prisms-center · landinjm · Jan 20, 2026 · Jan 20, 2026 · Jan 20, 2026 · Jan 20, 2026
diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
diff --git a/.github/workflows/compile_applications.yml b/.github/workflows/compile_applications.yml
@@ -1,13 +1,6 @@
 name: compile-applications
 
 on:
-  push:
-    branches:
-      - master
-    paths-ignore:
-      - 'doc/**'
-      - 'contrib/**'
-      - '**/*.md'
   merge_group:
     paths-ignore:
       - 'doc/**'

diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -1,14 +1,6 @@
 name: linux
 
 on:
-  push:
-    branches:
-      - master
-    paths-ignore:
-      - 'applications/**'
-      - 'doc/**'
-      - 'contrib/**'
-      - '**/*.md'
   pull_request:
   merge_group:
     branches:

diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
@@ -0,0 +1,23 @@
+name: pre-commit
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request'}}
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: 3.x
+    - uses: pre-commit/action@v3.0.1
+    - uses: pre-commit-ci/lite-action@v1.1.0
+      if: always()
diff --git a/.gitignore b/.gitignore
@@ -51,4 +51,4 @@ output.txt
 error.txt
 
 # generated by operating system
-.DS_Store
+.DS_Store
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -281,7 +281,8 @@ foreach(_build ${PRISMS_PF_BUILD_TYPES})
     PUBLIC
       $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/include>
       $<INSTALL_INTERFACE:include>
-    PRIVATE ${CMAKE_SOURCE_DIR}/src
+    PRIVATE
+      ${CMAKE_SOURCE_DIR}/src
   )
 
   target_compile_options(
@@ -339,7 +340,8 @@ install(
 
 # Install the headers
 install(
-  DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/
+  DIRECTORY
+    ${CMAKE_CURRENT_SOURCE_DIR}/include/
   DESTINATION include
   FILES_MATCHING
   PATTERN "*.h"
@@ -348,24 +350,28 @@ install(
 
 # Install the generated config.h
 install(
-  FILES ${CMAKE_CURRENT_BINARY_DIR}/include/prismspf/config.h
+  FILES
+    ${CMAKE_CURRENT_BINARY_DIR}/include/prismspf/config.h
   DESTINATION include/prismspf
 )
 
 # Install the cmake folder
 install(
-  DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/cmake/
+  DIRECTORY
+    ${CMAKE_CURRENT_SOURCE_DIR}/cmake/
   DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/prisms_pf
   FILES_MATCHING
   PATTERN "*.cmake"
   PATTERN "*.cc"
   PATTERN "CMakeLists.txt"
-  PATTERN "*.cmake.in" EXCLUDE
+  PATTERN "*.cmake.in"
+    EXCLUDE
 )
 
 # Install the generated Config file
 install(
-  FILES ${CMAKE_CURRENT_BINARY_DIR}/cmake/prisms_pf-config.cmake
+  FILES
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/prisms_pf-config.cmake
   DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/prisms_pf
 )
 
@@ -378,20 +384,15 @@ install(
 )
 
 # Install the VERSION file
-install(
-  FILES ${CMAKE_CURRENT_SOURCE_DIR}/VERSION
-  DESTINATION .
-)
+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/VERSION DESTINATION .)
 
 # Install the LICENSE file
-install(
-  FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE
-  DESTINATION .
-)
+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/LICENSE DESTINATION .)
 
 # Install the cmake/template file
 install(
-  FILES "${CMAKE_CURRENT_BINARY_DIR}/cmake/templates"
+  FILES
+    "${CMAKE_CURRENT_BINARY_DIR}/cmake/templates"
   DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/prisms_pf
 )
 

diff --git a/README.md b/README.md
@@ -1,8 +1,6 @@
 ![](logo_v2.png)
 
 [![GitHub Linux](https://github.com/prisms-center/phaseField/actions/workflows/linux.yml/badge.svg)](https://github.com/prisms-center/phaseField/actions/workflows/linux.yml)
-[![Clang-Format](https://github.com/prisms-center/phaseField/actions/workflows/clang-format.yml/badge.svg)](https://github.com/prisms-center/phaseField/actions/workflows/clang-format.yml)
-[![Clang-Tidy](https://github.com/prisms-center/phaseField/actions/workflows/clang-tidy.yml/badge.svg)](https://github.com/prisms-center/phaseField/actions/workflows/clang-tidy.yml)
 
