_cycle_T.pdf | Bin .../figures/convTaylorVortexFO.pdf | Bin .../figures/convTaylorVortexSO.pdf | Bin .../convTaylorVortexSO_ElemLagElemPf.pdf | Bin .../dgNonconformalCVFEM_3dTempMMS_OoC.pdf | Bin .../dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf | Bin ...gNonconformalCVFEM_3dTempMMS_tempField.pdf | Bin .../source/verification/figures/ew_aoa.pdf | Bin .../verification/figures/ew_dragcoeff.pdf | Bin .../figures/ew_dragforceperunitlength.pdf | Bin .../verification/figures/ew_liftcoeff.pdf | Bin .../figures/ew_liftforceperunitlength.pdf | Bin .../verification/figures/fw_bladeresults.png | Bin .../figures/fw_bladeschematic.png | Bin .../figures/hex8_tet4_one_two_ten_R0_R1.png | Bin .../figures/ho_heatCondMMM_dtdx.pdf | Bin .../verification/figures/ho_stvUandDpDx.pdf | Bin .../verification/figures/hybrid_T_L2.pdf | Bin .../verification/figures/hybrid_T_Loo.pdf | Bin .../verification/figures/hybrid_laplace.png | Bin .../verification/figures/openJetFlowStill.pdf | Bin .../verification/figures/openJetInlet.pdf | Bin .../figures/tquadEdgeCvfemTdiff.pdf | Bin .../verification/figures/tquadLaplaceMMS.pdf | Bin .../figures/tquadLaplaceMMSCVFEM.pdf | Bin .../source/verification/index.rst | 0 .../source/verification/introduction.rst | 0 .../source/verification/verification.rst | 0 docs/{ => sphinx}/zrefs.rst | 0 144 files changed, 665 insertions(+), 476 deletions(-) create mode 100644 .github/problem-matchers/gcc.json create mode 100644 .github/problem-matchers/sphinx.json create mode 100644 .github/workflows/docs.yml delete mode 100644 docs/CMakeLists.txt delete mode 100644 docs/Doxyfile.breathe.in delete mode 100644 docs/_static/.blank delete mode 100644 docs/conf.py rename docs/{Doxyfile.in => doxygen/Doxyfile} (91%) delete mode 100644 docs/requirements.txt create mode 100644 docs/sphinx/conf.py rename docs/{ => sphinx}/index.rst (100%) rename docs/{ => sphinx}/naluLowMach.jpg (100%) rename docs/{ => sphinx}/references/references.bib (100%) rename docs/{ => sphinx}/source/developer/apidocs/actuatorsources.rst (100%) rename docs/{ => sphinx}/source/developer/apidocs/eqsystems.rst (100%) rename docs/{ => sphinx}/source/developer/apidocs/linsys.rst (100%) rename docs/{ => sphinx}/source/developer/apidocs/masterelem.rst (100%) rename docs/{ => sphinx}/source/developer/apidocs/postprocess.rst (100%) rename docs/{ => sphinx}/source/developer/apidocs/realms.rst (100%) rename docs/{ => sphinx}/source/developer/apidocs/userfunc.rst (100%) rename docs/{ => sphinx}/source/developer/build_doc.rst (100%) rename docs/{ => sphinx}/source/developer/code.rst (100%) rename docs/{ => sphinx}/source/developer/contrib.rst (100%) rename docs/{ => sphinx}/source/developer/dox_example/example.h (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/class_example_class.xml (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/combine.xslt (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/compound.xsd (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/example_8h.xml (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/index.xml (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/index.xsd (100%) rename docs/{ => sphinx}/source/developer/dox_example/xml/namespacestd.xml (100%) rename docs/{ => sphinx}/source/developer/index.rst (100%) rename docs/{ => sphinx}/source/developer/infra.rst (100%) rename docs/{ => sphinx}/source/developer/mainpage.dox (100%) rename docs/{ => sphinx}/source/developer/style.rst (100%) rename docs/{ => sphinx}/source/developer/testing.rst (100%) rename docs/{ => sphinx}/source/developer/workflow.rst (100%) rename docs/{ => sphinx}/source/developer/write_developer_doc.rst (100%) rename docs/{ => sphinx}/source/developer/write_user_doc.rst (100%) rename docs/{ => sphinx}/source/theory/adaptivity.rst (100%) rename docs/{ => sphinx}/source/theory/advectionStabilization.rst (100%) rename docs/{ => sphinx}/source/theory/amsAbl_ransBelowKs.yaml (100%) rename docs/{ => sphinx}/source/theory/boundaryConditions.rst (100%) rename docs/{ => sphinx}/source/theory/codeAbstractions.rst (100%) rename docs/{ => sphinx}/source/theory/couplingApproach.rst (100%) rename docs/{ => sphinx}/source/theory/discretizationApproach.rst (100%) rename docs/{ => sphinx}/source/theory/images/actuatorDisk.png (100%) rename docs/{ => sphinx}/source/theory/images/contactSearchAndEval.pdf (100%) rename docs/{ => sphinx}/source/theory/images/cvfem_conv.png (100%) rename docs/{ => sphinx}/source/theory/images/cvfem_nodes.png (100%) rename docs/{ => sphinx}/source/theory/images/cvfem_onecv.png (100%) rename docs/{ => sphinx}/source/theory/images/cylinder_overset.png (100%) rename docs/{ => sphinx}/source/theory/images/dgHex8Tet4Duct.png (100%) rename docs/{ => sphinx}/source/theory/images/dgQuad4Quad9MMS.png (100%) rename docs/{ => sphinx}/source/theory/images/hadapt.pdf (100%) rename docs/{ => sphinx}/source/theory/images/hadapt2.pdf (100%) rename docs/{ => sphinx}/source/theory/images/hadapt3.pdf (100%) rename docs/{ => sphinx}/source/theory/images/hex.pdf (100%) rename docs/{ => sphinx}/source/theory/images/ordinate.pdf (100%) rename docs/{ => sphinx}/source/theory/images/oversetBlockOneTwo.png (100%) rename docs/{ => sphinx}/source/theory/images/oversetBlockOneTwoCut.png (100%) rename docs/{ => sphinx}/source/theory/images/oversetHC.png (100%) rename docs/{ => sphinx}/source/theory/images/oversetNodes.png (100%) rename docs/{ => sphinx}/source/theory/images/oversetSphere.png (100%) rename docs/{ => sphinx}/source/theory/images/pecletFactor.pdf (100%) rename docs/{ => sphinx}/source/theory/images/quadel.pdf (100%) rename docs/{ => sphinx}/source/theory/images/rotbox_overset.png (100%) rename docs/{ => sphinx}/source/theory/images/tioga_cyl_velocity.png (100%) rename docs/{ => sphinx}/source/theory/images/tioga_cyl_vorticity.png (100%) rename docs/{ => sphinx}/source/theory/images/twoBlockDiag.pdf (100%) rename docs/{ => sphinx}/source/theory/images/we_cvfem_p1.png (100%) rename docs/{ => sphinx}/source/theory/index.rst (100%) rename docs/{ => sphinx}/source/theory/lowMachNumberDerivation.rst (100%) rename docs/{ => sphinx}/source/theory/multiPhysics.rst (100%) rename docs/{ => sphinx}/source/theory/nso.rst (100%) rename docs/{ => sphinx}/source/theory/overset.rst (100%) rename docs/{ => sphinx}/source/theory/pressureStabilization.rst (100%) rename docs/{ => sphinx}/source/theory/propertyEvaluation.rst (100%) rename docs/{ => sphinx}/source/theory/ransAbl_momentum.yaml (100%) rename docs/{ => sphinx}/source/theory/ransAbl_wallUserData.yaml (100%) rename docs/{ => sphinx}/source/theory/rteStabilization.rst (100%) rename docs/{ => sphinx}/source/theory/supportedEquationSet.rst (100%) rename docs/{ => sphinx}/source/theory/symmetry.yaml (100%) rename docs/{ => sphinx}/source/theory/timeDiscretization.rst (100%) rename docs/{ => sphinx}/source/theory/topologicalSupport.rst (100%) rename docs/{ => sphinx}/source/theory/turbulenceModeling.rst (100%) rename docs/{ => sphinx}/source/theory/windEnergy.rst (100%) rename docs/{ => sphinx}/source/user/build_manually.rst (100%) rename docs/{ => sphinx}/source/user/build_spack.rst (100%) rename docs/{ => sphinx}/source/user/building.rst (100%) rename docs/{ => sphinx}/source/user/do-config-nalu-wind.sh (100%) rename docs/{ => sphinx}/source/user/do-config-trilinos.sh (100%) rename docs/{ => sphinx}/source/user/index.rst (100%) rename docs/{ => sphinx}/source/user/nalu_run/McAlisterLessonsLearned.rst (100%) rename docs/{ => sphinx}/source/user/nalu_run/abl_forcing.rst (100%) rename docs/{ => sphinx}/source/user/nalu_run/figures/ramp.png (100%) rename docs/{ => sphinx}/source/user/nalu_run/grid07_conformal10_surf_tip.png (100%) rename docs/{ => sphinx}/source/user/nalu_run/grid07_conformal10_surf_tip_close.png (100%) rename docs/{ => sphinx}/source/user/nalu_run/nalu.i (100%) rename docs/{ => sphinx}/source/user/nalu_run/nalu_inp.rst (100%) rename docs/{ => sphinx}/source/user/nalu_run/nalu_mesh.rst (100%) rename docs/{ => sphinx}/source/user/nalu_run/nalux.rst (100%) rename docs/{ => sphinx}/source/user/nalu_run/turbine_modeling.rst (100%) rename docs/{ => sphinx}/source/user/running.rst (100%) rename docs/{ => sphinx}/source/user/verify_installation.rst (100%) rename docs/{ => sphinx}/source/verification/figures/T_123.png (100%) rename docs/{ => sphinx}/source/verification/figures/T_linear_gradBC.png (100%) rename docs/{ => sphinx}/source/verification/figures/T_parabolic_gradBC.png (100%) rename docs/{ => sphinx}/source/verification/figures/U_x_CTV_subsequent_L2.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/U_x_precursor.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/Ux_123.png (100%) rename docs/{ => sphinx}/source/verification/figures/Ux_23.png (100%) rename docs/{ => sphinx}/source/verification/figures/Uz_L2_dp.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/abl_sub_check_one_two.png (100%) rename docs/{ => sphinx}/source/verification/figures/abl_sub_cycle_T.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/convTaylorVortexFO.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/convTaylorVortexSO.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/convTaylorVortexSO_ElemLagElemPf.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoC.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_tempField.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/ew_aoa.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/ew_dragcoeff.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/ew_dragforceperunitlength.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/ew_liftcoeff.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/ew_liftforceperunitlength.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/fw_bladeresults.png (100%) rename docs/{ => sphinx}/source/verification/figures/fw_bladeschematic.png (100%) rename docs/{ => sphinx}/source/verification/figures/hex8_tet4_one_two_ten_R0_R1.png (100%) rename docs/{ => sphinx}/source/verification/figures/ho_heatCondMMM_dtdx.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/ho_stvUandDpDx.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/hybrid_T_L2.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/hybrid_T_Loo.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/hybrid_laplace.png (100%) rename docs/{ => sphinx}/source/verification/figures/openJetFlowStill.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/openJetInlet.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/tquadEdgeCvfemTdiff.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/tquadLaplaceMMS.pdf (100%) rename docs/{ => sphinx}/source/verification/figures/tquadLaplaceMMSCVFEM.pdf (100%) rename docs/{ => sphinx}/source/verification/index.rst (100%) rename docs/{ => sphinx}/source/verification/introduction.rst (100%) rename docs/{ => sphinx}/source/verification/verification.rst (100%) rename docs/{ => sphinx}/zrefs.rst (100%) diff --git a/.github/problem-matchers/gcc.json b/.github/problem-matchers/gcc.json new file mode 100644 index 000000000..9ab06796a --- /dev/null +++ b/.github/problem-matchers/gcc.json @@ -0,0 +1,18 @@ +{ + "__comment": "Taken from vscode-cpptools's Extension/package.json gcc rule", + "problemMatcher": [ + { + "owner": "gcc-problem-matcher", + "pattern": [ + { + "regexp": "^(.*):(\\d+):(\\d+):\\s+(?:fatal\\s+)?(warning|error):\\s+(.*)$", + "file": 1, + "line": 2, + "column": 3, + "severity": 4, + "message": 5 + } + ] + } + ] +} diff --git a/.github/problem-matchers/sphinx.json b/.github/problem-matchers/sphinx.json new file mode 100644 index 000000000..6fcd3884e --- /dev/null +++ b/.github/problem-matchers/sphinx.json @@ -0,0 +1,40 @@ +{ + "problemMatcher": [ + { + "owner": "sphinx-problem-matcher", + "pattern": [ + { + "regexp": "^(.*):(\\d+):\\s+(\\w*):\\s+(.*)$", + "file": 1, + "line": 2, + "severity": 3, + "message": 4 + } + ] + }, + { + "owner": "sphinx-problem-matcher-loose", + "pattern": [ + { + "_comment": "A bit of a looser pattern, doesn't look for line numbers, just looks for file names relying on them to start with / and end with .rst", + "regexp": "(\/.*\\.rst):\\s+(\\w*):\\s+(.*)$", + "file": 1, + "severity": 2, + "message": 3 + } + ] + }, + { + "owner": "sphinx-problem-matcher-loose-no-severity", + "pattern": [ + { + "_comment": "Looks for file names ending with .rst and line numbers but without severity", + "regexp": "^(.*\\.rst):(\\d+):(.*)$", + "file": 1, + "line": 2, + "message": 3 + } + ] + } + ] +} diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml new file mode 100644 index 000000000..0d631d8ed --- /dev/null +++ b/.github/workflows/docs.yml @@ -0,0 +1,57 @@ +name: Nalu-Wind-Docs + +on: + push: + branches: [main] + pull_request: + branches: [main] + +concurrency: + group: ${{github.ref}}-${{github.head_ref}}-docs + cancel-in-progress: true + +jobs: + Docs: + runs-on: ubuntu-latest + steps: + - name: Clone + uses: actions/checkout@v4 + - name: Python + uses: actions/setup-python@v5 + with: + python-version: '3.x' + - name: Dependencies + run: | + export DEBIAN_FRONTEND=noninteractive + sudo apt-get update + sudo apt-get install -y --no-install-recommends doxygen graphviz + python3 -m pip install --upgrade pip + pip3 install sphinx sphinx_rtd_theme + - name: Build + # execute from top-level nalu-wind directory + run: | + echo "::add-matcher::.github/problem-matchers/sphinx.json" + sphinx-build -M html ./docs/sphinx ./build_docs/manual -W --keep-going -n 2>&1 | tee -a build-output.txt + # Doxygen output gets parsed wrong by the sphinx problem matcher so unregister it + echo "::remove-matcher owner=sphinx-problem-matcher-loose-no-severity::" + echo "::remove-matcher owner=sphinx-problem-matcher-loose::" + echo "::remove-matcher owner=sphinx-problem-matcher::" + doxygen ./docs/doxygen/Doxyfile + mv ./build_docs/manual/html ./documentation + mv ./build_docs/doxygen/html ./documentation/api_docs + touch ./documentation/.nojekyll + - name: Report + run: | + echo "::add-matcher::.github/problem-matchers/sphinx.json" + egrep "WARNING:" build-output.txt | sort | uniq | \ + awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > build-output-warnings.txt + cat build-output-warnings.txt + exit $(tail -n 1 build-output-warnings.txt | awk '{print $2}') + - name: Deploy + if: github.event_name == 'push' + uses: JamesIves/github-pages-deploy-action@releases/v3 + with: + GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} + BRANCH: gh-pages + FOLDER: documentation + SINGLE_COMMIT: true diff --git a/CMakeLists.txt b/CMakeLists.txt index 0058b0e90..5b9c2c72a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -10,8 +10,6 @@ option(ENABLE_ROCM "Enable build targeting AMD GPU" OFF) option(ENABLE_UMPIRE "Enable Umpire GPU memory pools" OFF) option(ENABLE_TESTS "Enable regression testing." OFF) option(ENABLE_UNIT_TESTS "Enable unit testing." ON) -option(ENABLE_DOCUMENTATION "Build documentation." OFF) -option(ENABLE_SPHINX_API_DOCS "Link Doxygen API docs to Sphinx" OFF) option(ENABLE_WIND_UTILS "Build wind utils along with Nalu-Wind" OFF) option(ENABLE_FFTW "Use the FFTW library to support ABLTopBC" OFF) option(ENABLE_HYPRE "Use HYPRE Solver library" ON) @@ -313,10 +311,6 @@ endif() include(CMakePackageConfigHelpers) include(GNUInstallDirs) -if(ENABLE_DOCUMENTATION) - add_subdirectory(docs) -endif() - if(ENABLE_TESTS) enable_testing() include(CTest) diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt deleted file mode 100644 index 859f4143b..000000000 --- a/docs/CMakeLists.txt +++ /dev/null @@ -1,62 +0,0 @@ -find_package(Doxygen) -find_package(Sphinx) - -if (DOXYGEN_FOUND OR SPHINX_FOUND) - add_custom_target(docs) -endif() - -if(DOXYGEN_FOUND) - configure_file(Doxyfile.in Doxyfile @ONLY) - add_custom_target(doxygen - COMMAND ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile" ) - add_dependencies(docs doxygen) -else() - message(WARNING "Skipping Doxygen documentation due to missing dependencies.") -endif() - -if(SPHINX_FOUND) - find_package(LATEX COMPONENTS PDFLATEX BIBTEX) - if (ENABLE_SPHINX_API_DOCS) - set(SPHINX_OPTS "-t" "use_breathe") - configure_file(Doxyfile.breathe.in Doxyfile.breathe @ONLY) - add_custom_command( - OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/doxygen/xml/index.xml - DEPENDS ${HEADER} - COMMAND ${DOXYGEN_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile.breathe") - set_source_files_properties( - ${CMAKE_CURRENT_BINARY_DIR}/doxygen/xml/index.xml - PROPERTIES GENERATED TRUE) - add_custom_target(sphinx - DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/doxygen/xml/index.xml - COMMAND ${SPHINX_EXECUTABLE} -M html - "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_BINARY_DIR}" - -c ${CMAKE_CURRENT_SOURCE_DIR} ${SPHINX_OPTS}) - add_dependencies(docs sphinx) - - # PDF documentation generation using sphinx -> latex -> pdflatex - if (LATEX_FOUND) - add_custom_target(sphinx-pdf - DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/doxygen/xml/index.xml - COMMAND ${SPHINX_EXECUTABLE} -M latexpdf - "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_BINARY_DIR}" - -c ${CMAKE_CURRENT_SOURCE_DIR} ${SPHINX_OPTS}) - endif() - else() - set(SPHINX_OPTS "") - add_custom_target(sphinx - COMMAND ${SPHINX_EXECUTABLE} -M html - "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_BINARY_DIR}" - -c ${CMAKE_CURRENT_SOURCE_DIR} ${SPHINX_OPTS}) - add_dependencies(docs sphinx) - - # PDF documentation generation using sphinx -> latex -> pdflatex - if (LATEX_FOUND) - add_custom_target(sphinx-pdf - COMMAND ${SPHINX_EXECUTABLE} -M latexpdf - "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_BINARY_DIR}" - -c ${CMAKE_CURRENT_SOURCE_DIR} ${SPHINX_OPTS}) - endif() - endif() -else() - message(WARNING "Skipping Sphinx documentation due to missing dependencies.") -endif() diff --git a/docs/Doxyfile.breathe.in b/docs/Doxyfile.breathe.in deleted file mode 100644 index 33df87447..000000000 --- a/docs/Doxyfile.breathe.in +++ /dev/null @@ -1,39 +0,0 @@ -# Minimal Doxygen configuration to interface with Sphinx Breathe - -DOXYFILE_ENCODING = UTF-8 -PROJECT_NAME = "Nalu-Wind" -JAVADOC_AUTOBRIEF = YES -QT_AUTOBRIEF = YES -MARKDOWN_SUPPORT = YES -BUILTIN_STL_SUPPORT = YES -EXTRACT_ALL = YES -EXTRACT_PRIVATE = YES -EXTRACT_PACKAGE = YES -EXTRACT_STATIC = YES -EXTRACT_LOCAL_CLASSES = YES -EXTRACT_ANON_NSPACES = NO -HAVE_DOT = NO -GENERATE_TODOLIST = NO -GENERATE_TESTLIST = NO -GENERATE_BUGLIST = NO -GENERATE_HTML = NO -GENERATE_DOCSET = NO -GENERATE_HTMLHELP = NO -GENERATE_CHI = NO -GENERATE_QHP = NO -GENERATE_ECLIPSEHELP = NO -GENERATE_TREEVIEW = NO -GENERATE_LATEX = NO -GENERATE_RTF = NO -GENERATE_MAN = NO -GENERATE_DOCBOOK = NO -GENERATE_AUTOGEN_DEF = NO -GENERATE_PERLMOD = NO -QUIET = YES -WARNINGS = NO -GENERATE_XML = YES - -FILE_PATTERNS = *.h *.hpp *.H -RECURSIVE = YES -INPUT = @CMAKE_SOURCE_DIR@/include -OUTPUT_DIRECTORY = @CMAKE_BINARY_DIR@/docs/doxygen diff --git a/docs/_static/.blank b/docs/_static/.blank deleted file mode 100644 index 5a5329651..000000000 --- a/docs/_static/.blank +++ /dev/null @@ -1 +0,0 @@ -Need this file so I can check in a blank _static directory. diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 198efab21..000000000 --- a/docs/conf.py +++ /dev/null @@ -1,237 +0,0 @@ -# -*- coding: utf-8 -*- -# -# Nalu-Wind documentation build configuration file, created by -# sphinx-quickstart on Wed Jan 25 13:52:07 2017. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# 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. - -import os -import sys -import subprocess -import re - -#sys.path.append(os.path.abspath('_extensions/')) - -readTheDocs = os.environ.get('READTHEDOCS', None) == 'True' -# Only link to API docs if the user specifically requests it. On RTD build it by default -use_breathe = tags.has("use_breathe") or readTheDocs - -if readTheDocs: - sourcedir = sys.argv[-2] - builddir = sys.argv[-1] -elif use_breathe: - sourcedir = sys.argv[-6] - builddir = sys.argv[-5] -else: - sourcedir = sys.argv[-2] - builddir = sys.argv[-1] - - -# This function was adapted from https://gitlab.kitware.com/cmb/smtk -# Only run when on readthedocs -def runDoxygen(doxyfileIn, doxyfileOut): - dx = open(os.path.join(sourcedir, doxyfileIn), 'r') - cfg = dx.read() - srcdir = os.path.abspath(os.path.join(os.getcwd(), os.pardir)) - bindir = srcdir - c2 = re.sub('@CMAKE_SOURCE_DIR@', srcdir, - re.sub('@CMAKE_BINARY_DIR@', bindir, cfg)) - doxname = os.path.join(sourcedir, doxyfileOut) - with open(doxname, 'w') as fh: - fh.write(c2) - print('Running Doxygen on %s' % doxyfileOut) - try: - subprocess.call(('doxygen', doxname)) - except: - # Gracefully bailout if doxygen encounters errors - use_breathe = False - -if readTheDocs: - runDoxygen('Doxyfile.breathe.in', 'Doxyfile') - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.5.2' - -# 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', - 'sphinx.ext.autosummary', - 'sphinx.ext.mathjax', - 'sphinx.ext.intersphinx', - 'sphinxcontrib.bibtex', - ] -bibtex_bibfiles = ['references/references.bib'] - -if use_breathe: - extensions.append('breathe') - -autodoc_default_flags = ['members','show-inheritance','undoc-members'] - -autoclass_content = 'both' - -mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' - - -# Add any paths that contain templates here, relative to this directory. -#templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = ['.rst'] - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = u'Nalu-Wind' -copyright = u'2019, Nalu-Wind Development Team' -author = u'Nalu-Wind Team' - -# 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. -# -# The short X.Y version. -version = u'1.2.0' -# The full version, including alpha/beta/rc tags. -release = u'1.2.0' - -# 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 = None -numfig = True - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - -# 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 = 'bizstyle' -if readTheDocs: - html_theme = 'default' -else: - html_theme = 'sphinx_rtd_theme' -html_logo = 'naluLowMach.jpg' - -# 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 = {} - -# 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'] - - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = 'Naludoc' - - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'Nalu.tex', u'Nalu-Wind Documentation', - u'Nalu-Wind Development Team', '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, 'nalu', u'Nalu-Wind 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, 'Nalu', u'Nalu-Wind Documentation', - author, 'Nalu', 'One line description of project.', - 'Miscellaneous'), -] - -# Breathe options -breathe_projects = { - 'nalu' : os.path.join(sourcedir if readTheDocs else builddir, - 'doxygen', 'xml'), - 'example_cpp' : os.path.join(sourcedir, - 'source', 'developer', 'dox_example', 'xml') -} - -# Assign nalu to be the default project -breathe_default_project = "nalu" - -# Set primary language to C++ for documentation instead of default `py:` -primary_domain = "cpp" - -def setup(app): - app.add_object_type("inpfile", "inpfile", - objname="Nalu-Wind Input File Parameter", - indextemplate="pair: %s; Nalu-Wind Input File Parameter") - - app.add_config_value("use_breathe", use_breathe, 'env') - app.add_config_value("on_rtd", readTheDocs, 'env') diff --git a/docs/Doxyfile.in b/docs/doxygen/Doxyfile similarity index 91% rename from docs/Doxyfile.in rename to docs/doxygen/Doxyfile index c9214b02d..69c1eb824 100644 --- a/docs/Doxyfile.in +++ b/docs/doxygen/Doxyfile @@ -1,4 +1,4 @@ -# Doxyfile 1.8.13 +# Doxyfile 1.8.17 # This file describes the settings to be used by the documentation system # doxygen (www.doxygen.org) for a project. @@ -17,11 +17,11 @@ # Project related configuration options #--------------------------------------------------------------------------- -# This tag specifies the encoding used for all characters in the config file -# that follow. The default is UTF-8 which is also the encoding used for all text -# before the first occurrence of this tag. Doxygen uses libiconv (or the iconv -# built into libc) for the transcoding. See http://www.gnu.org/software/libiconv -# for the list of possible encodings. +# This tag specifies the encoding used for all characters in the configuration +# file that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# https://www.gnu.org/software/libiconv/ for the list of possible encodings. # The default value is: UTF-8. DOXYFILE_ENCODING = UTF-8 @@ -38,27 +38,27 @@ PROJECT_NAME = "Nalu-Wind" # could be handy for archiving the generated documentation or if some version # control system is