Merge pull request dealii#17893 from jpthiele/precommit

marcfehling · web-flow · commit aa53ff944792 · 2024-12-02T10:07:10.000+01:00
Add pre-commit config and CI job
diff --git a/.github/workflows/indent.yml b/.github/workflows/indent.yml
@@ -68,16 +68,3 @@ jobs:
       with:
         name: doxygen_documentation
         path: build/doc/doxygen
-
-  typos:
-    # check for typos
-
-    name: typos
-    runs-on: [ubuntu-24.04]
-
-    steps:
-    - uses: actions/checkout@v4
-    - uses: crate-ci/typos@v1.27.3
-      with:
-        files: doc examples include source tests
-        config: ./.typos.toml
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,19 @@
+name: pre-commit
+
+on: [push, pull_request]
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+permissions:
+  contents: read
+
+env:
+  SKIP: clang-format, no-commit-to-branch
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+    - uses: pre-commit/action@v3.0.1
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,48 @@
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: check-added-large-files
+    args: [--maxkb=8192]
+  - id: check-merge-conflict
+  - id: check-json
+    exclude: tests/a-framework/parameter_file_3\.json
+  - id: check-toml
+  - id: check-yaml
+    args: [--allow-multiple-documents]
+  - id: end-of-file-fixer
+    exclude: |
+        (?x)(
+            \.output|
+            \.run_only|
+            \.diff|
+            ^bundled/
+        )
+  - id: no-commit-to-branch
+    args: [--branch,master]
+  - id: trailing-whitespace
+    files: |
+        (?x)(
+            \.(cc|h$|html|doc|txt)|
+            ^doc/news
+        )
+    exclude: ^bundled/
+- repo: https://github.com/gitleaks/gitleaks
+  rev: v8.21.2
+  hooks:
+  - id: gitleaks
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v16.0.6
+  hooks:
+  - id: clang-format
+    files: |
+        (?x)(
+            \.inst\.in |
+            \.cc |
+            \.h
+        )$
+- repo: https://github.com/crate-ci/typos
+  rev: v1.28.1
+  hooks:
+  - id: typos
+    files: (?x) ^(doc|examples|include|source|tests)/
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,4 +3,4 @@ Changes to deal.II between versions
 
 The list of changes between versions of deal.II is maintained as part of the
 regular documentation. You can find it
-[here](https://www.dealii.org/developer/doxygen/deal.II/pages.html).
+[here](https://www.dealii.org/developer/doxygen/deal.II/pages.html).
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -40,7 +40,7 @@ cmake_policy(VERSION 3.13.4)
 
 if(POLICY CMP0074)
   # Introduced in CMake 3.12: find_package(<PackageName>) also searches
-  # <PackageName>_ROOT CMake and environment variables when set to NEW. 
+  # <PackageName>_ROOT CMake and environment variables when set to NEW.
   cmake_policy(SET CMP0074 NEW)
 endif()
 
diff --git a/README.md b/README.md
@@ -82,4 +82,3 @@ by running, for example:
 The above command would drop you into an isolated environment, in which you 
 will find the latest version of deal.II (master development branch) installed
 under `/usr/local`.
-
diff --git a/cmake/config/CMakeLists.txt b/cmake/config/CMakeLists.txt
@@ -192,4 +192,3 @@ install(FILES
 #
 
 message(STATUS "Setting up project configuration - Done")
-
diff --git a/cmake/config/ConfigGit.cmake.in b/cmake/config/ConfigGit.cmake.in
@@ -21,4 +21,3 @@ set(DEAL_II_GIT_BRANCH "@DEAL_II_GIT_BRANCH@")
 set(DEAL_II_GIT_REVISION "@DEAL_II_GIT_REVISION@")
 set(DEAL_II_GIT_SHORTREV "@DEAL_II_GIT_SHORTREV@")
 set(DEAL_II_GIT_TAG "@DEAL_II_GIT_TAG@")
-
diff --git a/cmake/config/ConfigVersion.cmake.in b/cmake/config/ConfigVersion.cmake.in
@@ -14,4 +14,3 @@ else()
     set(PACKAGE_VERSION_EXACT TRUE)
   endif()
 endif()
-
diff --git a/cmake/configure/TestBoostBug/polymorphic_derived2.cpp b/cmake/configure/TestBoostBug/polymorphic_derived2.cpp
@@ -44,4 +44,4 @@ void polymorphic_derived2::serialize(
 );
 