 [![License: LGPL v2.1](https://img.shields.io/badge/License-lgpl-blue.svg)](https://www.gnu.org/licenses/lgpl-2.1)
 [![DOI](https://zenodo.org/badge/22602327.svg)](https://zenodo.org/badge/latestdoi/22602327)

diff --git a/applications/MgNd_precipitate_single_Bppp/CMakeLists.txt b/applications/MgNd_precipitate_single_Bppp/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/allen_cahn_explicit/CMakeLists.txt b/applications/allen_cahn_explicit/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(
@@ -21,7 +25,6 @@ if(PRISMS_PF_FOUND)
 
   # Set up the application
   prisms_pf_autopilot(${PRISMS_PF_CMAKE_DIR})
-
 else()
   message(FATAL_ERROR "PRISMS-PF package not found. Please make sure it is in path.")
 endif()
diff --git a/applications/alloy_solidification/CMakeLists.txt b/applications/alloy_solidification/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(
@@ -27,15 +31,17 @@ if(PRISMS_PF_FOUND)
     set_target_properties(
       main-debug
       PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}
+        RUNTIME_OUTPUT_DIRECTORY
+          ${CMAKE_SOURCE_DIR}
     )
   endif()
 
   if(TARGET main-release)
     set_target_properties(
       main-release
       PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}
+        RUNTIME_OUTPUT_DIRECTORY
+          ${CMAKE_SOURCE_DIR}
     )
   endif()
 else()

diff --git a/applications/blank/CMakeLists.txt b/applications/blank/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/cahn_hilliard_explicit/CMakeLists.txt b/applications/cahn_hilliard_explicit/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/coupled_allen_cahn_cahn_hilliard/CMakeLists.txt b/applications/coupled_allen_cahn_cahn_hilliard/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/eshelby_inclusion/CMakeLists.txt b/applications/eshelby_inclusion/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/nucleation/CMakeLists.txt b/applications/nucleation/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/precipitate_evolution/CMakeLists.txt b/applications/precipitate_evolution/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/applications/spinodal_decomposition/CMakeLists.txt b/applications/spinodal_decomposition/CMakeLists.txt
@@ -5,7 +5,11 @@
 cmake_minimum_required(VERSION 3.18)
 
 # Create a project for the application
-project(myapp C CXX)
+project(
+  myapp
+  C
+  CXX
+)
 
 # Find the PRISMS-PF package
 find_package(

diff --git a/cmake/macros/macro_expand_template_instantiations.cmake b/cmake/macros/macro_expand_template_instantiations.cmake
@@ -43,14 +43,12 @@ macro(expand_template_instantiations _target _inst_in_files)
       COMMAND
         ${_command}
       ARGS
-        ${_template_file} < 
-        ${CMAKE_CURRENT_SOURCE_DIR}/${_inst_in_file} >
+        ${_template_file} < ${CMAKE_CURRENT_SOURCE_DIR}/${_inst_in_file} >
         "${_final_output}.tmp"
       COMMAND
         ${CMAKE_COMMAND}
       ARGS
-        -E rename "${_final_output}.tmp"
-        "${_final_output}"
+        -E rename "${_final_output}.tmp" "${_final_output}"
     )
 
     # Append to a list of inst _inst_targets

diff --git a/cmake/macros/macro_prisms_pf_autopilot.cmake b/cmake/macros/macro_prisms_pf_autopilot.cmake
@@ -44,7 +44,8 @@ macro(prisms_pf_autopilot PRISMS_PF_CMAKE_DIR)
     set_target_properties(
       ${_target}
       PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+        RUNTIME_OUTPUT_DIRECTORY
+          "${CMAKE_CURRENT_SOURCE_DIR}"
     )
 
     add_dependencies(${_target} dummy_inst)

diff --git a/contrib/utilities/prm_remove_comments.sh b/contrib/utilities/prm_remove_comments.sh