Merge remote-tracking branch 'upstream/develop' into fix-optical-gen-energy

Author: amandalund

.github/CODEOWNERS

@@ -1,12 +1,9 @@
-#-----------------------------------------------------------------------------#
+#-----------------------------*- codeowners -*--------------------------------#
 # CELERITAS PROJECT CODEOWNERS
 # See discussion in /doc/development/administration.rst .
 # Note that later lines take precedence over earlier ones.
 #-----------------------------------------------------------------------------#
 
-# Default all changes to ping the code lead if not overridden below
-* @celeritas-project/code-lead
-
 #-------------------------------------#
 # Topics
 #-------------------------------------#
@@ -21,26 +18,30 @@
 /cmake/ @sethrj @pcanal
 /scripts/ci/ @sethrj @pcanal
 /scripts/docker/interactive @esseivaju
-/scripts/**/perlmutter.* @esseivaju
+
+# Input definitions
+/*/*/inp/ @sethrj
 
 # Core capabilities
-/src/corecel/ @sethrj
-/src/corecel/random/ @davidsgr @amandalund
-/src/corecel/sys/ @esseivaju
+/*/corecel/ @sethrj
+/*/corecel/random/**/Xorwow* @amandalund
+/*/corecel/random/**/Ranlux* @davidsgr @sethrj
+/*/corecel/sys/ @esseivaju
 
 # Physics
-/src/celeritas/em/ @amandalund @stognini @whokion
-/src/celeritas/field/ @sethrj @whokion
-/src/celeritas/neutron/ @whokion
-/src/celeritas/optical/ @amandalund @hhollenb @Rashika-Gupta @whokion
-/src/celeritas/phys/ @sethrj @amandalund
-/src/celeritas/track/ @amandalund @esseivaju @LSchwiebert
+/*/celeritas/decay/ @amandalund @stognini
+/*/celeritas/em/ @amandalund @stognini @whokion
+/*/celeritas/field/ @sethrj @whokion
+/*/celeritas/neutron/ @whokion
+/*/celeritas/optical/ @amandalund @hhollenb @whokion
+/*/celeritas/phys/ @sethrj @amandalund
+/*/celeritas/track/ @amandalund @esseivaju @LSchwiebert
 
 # Geometry
-/src/orange/ @elliottbiondo @esseivaju @sethrj
-/src/geocel/vg/ @mrguilima @sethrj
+/*/orange/ @elliottbiondo @sethrj
+/*/geocel/vg/ @mrguilima @sethrj
 
 # Integration
-/src/celeritas/g4/ @drbenmorgan @sethrj @stognini @whokion
-/src/celeritas/ext/ @drbenmorgan @sethrj @stognini @whokion
-/src/accel/ @drbenmorgan @esseivaju @rahmans1 @Rashika-Gupta @sethrj @stognini @whokion
+/*/celeritas/g4/ @drbenmorgan @stognini
+/*/celeritas/ext/ @drbenmorgan @stognini
+/*/accel/ @drbenmorgan @esseivaju @rahmans1 @Rashika-Gupta @sethrj @stognini @whokion

.github/workflows/build-docker.yml

@@ -75,7 +75,7 @@ jobs:
       # NOTE: checkout must occur *after* setting up environment for git tags to work
       # NOTE: depth must be enough to include the previous tag
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
         with:
           fetch-depth: 383
           fetch-tags: true
@@ -93,7 +93,10 @@ jobs:
       - name: Build Celeritas
         working-directory: build
         run: |
-          ninja
+          echo "::group::Build verbosely"
+          ninja -v -k0
+          echo "::endgroup::"
+          echo "::notice title=build-size::Build size is $(du -hs . | awk '{print $1}')"
 
       ### TEST ###
 
@@ -129,10 +132,19 @@ jobs:
       ### INSTALL ###
 
       - name: Install Celeritas
+        id: install
         working-directory: build
         run: |
+          echo "::group::Install"
           cmake --install .
+          echo "::endgroup::"
+          cmake --build . --target clean
       - name: Check installation
+        if: >-
+          ${{
+            !cancelled()
+            && steps.install.outcome == 'success'
+          }}
         working-directory: install
         run: |
           for exe in orange-update celer-export-geant \
@@ -144,7 +156,8 @@ jobs:
         # TODO: rocm+ndebug fails to propagate HIP library link
         if: >-
           ${{
-            !(matrix.image == 'ubuntu-rocm' && matrix.buildtype == 'ndebug')
+            steps.install.outcome == 'success'
+            && !(matrix.image == 'ubuntu-rocm' && matrix.buildtype == 'ndebug')
           }}
         run: |
           . /etc/profile