 // note: export has to be AFTER #includes for all archive classes
-BOOST_CLASS_EXPORT_IMPLEMENT(polymorphic_derived2)
+BOOST_CLASS_EXPORT_IMPLEMENT(polymorphic_derived2)
diff --git a/cmake/configure/TestBoostBug/polymorphic_derived2.hpp b/cmake/configure/TestBoostBug/polymorphic_derived2.hpp
@@ -39,4 +39,3 @@ BOOST_CLASS_TYPE_INFO(
 )
 
 #endif // POLYMORPHIC_DERIVED2_HPP
-
diff --git a/cmake/configure/configure_10_taskflow.cmake b/cmake/configure/configure_10_taskflow.cmake
@@ -46,4 +46,3 @@ endmacro()
 
 
 configure_feature(TASKFLOW)
-
diff --git a/cmake/configure/configure_30_kokkos.cmake b/cmake/configure/configure_30_kokkos.cmake
@@ -37,4 +37,3 @@ if(NOT DEAL_II_WITH_KOKKOS)
       )
   endif()
 endif()
-
diff --git a/cmake/configure/configure_50_arborx.cmake b/cmake/configure/configure_50_arborx.cmake
@@ -78,4 +78,3 @@ macro(feature_arborx_find_external var)
 endmacro()
 
 configure_feature(ARBORX)
-
diff --git a/cmake/configure/configure_50_complex_values.cmake b/cmake/configure/configure_50_complex_values.cmake
@@ -38,4 +38,3 @@ if(${DEAL_II_WITH_COMPLEX_VALUES})
        "LinearAlgebra::distributed::BlockVector<std::complex<float> >"
       )
 endif()
-
diff --git a/cmake/macros/check_compiler_setup/CMakeLists.txt b/cmake/macros/check_compiler_setup/CMakeLists.txt
@@ -8,4 +8,3 @@ add_executable(CheckCompilerSetupExec dummy.cpp)
 target_compile_options(CheckCompilerSetupExec PRIVATE ${TEST_COMPILE_OPTIONS})
 target_link_options(CheckCompilerSetupExec PRIVATE ${TEST_LINK_OPTIONS})
 target_link_libraries(CheckCompilerSetupExec ${TEST_LINK_LIBRARIES})
-
diff --git a/cmake/macros/macro_add_flags.cmake b/cmake/macros/macro_add_flags.cmake
@@ -27,4 +27,3 @@ macro(add_flags _variable _flags)
     string(STRIP "${${_variable}}" ${_variable})
   endif()
 endmacro()
-
diff --git a/cmake/macros/macro_check_cxx_compiler_bug.cmake b/cmake/macros/macro_check_cxx_compiler_bug.cmake
@@ -42,4 +42,3 @@ macro(check_cxx_compiler_bug _source _var)
     set(${_var} TRUE)
   endif()
 endmacro()
-
diff --git a/cmake/macros/macro_check_mpi_interface.cmake b/cmake/macros/macro_check_mpi_interface.cmake
@@ -66,4 +66,3 @@ macro(check_mpi_interface _feature _var)
     endif()
   endif()
 endmacro()
-
diff --git a/cmake/macros/macro_clear_cmake_required.cmake b/cmake/macros/macro_clear_cmake_required.cmake
@@ -24,4 +24,3 @@ macro(clear_cmake_required)
   set(CMAKE_REQUIRED_INCLUDES)
   set(CMAKE_REQUIRED_LIBRARIES)
 endmacro()
-
diff --git a/cmake/macros/macro_copy_target_properties.cmake b/cmake/macros/macro_copy_target_properties.cmake
@@ -154,4 +154,3 @@ function(copy_target_properties _destination_target)
     target_link_options(${_destination_target} INTERFACE ${_link_options})
   endif()
 endfunction()
-
diff --git a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
@@ -326,4 +326,3 @@ ${_switch_targets}#
   endif()
 