used. -PROJECT_NUMBER = +PROJECT_NUMBER = v0.1.0 # Using the PROJECT_BRIEF tag one can provide an optional one line description # for a project that appears at the top of each page and should give viewer a # quick idea about the purpose of the project. Keep the description short. -PROJECT_BRIEF = "A generalized unstructured massively parallel low Mach flow code designed to support a variety of energy applications of interest (most notably Wind ECP) built on the Sierra Toolkit and Trilinos solver Tpetra/Epetra stack. The open source BSD, clause 3 license model has been chosen for the code base. See LICENSE for more information." +PROJECT_BRIEF = "CFD solver for wind plant simulations" # With the PROJECT_LOGO tag one can specify a logo or an icon that is included # in the documentation. The maximum height of the logo should not exceed 55 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy # the logo to the output directory. -PROJECT_LOGO = @CMAKE_SOURCE_DIR@/docs/naluLowMach.jpg +PROJECT_LOGO = # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path # into which the generated documentation will be written. If a relative path is # entered, it will be relative to the location where doxygen was started. If -# left blank the current directory will be used. +# left blank the current directory will be used. -OUTPUT_DIRECTORY = @CMAKE_BINARY_DIR@/docs/doxygen +OUTPUT_DIRECTORY = ./build_docs/doxygen # If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- # directories (in 2 levels) under the output directory of each output format and @@ -93,6 +93,14 @@ ALLOW_UNICODE_NAMES = NO OUTPUT_LANGUAGE = English +# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all generated output in the proper direction. +# Possible values are: None, LTR, RTL and Context. +# The default value is: None. + +OUTPUT_TEXT_DIRECTION = None + # If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member # descriptions after the members that are listed in the file and class # documentation (similar to Javadoc). Set to NO to disable this. @@ -162,7 +170,7 @@ FULL_PATH_NAMES = NO # will be relative from the directory where doxygen is started. # This tag requires that the tag FULL_PATH_NAMES is set to YES. -STRIP_FROM_PATH = +STRIP_FROM_PATH = # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the # path mentioned in the documentation of a class, which tells the reader which @@ -171,7 +179,7 @@ STRIP_FROM_PATH = # specify the list of include paths that are normally passed to the compiler # using the -I flag. -STRIP_FROM_INC_PATH = +STRIP_FROM_INC_PATH = # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but # less readable) file names. This can be useful is your file systems doesn't @@ -189,6 +197,16 @@ SHORT_NAMES = NO JAVADOC_AUTOBRIEF = YES +# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line +# such as +# /*************** +# as being the beginning of a Javadoc-style comment "banner". If set to NO, the +# Javadoc-style will behave just like regular comments and it will not be +# interpreted by doxygen. +# The default value is: NO. + +JAVADOC_BANNER = NO + # If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first # line (until the first dot) of a Qt-style comment as the brief description. If # set to NO, the Qt-style will behave just like regular Qt-style comments (thus @@ -236,7 +254,12 @@ TAB_SIZE = 4 # will allow you to put the command \sideeffect (or @sideeffect) in the # documentation, which will result in a user-defined paragraph with heading # "Side Effects:". You can put \n's in the value part of an alias to insert -# newlines. +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. +# When you need a literal { or } or , in the value part of an alias you have to +# escape them by means of a backslash (\), this can lead to conflicts with the +# commands \{ and \} for these it is advised to use the version @{ and @} or use +# a double escape (\\{ and \\}) ALIASES = @@ -274,17 +297,26 @@ OPTIMIZE_FOR_FORTRAN = NO OPTIMIZE_OUTPUT_VHDL = NO +# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice +# sources only. Doxygen will then generate output that is more tailored for that +# language. For instance, namespaces will be presented as modules, types will be +# separated into more groups, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_SLICE = NO + # Doxygen selects the parser to use depending on the extension of the files it # parses. With this tag you can assign which parser to use for a given # extension. Doxygen has a built-in mapping, but you can override or extend it # using this tag. The format is ext=language, where ext is a file extension, and -# language is one of the parsers supported by doxygen: IDL, Java, Javascript, -# C#, C, C++, D, PHP, Objective-C, Python, Fortran (fixed format Fortran: -# FortranFixed, free formatted Fortran: FortranFree, unknown formatted Fortran: -# Fortran. In the later case the parser tries to guess whether the code is fixed -# or free formatted code, this is the default for Fortran type files), VHDL. For -# instance to make doxygen treat .inc files as Fortran files (default is PHP), -# and .f files as C (default is Fortran), use: inc=Fortran f=C. +# language is one of the parsers supported by doxygen: IDL, Java, JavaScript, +# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, +# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: +# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser +# tries to guess whether the code is fixed or free formatted code, this is the +# default for Fortran type files), VHDL, tcl. For instance to make doxygen treat +# .inc files as Fortran files (default is PHP), and .f files as C (default is +# Fortran), use: inc=Fortran f=C. # # Note: For files without extension you can use no_extension as a placeholder. # @@ -295,7 +327,7 @@ EXTENSION_MAPPING = # If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments # according to the Markdown format, which allows for more readable -# documentation. See http://daringfireball.net/projects/markdown/ for details. +# documentation. See https://daringfireball.net/projects/markdown/ for details. # The output of markdown processing is further processed by doxygen, so you can # mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in # case of backward compatibilities issues. @@ -307,10 +339,10 @@ MARKDOWN_SUPPORT = YES # to that level are automatically included in the table of contents, even if # they do not have an id attribute. # Note: This feature currently applies only to Markdown headings. -# Minimum value: 0, maximum value: 99, default value: 0. +# Minimum value: 0, maximum value: 99, default value: 5. # This tag requires that the tag MARKDOWN_SUPPORT is set to YES. -TOC_INCLUDE_HEADINGS = 0 +TOC_INCLUDE_HEADINGS = 5 # When enabled doxygen tries to link words that correspond to documented # classes, or namespaces to their corresponding documentation. Such a link can @@ -337,7 +369,7 @@ BUILTIN_STL_SUPPORT = YES CPP_CLI_SUPPORT = NO # Set the SIP_SUPPORT tag to YES if your project consists of sip (see: -# http://www.riverbankcomputing.co.uk/software/sip/intro) sources only. Doxygen +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen # will parse them like normal C++ but will assume all classes use public instead # of private inheritance when no explicit protection keyword is present. # The default value is: NO. @@ -352,7 +384,7 @@ SIP_SUPPORT = NO # should set this option to NO. # The default value is: YES. -IDL_PROPERTY_SUPPORT = NO +IDL_PROPERTY_SUPPORT = YES # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC # tag is set to YES then doxygen will reuse the documentation of the first @@ -443,11 +475,17 @@ EXTRACT_ALL = YES EXTRACT_PRIVATE = YES +# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual +# methods of a class will be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIV_VIRTUAL = NO + # If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal # scope will be included in the documentation. # The default value is: NO. -EXTRACT_PACKAGE = YES +EXTRACT_PACKAGE = NO # If the EXTRACT_STATIC tag is set to YES, all static members of a file will be # included in the documentation. @@ -469,7 +507,7 @@ EXTRACT_LOCAL_CLASSES = YES # included. # The default value is: NO. -EXTRACT_LOCAL_METHODS = YES +EXTRACT_LOCAL_METHODS = NO # If this flag is set to YES, the members of anonymous namespaces will be # extracted and appear in the documentation as a namespace called @@ -478,7 +516,7 @@ EXTRACT_LOCAL_METHODS = YES # are hidden. # The default value is: NO. -EXTRACT_ANON_NSPACES = YES +EXTRACT_ANON_NSPACES = NO # If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all # undocumented members inside documented classes or files. If set to NO these @@ -497,8 +535,8 @@ HIDE_UNDOC_MEMBERS = NO HIDE_UNDOC_CLASSES = NO # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend -# (class|struct|union) declarations. If set to NO, these declarations will be -# included in the documentation. +# declarations. If set to NO, these declarations will be included in the +# documentation. # The default value is: NO. HIDE_FRIEND_COMPOUNDS = NO @@ -508,7 +546,7 @@ HIDE_FRIEND_COMPOUNDS = NO # blocks will be appended to the function's detailed documentation block. # The default value is: NO. -HIDE_IN_BODY_DOCS = NO +HIDE_IN_BODY_DOCS = YES # The INTERNAL_DOCS tag determines if documentation that is typed after a # \internal command is included. If the tag is set to NO then the documentation @@ -521,7 +559,7 @@ INTERNAL_DOCS = NO # names in lower-case letters. If set to YES, upper-case letters are also # allowed. This is useful if you have classes or files whose names only differ # in case and if your file system supports case sensitive file names. Windows -# and Mac users are advised to set this option to NO. +# (including Cygwin) ands Mac users are advised to set this option to NO. # The default value is: system dependent. CASE_SENSE_NAMES = NO @@ -623,7 +661,7 @@ STRICT_PROTO_MATCHING = NO # list. This list is created by putting \todo commands in the documentation. # The default value is: YES. -GENERATE_TODOLIST = YES +GENERATE_TODOLIST = NO # The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test # list. This list is created by putting \test commands in the documentation. @@ -708,7 +746,7 @@ LAYOUT_FILE = # The CITE_BIB_FILES tag can be used to specify one or more bib files containing # the reference definitions. This must be a list of .bib files. The .bib # extension is automatically appended if omitted. This requires the bibtex tool -# to be installed. See also http://en.wikipedia.org/wiki/BibTeX for more info. +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. # For LaTeX the style of the bibliography can be controlled using # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the # search path. See also \cite for info how to create references. @@ -753,7 +791,8 @@ WARN_IF_DOC_ERROR = YES # This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that # are documented, but have no documentation for their parameters or return # value. If set to NO, doxygen will only warn about wrong or incomplete -# parameter documentation, but not about the absence of documentation. +# parameter documentation, but not about the absence of documentation. If +# EXTRACT_ALL is set to YES then this flag will automatically be disabled. # The default value is: NO. WARN_NO_PARAMDOC = NO @@ -790,18 +829,13 @@ WARN_LOGFILE = # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING # Note: If this tag is empty the current directory is searched. -INPUT = @CMAKE_SOURCE_DIR@/docs/source/developer/mainpage.dox \ - @CMAKE_SOURCE_DIR@/docs/source/developer/example.h \ - @CMAKE_SOURCE_DIR@/nalu.C \ - @CMAKE_SOURCE_DIR@/unit_tests.C \ - @CMAKE_SOURCE_DIR@/src \ - @CMAKE_SOURCE_DIR@/include \ - @CMAKE_SOURCE_DIR@/unit_tests +INPUT = ./src \ + ./docs/doxygen/main_page.md # This tag can be used to specify the character encoding of the source files # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses # libiconv (or the iconv built into libc) for the transcoding. See the libiconv -# documentation (see: http://www.gnu.org/software/libiconv) for the list of +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of # possible encodings. # The default value is: UTF-8. @@ -818,15 +852,19 @@ INPUT_ENCODING = UTF-8 # If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, # *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, # *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, -# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, -# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf and *.qsf. - -FILE_PATTERNS = *.C \ - *.c \ +# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment), +# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen +# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f, *.for, *.tcl, *.vhd, +# *.vhdl, *.ucf, *.qsf and *.ice. