Merge branch 'master' into levelset-refactor

Author: sbryngelson

.pr_agent.toml

@@ -1,7 +1,12 @@
 # .pr_agent.toml
 [github_app]
-# Run these tools automatically on every new PR:
-pr_commands = ["/describe", "/review", "/improve"]
+pr_commands = [
+  "/review",
+  "/improve",
+]
+
+handle_push_trigger = true
+push_commands = ["/improve"]
 
 [pr_reviewer]                # (all fields optional)
 num_max_findings        = 10  # how many items to surface

.typos.toml

@@ -30,4 +30,4 @@ unknwn = "unknwn"     # typo for "unknown" - tests unknown param detection
 tru = "tru"           # typo for "true" in "when_tru" - tests dependency keys
 
 [files]
-extend-exclude = ["docs/documentation/references*", "tests/", "toolchain/cce_simulation_workgroup_256.sh", "build-docs/"]
+extend-exclude = ["docs/documentation/references*", "docs/references.bib", "tests/", "toolchain/cce_simulation_workgroup_256.sh", "build-docs/"]

CMakeLists.txt

@@ -720,6 +720,7 @@ if (MFC_DOCUMENTATION)
         set(DOXYGEN_HTML_OUTPUT      "\"${CMAKE_CURRENT_BINARY_DIR}/${target}\"")
         set(DOXYGEN_MATHJAX_CODEFILE "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/config.js\"")
         set(DOXYGEN_PROJECT_LOGO     "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/res/icon.ico\"")
+        set(DOXYGEN_CITE_BIB_FILES   "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/references.bib\"")
         set(DOXYGEN_IMAGE_PATH       "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/res\"\
                                       \"${CMAKE_CURRENT_SOURCE_DIR}/docs/${target}\"")
 
@@ -752,6 +753,8 @@ if (MFC_DOCUMENTATION)
                     "${opt_parameters_dependency}"
                     "${${target}_SRCs}" "${${target}_DOCs}"
             COMMAND "${DOXYGEN_EXECUTABLE}" "${target}-Doxyfile"
+            COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/postprocess_citations.py"
+                    "${CMAKE_CURRENT_BINARY_DIR}/${target}"
             WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
             COMMENT "${target}: Generating documentation"
         )
@@ -771,6 +774,7 @@ if (MFC_DOCUMENTATION)
     add_custom_target(documentation)
 
     find_package(Doxygen REQUIRED dot REQUIRED)
+    find_package(Python3 REQUIRED COMPONENTS Interpreter)
 
     # > Fetch CSS Theme
     ExternalProject_Add(doxygen-awesome-css

docs/Doxyfile.in

@@ -740,7 +740,7 @@ LAYOUT_FILE            =
 # 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.
 
-CITE_BIB_FILES         =
+CITE_BIB_FILES         = @DOXYGEN_CITE_BIB_FILES@
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages