Fix: Fix coverage test

.github/workflows/coverage.yml

@@ -13,24 +13,76 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v5
-      - name: Install Requirements for Coverage Testing
+        with:
+          submodules: recursive
+
+      - name: Install Perl Dependencies and Coverage Tools
         run: |
-          apt update && apt install -y lcov gpg curl jq ca-certificates
-      - name: Building
+          apt update && apt install -y curl jq ca-certificates python3-pip
+          apt install -y lcov perl-modules
+          apt install -y libcapture-tiny-perl libdatetime-perl libjson-perl libperlio-gzip-perl
+          lcov --version
+
+      - name: Building with Coverage
         run: |
-          cmake -B build -DENABLE_COVERAGE=ON -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON
+          rm -rf build/
+          rm -f CMakeCache.txt
+
+          mkdir -p build
+          chmod -R 755 build/
+
+          cmake -B build \
+            -DENABLE_COVERAGE=ON \
+            -DBUILD_TESTING=ON \
+            -DENABLE_MLALGO=ON \
+            -DENABLE_LIBXC=ON \
+            -DENABLE_LIBRI=ON \
+            -DENABLE_GOOGLEBENCH=ON \
+            -DENABLE_RAPIDJSON=ON \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DCMAKE_CXX_FLAGS="--coverage -fprofile-arcs -ftest-coverage" \
+            -DCMAKE_EXE_LINKER_FLAGS="--coverage"
           cmake --build build -j`nproc`
           cmake --install build
+
       - name: Testing
         env:
           OMP_NUM_THREADS: 1
         run: |
-          cmake --build build --target test ARGS="-V --timeout 21600" || exit 0
+          chmod -R 755 build/
+          cmake --build build --target test ARGS="-V --timeout 21600" || echo "Some tests failed but continuing for coverage"
+
+      - name: Generate Coverage Data
+        run: |
+          cd build
+
+          lcov --directory . --capture --output-file coverage.info
+
+          lcov --remove coverage.info '/usr/*' '*/test/*' '*/external/*' '*/build/*' --output-file coverage.filtered.info
+
+          genhtml coverage.filtered.info --output-directory coverage-report
+
+          cd ..
+
       - name: Upload Coverage to Codecov
         uses: codecov/codecov-action@v5
         if: ${{ ! cancelled() }}
         with:
           fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}
-          skip_validation: true
+          files: ./build/coverage.xml,./build/coverage.info
+          directory: ./build/
+          flags: unittests
+          name: codecov-umbrella
           verbose: true
+
+      - name: Upload Coverage Report Artifact
+        uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: coverage-report
+          path: |
+            build/coverage-report/
+            build/coverage.info
+            build/coverage.xml
+          retention-days: 30

CMakeLists.txt

@@ -156,10 +156,14 @@ if(ENABLE_COVERAGE)
     include(FetchContent)
     FetchContent_Declare(
       cmakecodecov
-      URL https://github.com/baixiaokuang/CMake-codecov/archive/refs/heads/master.zip
+      GIT_REPOSITORY https://github.com/RWTH-HPC/CMake-codecov.git
+      GIT_TAG master
+      GIT_SHALLOW TRUE
+      GIT_PROGRESS TRUE
     )
     FetchContent_Populate(cmakecodecov)
     list(APPEND CMAKE_MODULE_PATH ${cmakecodecov_SOURCE_DIR}/cmake)
+    set(CMAKE_MODULE_PATH "${cmakecodecov_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
     find_package(codecov REQUIRED)
   endif()
 endif()

source/source_cell/test_pw/CMakeLists.txt

@@ -15,7 +15,7 @@ AddTest(
   ../read_stru.cpp   ../read_atom_species.cpp
 	../read_pp_vwr.cpp ../read_pp_blps.cpp ../../source_io/output.cpp
   ../../source_estate/read_pseudo.cpp ../../source_estate/cal_nelec_nband.cpp
-  ../../source_estate/read_orb.cpp    ../../source_cell/print_cell.cpp
+  ../../source_estate/read_orb.cpp    ../print_cell.cpp
   ../../source_estate/cal_wfc.cpp  ../sep.cpp   ../sep_cell.cpp
 )
 