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.H \ *.h \ - *.hpp \ - *.f90 \ - *.F + *.hpp # The RECURSIVE tag can be used to specify whether or not subdirectories should # be searched for input files as well. @@ -841,12 +879,7 @@ RECURSIVE = YES # Note that relative paths are relative to the directory from which doxygen is # run. -EXCLUDE_PATTERNS = */.git/* \ -# */build/* \ -# */SQA/* \ -# */cmake/* \ -# */docs/* \ -# */nightly_build/* +EXCLUDE = # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or # directories that are symbolic links (a Unix file system feature) are excluded @@ -862,6 +895,8 @@ EXCLUDE_SYMLINKS = NO # Note that the wildcards are matched against the file with absolute path, so to # exclude all test directories for example use the pattern */test/* +EXCLUDE_PATTERNS = + # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names # (namespaces, classes, functions, etc.) that should be excluded from the # output. The symbol name can be a fully qualified name, a word, or if the @@ -982,16 +1017,16 @@ INLINE_SOURCES = NO STRIP_CODE_COMMENTS = YES # If the REFERENCED_BY_RELATION tag is set to YES then for each documented -# function all documented functions referencing it will be listed. +# entity all documented functions referencing it will be listed. # The default value is: NO. -REFERENCED_BY_RELATION = YES +REFERENCED_BY_RELATION = NO # If the REFERENCES_RELATION tag is set to YES then for each documented function # all documented entities called/used by that function will be listed. # The default value is: NO. -REFERENCES_RELATION = YES +REFERENCES_RELATION = NO # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set # to YES then the hyperlinks from functions in REFERENCES_RELATION and @@ -1014,12 +1049,12 @@ SOURCE_TOOLTIPS = YES # If the USE_HTAGS tag is set to YES then the references to source code will # point to the HTML generated by the htags(1) tool instead of doxygen built-in # source browser. The htags tool is part of GNU's global source tagging system -# (see http://www.gnu.org/software/global/global.html). You will need version +# (see https://www.gnu.org/software/global/global.html). You will need version # 4.8.6 or higher. # # To use it do the following: # - Install the latest version of global -# - Enable SOURCE_BROWSER and USE_HTAGS in the config file +# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file # - Make sure the INPUT points to the root of the source tree # - Run doxygen as normal # @@ -1159,7 +1194,7 @@ HTML_EXTRA_FILES = # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen # will adjust the colors in the style sheet and background images according to # this color. Hue is specified as an angle on a colorwheel, see -# http://en.wikipedia.org/wiki/Hue for more information. For instance the value +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value # 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 # purple, and 360 is red again. # Minimum value: 0, maximum value: 359, default value: 220. @@ -1195,6 +1230,17 @@ HTML_COLORSTYLE_GAMMA = 80 HTML_TIMESTAMP = NO +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via JavaScript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have JavaScript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = YES + # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML # documentation will contain sections that can be hidden and shown after the # page has loaded. @@ -1218,13 +1264,13 @@ HTML_INDEX_NUM_ENTRIES = 100 # If the GENERATE_DOCSET tag is set to YES, additional index files will be # generated that can be used as input for Apple's Xcode 3 integrated development -# environment (see: http://developer.apple.com/tools/xcode/), introduced with -# OSX 10.5 (Leopard). To create a documentation set, doxygen will generate a +# environment (see: https://developer.apple.com/xcode/), introduced with OSX +# 10.5 (Leopard). To create a documentation set, doxygen will generate a # Makefile in the HTML output directory. Running make will produce the docset in # that directory and running make install will install the docset in # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at -# startup. See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html -# for more information. +# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy +# genXcode/_index.html for more information. # The default value is: NO. # This tag requires that the tag GENERATE_HTML is set to YES. @@ -1263,7 +1309,7 @@ DOCSET_PUBLISHER_NAME = Publisher # If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three # additional HTML index files: index.hhp, index.hhc, and index.hhk. The # index.hhp is a project file that can be read by Microsoft's HTML Help Workshop -# (see: http://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on # Windows. # # The HTML Help Workshop contains a compiler that can convert all HTML output @@ -1339,7 +1385,7 @@ QCH_FILE = # The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help # Project output. For more information please see Qt Help Project / Namespace -# (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#namespace). +# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). # The default value is: org.doxygen.Project. # This tag requires that the tag GENERATE_QHP is set to YES. @@ -1347,7 +1393,7 @@ QHP_NAMESPACE = org.doxygen.Project # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt # Help Project output. For more information please see Qt Help Project / Virtual -# Folders (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#virtual- +# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual- # folders). # The default value is: doc. # This tag requires that the tag GENERATE_QHP is set to YES. @@ -1356,7 +1402,7 @@ QHP_VIRTUAL_FOLDER = doc # If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom # filter to add. For more information please see Qt Help Project / Custom -# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- # filters). # This tag requires that the tag GENERATE_QHP is set to YES. @@ -1364,7 +1410,7 @@ QHP_CUST_FILTER_NAME = # The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the # custom filter to add. For more information please see Qt Help Project / Custom -# Filters (see: http://qt-project.org/doc/qt-4.8/qthelpproject.html#custom- +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- # filters). # This tag requires that the tag GENERATE_QHP is set to YES. @@ -1372,7 +1418,7 @@ QHP_CUST_FILTER_ATTRS = # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this # project's filter section matches. Qt Help Project / Filter Attributes (see: -# http://qt-project.org/doc/qt-4.8/qthelpproject.html#filter-attributes). +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). # This tag requires that the tag GENERATE_QHP is set to YES. QHP_SECT_FILTER_ATTRS = @@ -1465,7 +1511,7 @@ EXT_LINKS_IN_WINDOW = NO FORMULA_FONTSIZE = 10 -# Use the FORMULA_TRANPARENT tag to determine whether or not the images +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images # generated for formulas are transparent PNGs. Transparent PNGs are not # supported properly for IE 6.0, but are supported on all modern browsers. # @@ -1476,8 +1522,14 @@ FORMULA_FONTSIZE = 10 FORMULA_TRANSPARENT = YES +# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands +# to create new LaTeX commands to be used in formulas as building blocks. See +# the section "Including formulas" for details. + +FORMULA_MACROFILE = + # Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see -# http://www.mathjax.org) which uses client side Javascript for the rendering +# https://www.mathjax.org) which uses client side JavaScript for the rendering # instead of using pre-rendered bitmaps. Use this if you do not have LaTeX # installed or if you want to formulas look prettier in the HTML output. When # enabled you may also need to install MathJax separately and configure the path @@ -1496,6 +1548,7 @@ USE_MATHJAX = YES # This tag requires that the tag USE_MATHJAX is set to YES. MATHJAX_FORMAT = HTML-CSS +# MATHJAX_FORMAT = SVG # When MathJax is enabled you need to specify the location relative to the HTML # output directory using the MATHJAX_RELPATH option. The destination directory @@ -1504,11 +1557,11 @@ MATHJAX_FORMAT = HTML-CSS # MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax # Content Delivery Network so you can quickly see the result without installing # MathJax. However, it is strongly recommended to install a local copy of -# MathJax from http://www.mathjax.org before deployment. -# The default value is: http://cdn.mathjax.org/mathjax/latest. +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/. # This tag requires that the tag USE_MATHJAX is set to YES. -MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest +MATHJAX_RELPATH = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/ # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax # extension names that should be enabled during MathJax rendering. For example @@ -1544,10 +1597,10 @@ MATHJAX_CODEFILE = # The default value is: YES. # This tag requires that the tag GENERATE_HTML is set to YES. -SEARCHENGINE = NO +SEARCHENGINE = YES # When the SERVER_BASED_SEARCH tag is enabled the search engine will be -# implemented using a web server instead of a web client using Javascript. There +# implemented using a web server instead of a web client using JavaScript. There # are two flavors of web server based searching depending on the EXTERNAL_SEARCH # setting. When disabled, doxygen will generate a PHP script for searching and # an index file used by the script. When EXTERNAL_SEARCH is enabled the indexing @@ -1566,7 +1619,7 @@ SERVER_BASED_SEARCH = NO # # Doxygen ships with an example indexer (doxyindexer) and search engine # (doxysearch.cgi) which are based on the open source search engine library -# Xapian (see: http://xapian.org/). +# Xapian (see: https://xapian.org/). # # See the section "External Indexing and Searching" for details. # The default value is: NO. @@ -1579,7 +1632,7 @@ EXTERNAL_SEARCH = NO # # Doxygen ships with an example indexer (doxyindexer) and search engine # (doxysearch.cgi) which are based on the open source search engine library -# Xapian (see: http://xapian.org/). See the section "External Indexing and +# Xapian (see: https://xapian.org/). See the section "External Indexing and # Searching" for details. # This tag requires that the tag SEARCHENGINE is set to YES. @@ -1631,21 +1684,35 @@ LATEX_OUTPUT = latex # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be # invoked. # -# Note that when enabling USE_PDFLATEX this option is only used for generating -# bitmaps for formulas in the HTML output, but not in the Makefile that is -# written to the output directory. -# The default file is: latex. +# Note that when not enabling USE_PDFLATEX the default is latex when enabling +# USE_PDFLATEX the default is pdflatex and when in the later case latex is +# chosen this is overwritten by pdflatex. For specific output languages the +# default can have been set differently, this depends on the implementation of +# the output language. # This tag requires that the tag GENERATE_LATEX is set to YES. -LATEX_CMD_NAME = latex +LATEX_CMD_NAME = # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to generate # index for LaTeX. +# Note: This tag is used in the Makefile / make.bat. +# See also: LATEX_MAKEINDEX_CMD for the part in the generated output file +# (.tex). # The default file is: makeindex. # This tag requires that the tag GENERATE_LATEX is set to YES. MAKEINDEX_CMD_NAME = makeindex +# The LATEX_MAKEINDEX_CMD tag can be used to specify the command name to +# generate index for LaTeX. In case there is no backslash (\) as first character +# it will be automatically added in the LaTeX code. +# Note: This tag is used in the generated output file (.tex). +# See also: MAKEINDEX_CMD_NAME for the part in the Makefile / make.bat. +# The default value is: makeindex. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_MAKEINDEX_CMD = makeindex + # If the COMPACT_LATEX tag is set to YES, doxygen generates more compact LaTeX # documents. This may be useful for small projects and may help to save some # trees in general. @@ -1766,7 +1833,7 @@ LATEX_SOURCE_CODE = NO # The LATEX_BIB_STYLE tag can be used to specify the style to use for the # bibliography, e.g. plainnat, or ieeetr. See -# http://en.wikipedia.org/wiki/BibTeX and \cite for more info. +# https://en.wikipedia.org/wiki/BibTeX and \cite for more info. # The default value is: plain. # This tag requires that the tag GENERATE_LATEX is set to YES. @@ -1780,6 +1847,14 @@ LATEX_BIB_STYLE = plain LATEX_TIMESTAMP = NO +# The LATEX_EMOJI_DIRECTORY tag is used to specify the (relative or absolute) +# path from which the emoji images will be read. If a relative path is entered, +# it will be relative to the LATEX_OUTPUT directory. If left blank the +# LATEX_OUTPUT directory will be used. +# This tag requires that the tag GENERATE_LATEX is set to YES. + +LATEX_EMOJI_DIRECTORY = + #--------------------------------------------------------------------------- # Configuration options related to the RTF output #--------------------------------------------------------------------------- @@ -1819,9 +1894,9 @@ COMPACT_RTF = NO RTF_HYPERLINKS = NO -# Load stylesheet definitions from file. Syntax is similar to doxygen's config -# file, i.e. a series of assignments. You only have to provide replacements, -# missing definitions are set to their default value. +# Load stylesheet definitions from file. Syntax is similar to doxygen's +# configuration file, i.e. a series of assignments. You only have to provide +# replacements, missing definitions are set to their default value. # # See also section "Doxygen usage" for information on how to generate the # default style sheet that doxygen normally uses. @@ -1830,8 +1905,8 @@ RTF_HYPERLINKS = NO RTF_STYLESHEET_FILE = # Set optional variables used in the generation of an RTF document. Syntax is -# similar to doxygen's config file. A template extensions file can be generated -# using doxygen -e rtf extensionFile. +# similar to doxygen's configuration file. A template extensions file can be +# generated using doxygen -e rtf extensionFile. # This tag requires that the tag GENERATE_RTF is set to YES. RTF_EXTENSIONS_FILE = @@ -1917,6 +1992,13 @@ XML_OUTPUT = xml XML_PROGRAMLISTING = YES +# If the XML_NS_MEMB_FILE_SCOPE tag is set to YES, doxygen will include +# namespace members in file scope as well, matching the HTML output. +# The default value is: NO. +# This tag requires that the tag GENERATE_XML is set to YES. + +XML_NS_MEMB_FILE_SCOPE = NO + #--------------------------------------------------------------------------- # Configuration options related to the DOCBOOK output #--------------------------------------------------------------------------- @@ -1949,9 +2031,9 @@ DOCBOOK_PROGRAMLISTING = NO #--------------------------------------------------------------------------- # If the GENERATE_AUTOGEN_DEF tag is set to YES, doxygen will generate an -# AutoGen Definitions (see http://autogen.sf.net) file that captures the -# structure of the code including all documentation. Note that this feature is -# still experimental and incomplete at the moment. +# AutoGen Definitions (see http://autogen.sourceforge.net/) file that captures +# the structure of the code including all documentation. Note that this feature +# is still experimental and incomplete at the moment. # The default value is: NO. GENERATE_AUTOGEN_DEF = NO @@ -2011,7 +2093,7 @@ ENABLE_PREPROCESSING = YES # The default value is: NO. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. -MACRO_EXPANSION = NO +MACRO_EXPANSION = YES # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then # the macro expansion is limited to the macros specified with the PREDEFINED and @@ -2019,7 +2101,7 @@ MACRO_EXPANSION = NO # The default value is: NO. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. -EXPAND_ONLY_PREDEF = NO +EXPAND_ONLY_PREDEF = YES # If the SEARCH_INCLUDES tag is set to YES, the include files in the # INCLUDE_PATH will be searched if a #include is found. @@ -2033,7 +2115,7 @@ SEARCH_INCLUDES = YES # preprocessor. # This tag requires that the tag SEARCH_INCLUDES is set to YES. -INCLUDE_PATH = @CMAKE_SOURCE_DIR@/include +INCLUDE_PATH = # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard # patterns (like *.h and *.hpp) to filter out the header-files in the @@ -2041,7 +2123,7 @@ INCLUDE_PATH = @CMAKE_SOURCE_DIR@/include # used. # This tag requires that the tag ENABLE_PREPROCESSING is set to YES. -INCLUDE_FILE_PATTERNS = *.h *.hpp +INCLUDE_FILE_PATTERNS = # The PREDEFINED tag can be used to specify one or more macro names that are # defined before the preprocessor is started (similar to the -D option of e.g. @@ -2089,12 +2171,14 @@ SKIP_FUNCTION_MACROS = YES # the path). If a tag file is not located in the directory in which doxygen is # run, you must also specify the path to the tagfile here. -GENERATE_TAGFILE = @CMAKE_BINARY_DIR@/docs/nalu.tag +TAGFILES = # When a file name is specified after GENERATE_TAGFILE, doxygen will create a # tag file that is based on the input files it reads. See section "Linking to # external documentation" for more information about the usage of tag files. +GENERATE_TAGFILE = + # If the ALLEXTERNALS tag is set to YES, all external class will be listed in # the class index. If set to NO, only the inherited external classes will be # listed. @@ -2116,12 +2200,6 @@ EXTERNAL_GROUPS = YES EXTERNAL_PAGES = YES -# The PERL_PATH should be the absolute path and name of the perl script -# interpreter (i.e. the result of 'which perl'). -# The default file (with absolute path) is: /usr/bin/perl. - -PERL_PATH = /usr/bin/perl - #--------------------------------------------------------------------------- # Configuration options related to the dot tool #--------------------------------------------------------------------------- @@ -2135,15 +2213,6 @@ PERL_PATH = /usr/bin/perl CLASS_DIAGRAMS = YES -# You can define message sequence charts within doxygen comments using the \msc -# command. Doxygen will then run the mscgen tool (see: -# http://www.mcternan.me.uk/mscgen/)) to produce the chart and insert it in the -# documentation. The MSCGEN_PATH tag allows you to specify the directory where -# the mscgen tool resides. If left empty the tool is assumed to be found in the -# default search path. - -MSCGEN_PATH = - # You can include diagrams made with dia in doxygen documentation. Doxygen will # then run dia to produce the diagram and insert it in the documentation. The # DIA_PATH tag allows you to specify the directory where the dia binary resides. @@ -2164,7 +2233,7 @@ HIDE_UNDOC_RELATIONS = YES # set to NO # The default value is: NO. -HAVE_DOT = NO +HAVE_DOT = YES # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed # to run in parallel. When set to 0 doxygen will base this on the number of @@ -2251,7 +2320,7 @@ UML_LIMIT_NUM_FIELDS = 10 # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. -TEMPLATE_RELATIONS = NO +TEMPLATE_RELATIONS = YES # If the INCLUDE_GRAPH, ENABLE_PREPROCESSING and SEARCH_INCLUDES tags are set to # YES then doxygen will generate a graph for each documented file showing the @@ -2281,7 +2350,7 @@ INCLUDED_BY_GRAPH = YES # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. -CALL_GRAPH = YES +CALL_GRAPH = NO # If the CALLER_GRAPH tag is set to YES then doxygen will generate a caller # dependency graph for every global function or class method. @@ -2293,7 +2362,7 @@ CALL_GRAPH = YES # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. -CALLER_GRAPH = YES +CALLER_GRAPH = NO # If the GRAPHICAL_HIERARCHY tag is set to YES then doxygen will graphical # hierarchy of all classes instead of a textual one. @@ -2324,7 +2393,7 @@ DIRECTORY_GRAPH = YES # The default value is: png. # This tag requires that the tag HAVE_DOT is set to YES. -DOT_IMAGE_FORMAT = jpg +DOT_IMAGE_FORMAT = svg # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to # enable generation of interactive SVG images that allow zooming and panning. @@ -2336,7 +2405,7 @@ DOT_IMAGE_FORMAT = jpg # The default value is: NO. # This tag requires that the tag HAVE_DOT is set to YES. -INTERACTIVE_SVG = NO +INTERACTIVE_SVG = YES # The DOT_PATH tag can be used to specify the path where the dot tool can be # found. If left blank, it is assumed the dot tool can be found in the path. @@ -2391,7 +2460,7 @@ PLANTUML_INCLUDE_PATH = # Minimum value: 0, maximum value: 10000, default value: 50. # This tag requires that the tag HAVE_DOT is set to YES. -DOT_GRAPH_MAX_NODES = 100 +DOT_GRAPH_MAX_NODES = 50 # The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the graphs # generated by dot. A depth value of 3 means that only nodes reachable from the @@ -2403,7 +2472,7 @@ DOT_GRAPH_MAX_NODES = 100 # Minimum value: 0, maximum value: 1000, default value: 0. # This tag requires that the tag HAVE_DOT is set to YES. -MAX_DOT_GRAPH_DEPTH = 3 +MAX_DOT_GRAPH_DEPTH = 0 # Set the DOT_TRANSPARENT tag to YES to generate images with a transparent # background. This is disabled by default, because dot on Windows does not seem diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 7cefca76f..000000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,6 +0,0 @@ -breathe==4.13.1 -docutils==0.14 -Pygments==2.15.0 -pyparsing==2.4.2 -Sphinx==2.1.2 -sphinxcontrib-bibtex==0.4.2 diff --git a/docs/sphinx/conf.py b/docs/sphinx/conf.py new file mode 100644 index 000000000..749ff5622 --- /dev/null +++ b/docs/sphinx/conf.py @@ -0,0 +1,356 @@ +# -*- coding: utf-8 -*- +# +# Nalu-Wind documentation build configuration file +# +# This file is execfile()d with the current directory set to its +# containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +# 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. +# +# import os +import sys +# sys.path.insert(0, os.path.abspath('.')) +#sys.path.append("../breathe") + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# +# needs_sphinx = '1.0' + +# 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.mathjax'] + + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] +#breathe_projects = {"Nalu-Wind": "../doxygen_output/xml/"} +#breathe_default_project = "Nalu-Wind" + +fortran_src ='../../src/' +#fortran_ext =[' 'F90'] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +# +# source_suffix = ['.rst', '.md'] +source_suffix = '.rst' + +# The encoding of source files. +# +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'Nalu-Wind' +copyright = u'ExaWind team' +author = u'ExaWind team' + +# 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. +# +# The short X.Y version. +version = u'0.1' +# The full version, including alpha/beta/rc tags. +release = u'0.1' + +# 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 + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# +# today = '' +# +# Else, today_fmt is used as the format for a strftime call. +# +# today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This patterns also effect to html_static_path and html_extra_path +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +# modindex_common_prefix = [] + +# If true, keep warnings as "system message" paragraphs in the built documents. +# keep_warnings = False + +# If true, `todo` and `todoList` produce output, else they produce nothing. +todo_include_todos = False + +numfig = True +numfig_format = {'figure': '%s', 'table': '%s', 'code-block': '%s'} + +# -- 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 = 'nature' +html_theme = 'sphinx_rtd_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 = {} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. +# " v documentation" by default. +# +# html_title = u'Nalu-Wind v0.01' + +# A shorter title for the navigation bar. Default is the same as html_title. +# +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +# +# html_logo = None + +# The name of an image file (relative to this directory) to use as a favicon of +# the docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +# +# html_favicon = None + +# 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_static_path = [] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# +# html_extra_path = [] + +# If not None, a 'Last updated on:' timestamp is inserted at every page +# bottom, using the given strftime format. +# The empty string is equivalent to '%b %d, %Y'. +# +# html_last_updated_fmt = None + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# +# html_additional_pages = {} + +# 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 = False + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Language to be used for generating the HTML full-text search index. +# Sphinx supports the following languages: +# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' +# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh' +# +# html_search_language = 'en' + +# A dictionary with options for the search language support, empty by default. +# 'ja' uses this config value. +# 'zh' user can custom change `jieba` dictionary path. +# +# html_search_options = {'type': 'default'} + +# The name of a javascript file (relative to the configuration directory) that +# implements a search results scorer. If empty, the default will be used. +# +# html_search_scorer = 'scorer.js' + +# Output file base name for HTML help builder. +htmlhelp_basename = 'nalu-wind-doc' + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { + # The paper size ('letterpaper' or 'a4paper'). + # + # 'papersize': 'letterpaper', + + # The font size ('10pt', '11pt' or '12pt'). + # + # 'pointsize': '10pt', + + # Additional stuff for the LaTeX preamble. + # + # 'preamble': '', + + # Latex figure (float) alignment + # + # 'figure_align': 'htbp', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + (master_doc, 'nalu_wind.tex', u'Nalu-Wind Documentation', + author, 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +# +# latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +# +# latex_use_parts = False + +# If true, show page references after internal links. +# +# latex_show_pagerefs = False + +# If true, show URL addresses after external links. +# +# latex_show_urls = False + +# Documents to append as an appendix to all manuals. +# +# latex_appendices = [] + +# It false, will not define \strong, \code, itleref, \crossref ... but only +# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added +# packages. +# +# latex_keep_old_macro_names = True + +# If false, no module index is generated. +# +# latex_domain_indices = True + + +# -- 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, 'nalu-wind', u'Nalu-Wind Documentation', + [author], 1) +] + +# If true, show URL addresses after external links. +# +# man_show_urls = False + + +# -- 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, 'nalu_wind', u'Nalu-Wind Documentation', + author, 'Nalu-Wind', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +# +# texinfo_appendices = [] + +# If false, no module index is generated. +# +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# +# texinfo_no_detailmenu = False + +def setup(app): + app.add_object_type("cmakeval", "cmakeval", + objname="CMake configuration value", + indextemplate="pair: %s; CMake configuration") + app.add_object_type("input_param", "input_param", + objname="Nalu-Wind input parameter", + indextemplate="pair: %s; Nalu-Wind input parameter") diff --git a/docs/index.rst b/docs/sphinx/index.rst similarity index 100% rename from docs/index.rst rename to docs/sphinx/index.rst diff --git a/docs/naluLowMach.jpg b/docs/sphinx/naluLowMach.jpg similarity index 100% rename from docs/naluLowMach.jpg rename to docs/sphinx/naluLowMach.jpg diff --git a/docs/references/references.bib b/docs/sphinx/references/references.bib similarity index 100% rename from docs/references/references.bib rename to docs/sphinx/references/references.bib diff --git a/docs/source/developer/apidocs/actuatorsources.rst b/docs/sphinx/source/developer/apidocs/actuatorsources.rst similarity index 100% rename from docs/source/developer/apidocs/actuatorsources.rst rename to docs/sphinx/source/developer/apidocs/actuatorsources.rst diff --git a/docs/source/developer/apidocs/eqsystems.rst b/docs/sphinx/source/developer/apidocs/eqsystems.rst similarity index 100% rename from docs/source/developer/apidocs/eqsystems.rst rename to docs/sphinx/source/developer/apidocs/eqsystems.rst diff --git a/docs/source/developer/apidocs/linsys.rst b/docs/sphinx/source/developer/apidocs/linsys.rst similarity index 100% rename from docs/source/developer/apidocs/linsys.rst rename to docs/sphinx/source/developer/apidocs/linsys.rst diff --git a/docs/source/developer/apidocs/masterelem.rst b/docs/sphinx/source/developer/apidocs/masterelem.rst similarity index 100% rename from docs/source/developer/apidocs/masterelem.rst rename to docs/sphinx/source/developer/apidocs/masterelem.rst diff --git a/docs/source/developer/apidocs/postprocess.rst b/docs/sphinx/source/developer/apidocs/postprocess.rst similarity index 100% rename from docs/source/developer/apidocs/postprocess.rst rename to docs/sphinx/source/developer/apidocs/postprocess.rst diff --git a/docs/source/developer/apidocs/realms.rst b/docs/sphinx/source/developer/apidocs/realms.rst similarity index 100% rename from docs/source/developer/apidocs/realms.rst rename to docs/sphinx/source/developer/apidocs/realms.rst diff --git a/docs/source/developer/apidocs/userfunc.rst b/docs/sphinx/source/developer/apidocs/userfunc.rst similarity index 100% rename from docs/source/developer/apidocs/userfunc.rst rename to docs/sphinx/source/developer/apidocs/userfunc.rst diff --git a/docs/source/developer/build_doc.rst b/docs/sphinx/source/developer/build_doc.rst similarity index 100% rename from docs/source/developer/build_doc.rst rename to docs/sphinx/source/developer/build_doc.rst diff --git a/docs/source/developer/code.rst b/docs/sphinx/source/developer/code.rst similarity index 100% rename from docs/source/developer/code.rst rename to docs/sphinx/source/developer/code.rst diff --git a/docs/source/developer/contrib.rst b/docs/sphinx/source/developer/contrib.rst similarity index 100% rename from docs/source/developer/contrib.rst rename to docs/sphinx/source/developer/contrib.rst diff --git a/docs/source/developer/dox_example/example.h b/docs/sphinx/source/developer/dox_example/example.h similarity index 100% rename from docs/source/developer/dox_example/example.h rename to docs/sphinx/source/developer/dox_example/example.h diff --git a/docs/source/developer/dox_example/xml/class_example_class.xml b/docs/sphinx/source/developer/dox_example/xml/class_example_class.xml similarity index 100% rename from docs/source/developer/dox_example/xml/class_example_class.xml rename to docs/sphinx/source/developer/dox_example/xml/class_example_class.xml diff --git a/docs/source/developer/dox_example/xml/combine.xslt b/docs/sphinx/source/developer/dox_example/xml/combine.xslt similarity index 100% rename from docs/source/developer/dox_example/xml/combine.xslt rename to docs/sphinx/source/developer/dox_example/xml/combine.xslt diff --git a/docs/source/developer/dox_example/xml/compound.xsd b/docs/sphinx/source/developer/dox_example/xml/compound.xsd similarity index 100% rename from docs/source/developer/dox_example/xml/compound.xsd rename to docs/sphinx/source/developer/dox_example/xml/compound.xsd diff --git a/docs/source/developer/dox_example/xml/example_8h.xml b/docs/sphinx/source/developer/dox_example/xml/example_8h.xml similarity index 100% rename from docs/source/developer/dox_example/xml/example_8h.xml rename to docs/sphinx/source/developer/dox_example/xml/example_8h.xml diff --git a/docs/source/developer/dox_example/xml/index.xml b/docs/sphinx/source/developer/dox_example/xml/index.xml similarity index 100% rename from docs/source/developer/dox_example/xml/index.xml rename to docs/sphinx/source/developer/dox_example/xml/index.xml diff --git a/docs/source/developer/dox_example/xml/index.xsd b/docs/sphinx/source/developer/dox_example/xml/index.xsd similarity index 100% rename from docs/source/developer/dox_example/xml/index.xsd rename to docs/sphinx/source/developer/dox_example/xml/index.xsd diff --git a/docs/source/developer/dox_example/xml/namespacestd.xml b/docs/sphinx/source/developer/dox_example/xml/namespacestd.xml similarity index 100% rename from docs/source/developer/dox_example/xml/namespacestd.xml rename to docs/sphinx/source/developer/dox_example/xml/namespacestd.xml diff --git a/docs/source/developer/index.rst b/docs/sphinx/source/developer/index.rst similarity index 100% rename from docs/source/developer/index.rst rename to docs/sphinx/source/developer/index.rst diff --git a/docs/source/developer/infra.rst b/docs/sphinx/source/developer/infra.rst similarity index 100% rename from docs/source/developer/infra.rst rename to docs/sphinx/source/developer/infra.rst diff --git a/docs/source/developer/mainpage.dox b/docs/sphinx/source/developer/mainpage.dox similarity index 100% rename from docs/source/developer/mainpage.dox rename to docs/sphinx/source/developer/mainpage.dox diff --git a/docs/source/developer/style.rst b/docs/sphinx/source/developer/style.rst similarity index 100% rename from docs/source/developer/style.rst rename to docs/sphinx/source/developer/style.rst diff --git a/docs/source/developer/testing.rst b/docs/sphinx/source/developer/testing.rst similarity index 100% rename from docs/source/developer/testing.rst rename to docs/sphinx/source/developer/testing.rst diff --git a/docs/source/developer/workflow.rst b/docs/sphinx/source/developer/workflow.rst similarity index 100% rename from docs/source/developer/workflow.rst rename to docs/sphinx/source/developer/workflow.rst diff --git a/docs/source/developer/write_developer_doc.rst b/docs/sphinx/source/developer/write_developer_doc.rst similarity index 100% rename from docs/source/developer/write_developer_doc.rst rename to docs/sphinx/source/developer/write_developer_doc.rst diff --git a/docs/source/developer/write_user_doc.rst b/docs/sphinx/source/developer/write_user_doc.rst similarity index 100% rename from docs/source/developer/write_user_doc.rst rename to docs/sphinx/source/developer/write_user_doc.rst diff --git a/docs/source/theory/adaptivity.rst b/docs/sphinx/source/theory/adaptivity.rst similarity index 100% rename from docs/source/theory/adaptivity.rst rename to docs/sphinx/source/theory/adaptivity.rst diff --git a/docs/source/theory/advectionStabilization.rst b/docs/sphinx/source/theory/advectionStabilization.rst similarity index 100% rename from docs/source/theory/advectionStabilization.rst rename to docs/sphinx/source/theory/advectionStabilization.rst diff --git a/docs/source/theory/amsAbl_ransBelowKs.yaml b/docs/sphinx/source/theory/amsAbl_ransBelowKs.yaml similarity index 100% rename from docs/source/theory/amsAbl_ransBelowKs.yaml rename to docs/sphinx/source/theory/amsAbl_ransBelowKs.yaml diff --git a/docs/source/theory/boundaryConditions.rst b/docs/sphinx/source/theory/boundaryConditions.rst similarity index 100% rename from docs/source/theory/boundaryConditions.rst rename to docs/sphinx/source/theory/boundaryConditions.rst diff --git a/docs/source/theory/codeAbstractions.rst b/docs/sphinx/source/theory/codeAbstractions.rst similarity index 100% rename from docs/source/theory/codeAbstractions.rst rename to docs/sphinx/source/theory/codeAbstractions.rst diff --git a/docs/source/theory/couplingApproach.rst b/docs/sphinx/source/theory/couplingApproach.rst similarity index 100% rename from docs/source/theory/couplingApproach.rst rename to docs/sphinx/source/theory/couplingApproach.rst diff --git a/docs/source/theory/discretizationApproach.rst b/docs/sphinx/source/theory/discretizationApproach.rst similarity index 100% rename from docs/source/theory/discretizationApproach.rst rename to docs/sphinx/source/theory/discretizationApproach.rst diff --git a/docs/source/theory/images/actuatorDisk.png b/docs/sphinx/source/theory/images/actuatorDisk.png similarity index 100% rename from docs/source/theory/images/actuatorDisk.png rename to docs/sphinx/source/theory/images/actuatorDisk.png