.github/workflows/build-fast.yml

@@ -58,7 +58,7 @@ jobs:
       }}
     steps:
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
 
       ### ENVIRONMENT ###
 
@@ -162,7 +162,7 @@ jobs:
     runs-on: windows-latest
     steps:
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
 
       ### ENVIRONMENT ###
 

.github/workflows/build-spack.yml

@@ -105,7 +105,7 @@ jobs:
     continue-on-error: false
     steps:
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
         with:
           fetch-depth: ${{format('{0}', matrix.special != 'tidy' && 383 || 0)}}
           fetch-tags: true # to get version information
@@ -122,6 +122,7 @@ jobs:
           path: spack-src
       - name: Initialize spack environment
         run: |
+          echo "::notice title=spack-arch::Spack architecture is $(spack arch)"
           sed -e 's/cxxstd=default/cxxstd=${{env.CXXSTD}}/' \
             scripts/ci/spack.yaml > spack.yaml
           if ${{matrix.geometry == 'vecgeom'}}; then
@@ -144,7 +145,9 @@ jobs:
                 && matrix.geant != ''}}; then
             spack -e . add [email protected]
           fi
+          echo "::group::Find compilers"
           spack -vd -e . compiler find --mixed-toolchain
+          echo "::endgroup::"
           # Add the spack ref so that updating spack will reconcretize
           echo "# Concretized with ${{env.SPACK_REF}}" >> spack.yaml
       - name: Cache concretization
@@ -159,7 +162,6 @@ jobs:
         run: |
           spack -e . -v concretize || (
             ERR=$?
-            spack arch
             cat spack.yaml
             exit $ERR
           )
@@ -188,8 +190,6 @@ jobs:
 
       - name: Configure Celeritas
         run: |
-          # NOTE: tags have issues, see https://github.com/actions/checkout/issues/2041
-          git fetch --tags
           ln -fs scripts/cmake-presets/ci-ubuntu-github.json CMakeUserPresets.json
           if ${{matrix.geant == '11.0'}}; then
             # Test overriding of Geant4 environment variables
@@ -244,7 +244,10 @@ jobs:
         working-directory: build
         run: |
           ccache -z
+          echo "::group::Build verbosely"
           ninja -v -k0
+          echo "::endgroup::"
+          echo "::notice title=build-size::Build size is $(du -hs . | awk '{print $1}')"
       - name: Show ccache stats
         if: ${{!cancelled() && steps.installdeps.outcome == 'success'}}
         run: |
@@ -356,7 +359,10 @@ jobs:
           }}
         working-directory: build
         run: |
-          ninja install
+          echo "::group::Install"
+          cmake --install .
+          echo "::endgroup::"
+          ninja clean
       - name: Check installation
         if: >-
           ${{
@@ -372,13 +378,12 @@ jobs:
           ./bin/celer-sim --config
       - name: Build examples
         env:
-          CELER_DISABLE_G4_EXAMPLES: >-
-            ${{(!matrix.geant) && '1' || ''}}
-        # Special clang features require downstream flags that don't propagate
+          CELER_DISABLE_G4_EXAMPLES: ${{(!matrix.geant) && '1' || ''}}
+        # `asanlite` requires downstream flags that don't propagate
         if: >-
           ${{
-            matrix.special != 'asanlite'
-            && matrix.special != 'tidy'
+            steps.install.outcome == 'success'
+            && matrix.special != 'asanlite'
           }}
         run: |
           . ${SPACK_VIEW}/rc

.github/workflows/build-ultralite.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-24.04
     steps:
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
 
       ### ENVIRONMENT ###
 
@@ -121,7 +121,7 @@ jobs:
     runs-on: windows-latest
     steps:
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
 
       ### ENVIRONMENT ###
 

.github/workflows/deploy-pages.yml

@@ -30,7 +30,7 @@ jobs:
     needs: build-docs
     steps:
       - name: Check out Celeritas doc base
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
         with:
           ref: doc/gh-pages-base
       - uses: actions/setup-python@v5

