Apply a pre-commit config

.clang-format

@@ -1,3 +1,10 @@
+# SPDX-FileCopyrightText: 2021 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-LicenseComments: Full text under /LICENSE and /LICENSES/
+#
+# SPDX-FileContributor: Author lists in /AUTHORS and /CITATION.cff
+
 Language:        Cpp
 AccessModifierOffset: -4
 AlignAfterOpenBracket: Align
@@ -19,9 +26,9 @@ AllowShortLoopsOnASingleLine: false
 AlwaysBreakAfterDefinitionReturnType: None
 AlwaysBreakAfterReturnType: None
 AlwaysBreakBeforeMultilineStrings: false
-AlwaysBreakTemplateDeclarations: MultiLine
-BinPackArguments: true
-BinPackParameters: true
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
 BraceWrapping:
   AfterCaseLabel:  false
   AfterClass:      false
@@ -63,19 +70,22 @@ ForEachMacros:
   - foreach
   - Q_FOREACH
   - BOOST_FOREACH
-IncludeBlocks:   Preserve
+IncludeBlocks:   Regroup
 IncludeCategories:
+  # keep the doctest headers in front
+  - Regex:           '^(<|")doctest'
+    Priority:        1
   - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
-    Priority:        2
-  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
     Priority:        3
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        4
   - Regex:           '.*'
-    Priority:        1
+    Priority:        2
 IncludeIsMainRegex: '(Test)?$'
 IndentCaseLabels: false
 IndentPPDirectives: None
-IndentWidth:     4
-IndentWrappedFunctionNames: false
+IndentWidth:     2
+IndentWrappedFunctionNames: true
 JavaScriptQuotes: Leave
 JavaScriptWrapImports: true
 KeepEmptyLinesAtTheStartOfBlocks: true
@@ -96,6 +106,7 @@ PenaltyBreakTemplateDeclaration: 10
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 60
 PointerAlignment: Left
+QualifierAlignment: Left
 ReflowComments:  true
 SortIncludes:    true
 SortUsingDeclarations: true
@@ -121,4 +132,3 @@ StatementMacros:
   - QT_REQUIRE_VERSION
 TabWidth:        8
 UseTab:          Never
-

.flake8

@@ -0,0 +1,20 @@
+# SPDX-FileCopyrightText: 2024 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-LicenseComments: Full text under /LICENSE and /LICENSES/
+#
+# SPDX-FileContributor: Author lists in /AUTHORS and /CITATION.cff
+
+# reason for rule exclusion:
+# * BLK100: conflicts with isort, i.e. I001,..,I005 (which is more important to be adhered)
+# * E501: hard to enforce; makes tensor operations partially unreadable
+# * E731: decreases readability
+# * E203: decreases readability; actually applied by black
+#
+# reason(s) for directory exclusion:
+# * preprocessing: TODO, to be exluded from the repository
+# * postprocessing: TODO, to be exluded from the repository
+# * submodules: submodules, need to be handled separately
+
+[flake8]
+extend-ignore = BLK100,E501,E731,E203

.gitignore

@@ -38,4 +38,3 @@ build*/
 *.exe
 *.out
 *.app
-

.pre-commit-config.yaml

@@ -0,0 +1,89 @@
+# SPDX-FileCopyrightText: 2025 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+# SPDX-LicenseComments: Full text under /LICENSE and /LICENSES/
+#
+# SPDX-FileContributor: Author lists in /AUTHORS and /CITATION.cff
+
+---
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: check-merge-conflict
+        name: '[GENERIC] merge conflict check'
+    -   id: check-symlinks
+        name: '[GENERIC] symlink check'
+    -   id: destroyed-symlinks
+        name: '[GENERIC] detect broken symlinks'
+    -   id: detect-private-key
+        name: '[GENERIC] detect private keys uploaded by accident'
+    -   id: check-case-conflict
+        name: '[GENERIC] detect OS file naming case conflicts'
+    -   id: check-executables-have-shebangs
+        name: '[GENERIC] check for shebangs in executable files'
+    -   id: check-illegal-windows-names
+        name: '[GENERIC] detect illegal Windows file names'
+    -   id: check-json
+        name: '[JSON] check'
+    -   id: check-xml
+        name: '[XML] check'
+
+-   repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.18.1
+    hooks:
+    -   id: markdownlint-cli2
+        name: '[MARKDOWN] lint'
+
+#-   repo: https://github.com/fsfe/reuse-tool
+#    rev: v6.0.0
+#    hooks:
+#    -   id: reuse
+#        name: '[GENERIC] REUSE compatibiltiy'
+
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 25.1.0
+    hooks:
+    -   id: black
+        files: ^(?!preprocessing|postprocessing)
+        name: '[PYTHON] black'
+-   repo: https://github.com/pycqa/isort
+    rev: 6.0.1
+    hooks:
+    -   id: isort
+        files: ^(?!preprocessing|postprocessing)
+        args: ["--profile", "black"]
+        name: '[PYTHON] isort'
+-   repo: https://github.com/pycqa/bandit
+    rev: 1.8.6
+    hooks:
+    -   id: bandit
+        args: ["--confidence-level", "high", "--severity-level", "high"]
+        name: '[PYTHON] bandit'
+-   repo: https://github.com/pycqa/flake8
+    rev: '7.3.0'
+    hooks:
+    -   id: flake8
+        files: ^(?!preprocessing|postprocessing)
+        name: '[PYTHON] Flake8'
+
+-   repo: https://github.com/sphinx-contrib/sphinx-lint
+    rev: 'v1.0.0'
+    hooks:
+    -   id: sphinx-lint
+        name: '[SPHINX/RST] sphinx lint'
+
+-   repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: 'v21.1.0'
+    hooks:
+    -   id: clang-format
+        name: '[C++] clang-format'
+
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+    -   id: end-of-file-fixer
+        name: '[GENERIC] newline eof'
+    -   id: trailing-whitespace
+        name: '[GENERIC] remove trailing whitespace'

