Add pre-commit config

.github/workflows/test.yml

@@ -26,9 +26,9 @@ env:
     ninja
     cmake
     gcovr
+
 jobs:
   gcc-build:
-    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
@@ -43,6 +43,11 @@ jobs:
             sanitizer: none
             buildtype: release
 
+    runs-on: ${{ matrix.os }}
+
+    permissions:
+      contents: read
+
     env:
       FC: gfortran
       CC: gcc
@@ -52,7 +57,9 @@ jobs:
 
     steps:
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+        with:
+          persist-credentials: false
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -62,23 +69,29 @@ jobs:
       - name: Install GCC ${{ matrix.GCC_V }} (OSX)
         if: contains(matrix.os, 'macos')
         run: |
-          ln -s /usr/local/bin/gfortran-${{ env.GCC_V }} /usr/local/bin/gfortran
-          ln -s /usr/local/bin/gcc-${{ env.GCC_V }} /usr/local/bin/gcc
-          ln -s /usr/local/bin/g++-${{ env.GCC_V }} /usr/local/bin/g++
+          ln -s /usr/local/bin/gfortran-${GCC_V} /usr/local/bin/gfortran
+          ln -s /usr/local/bin/gcc-${GCC_V} /usr/local/bin/gcc
+          ln -s /usr/local/bin/g++-${GCC_V} /usr/local/bin/g++
+        env:
+          GCC_V: ${{ env.GCC_V }}
 
       - name: Install GCC (Linux)
         run: |
           sudo add-apt-repository ppa:ubuntu-toolchain-r/test
           sudo apt-get update
-          sudo apt-get install gcc-${{ env.GCC_V }} g++-${{ env.GCC_V }} gfortran-${{ env.GCC_V }}
+          sudo apt-get install gcc-${GCC_V} g++-${GCC_V} gfortran-${GCC_V}
+        env:
+          GCC_V: ${{ env.GCC_V }}
 
       - name: Set GCC Version (Linux)
         if: contains(matrix.os, 'ubuntu')
         run: >-
           sudo update-alternatives
-          --install /usr/bin/gcc gcc /usr/bin/gcc-${{ env.GCC_V }} 100
-          --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${{ env.GCC_V }}
-          --slave /usr/bin/gcov gcov /usr/bin/gcov-${{ env.GCC_V }}
+          --install /usr/bin/gcc gcc /usr/bin/gcc-${GCC_V} 100
+          --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${GCC_V}
+          --slave /usr/bin/gcov gcov /usr/bin/gcov-${GCC_V}
+        env:
+          GCC_V: ${{ env.GCC_V }}
 
       - name: Install CBLAS and LAPACKE
         if: contains(matrix.os, 'ubuntu')
@@ -95,7 +108,7 @@ jobs:
           --libdir=lib
           --warnlevel=0
           -Dsanitizer=${{ matrix.sanitizer }}
-          -Db_coverage=${{ env.COVERAGE }}
+          -Db_coverage=${COVERAGE}
         env:
           COVERAGE: ${{ contains(matrix.os, 'ubuntu') && 'true' || 'false' }}
 
@@ -107,7 +120,7 @@ jobs:
           meson test -C ${{ env.M_BUILD_DIR }} --print-errorlogs --no-rebuild --num-processes 2 -t 2
 
       - name: Create coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.GCC_V == '11'
+        if: matrix.os == 'ubuntu-latest' && matrix.GCC_V == '12'
         run: |
           ninja -C ${{ env.M_BUILD_DIR }} coverage
 
@@ -117,7 +130,8 @@ jobs:
           echo "DFTD4_PREFIX=$PWD/_dist" >> $GITHUB_ENV
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.GCC_V == '11'
+        uses: codecov/codecov-action@7f8b4b4bde536c465e797be725718b88c5d95e0e # 5.1.1
+        if: matrix.os == 'ubuntu-latest' && matrix.GCC_V == '12'
         with:
           files: ./coverage.xml # optional
+          verbose: true # optional (default = false)

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-shebang-scripts-are-executable
+      - id: check-toml
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ["--maxkb=20000"]
+
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v21.1.7
+    hooks:
+    - id: clang-format
+      types_or: [c++, c, cuda]
+
+  - repo: https://github.com/woodruffw/zizmor-pre-commit
+    rev: v1.18.0
+    hooks:
+      - id: zizmor

app/main.cpp

@@ -96,7 +96,7 @@ void help() {
 
    <file> is a valid xmol file (coordinates in Ångström).
    (Turbomole coordinate file (coordinates in Bohr) not yet supported!)
-   
+
 
    Options:
 