 endmacro()
-
diff --git a/cmake/macros/macro_enable_if_supported.cmake b/cmake/macros/macro_enable_if_supported.cmake
@@ -56,4 +56,3 @@ macro(enable_if_supported _variable _flag)
 
   unset(CMAKE_REQUIRED_FLAGS)
 endmacro()
-
diff --git a/cmake/macros/macro_expand_instantiations.cmake b/cmake/macros/macro_expand_instantiations.cmake
@@ -92,4 +92,3 @@ macro(expand_instantiations _target _inst_in_files)
   endforeach()
 
 endmacro()
-
diff --git a/cmake/macros/macro_item_matches.cmake b/cmake/macros/macro_item_matches.cmake
@@ -30,4 +30,3 @@ macro(item_matches _var _regex)
     endif()
   endforeach()
 endmacro()
-
diff --git a/cmake/macros/macro_print_target_properties.cmake b/cmake/macros/macro_print_target_properties.cmake
@@ -56,4 +56,3 @@ function(print_target_properties _target)
     set(${ARGN} "${_messages}" PARENT_SCOPE)
   endif()
 endfunction()
-
diff --git a/cmake/macros/macro_reset_cmake_required.cmake b/cmake/macros/macro_reset_cmake_required.cmake
@@ -25,4 +25,3 @@ macro(reset_cmake_required)
   set(CMAKE_REQUIRED_INCLUDES)
   set(CMAKE_REQUIRED_LIBRARIES ${DEAL_II_LINKER_FLAGS_SAVED})
 endmacro()
-
diff --git a/cmake/macros/macro_strip_flag.cmake b/cmake/macros/macro_strip_flag.cmake
@@ -27,4 +27,3 @@ macro(strip_flag _variable _flag)
   string(REPLACE "  " " " ${_variable} "${${_variable}}")
   string(STRIP "${${_variable}}" ${_variable})
 endmacro()
-
diff --git a/cmake/macros/macro_strip_known_generator_expressions.cmake b/cmake/macros/macro_strip_known_generator_expressions.cmake
@@ -30,4 +30,3 @@ macro(strip_known_generator_expressions _variable)
     string(REGEX REPLACE ${expression} "\\1" ${_variable} "${${_variable}}")
   endforeach()
 endmacro()
-
diff --git a/cmake/modules/FindDEAL_II_TRILINOS.cmake b/cmake/modules/FindDEAL_II_TRILINOS.cmake
@@ -196,4 +196,3 @@ else()
       EPETRA_CONFIG_H ${_libraries} TRILINOS_CXX_SUPPORTS_SACADO_COMPLEX_RAD
     )
 endif()
-
diff --git a/cmake/setup_compiler_flags_intel.cmake b/cmake/setup_compiler_flags_intel.cmake
@@ -184,4 +184,3 @@ if (CMAKE_BUILD_TYPE MATCHES "Debug")
   enable_if_supported(DEAL_II_CXX_FLAGS_DEBUG "-gdwarf-2")
   enable_if_supported(DEAL_II_CXX_FLAGS_DEBUG "-grecord-gcc-switches")
 endif()
-
diff --git a/cmake/setup_compiler_flags_msvc.cmake b/cmake/setup_compiler_flags_msvc.cmake
@@ -118,4 +118,3 @@ if (CMAKE_BUILD_TYPE MATCHES "Debug")
   # generate some debug info:
   enable_if_supported(DEAL_II_CXX_FLAGS_DEBUG "/Zi /MDd /Od")
 endif()
-
diff --git a/cmake/setup_finalize.cmake b/cmake/setup_finalize.cmake
@@ -67,4 +67,3 @@ file(WRITE ${CMAKE_BINARY_DIR}/revision.log
 #
 ###"
   )
-
diff --git a/contrib/python-bindings/tests/manifold_wrapper.vtk b/contrib/python-bindings/tests/manifold_wrapper.vtk
@@ -103,4 +103,3 @@ SCALARS ManifoldID int 1
 LOOKUP_TABLE default
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 
-
diff --git a/contrib/utilities/checkdoxygen.py b/contrib/utilities/checkdoxygen.py
@@ -133,4 +133,3 @@ def check_multiple_defined_headers(lines):
     
