Merge branch 'main' into sc/add-dependabot

samcunliffe · web-flow · commit 17888f82b8c2 · 2025-06-05T15:00:33.000+01:00
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,28 +8,31 @@ name: Build and test
 # time we only run the full system tests on Ubuntu (although this can easily be
 # changed).
 
-
 on:
   push:
     branches: ["main"]
   pull_request:
   merge_group:
+  schedule:
+    - cron: "0 9 15 * *"
   workflow_dispatch:
 
-
 concurrency:
   # Skip intermediate builds: always.
   # Cancel intermediate builds: always.
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
-
 jobs:
   linting:
     name: Linting checks with pre-commit
     runs-on: ubuntu-latest
     steps:
-      - uses: ucl/composite-actions/pre-commit@v1
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v4
+      - name: Check clang-format version
+        run: clang-format --version
+      - uses: pre-commit/action@v3.0.1
 
   build:
     name: ${{ matrix.build_type }} build on ${{ matrix.os }} with build testing ${{ matrix.build_testing }}
@@ -38,7 +41,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, ubuntu-20.04, windows-latest, macos-latest]
+        os: [ubuntu-latest, windows-latest, macos-latest]
         build_type: [Debug, Release]
         build_testing: [ON, OFF]
         exclude:
@@ -49,15 +52,15 @@ jobs:
 
     steps:
       - name: Check out repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1.2.3
+        uses: matlab-actions/setup-matlab@v2.5.0
 
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.9'
+          python-version: "3.9"
 
       # -------------------------------------------------------------------------------
       # Ubuntu
@@ -89,7 +92,7 @@ jobs:
       # MacOS
       - name: Install dependencies for MacOS
         if: ${{ contains(matrix.os, 'macos') }}
-        run: brew install fftw hdf5
+        run: brew install fftw hdf5 libomp
 
       - name: Fix omp headers not linked on MacOS
         if: ${{ contains(matrix.os, 'macos') }}
@@ -148,7 +151,7 @@ jobs:
       # Unit tests
       - name: Produce MATLAB unit test data
         if: matrix.build_testing == 'ON'
-        uses: matlab-actions/run-command@v1
+        uses: matlab-actions/run-command@v2
         with:
           command: cd('tdms/tests/unit/benchmark_scripts/'), setup_unit_tests
 
@@ -175,8 +178,8 @@ jobs:
           lcov --capture --directory ${{ runner.workspace }}/build/CMakeFiles/tdms_tests.dir/src --output-file coverage.info
           lcov --remove coverage.info '/usr/*' --output-file coverage.info
           lcov --remove coverage.info '*/_deps/*' --output-file coverage.info
-          lcov --remove coverage.info '/Library/*' --output-file coverage.info
-          lcov --remove coverage.info '/Applications/*' --output-file coverage.info
+          lcov --ignore-errors unused --remove coverage.info '/Library/*' --output-file coverage.info
+          lcov --ignore-errors unused --remove coverage.info '/Applications/*' --output-file coverage.info
           lcov --list coverage.info
 
       - name: Upload coverage reports to Codecov
@@ -196,7 +199,7 @@ jobs:
         if: matrix.build_testing == 'OFF' && matrix.build_type == 'Debug'
         # If we use the build with testing ON, we'd also need to copy over (and
         # install) the libtdms.so so use the OFF build for simplicity.
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: tdms_build_${{ matrix.os }}
           path: ${{ runner.workspace }}/build/tdms_build.tar
@@ -218,7 +221,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1.2.3
+        uses: matlab-actions/setup-matlab@v2.5.0
 
       - name: Install HDF5 libraries for Ubuntu
         if: ${{ contains(matrix.os, 'ubuntu') }}
@@ -232,7 +235,7 @@ jobs:
           python3 -m pip install -r ${GITHUB_WORKSPACE}/tdms/tests/requirements.txt
 
       - name: Download build result
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: tdms_build_${{ matrix.os }}
           path: ${{ runner.workspace }}
@@ -244,7 +247,7 @@ jobs:
 
       - name: Setup cache of test data
         id: cache-test-data
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ github.workspace }}/tdms/tests/system/data
           key: test_data
diff --git a/.github/workflows/doxygen-gh-pages.yml b/.github/workflows/doxygen-gh-pages.yml
@@ -20,7 +20,7 @@ jobs:
     steps:
 
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: "true"
 