CMakeLists.txt

@@ -257,7 +257,7 @@ if(EASICUBE)
         set_target_properties (easicube PROPERTIES
             INSTALL_RPATH_USE_LINK_PATH TRUE
         )
-    
+
         install (TARGETS easicube)
     else()
         message(WARNING "easicube needs easi to be compiled with ASAGI. Since this is not the case, easicube will be skipped.")

README.md

@@ -2,15 +2,20 @@
 
 [![Documentation Status](https://readthedocs.org/projects/easyinit/badge/?version=latest)](https://easyinit.readthedocs.io/en/latest/?badge=latest)
 
-
-easi is a library for the **E**asy **I**nitialization of models in three (or less or more) dimensional domains.
-The purpose of easi is to evaluate functions f : R^m -> R^n,
+easi is a library for the **E**asy **I**nitialization of models
+in three (or less or more) dimensional domains.
+The purpose of easi is to evaluate functions $f : R^m \rightarrow R^n$,
 which are described in a [YAML](http://yaml.org) configuration file.
 In grid-based simulation software, such as [SeisSol](http://www.seissol.org>),
 easi may be used to define models.
-In SeisSol, the function f maps every point in space (say x,y,z) to a vector of parameters (e.g. ρ, μ, and λ),
+In SeisSol, the function $f$ maps every point in space
+(say $x,y,z$) to a vector of parameters (e.g. $\rho$, $\mu$, and $\lambda$),
 which define a rheological model.
-Here, over 5000 lines of model-specific Fortran code could be replaced with YAML files.
+Here, over 5000 lines of model-specific Fortran
+code could be replaced with YAML files.
 
 ## Documentation
-The reference documentation can be found on [Read the Docs](https://easyinit.readthedocs.io) or be downloaded as [PDF manual](http://readthedocs.org/projects/easyinit/downloads/pdf/latest/).
+
+The reference documentation can be found on
+[Read the Docs](https://easyinit.readthedocs.io)
+or be downloaded as a [PDF manual](http://readthedocs.org/projects/easyinit/downloads/pdf/latest/).

cmake/FindFILESYSTEM.cmake

@@ -6,7 +6,7 @@
 #
 #  NOTE: it is not an official cmake search file
 #  authors: Carsten Uphoff, Ravil Dorozhinskii
-#  email: uphoff@in.tum.de, ravil.dorozhinskii@tum.de 
+#  email: uphoff@in.tum.de, ravil.dorozhinskii@tum.de
 #
 
 

cmake/FindNetCDF.cmake

@@ -141,4 +141,3 @@ include(FindPackageHandleStandardArgs)
 find_package_handle_standard_args(NetCDF
   REQUIRED_VARS NetCDF_LIBRARY NetCDF_INCLUDE_DIR
   VERSION_VAR NetCDF_VERSION)
-

cmake/easiConfig.cmake.in

@@ -16,4 +16,3 @@ endif()
 if (NOT TARGET easi::easi)
     include ("${CMAKE_CURRENT_LIST_DIR}/easiTargets.cmake")
 endif ()
-

doc/Makefile

@@ -16,4 +16,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/builders.rst

@@ -13,7 +13,7 @@ Defines parameters at nodes, which are interpolated inbetween nodes.
 
     !LayeredModel
     map: <map> # Mapping to 1D (root component)
-    interpolation: (lower|upper|linear) 
+    interpolation: (lower|upper|linear)
     parameters: [<dimension>, <dimension>, ...] # order of dimension
     nodes:
       <double>: [<double>, <double>, ...] # key: node position, value: dimension values

doc/compiling_dependencies.rst

@@ -21,7 +21,7 @@ Alternatively for gcc compilers on SupermucNG:
     export CC=mpigcc
 
 2. Asagi
- 
+
 See https://seissol.readthedocs.io/en/latest/asagi.html.
 
 3. yaml-cpp
@@ -32,7 +32,7 @@ On SupermucNG and with intel compilers:
 
     module load yaml-cpp/0.7.0-intel21
 
-    
+
 Alternatively you can build from source:
 
 .. code-block:: bash
@@ -46,15 +46,15 @@ Alternatively you can build from source:
     make -j 4
     make install
     cd ../..
-
 
-4. ImpalaJIT 
+
+4. ImpalaJIT
 
 .. code-block:: bash
 
     git clone git@github.com:uphoffc/ImpalaJIT
     # git clone https://github.com/uphoffc/ImpalaJIT.git
-    cd ImpalaJIT 
+    cd ImpalaJIT
     mkdir build && cd build
     cmake ..  -DCMAKE_INSTALL_PREFIX=$HOME
     make -j 4
@@ -73,4 +73,3 @@ Alternatively you can build from source:
     make local
     cp -r install/* ~
     cd ..
-