     # check the file group
     check_multiple_defined_headers(lines)
-
diff --git a/contrib/utilities/count_lines.sh b/contrib/utilities/count_lines.sh
@@ -128,4 +128,3 @@ for commit in $commits ; do
 done
 
 git checkout -q ${current_branch}
-
diff --git a/contrib/utilities/parse_ctest_output.py b/contrib/utilities/parse_ctest_output.py
@@ -298,5 +298,3 @@ def parse_revision(dirname):
 
 
 f.write('</body></html>')
-
-
diff --git a/contrib/utilities/relocate_libraries.py b/contrib/utilities/relocate_libraries.py
@@ -116,7 +116,3 @@ def get_libs():
             print('Last command failed!')
             print(" ".join(command))
             print('*********************************************\n\n')
-
-
-
-
diff --git a/contrib/utilities/run_clang_tidy.sh b/contrib/utilities/run_clang_tidy.sh
@@ -75,4 +75,3 @@ fi
 
 echo "OK"
 exit 0
-
diff --git a/contrib/utilities/update-copyright.sh b/contrib/utilities/update-copyright.sh
@@ -182,4 +182,3 @@ process()
 
 process "."  "CMakeLists.txt|CTestConfig.cmake" update_copyright
 process "cmake contrib doc examples include source tests" ".*" update_copyright
-
diff --git a/contrib/utilities/wrapcomments.py b/contrib/utilities/wrapcomments.py
@@ -592,8 +592,3 @@ def format_block(lines, infostr=""):
 
 for line in out:
     print (line)
-
-
-
-
-
diff --git a/doc/news/changes/README.md b/doc/news/changes/README.md
@@ -1,22 +1,22 @@
 This folder contains changelog entries
 ======================================
 
-Changes between different releases in deal.II are documented in the file 
+Changes between different releases in deal.II are documented in the file
 "changes.h" that is automatically created from the files in the directories
 
-  * "major", 
-  * "minor" and 
+  * "major",
+  * "minor" and
   * "incompatibilities".
 
 Each of these files contain a short description of a change, the authors' names
-and the date where the latter two a separated by "<br>" from the first one. 
+and the date where the latter two a separated by "<br>" from the first one.
 A typical file could look like this:
 
     New: We can do fancy stuff now.
     <br>
     (John Doe, YYYY/MM/DD)
 
-and is named "YYYYMMDDJohnDoe". File names for multiple contributions from the 
+and is named "YYYYMMDDJohnDoe". File names for multiple contributions from the
 same author on one day have a number appended, e.g. "YYYMMDDJohnDoe\_1".
 Only the file name is used to have a proper order in "changes.h". This
 means that the file can in principle have an arbitrary name as long as the date
@@ -25,7 +25,7 @@ in the file and in the file name match.
 incompatibilities
 -----------------
 
-The "incompatibilities" section contains modifications to the library that 
+The "incompatibilities" section contains modifications to the library that
 are incompatible with previous versions of the library, but which are
 necessary for the future maintainability of the library.
 
