diff --git a/.github/workflows/clang-format.yml b/.github/workflows/clang-format.yml
deleted file mode 100644
index 95a8999c5..000000000
--- a/.github/workflows/clang-format.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-name: Clang-Format Check
-
-on:
-  push:
-    branches:
-      - master
-  pull_request:
-  merge_group:
-    paths-ignore:
-      - 'doc/**'
-      - 'contrib/**'
-
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{ github.event_name == 'pull_request'}}
-
-permissions:
-  contents: read
-
-jobs:
-  clang-format-check:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout repo
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 30
-
-    - name: Run Clang-Format
-      uses: jidicula/clang-format-action@v4.13.0
-      with:
-        clang-format-version: '18'
-        exclude-regex: 'contrib/catch/.*'
diff --git a/.github/workflows/compile_applications.yml b/.github/workflows/compile_applications.yml
index 39980ce53..f48210602 100644
--- 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
index 791e78d77..d7ce86eec 100644
--- 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
new file mode 100644
index 000000000..c5365755c
--- /dev/null
+++ 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
index 4ae4e7845..8e57ff982 100644
--- a/.gitignore
+++ b/.gitignore
@@ -51,4 +51,4 @@ output.txt
 error.txt
 
 # generated by operating system
-.DS_Store
\ No newline at end of file
+.DS_Store
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f1e081393..0c5be9409 100644
--- 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
index 2ec452621..a26690320 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 9bef0eaab..e8236bd4f 100644
--- 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
index 879e37e61..df9656265 100644
--- 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(
@@ -27,7 +31,8 @@ if(PRISMS_PF_FOUND)
     set_target_properties(
       main-debug
       PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}
+        RUNTIME_OUTPUT_DIRECTORY
+          ${CMAKE_SOURCE_DIR}
     )
   endif()
 
@@ -35,7 +40,8 @@ if(PRISMS_PF_FOUND)
     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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 1db24ddd3..e8236bd4f 100644
--- 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
index 9b7c81f14..70f708b24 100644
--- 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
index d622f92c4..6a86a5875 100644
--- 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(${_target} dummy_inst)
diff --git a/contrib/utilities/prm_remove_comments.sh b/contrib/utilities/prm_remove_comments.sh
deleted file mode 100755
index cfdac86a8..000000000
--- a/contrib/utilities/prm_remove_comments.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-# SPDX-FileCopyrightText: © 2025 PRISMS Center at the University of Michigan
-# SPDX-License-Identifier: GNU Lesser General Public Version 2.1
-#
-# This script removes all comments from all .prm files
-#
-#
-# Usage:
-# ./contrib/utilities/prm_remove_comments.sh
-#
-
-if test ! -d src -o ! -d include -o ! -d applications; then
-	echo "This script must be run from the top-level directory of PRISMS-PF"
-	exit 1
-fi
-
-SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
-MAIN_DIR="$SCRIPT_DIR/../../"
-
-find "$MAIN_DIR" -type f -name "*.prm" -exec sed -i -E 's/^\s*#.*//; s/\s+#.*//' {} +
-
-echo "Done"
-exit 0
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 1a7386d02..e178d1e74 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -10,9 +10,7 @@ endforeach()
 
 # Handles the install path
 foreach(_target ${PRISMS_PF_TARGETS})
-    target_include_directories(${_target} PUBLIC 
-        $<INSTALL_INTERFACE:include>
-    )
+  target_include_directories(${_target} PUBLIC $<INSTALL_INTERFACE:include>)
 endforeach()
 
 # Add the dummy.cc
diff --git a/tests/regression_tests/allen_cahn_explicit/CMakeLists.txt b/tests/regression_tests/allen_cahn_explicit/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/allen_cahn_explicit/CMakeLists.txt
+++ b/tests/regression_tests/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(
diff --git a/tests/regression_tests/allen_cahn_implicit/CMakeLists.txt b/tests/regression_tests/allen_cahn_implicit/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/allen_cahn_implicit/CMakeLists.txt
+++ b/tests/regression_tests/allen_cahn_implicit/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/tests/regression_tests/cahn_hilliard_explicit/CMakeLists.txt b/tests/regression_tests/cahn_hilliard_explicit/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/cahn_hilliard_explicit/CMakeLists.txt
+++ b/tests/regression_tests/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/tests/regression_tests/cahn_hilliard_implicit/CMakeLists.txt b/tests/regression_tests/cahn_hilliard_implicit/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/cahn_hilliard_implicit/CMakeLists.txt
+++ b/tests/regression_tests/cahn_hilliard_implicit/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/tests/regression_tests/cavity_flow/CMakeLists.txt b/tests/regression_tests/cavity_flow/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/cavity_flow/CMakeLists.txt
+++ b/tests/regression_tests/cavity_flow/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/tests/regression_tests/fracture/CMakeLists.txt b/tests/regression_tests/fracture/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/fracture/CMakeLists.txt
+++ b/tests/regression_tests/fracture/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/tests/regression_tests/heat_equation_steady_state/CMakeLists.txt b/tests/regression_tests/heat_equation_steady_state/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/heat_equation_steady_state/CMakeLists.txt
+++ b/tests/regression_tests/heat_equation_steady_state/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/tests/regression_tests/linear_solve_old_solution/CMakeLists.txt b/tests/regression_tests/linear_solve_old_solution/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/linear_solve_old_solution/CMakeLists.txt
+++ b/tests/regression_tests/linear_solve_old_solution/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/tests/regression_tests/mechanics/CMakeLists.txt b/tests/regression_tests/mechanics/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/mechanics/CMakeLists.txt
+++ b/tests/regression_tests/mechanics/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/tests/regression_tests/precipitate_explicit/CMakeLists.txt b/tests/regression_tests/precipitate_explicit/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/precipitate_explicit/CMakeLists.txt
+++ b/tests/regression_tests/precipitate_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/tests/regression_tests/solution_blocks/CMakeLists.txt b/tests/regression_tests/solution_blocks/CMakeLists.txt
index 1db24ddd3..e8236bd4f 100644
--- a/tests/regression_tests/solution_blocks/CMakeLists.txt
+++ b/tests/regression_tests/solution_blocks/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(