@@ -45,7 +45,7 @@ jobs:
       shell: bash
 
     - name: Upload the website
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: tdms_website
         path: html/*
@@ -61,7 +61,7 @@ jobs:
       uses: actions/checkout@v3
 
     - name: Download the content for deployment
-      uses: actions/download-artifact@v3
+      uses: actions/download-artifact@v4
       with:
         name: tdms_website
         path: html
diff --git a/.github/workflows/matlab_tests.yml b/.github/workflows/matlab_tests.yml
@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up MATLAB
-        uses: matlab-actions/setup-matlab@v1.2.3
+        uses: matlab-actions/setup-matlab@v2.5.0
 
       - name: Run script
         uses: matlab-actions/run-command@v1
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,23 +1,23 @@
 repos:
     # Sort order of Python imports
     - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
+      rev: 6.0.1
       hooks:
           - id: isort
     # Python code formatting
     - repo: https://github.com/psf/black
-      rev: 22.3.0
+      rev: 25.1.0
       hooks:
           - id: black
     # Remove unused Python imports
     - repo: https://github.com/myint/autoflake
-      rev: v1.4
+      rev: v2.3.1
       hooks:
         - id: autoflake
           args: ["--in-place", "--remove-all-unused-imports"]
     # Remove whitespace at line end, ensure newline at the end of files
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0  # Use the ref you want to point at
+      rev: v5.0.0  # Use the ref you want to point at
       hooks:
         - id: trailing-whitespace
         - id: end-of-file-fixer
diff --git a/tdms/CMakeLists.txt b/tdms/CMakeLists.txt
@@ -37,9 +37,6 @@ include_directories(${CMAKE_SOURCE_DIR}/matlabio/)
 find_package(Matlab REQUIRED MAT_LIBRARY)
 include_directories(${Matlab_INCLUDE_DIRS})
 
-# Currently matlab only has x84 libraries on Mac (no arm)
-set(CMAKE_OSX_ARCHITECTURES "x86_64")
-
 # Set the RPATH for the executable to find the dynamically linked libraries
 get_filename_component(MATLAB_LIB_ROOT "${Matlab_MAT_LIBRARY}" DIRECTORY)
 set(CMAKE_INSTALL_RPATH ${MATLAB_LIB_ROOT})
diff --git a/tdms/src/simulation_manager/execute_detector_subfunctions.cpp b/tdms/src/simulation_manager/execute_detector_subfunctions.cpp
@@ -81,7 +81,7 @@ void SimulationManager::compute_detector_functions(unsigned int tind,
         values from the detector arrays. Ergo, we can handle computing phasors
         at different frequencies simultaneously. */
 #pragma omp parallel default(shared) private(lambda_an_t, Idxt, Idyt, kprop,   \
-                                             phaseTermE, cphaseTermE)
+                                                     phaseTermE, cphaseTermE)
     {
       // For each frequency
 /**
@@ -168,6 +168,6 @@ void SimulationManager::compute_detector_functions(unsigned int tind,
         outputs.ID.y[ifx][im] += Idyt * cphaseTermE;
 
       }// end of loop on frequencies
-    }  // end of pragma omp parallel
-  }    // end of loop over each mode
+    }// end of pragma omp parallel
+  }// end of loop over each mode
 }
diff --git a/tdms/src/simulation_manager/execute_simulation.cpp b/tdms/src/simulation_manager/execute_simulation.cpp
@@ -128,8 +128,9 @@ void SimulationManager::execute() {
              // warning
 
 #pragma omp parallel default(shared) private(                                  \
-        i, j, k, n, rho, k_loc, array_ind, Ca, Cb, Cc, alpha_l, beta_l,        \
-        gamma_l, kappa_l, sigma_l, Enp1, Jnp1)//,ca_vec,cb_vec,eh_vec)
+                i, j, k, n, rho, k_loc, array_ind, Ca, Cb, Cc, alpha_l,        \
+                        beta_l, gamma_l, kappa_l, sigma_l, Enp1,               \
+                        Jnp1)//,ca_vec,cb_vec,eh_vec)
     {
       n = omp_get_thread_num();
       Enp1 = 0.0;
@@ -803,7 +804,7 @@ void SimulationManager::execute() {
           // PSTD, E_s.yz
         }// if (solver_method == DerivativeMethod::FiniteDifference) (else
          // PseudoSpectral)
-      }  // if(params.dimension==THREE || params.dimension==TE)
+      }// if(params.dimension==THREE || params.dimension==TE)
 