@@ -146,7 +146,8 @@ int main(int argc, char **argv) {
   } else if (args.getflag("-f")) {
     func = args.getopt("-f");
   } else {
-    printf("WARNING: No functional given (via '--func'). Defaulting to PBE.\n\n"
+    printf(
+      "WARNING: No functional given (via '--func'). Defaulting to PBE.\n\n"
     );
     func = "pbe";
   }

include/dftd_cblas.h

@@ -1,13 +1,16 @@
 /*
  * This file contains code adapted from the ORCA quantum chemistry program.
- * ORCA is developed by the group of Prof. Frank Neese at the Max-Planck-Institut für Kohlenforschung,
- * Mülheim an der Ruhr and FAccTs GmbH. ORCA is licensed by the Max-Planck-Institut für Kohlenforschung and FAccTs GmbH.
+ * ORCA is developed by the group of Prof. Frank Neese at the
+ * Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr and FAccTs GmbH.
+ * ORCA is licensed by the Max-Planck-Institut für Kohlenforschung and FAccTs
+ * GmbH.
  *
- * The inclusion of ORCA code in this file has been done with the explicit permission
- * of the ORCA developers.
+ * The inclusion of ORCA code in this file has been done with the explicit
+ * permission of the ORCA developers.
  *
- * For reuse or licensing of this code, please contact the ORCA team at the Max-Planck-Institut
- * für Kohlenforschung (https://orcaforum.kofo.mpg.de/) or FAccTs GmbH (https://www.faccts.de/).
+ * For reuse or licensing of this code, please contact the ORCA team at the
+ * Max-Planck-Institut für Kohlenforschung (https://orcaforum.kofo.mpg.de/) or
+ * FAccTs GmbH (https://www.faccts.de/).
  */
 #pragma once
 
@@ -35,8 +38,8 @@ inline int BLAS_Add_Mat_x_Vec(
   bool Transpose,
   double alpha
 ) {
-    if (Transpose) {
-      if (A.cols == C.N && A.rows == V.N) {
+  if (Transpose) {
+    if (A.cols == C.N && A.rows == V.N) {
       cblas_dgemv(
         CblasRowMajor,
         CblasTrans,
@@ -54,7 +57,7 @@ inline int BLAS_Add_Mat_x_Vec(
       return EXIT_SUCCESS;
     };
   } else {
-      if (A.rows == C.N && A.cols == V.N) {
+    if (A.rows == C.N && A.cols == V.N) {
       cblas_dgemv(
         CblasRowMajor,
         CblasNoTrans,
@@ -98,7 +101,7 @@ inline int BLAS_Add_Mat_x_Mat(
   // check for size 0 matrices
   if (A.cols == 0 || A.rows == 0 || B.cols == 0 || B.rows == 0 || C.cols == 0 ||
       C.rows == 0) {
-      exit(EXIT_FAILURE);
+    exit(EXIT_FAILURE);
   };
 
   // check for transpositions
@@ -221,9 +224,9 @@ inline int BLAS_InvertMatrix(TMatrix<double> &a) {
     (lapack_int)a.cols,
     ipiv
   );
-  if (info != 0) { 
+  if (info != 0) {
     delete[] ipiv;
-    return EXIT_FAILURE; 
+    return EXIT_FAILURE;
   }
 
   // Inverse of an LU-factored general matrix
@@ -240,19 +243,19 @@ inline int BLAS_InvertMatrix(TMatrix<double> &a) {
 /**
  * @brief Solve a symmetric linear system A * X = B for X.
  *
- * This routine factorizes a symmetric matrix A using Bunch-Kaufman factorization
- * and solves for the right-hand side vector B. The matrix A is overwritten
- * by its factorization. The solution overwrites B.
+ * This routine factorizes a symmetric matrix A using Bunch-Kaufman
+ * factorization and solves for the right-hand side vector B. The matrix A is
+ * overwritten by its factorization. The solution overwrites B.
  *
  * @param A Symmetric matrix of size (m x m). Overwritten by the factorization.
  * @param B Right-hand side vector of size m. Overwritten by the solution.
  * @return int Returns EXIT_SUCCESS (0) on success, EXIT_FAILURE (1) on error.
  */
 inline int BLAS_SolveSymmetric(
-  TMatrix<double> &A,   // symmetric matrix
-  TVector<double> &B    // RHS vector (becomes solution)
+  TMatrix<double> &A, // symmetric matrix
+  TVector<double> &B  // RHS vector (becomes solution)
 ) {
-  const lapack_int m    = A.rows;
+  const lapack_int m = A.rows;
   const lapack_int nrhs = 1;
 
   if (A.cols != m || B.N != m) {
@@ -272,7 +275,8 @@ inline int BLAS_SolveSymmetric(
   }
 
   // Solve for all RHS columns
-  info = LAPACKE_dsytrs(LAPACK_ROW_MAJOR, 'L', m, nrhs, A.p, m, ipiv, B.p, nrhs);
+  info =
+    LAPACKE_dsytrs(LAPACK_ROW_MAJOR, 'L', m, nrhs, A.p, m, ipiv, B.p, nrhs);
   delete[] ipiv;
 
   if (info != 0) {