diff --git a/docs/source/theory/images/contactSearchAndEval.pdf b/docs/sphinx/source/theory/images/contactSearchAndEval.pdf similarity index 100% rename from docs/source/theory/images/contactSearchAndEval.pdf rename to docs/sphinx/source/theory/images/contactSearchAndEval.pdf diff --git a/docs/source/theory/images/cvfem_conv.png b/docs/sphinx/source/theory/images/cvfem_conv.png similarity index 100% rename from docs/source/theory/images/cvfem_conv.png rename to docs/sphinx/source/theory/images/cvfem_conv.png diff --git a/docs/source/theory/images/cvfem_nodes.png b/docs/sphinx/source/theory/images/cvfem_nodes.png similarity index 100% rename from docs/source/theory/images/cvfem_nodes.png rename to docs/sphinx/source/theory/images/cvfem_nodes.png diff --git a/docs/source/theory/images/cvfem_onecv.png b/docs/sphinx/source/theory/images/cvfem_onecv.png similarity index 100% rename from docs/source/theory/images/cvfem_onecv.png rename to docs/sphinx/source/theory/images/cvfem_onecv.png diff --git a/docs/source/theory/images/cylinder_overset.png b/docs/sphinx/source/theory/images/cylinder_overset.png similarity index 100% rename from docs/source/theory/images/cylinder_overset.png rename to docs/sphinx/source/theory/images/cylinder_overset.png diff --git a/docs/source/theory/images/dgHex8Tet4Duct.png b/docs/sphinx/source/theory/images/dgHex8Tet4Duct.png similarity index 100% rename from docs/source/theory/images/dgHex8Tet4Duct.png rename to docs/sphinx/source/theory/images/dgHex8Tet4Duct.png diff --git a/docs/source/theory/images/dgQuad4Quad9MMS.png b/docs/sphinx/source/theory/images/dgQuad4Quad9MMS.png similarity index 100% rename from docs/source/theory/images/dgQuad4Quad9MMS.png rename to docs/sphinx/source/theory/images/dgQuad4Quad9MMS.png diff --git a/docs/source/theory/images/hadapt.pdf b/docs/sphinx/source/theory/images/hadapt.pdf similarity index 100% rename from docs/source/theory/images/hadapt.pdf rename to docs/sphinx/source/theory/images/hadapt.pdf diff --git a/docs/source/theory/images/hadapt2.pdf b/docs/sphinx/source/theory/images/hadapt2.pdf similarity index 100% rename from docs/source/theory/images/hadapt2.pdf rename to docs/sphinx/source/theory/images/hadapt2.pdf diff --git a/docs/source/theory/images/hadapt3.pdf b/docs/sphinx/source/theory/images/hadapt3.pdf similarity index 100% rename from docs/source/theory/images/hadapt3.pdf rename to docs/sphinx/source/theory/images/hadapt3.pdf diff --git a/docs/source/theory/images/hex.pdf b/docs/sphinx/source/theory/images/hex.pdf similarity index 100% rename from docs/source/theory/images/hex.pdf rename to docs/sphinx/source/theory/images/hex.pdf diff --git a/docs/source/theory/images/ordinate.pdf b/docs/sphinx/source/theory/images/ordinate.pdf similarity index 100% rename from docs/source/theory/images/ordinate.pdf rename to docs/sphinx/source/theory/images/ordinate.pdf diff --git a/docs/source/theory/images/oversetBlockOneTwo.png b/docs/sphinx/source/theory/images/oversetBlockOneTwo.png similarity index 100% rename from docs/source/theory/images/oversetBlockOneTwo.png rename to docs/sphinx/source/theory/images/oversetBlockOneTwo.png diff --git a/docs/source/theory/images/oversetBlockOneTwoCut.png b/docs/sphinx/source/theory/images/oversetBlockOneTwoCut.png similarity index 100% rename from docs/source/theory/images/oversetBlockOneTwoCut.png rename to docs/sphinx/source/theory/images/oversetBlockOneTwoCut.png diff --git a/docs/source/theory/images/oversetHC.png b/docs/sphinx/source/theory/images/oversetHC.png similarity index 100% rename from docs/source/theory/images/oversetHC.png rename to docs/sphinx/source/theory/images/oversetHC.png diff --git a/docs/source/theory/images/oversetNodes.png b/docs/sphinx/source/theory/images/oversetNodes.png similarity index 100% rename from docs/source/theory/images/oversetNodes.png rename to docs/sphinx/source/theory/images/oversetNodes.png diff --git a/docs/source/theory/images/oversetSphere.png b/docs/sphinx/source/theory/images/oversetSphere.png similarity index 100% rename from docs/source/theory/images/oversetSphere.png rename to docs/sphinx/source/theory/images/oversetSphere.png diff --git a/docs/source/theory/images/pecletFactor.pdf b/docs/sphinx/source/theory/images/pecletFactor.pdf similarity index 100% rename from docs/source/theory/images/pecletFactor.pdf rename to docs/sphinx/source/theory/images/pecletFactor.pdf diff --git a/docs/source/theory/images/quadel.pdf b/docs/sphinx/source/theory/images/quadel.pdf similarity index 100% rename from docs/source/theory/images/quadel.pdf rename to docs/sphinx/source/theory/images/quadel.pdf diff --git a/docs/source/theory/images/rotbox_overset.png b/docs/sphinx/source/theory/images/rotbox_overset.png similarity index 100% rename from docs/source/theory/images/rotbox_overset.png rename to docs/sphinx/source/theory/images/rotbox_overset.png diff --git a/docs/source/theory/images/tioga_cyl_velocity.png b/docs/sphinx/source/theory/images/tioga_cyl_velocity.png similarity index 100% rename from docs/source/theory/images/tioga_cyl_velocity.png rename to docs/sphinx/source/theory/images/tioga_cyl_velocity.png diff --git a/docs/source/theory/images/tioga_cyl_vorticity.png b/docs/sphinx/source/theory/images/tioga_cyl_vorticity.png similarity index 100% rename from docs/source/theory/images/tioga_cyl_vorticity.png rename to docs/sphinx/source/theory/images/tioga_cyl_vorticity.png diff --git a/docs/source/theory/images/twoBlockDiag.pdf b/docs/sphinx/source/theory/images/twoBlockDiag.pdf similarity index 100% rename from docs/source/theory/images/twoBlockDiag.pdf rename to docs/sphinx/source/theory/images/twoBlockDiag.pdf diff --git a/docs/source/theory/images/we_cvfem_p1.png b/docs/sphinx/source/theory/images/we_cvfem_p1.png similarity index 100% rename from docs/source/theory/images/we_cvfem_p1.png rename to docs/sphinx/source/theory/images/we_cvfem_p1.png diff --git a/docs/source/theory/index.rst b/docs/sphinx/source/theory/index.rst similarity index 100% rename from docs/source/theory/index.rst rename to docs/sphinx/source/theory/index.rst diff --git a/docs/source/theory/lowMachNumberDerivation.rst b/docs/sphinx/source/theory/lowMachNumberDerivation.rst similarity index 100% rename from docs/source/theory/lowMachNumberDerivation.rst rename to docs/sphinx/source/theory/lowMachNumberDerivation.rst diff --git a/docs/source/theory/multiPhysics.rst b/docs/sphinx/source/theory/multiPhysics.rst similarity index 100% rename from docs/source/theory/multiPhysics.rst rename to docs/sphinx/source/theory/multiPhysics.rst diff --git a/docs/source/theory/nso.rst b/docs/sphinx/source/theory/nso.rst similarity index 100% rename from docs/source/theory/nso.rst rename to docs/sphinx/source/theory/nso.rst diff --git a/docs/source/theory/overset.rst b/docs/sphinx/source/theory/overset.rst similarity index 100% rename from docs/source/theory/overset.rst rename to docs/sphinx/source/theory/overset.rst diff --git a/docs/source/theory/pressureStabilization.rst b/docs/sphinx/source/theory/pressureStabilization.rst similarity index 100% rename from docs/source/theory/pressureStabilization.rst rename to docs/sphinx/source/theory/pressureStabilization.rst diff --git a/docs/source/theory/propertyEvaluation.rst b/docs/sphinx/source/theory/propertyEvaluation.rst similarity index 100% rename from docs/source/theory/propertyEvaluation.rst rename to docs/sphinx/source/theory/propertyEvaluation.rst diff --git a/docs/source/theory/ransAbl_momentum.yaml b/docs/sphinx/source/theory/ransAbl_momentum.yaml similarity index 100% rename from docs/source/theory/ransAbl_momentum.yaml rename to docs/sphinx/source/theory/ransAbl_momentum.yaml diff --git a/docs/source/theory/ransAbl_wallUserData.yaml b/docs/sphinx/source/theory/ransAbl_wallUserData.yaml similarity index 100% rename from docs/source/theory/ransAbl_wallUserData.yaml rename to docs/sphinx/source/theory/ransAbl_wallUserData.yaml diff --git a/docs/source/theory/rteStabilization.rst b/docs/sphinx/source/theory/rteStabilization.rst similarity index 100% rename from docs/source/theory/rteStabilization.rst rename to docs/sphinx/source/theory/rteStabilization.rst diff --git a/docs/source/theory/supportedEquationSet.rst b/docs/sphinx/source/theory/supportedEquationSet.rst similarity index 100% rename from docs/source/theory/supportedEquationSet.rst rename to docs/sphinx/source/theory/supportedEquationSet.rst diff --git a/docs/source/theory/symmetry.yaml b/docs/sphinx/source/theory/symmetry.yaml similarity index 100% rename from docs/source/theory/symmetry.yaml rename to docs/sphinx/source/theory/symmetry.yaml diff --git a/docs/source/theory/timeDiscretization.rst b/docs/sphinx/source/theory/timeDiscretization.rst similarity index 100% rename from docs/source/theory/timeDiscretization.rst rename to docs/sphinx/source/theory/timeDiscretization.rst diff --git a/docs/source/theory/topologicalSupport.rst b/docs/sphinx/source/theory/topologicalSupport.rst similarity index 100% rename from docs/source/theory/topologicalSupport.rst rename to docs/sphinx/source/theory/topologicalSupport.rst diff --git a/docs/source/theory/turbulenceModeling.rst b/docs/sphinx/source/theory/turbulenceModeling.rst similarity index 100% rename from docs/source/theory/turbulenceModeling.rst rename to docs/sphinx/source/theory/turbulenceModeling.rst diff --git a/docs/source/theory/windEnergy.rst b/docs/sphinx/source/theory/windEnergy.rst similarity index 100% rename from docs/source/theory/windEnergy.rst rename to docs/sphinx/source/theory/windEnergy.rst diff --git a/docs/source/user/build_manually.rst b/docs/sphinx/source/user/build_manually.rst similarity index 100% rename from docs/source/user/build_manually.rst rename to docs/sphinx/source/user/build_manually.rst diff --git a/docs/source/user/build_spack.rst b/docs/sphinx/source/user/build_spack.rst similarity index 100% rename from docs/source/user/build_spack.rst rename to docs/sphinx/source/user/build_spack.rst diff --git a/docs/source/user/building.rst b/docs/sphinx/source/user/building.rst similarity index 100% rename from docs/source/user/building.rst rename to docs/sphinx/source/user/building.rst diff --git a/docs/source/user/do-config-nalu-wind.sh b/docs/sphinx/source/user/do-config-nalu-wind.sh similarity index 100% rename from docs/source/user/do-config-nalu-wind.sh rename to docs/sphinx/source/user/do-config-nalu-wind.sh diff --git a/docs/source/user/do-config-trilinos.sh b/docs/sphinx/source/user/do-config-trilinos.sh similarity index 100% rename from docs/source/user/do-config-trilinos.sh rename to docs/sphinx/source/user/do-config-trilinos.sh diff --git a/docs/source/user/index.rst b/docs/sphinx/source/user/index.rst similarity index 100% rename from docs/source/user/index.rst rename to docs/sphinx/source/user/index.rst diff --git a/docs/source/user/nalu_run/McAlisterLessonsLearned.rst b/docs/sphinx/source/user/nalu_run/McAlisterLessonsLearned.rst similarity index 100% rename from docs/source/user/nalu_run/McAlisterLessonsLearned.rst rename to docs/sphinx/source/user/nalu_run/McAlisterLessonsLearned.rst diff --git a/docs/source/user/nalu_run/abl_forcing.rst b/docs/sphinx/source/user/nalu_run/abl_forcing.rst similarity index 100% rename from docs/source/user/nalu_run/abl_forcing.rst rename to docs/sphinx/source/user/nalu_run/abl_forcing.rst diff --git a/docs/source/user/nalu_run/figures/ramp.png b/docs/sphinx/source/user/nalu_run/figures/ramp.png similarity index 100% rename from docs/source/user/nalu_run/figures/ramp.png rename to docs/sphinx/source/user/nalu_run/figures/ramp.png diff --git a/docs/source/user/nalu_run/grid07_conformal10_surf_tip.png b/docs/sphinx/source/user/nalu_run/grid07_conformal10_surf_tip.png similarity index 100% rename from docs/source/user/nalu_run/grid07_conformal10_surf_tip.png rename to docs/sphinx/source/user/nalu_run/grid07_conformal10_surf_tip.png diff --git a/docs/source/user/nalu_run/grid07_conformal10_surf_tip_close.png b/docs/sphinx/source/user/nalu_run/grid07_conformal10_surf_tip_close.png similarity index 100% rename from docs/source/user/nalu_run/grid07_conformal10_surf_tip_close.png rename to docs/sphinx/source/user/nalu_run/grid07_conformal10_surf_tip_close.png diff --git a/docs/source/user/nalu_run/nalu.i