.github/workflows/doc.yml

@@ -36,16 +36,14 @@ jobs:
             sudo apt-get -y install \
                 cmake graphviz ninja-build doxygen nlohmann-json3-dev
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
         with:
           fetch-depth: 383
           fetch-tags: true
       - name: Configure celeritas
         # Turn warnings into errors only for PRs
         # Disable expensive graphs for PRs also
         run: |
-          # NOTE: tags have issues, see https://github.com/actions/checkout/issues/2041
-          git fetch --tags
           ln -fs scripts/cmake-presets/ci-ubuntu-github.json CMakeUserPresets.json
           mkdir build && cd build
           cmake --preset=${CMAKE_PRESET} --log-level=VERBOSE \
@@ -79,7 +77,7 @@ jobs:
             sudo apt-get -y install \
                 cmake graphviz ninja-build doxygen nlohmann-json3-dev
       - name: Check out Celeritas
-        uses: actions/checkout@v4
+        uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8  # v6.0.1 (2 Dec 2025)
         with:
           fetch-depth: 383
           fetch-tags: true
@@ -92,13 +90,11 @@ jobs:
             pip install -r scripts/doc-requirements.txt
       - name: Configure celeritas
         run: |
-          # NOTE: tags have issues, see https://github.com/actions/checkout/issues/2041
-          git fetch --tags
           ln -fs scripts/cmake-presets/ci-ubuntu-github.json CMakeUserPresets.json
           mkdir build && cd build
           cmake --preset=${CMAKE_PRESET} --log-level=VERBOSE \
             ${{ github.workflow == 'pull_request'
-             && '-DDOXYGEN_WARN_AS_ERROR="YES" -DCELERITAS_SPHINX_USER_HTML_ARGS="-W;--keep-going"'
+             && '-DDOXYGEN_WARN_AS_ERROR="YES" -DCELERITAS_SPHINX_ARGS="-W;--keep-going"'
              || ''}} \
             ..
       - name: Build documentation

doc/CMakeLists.txt

@@ -110,6 +110,7 @@ if(CELERITAS_PYTHONPATH_RERUN)
   unset(CELERITAS_PYTHONPATH_RERUN CACHE)
 endif()
 
+
 if(NOT Sphinx_FOUND)
   function(celeritas_build_sphinx type output depends)
     add_custom_command(
@@ -125,6 +126,10 @@ if(NOT Sphinx_FOUND)
     )
   endfunction()
 else()
+  set(CELERITAS_SPHINX_ARGS "" CACHE STRING
+    "Additional arguments to pass to Sphinx to build user docs")
+  mark_as_advanced(CELERITAS_SPHINX_ARGS)
+
   celeritas_get_pyenv(CELER_PYTHONENV)
   function(celeritas_build_sphinx type output depends)
     if(NOT type STREQUAL "dummy")
@@ -139,7 +144,7 @@ else()
         "$<TARGET_FILE:Python::Interpreter>" -m sphinx.cmd.build -q
           -d "${CMAKE_CURRENT_BINARY_DIR}/doctrees"
           -b ${type}
-          ${ARGN}
+          ${CELERITAS_SPHINX_ARGS}
           "${CMAKE_CURRENT_SOURCE_DIR}"
           "${CMAKE_CURRENT_BINARY_DIR}/${type}"
       COMMENT "${_comment}"
@@ -272,7 +277,7 @@ doxygen_add_docs(doxygen_xml
 )
 
 #-----------------------------------------------------------------------------#
-# MMD PROCESSING
+# GRAPHICS PROCESSING
 
 # Note that *all* dot files must be present at the same time to prevent
 # errors when doing separate HTML/PDF builds: the doctrees directory caches the
@@ -338,12 +343,8 @@ add_custom_target(doc_preprocess DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/${_doctree
 
 #-----------------------------------------------------------------------------#
 # HTML
-set(CELERITAS_SPHINX_USER_HTML_ARGS "" CACHE STRING
-  "Additional arguments to pass to Sphinx to build HTML user docs")
-mark_as_advanced(CELERITAS_SPHINX_USER_HTML_ARGS)
-
 set(_doc_html "html/index.html")
-celeritas_build_sphinx(html "${_doc_html}" "${_doctree_env}" ${CELERITAS_SPHINX_USER_HTML_ARGS})
+celeritas_build_sphinx(html "${_doc_html}" "${_doctree_env}")
 add_custom_target(doc DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/${_doc_html}")
 
 install(DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/html/"

doc/implementation/geometry/orange/translation.rst

@@ -138,5 +138,5 @@ Configuration
 For debugging purposes, a special struct can be deserialized from a JSON input
 file specified with the ``G4ORG_OPTIONS`` environment variable.
 
-.. doxygenenum:: celeritas::g4org::InlineSingletons
-.. celerstruct:: g4org::Options
+.. doxygenenum:: celeritas::inp::InlineSingletons
+.. celerstruct:: inp::OrangeGeoFromGeant

doc/implementation/mucf-physics.rst

@@ -101,7 +101,7 @@ muonic atom spin flip. The muon-catalyzed fusion process is activated by
 enabling the ``mucf_physics`` option in
 :cpp:class:`celeritas::ext::GeantPhysicsOptions`.
 
-.. doxygenclass:: celeritas::inp::MucfPhysics
+.. celerstruct:: inp::MucfPhysics
 
 .. todo:: Expand description when hardcoded data is finalized.