       if (inputs.params.dimension == THREE ||
           inputs.params.dimension == Dimension::TRANSVERSE_ELECTRIC) {
@@ -1128,7 +1129,7 @@ void SimulationManager::execute() {
           // PSTD, E_s.zx
         }// if (solver_method == DerivativeMethod::FiniteDifference) (else
          // PseudoSpectral)
-      }  //(params.dimension==THREE || params.dimension==TE)
+      }//(params.dimension==THREE || params.dimension==TE)
       else {
 #pragma omp for
         // E_s.zx updates
@@ -1565,7 +1566,7 @@ void SimulationManager::execute() {
           // PSTD, E_s.zy
         }// if (solver_method == DerivativeMethod::FiniteDifference) (else
          // PseudoSpectral)
-      }  //(params.dimension==THREE || params.dimension==TE)
+      }//(params.dimension==THREE || params.dimension==TE)
       else {
 #pragma omp for
         for (k = 0; k <= K_tot; k++)
@@ -1719,7 +1720,7 @@ void SimulationManager::execute() {
     /********************/
     // begin parallel
 #pragma omp parallel default(shared) private(                                  \
-        i, j, k, n, k_loc, array_ind)//,ca_vec,cb_vec,eh_vec)
+                i, j, k, n, k_loc, array_ind)//,ca_vec,cb_vec,eh_vec)
     {
       n = omp_get_thread_num();
 
@@ -2153,7 +2154,7 @@ void SimulationManager::execute() {
           // PSTD, H_s.yz
         }// if (solver_method == DerivativeMethod::FiniteDifference) (else
          // PseudoSpectral)
-      }  //(params.dimension==THREE || params.dimension==TE)
+      }//(params.dimension==THREE || params.dimension==TE)
       else {
 
 #pragma omp for
@@ -2480,8 +2481,8 @@ void SimulationManager::execute() {
           // PSTD, H_s.zx
         }// if (solver_method == DerivativeMethod::FiniteDifference) (else
          // PseudoSpectral)
-      }  //(params.dimension==THREE || params.dimension==TE)
-    }    // end parallel
+      }//(params.dimension==THREE || params.dimension==TE)
+    }// end parallel
     if (TIME_EXEC) { timers.click_timer(TimersTrackingLoop::INTERNAL); }
 
     /* Update source terms for self consistency across scattered/total interface
diff --git a/tdms/src/simulation_parameters.cpp b/tdms/src/simulation_parameters.cpp
@@ -17,7 +17,7 @@ SimulationParameters::SimulationParameters() = default;
 
 void SimulationParameters::set_source_mode(string mode_string) {
 
-  auto s = move(mode_string);
+  auto s = std::move(mode_string);
   if (s == "steadystate") {
     source_mode = SourceMode::steadystate;
   } else if (s == "pulsed") {
@@ -29,7 +29,7 @@ void SimulationParameters::set_source_mode(string mode_string) {
 
 void SimulationParameters::set_run_mode(string mode_string) {
 
-  auto s = move(mode_string);
+  auto s = std::move(mode_string);
   if (s == "complete") {
     run_mode = RunMode::complete;
   } else if (s == "analyse") {
@@ -41,7 +41,7 @@ void SimulationParameters::set_run_mode(string mode_string) {
 
 void SimulationParameters::set_dimension(string mode_string) {
 
-  auto s = move(mode_string);
+  auto s = std::move(mode_string);
   if (s == "3") {
     dimension = Dimension::THREE;
   } else if (s == "TE") {
diff --git a/tdms/tests/system/utils.py b/tdms/tests/system/utils.py
@@ -1,6 +1,7 @@
 """
 Common utilities for running TDMS system tests
 """
+
 import os
 import shutil
 from dataclasses import dataclass
diff --git a/tdms/tests/unit/test_interpolation_functions.cpp b/tdms/tests/unit/test_interpolation_functions.cpp
@@ -144,8 +144,7 @@ TEST_CASE("BLi: interpolation-coefficient sums match") {
   coeff_sums[7] = BL7.interpolate(a);
   // now check that the entries of coeff_sums are the same
   int n = 8;
-  while (--n > 0 && abs(coeff_sums[n] - coeff_sums[0]) < tol)
-    ;
+  while (--n > 0 && abs(coeff_sums[n] - coeff_sums[0]) < tol);
   // we only reach the end of the while loop, IE get to n==0, when all elements
   // in the array are the same
   REQUIRE(n == 0);