diff --git a/doc/news/changes/minor/20241127Thiele b/doc/news/changes/minor/20241127Thiele
@@ -0,0 +1,7 @@
+New: Configuration and CI job for pre-commit.
+The tool pre-commit can install hooks into the local git repo.
+These will be run on every call to git commit and perform some quick checks
+on the changeset.
+The CI job runs these checks on the whole codebase.
+<br>
+(Jan Philipp Thiele, 2024/11/27)
diff --git a/doc/users/CMakeLists.txt.sample2 b/doc/users/CMakeLists.txt.sample2
@@ -14,7 +14,7 @@ set(TARGET "step-1")
 # you may want to either replace the following statement by something like
 #    FILE(GLOB_RECURSE TARGET_SRC  "source/*.cc")
 #    FILE(GLOB_RECURSE TARGET_INC  "include/*.h")
-#    SET(TARGET_SRC ${TARGET_SRC}  ${TARGET_INC}) 
+#    SET(TARGET_SRC ${TARGET_SRC}  ${TARGET_INC})
 # or switch altogether to the large project CMakeLists.txt file discussed
 # in the "CMake in user projects" page accessible from the "User info"
 # page of the documentation.
diff --git a/doc/users/CMakeLists.txt.sample3 b/doc/users/CMakeLists.txt.sample3
@@ -14,7 +14,7 @@ set(TARGET "step-1")
 # you may want to either replace the following statement by something like
 #    FILE(GLOB_RECURSE TARGET_SRC  "source/*.cc")
 #    FILE(GLOB_RECURSE TARGET_INC  "include/*.h")
-#    SET(TARGET_SRC ${TARGET_SRC}  ${TARGET_INC}) 
+#    SET(TARGET_SRC ${TARGET_SRC}  ${TARGET_INC})
 # or switch altogether to the large project CMakeLists.txt file discussed
 # in the "CMake in user projects" page accessible from the "User info"
 # page of the documentation.
diff --git a/examples/step-1/doc/builds-on b/examples/step-1/doc/builds-on
@@ -1 +0,0 @@
-
diff --git a/examples/step-11/doc/tooltip b/examples/step-11/doc/tooltip
@@ -1,2 +1 @@
 Higher order mappings. Dealing with constraints.
-
diff --git a/examples/step-33/slide.inp b/examples/step-33/slide.inp
@@ -3557,4 +3557,3 @@
 1824 4 line 31 32 
 1825 4 line 32 33 
 1826 4 line 33 9 
-
diff --git a/examples/step-57/doc/gnuplot.gpl b/examples/step-57/doc/gnuplot.gpl
@@ -61,5 +61,3 @@ plot "7500-line-0.txt" using 2:1 w l ls 1 title "Refinement 0", \
 "7500-line-4.txt" using 2:1 w l ls 5 title "Refinement 4", \
 "ref_2d_ghia_u.txt" using 7:1 ls 10 pt 4 w p  title "Reference [Ghia 82]", \
 "ref_2d_erturk_u.txt" using 5:1 ls 11 pt 6 w p  title "Reference [Erturk]"
-
-
diff --git a/examples/step-58/doc/kind b/examples/step-58/doc/kind
@@ -1,2 +1 @@
 time dependent
-
diff --git a/examples/step-6/doc/tooltip b/examples/step-6/doc/tooltip
@@ -1 +1 @@
-Adaptive local refinement. Higher order elements.
+Adaptive local refinement. Higher order elements.
diff --git a/examples/step-60/parameters.prm b/examples/step-60/parameters.prm
@@ -187,5 +187,3 @@ subsection Distributed Lagrange<1,2>
   end
 
 end
-
-
diff --git a/examples/step-71/doc/builds-on b/examples/step-71/doc/builds-on
@@ -1 +0,0 @@
-
diff --git a/examples/step-71/parameters.prm b/examples/step-71/parameters.prm
@@ -27,5 +27,3 @@ subsection Coupled Constitutive Laws
   end
 