b/docs/sphinx/source/user/nalu_run/nalu.i similarity index 100% rename from docs/source/user/nalu_run/nalu.i rename to docs/sphinx/source/user/nalu_run/nalu.i diff --git a/docs/source/user/nalu_run/nalu_inp.rst b/docs/sphinx/source/user/nalu_run/nalu_inp.rst similarity index 100% rename from docs/source/user/nalu_run/nalu_inp.rst rename to docs/sphinx/source/user/nalu_run/nalu_inp.rst diff --git a/docs/source/user/nalu_run/nalu_mesh.rst b/docs/sphinx/source/user/nalu_run/nalu_mesh.rst similarity index 100% rename from docs/source/user/nalu_run/nalu_mesh.rst rename to docs/sphinx/source/user/nalu_run/nalu_mesh.rst diff --git a/docs/source/user/nalu_run/nalux.rst b/docs/sphinx/source/user/nalu_run/nalux.rst similarity index 100% rename from docs/source/user/nalu_run/nalux.rst rename to docs/sphinx/source/user/nalu_run/nalux.rst diff --git a/docs/source/user/nalu_run/turbine_modeling.rst b/docs/sphinx/source/user/nalu_run/turbine_modeling.rst similarity index 100% rename from docs/source/user/nalu_run/turbine_modeling.rst rename to docs/sphinx/source/user/nalu_run/turbine_modeling.rst diff --git a/docs/source/user/running.rst b/docs/sphinx/source/user/running.rst similarity index 100% rename from docs/source/user/running.rst rename to docs/sphinx/source/user/running.rst diff --git a/docs/source/user/verify_installation.rst b/docs/sphinx/source/user/verify_installation.rst similarity index 100% rename from docs/source/user/verify_installation.rst rename to docs/sphinx/source/user/verify_installation.rst diff --git a/docs/source/verification/figures/T_123.png b/docs/sphinx/source/verification/figures/T_123.png similarity index 100% rename from docs/source/verification/figures/T_123.png rename to docs/sphinx/source/verification/figures/T_123.png diff --git a/docs/source/verification/figures/T_linear_gradBC.png b/docs/sphinx/source/verification/figures/T_linear_gradBC.png similarity index 100% rename from docs/source/verification/figures/T_linear_gradBC.png rename to docs/sphinx/source/verification/figures/T_linear_gradBC.png diff --git a/docs/source/verification/figures/T_parabolic_gradBC.png b/docs/sphinx/source/verification/figures/T_parabolic_gradBC.png similarity index 100% rename from docs/source/verification/figures/T_parabolic_gradBC.png rename to docs/sphinx/source/verification/figures/T_parabolic_gradBC.png diff --git a/docs/source/verification/figures/U_x_CTV_subsequent_L2.pdf b/docs/sphinx/source/verification/figures/U_x_CTV_subsequent_L2.pdf similarity index 100% rename from docs/source/verification/figures/U_x_CTV_subsequent_L2.pdf rename to docs/sphinx/source/verification/figures/U_x_CTV_subsequent_L2.pdf diff --git a/docs/source/verification/figures/U_x_precursor.pdf b/docs/sphinx/source/verification/figures/U_x_precursor.pdf similarity index 100% rename from docs/source/verification/figures/U_x_precursor.pdf rename to docs/sphinx/source/verification/figures/U_x_precursor.pdf diff --git a/docs/source/verification/figures/Ux_123.png b/docs/sphinx/source/verification/figures/Ux_123.png similarity index 100% rename from docs/source/verification/figures/Ux_123.png rename to docs/sphinx/source/verification/figures/Ux_123.png diff --git a/docs/source/verification/figures/Ux_23.png b/docs/sphinx/source/verification/figures/Ux_23.png similarity index 100% rename from docs/source/verification/figures/Ux_23.png rename to docs/sphinx/source/verification/figures/Ux_23.png diff --git a/docs/source/verification/figures/Uz_L2_dp.pdf b/docs/sphinx/source/verification/figures/Uz_L2_dp.pdf similarity index 100% rename from docs/source/verification/figures/Uz_L2_dp.pdf rename to docs/sphinx/source/verification/figures/Uz_L2_dp.pdf diff --git a/docs/source/verification/figures/abl_sub_check_one_two.png b/docs/sphinx/source/verification/figures/abl_sub_check_one_two.png similarity index 100% rename from docs/source/verification/figures/abl_sub_check_one_two.png rename to docs/sphinx/source/verification/figures/abl_sub_check_one_two.png diff --git a/docs/source/verification/figures/abl_sub_cycle_T.pdf b/docs/sphinx/source/verification/figures/abl_sub_cycle_T.pdf similarity index 100% rename from docs/source/verification/figures/abl_sub_cycle_T.pdf rename to docs/sphinx/source/verification/figures/abl_sub_cycle_T.pdf diff --git a/docs/source/verification/figures/convTaylorVortexFO.pdf b/docs/sphinx/source/verification/figures/convTaylorVortexFO.pdf similarity index 100% rename from docs/source/verification/figures/convTaylorVortexFO.pdf rename to docs/sphinx/source/verification/figures/convTaylorVortexFO.pdf diff --git a/docs/source/verification/figures/convTaylorVortexSO.pdf b/docs/sphinx/source/verification/figures/convTaylorVortexSO.pdf similarity index 100% rename from docs/source/verification/figures/convTaylorVortexSO.pdf rename to docs/sphinx/source/verification/figures/convTaylorVortexSO.pdf diff --git a/docs/source/verification/figures/convTaylorVortexSO_ElemLagElemPf.pdf b/docs/sphinx/source/verification/figures/convTaylorVortexSO_ElemLagElemPf.pdf similarity index 100% rename from docs/source/verification/figures/convTaylorVortexSO_ElemLagElemPf.pdf rename to docs/sphinx/source/verification/figures/convTaylorVortexSO_ElemLagElemPf.pdf diff --git a/docs/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoC.pdf b/docs/sphinx/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoC.pdf similarity index 100% rename from docs/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoC.pdf rename to docs/sphinx/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoC.pdf diff --git a/docs/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf b/docs/sphinx/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf similarity index 100% rename from docs/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf rename to docs/sphinx/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_OoCPNG.pdf diff --git a/docs/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_tempField.pdf b/docs/sphinx/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_tempField.pdf similarity index 100% rename from docs/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_tempField.pdf rename to docs/sphinx/source/verification/figures/dgNonconformalCVFEM_3dTempMMS_tempField.pdf diff --git a/docs/source/verification/figures/ew_aoa.pdf b/docs/sphinx/source/verification/figures/ew_aoa.pdf similarity index 100% rename from docs/source/verification/figures/ew_aoa.pdf rename to docs/sphinx/source/verification/figures/ew_aoa.pdf diff --git a/docs/source/verification/figures/ew_dragcoeff.pdf b/docs/sphinx/source/verification/figures/ew_dragcoeff.pdf similarity index 100% rename from docs/source/verification/figures/ew_dragcoeff.pdf rename to docs/sphinx/source/verification/figures/ew_dragcoeff.pdf diff --git a/docs/source/verification/figures/ew_dragforceperunitlength.pdf b/docs/sphinx/source/verification/figures/ew_dragforceperunitlength.pdf similarity index 100% rename from docs/source/verification/figures/ew_dragforceperunitlength.pdf rename to docs/sphinx/source/verification/figures/ew_dragforceperunitlength.pdf diff --git a/docs/source/verification/figures/ew_liftcoeff.pdf b/docs/sphinx/source/verification/figures/ew_liftcoeff.pdf similarity index 100% rename from docs/source/verification/figures/ew_liftcoeff.pdf rename to docs/sphinx/source/verification/figures/ew_liftcoeff.pdf diff --git a/docs/source/verification/figures/ew_liftforceperunitlength.pdf b/docs/sphinx/source/verification/figures/ew_liftforceperunitlength.pdf similarity index 100% rename from docs/source/verification/figures/ew_liftforceperunitlength.pdf rename to docs/sphinx/source/verification/figures/ew_liftforceperunitlength.pdf diff --git a/docs/source/verification/figures/fw_bladeresults.png b/docs/sphinx/source/verification/figures/fw_bladeresults.png similarity index 100% rename from docs/source/verification/figures/fw_bladeresults.png rename to docs/sphinx/source/verification/figures/fw_bladeresults.png diff --git a/docs/source/verification/figures/fw_bladeschematic.png b/docs/sphinx/source/verification/figures/fw_bladeschematic.png similarity index 100% rename from docs/source/verification/figures/fw_bladeschematic.png rename to docs/sphinx/source/verification/figures/fw_bladeschematic.png diff --git a/docs/source/verification/figures/hex8_tet4_one_two_ten_R0_R1.png b/docs/sphinx/source/verification/figures/hex8_tet4_one_two_ten_R0_R1.png similarity index 100% rename from docs/source/verification/figures/hex8_tet4_one_two_ten_R0_R1.png rename to docs/sphinx/source/verification/figures/hex8_tet4_one_two_ten_R0_R1.png diff --git a/docs/source/verification/figures/ho_heatCondMMM_dtdx.pdf b/docs/sphinx/source/verification/figures/ho_heatCondMMM_dtdx.pdf similarity index 100% rename from docs/source/verification/figures/ho_heatCondMMM_dtdx.pdf rename to docs/sphinx/source/verification/figures/ho_heatCondMMM_dtdx.pdf diff --git a/docs/source/verification/figures/ho_stvUandDpDx.pdf b/docs/sphinx/source/verification/figures/ho_stvUandDpDx.pdf similarity index 100% rename from docs/source/verification/figures/ho_stvUandDpDx.pdf rename to docs/sphinx/source/verification/figures/ho_stvUandDpDx.pdf diff --git a/docs/source/verification/figures/hybrid_T_L2.pdf b/docs/sphinx/source/verification/figures/hybrid_T_L2.pdf similarity index 100% rename from docs/source/verification/figures/hybrid_T_L2.pdf rename to docs/sphinx/source/verification/figures/hybrid_T_L2.pdf diff --git a/docs/source/verification/figures/hybrid_T_Loo.pdf b/docs/sphinx/source/verification/figures/hybrid_T_Loo.pdf similarity index 100% rename from docs/source/verification/figures/hybrid_T_Loo.pdf rename to docs/sphinx/source/verification/figures/hybrid_T_Loo.pdf diff --git a/docs/source/verification/figures/hybrid_laplace.png b/docs/sphinx/source/verification/figures/hybrid_laplace.png similarity index 100% rename from docs/source/verification/figures/hybrid_laplace.png rename to docs/sphinx/source/verification/figures/hybrid_laplace.png diff --git a/docs/source/verification/figures/openJetFlowStill.pdf b/docs/sphinx/source/verification/figures/openJetFlowStill.pdf similarity index 100% rename from docs/source/verification/figures/openJetFlowStill.pdf rename to docs/sphinx/source/verification/figures/openJetFlowStill.pdf diff --git a/docs/source/verification/figures/openJetInlet.pdf b/docs/sphinx/source/verification/figures/openJetInlet.pdf similarity index 100% rename from docs/source/verification/figures/openJetInlet.pdf rename to docs/sphinx/source/verification/figures/openJetInlet.pdf diff --git a/docs/source/verification/figures/tquadEdgeCvfemTdiff.pdf b/docs/sphinx/source/verification/figures/tquadEdgeCvfemTdiff.pdf similarity index 100% rename from docs/source/verification/figures/tquadEdgeCvfemTdiff.pdf rename to docs/sphinx/source/verification/figures/tquadEdgeCvfemTdiff.pdf diff --git a/docs/source/verification/figures/tquadLaplaceMMS.pdf b/docs/sphinx/source/verification/figures/tquadLaplaceMMS.pdf similarity index 100% rename from docs/source/verification/figures/tquadLaplaceMMS.pdf rename to docs/sphinx/source/verification/figures/tquadLaplaceMMS.pdf diff --git a/docs/source/verification/figures/tquadLaplaceMMSCVFEM.pdf b/docs/sphinx/source/verification/figures/tquadLaplaceMMSCVFEM.pdf similarity index 100% rename from docs/source/verification/figures/tquadLaplaceMMSCVFEM.pdf rename to docs/sphinx/source/verification/figures/tquadLaplaceMMSCVFEM.pdf diff --git a/docs/source/verification/index.rst b/docs/sphinx/source/verification/index.rst similarity index 100% rename from docs/source/verification/index.rst rename to docs/sphinx/source/verification/index.rst diff --git a/docs/source/verification/introduction.rst b/docs/sphinx/source/verification/introduction.rst similarity index 100% rename from docs/source/verification/introduction.rst rename to docs/sphinx/source/verification/introduction.rst diff --git a/docs/source/verification/verification.rst b/docs/sphinx/source/verification/verification.rst similarity index 100% rename from docs/source/verification/verification.rst rename to docs/sphinx/source/verification/verification.rst diff --git a/docs/zrefs.rst b/docs/sphinx/zrefs.rst similarity index 100% rename from docs/zrefs.rst rename to docs/sphinx/zrefs.rst