source/source_lcao/module_deepks/test/CMakeLists.txt

@@ -29,18 +29,18 @@ add_executable(
     ../../../source_estate/cal_nelec_nband.cpp
     ../../../source_estate/module_dm/density_matrix.cpp
     ../../../source_estate/module_dm/density_matrix_io.cpp
-    ../../../source_lcao/module_hcontainer/base_matrix.cpp
-    ../../../source_lcao/module_hcontainer/hcontainer.cpp
-    ../../../source_lcao/module_hcontainer/atom_pair.cpp
-    ../../../source_lcao/module_hcontainer/func_transfer.cpp
-    ../../../source_lcao/module_hcontainer/func_folding.cpp
-    ../../../source_lcao/module_hcontainer/transfer.cpp
-    ../../../source_lcao/module_hcontainer/output_hcontainer.cpp
-    ../../../source_lcao/module_operator_lcao/deepks_lcao.cpp
-    ../../../source_lcao/module_operator_lcao/operator_lcao.cpp
+    ../../module_hcontainer/base_matrix.cpp
+    ../../module_hcontainer/hcontainer.cpp
+    ../../module_hcontainer/atom_pair.cpp
+    ../../module_hcontainer/func_transfer.cpp
+    ../../module_hcontainer/func_folding.cpp
+    ../../module_hcontainer/transfer.cpp
+    ../../module_hcontainer/output_hcontainer.cpp
+    ../../module_operator_lcao/deepks_lcao.cpp
+    ../../module_operator_lcao/operator_lcao.cpp
     ../../../source_hamilt/operator.cpp
-    ../../../source_lcao/module_rt/td_info.cpp
-    ../../../source_lcao/module_rt/td_folding.cpp
+    ../../module_rt/td_info.cpp
+    ../../module_rt/td_folding.cpp
     ../../../source_estate/module_pot/H_TDDFT_pw.cpp
 )
 

source/source_lcao/module_operator_lcao/test/CMakeLists.txt

@@ -9,8 +9,8 @@ AddTest(
   ../../../source_basis/module_ao/parallel_orbitals.cpp 
   ../../../source_basis/module_ao/ORB_atomic_lm.cpp
   tmp_mocks.cpp ../../../source_hamilt/operator.cpp
-  ../../../source_lcao/module_rt/td_info.cpp
-  ../../../source_lcao/module_rt/td_folding.cpp
+  ../../module_rt/td_info.cpp
+  ../../module_rt/td_folding.cpp
   ../../../source_estate/module_pot/H_TDDFT_pw.cpp
 )
 
@@ -22,8 +22,8 @@ AddTest(
   ../../../source_basis/module_ao/parallel_orbitals.cpp 
   ../../../source_basis/module_ao/ORB_atomic_lm.cpp
   tmp_mocks.cpp ../../../source_hamilt/operator.cpp
-  ../../../source_lcao/module_rt/td_info.cpp
-  ../../../source_lcao/module_rt/td_folding.cpp
+  ../../module_rt/td_info.cpp
+  ../../module_rt/td_folding.cpp
   ../../../source_estate/module_pot/H_TDDFT_pw.cpp
 )
 

tests/integrate/CMakeLists.txt

@@ -1,5 +1,14 @@
 find_program(BASH bash)
 find_package(Python3 REQUIRED)
+
+add_executable(sum_cube ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
+install(TARGETS sum_cube DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
+message(STATUS "Target sum_cube has been defined in ${CMAKE_CURRENT_SOURCE_DIR}") # 添加此行
+
+if(ENABLE_COVERAGE)
+  add_coverage(sum_cube)
+endif()
+
 if(ENABLE_ASAN)
     add_test(
         NAME integrated_test_with_asan
@@ -13,10 +22,4 @@ else()
         COMMAND ${BASH} Autotest.sh -a ${ABACUS_BIN_PATH} -n 4
         WORKING_DIRECTORY ${ABACUS_TEST_DIR}/integrate
     )
-    add_executable(sum_cube.exe ${ABACUS_TEST_DIR}/integrate/tools/sum_cube.cpp)
-    install(TARGETS sum_cube.exe DESTINATION ${ABACUS_TEST_DIR}/integrate/tools/)
-
-    if(ENABLE_COVERAGE)
-      add_coverage(sum_cube.exe)
-    endif()
-endif()
+endif()

tests/integrate/clean.sh

@@ -55,7 +55,7 @@ for directory in `ls | grep $module`; do
 	#--------------------------------------------
 	# delete exec files in tools directory (if it exists)
 	#--------------------------------------------
-	sumfile1="$directory/sum_cube.exe"
+	sumfile1="$directory/sum_cube"
 	test -e "$sumfile1" && rm -rf $sumfile1
 
 	#--------------------------------------------

tests/integrate/tools/catch_properties.sh

@@ -3,7 +3,7 @@
 # mohan add 2025-05-03
 # this compare script is used in different integrate tests
 COMPARE_SCRIPT="../../integrate/tools/CompareFile.py"
-SUM_CUBE_EXE="../../integrate/tools/sum_cube.exe"
+SUM_CUBE_EXE="../../integrate/tools/sum_cube"
 
 
 sum_file(){