 end
-
-
diff --git a/examples/step-86/doc/results.dox b/examples/step-86/doc/results.dox
@@ -278,4 +278,3 @@ you have somewhere in the range of 50,000 to 100,000 unknowns *per MPI
 process*. But it is not difficult to adapt the program at hand here to
 run with a much finer mesh, or perhaps in 3d, so that one is beyond
 that limit and sees the benefits of parallel computing.
-
diff --git a/examples/step-89/CMakeLists.txt b/examples/step-89/CMakeLists.txt
diff --git a/source/differentiation/ad/ad_drivers.inst1.in b/source/differentiation/ad/ad_drivers.inst1.in
diff --git a/source/grid/grid_out.cc b/source/grid/grid_out.cc
diff --git a/source/grid/tria_accessor.inst.in b/source/grid/tria_accessor.inst.in
diff --git a/tests/cgal/input_grids/cube.off b/tests/cgal/input_grids/cube.off
diff --git a/tests/cgal/input_grids/hedra.off b/tests/cgal/input_grids/hedra.off
diff --git a/tests/cgal/input_grids/octahedron.off b/tests/cgal/input_grids/octahedron.off
diff --git a/tests/cgal/input_grids/tripod.off b/tests/cgal/input_grids/tripod.off
diff --git a/tests/codim_one/grids/sphere_0.inp b/tests/codim_one/grids/sphere_0.inp
diff --git a/tests/examples/step-9.diff b/tests/examples/step-9.diff
diff --git a/tests/grid/grid_in_gmsh_03.geo b/tests/grid/grid_in_gmsh_03.geo
diff --git a/tests/grid/grid_in_gmsh_03.msh b/tests/grid/grid_in_gmsh_03.msh
diff --git a/tests/grid/grid_in_msh_02/mesh.msh b/tests/grid/grid_in_msh_02/mesh.msh
diff --git a/tests/grid/grid_in_ucd_02_grids/grid_2.inp b/tests/grid/grid_in_ucd_02_grids/grid_2.inp
diff --git a/tests/grid/grid_in_ucd_02_grids/grid_3.inp b/tests/grid/grid_in_ucd_02_grids/grid_3.inp
diff --git a/tests/grid/grid_in_vtk_1d_3d.tria1.vtk b/tests/grid/grid_in_vtk_1d_3d.tria1.vtk
diff --git a/tests/grid/grid_in_vtk_1d_3d.tria2.vtk b/tests/grid/grid_in_vtk_1d_3d.tria2.vtk
diff --git a/tests/grid/grids/abaqus/2d/2d_short_handwritten.inp b/tests/grid/grids/abaqus/2d/2d_short_handwritten.inp
diff --git a/tests/grid/grids/abaqus/3d/codim_1-jagged_surface.inp b/tests/grid/grids/abaqus/3d/codim_1-jagged_surface.inp
diff --git a/tests/grid/grids/abaqus/3d/codim_1-tube.inp b/tests/grid/grids/abaqus/3d/codim_1-tube.inp
diff --git a/tests/grid/grids/comsol/mesh_example_with_domain_geom_info_1_7.mphtxt b/tests/grid/grids/comsol/mesh_example_with_domain_geom_info_1_7.mphtxt
diff --git a/tests/parameter_handler/parameter_handler_1_include_in.prm2 b/tests/parameter_handler/parameter_handler_1_include_in.prm2

Original file line number	Diff line number	Diff line change
`@@ -192,4 +192,3 @@ install(FILES`
`192`	`192`	`#`
`193`	`193`
`194`	`194`	`message(STATUS "Setting up project configuration - Done")`
`195`		`-`
-Original file line number
+Diff line change
     set(PACKAGE_VERSION_EXACT TRUE)
   endif()
 endif()
+-