Test for correct use of the thread ID in parallelize() calls.

This requires an additional test executable where subpar's silly test parallelization has been enabled. Also made sure that all thread IDs were passed around as int's for consistency with tatami's parallelize.
libscran · Sep 16, 2024 · 3fccec5 · 3fccec5
1 parent 2dd81e4
commit 3fccec5
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Showing 2 changed files with 36 additions and 20 deletions.
diff --git a/include/scran_qc/per_cell_qc_metrics.hpp b/include/scran_qc/per_cell_qc_metrics.hpp
@@ -155,7 +155,7 @@ void compute_qc_direct_dense(
         }
     }
 
-    tatami::parallelize([&](size_t, Index_ start, Index_ length) {
+    tatami::parallelize([&](int, Index_ start, Index_ length) {
         auto NR = mat.nrow();
         auto ext = tatami::consecutive_extractor<false>(&mat, false, start, length);
         std::vector<Value_> vbuffer(NR);
@@ -261,7 +261,7 @@ void compute_qc_direct_sparse(
 {
     auto is_in_subset = boolify_subsets(mat.nrow(), subsets, output);
 
-    tatami::parallelize([&](size_t, Index_ start, Index_ length) {
+    tatami::parallelize([&](int, Index_ start, Index_ length) {
         auto NR = mat.nrow();
         auto ext = tatami::consecutive_extractor<true>(&mat, false, start, length);
         std::vector<Value_> vbuffer(NR);
@@ -362,7 +362,7 @@ void compute_qc_direct_sparse(
 template<typename Sum_, typename Detected_, typename Value_, typename Index_>
 class PerCellQcMetricsRunningBuffers {
 public:
-    PerCellQcMetricsRunningBuffers(const PerCellQcMetricsBuffers<Sum_, Detected_, Value_, Index_>& output, size_t thread, Index_ start, Index_ len) {
+    PerCellQcMetricsRunningBuffers(const PerCellQcMetricsBuffers<Sum_, Detected_, Value_, Index_>& output, int thread, Index_ start, Index_ len) {
         if (output.sum) {
             my_sum = tatami_stats::LocalOutputBuffer<Sum_>(thread, start, len, output.sum);
         }
@@ -481,7 +481,7 @@ void compute_qc_running_dense(
 {
     auto is_in_subset = boolify_subsets(mat.nrow(), subsets, output);
 
-    tatami::parallelize([&](size_t thread, Index_ start, Index_ len) {
+    tatami::parallelize([&](int thread, Index_ start, Index_ len) {
         auto NR = mat.nrow();
         auto ext = tatami::consecutive_extractor<false>(&mat, true, static_cast<Index_>(0), NR, start, len);
         std::vector<Value_> vbuffer(len);
@@ -576,7 +576,7 @@ void compute_qc_running_sparse(
     opt.sparse_ordered_index = false;
     auto is_in_subset = boolify_subsets(mat.nrow(), subsets, output);
 
-    tatami::parallelize([&](size_t thread, Index_ start, Index_ len) {
+    tatami::parallelize([&](int thread, Index_ start, Index_ len) {
         auto NR = mat.nrow();
         auto ext = tatami::consecutive_extractor<true>(&mat, true, static_cast<Index_>(0), NR, start, len, opt);
         std::vector<Value_> vbuffer(len);

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
@@ -6,6 +6,31 @@ FetchContent_Declare(
 )
 FetchContent_MakeAvailable(scran_tests)
 
+option(CODE_COVERAGE "Enable coverage testing" OFF)
+set(DO_CODE_COVERAGE OFF)
+if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
+    set(DO_CODE_COVERAGE ON)
+endif()
+
+include(GoogleTest)
+
+macro(decorate_executable target)
+    target_link_libraries(
+        ${target}
+        scran_qc
+        scran_tests
+    )
+
+    target_compile_options(${target} PRIVATE -Wall -Werror -Wpedantic -Wextra)
+
+    if(DO_CODE_COVERAGE)
+        target_compile_options(${target} PRIVATE -O0 -g --coverage)
+        target_link_options(${target} PRIVATE --coverage)
+    endif()
+
+    gtest_discover_tests(${target})
+endmacro()
+
 add_executable(
     libtest 
     src/per_cell_qc_metrics.cpp
@@ -16,20 +41,11 @@ add_executable(
     src/crispr_quality_control.cpp
     src/format_filters.cpp
 )
+decorate_executable(libtest)
 
-target_link_libraries(
-    libtest
-    scran_qc
-    scran_tests
+add_executable(
+    cuspartest 
+    src/per_cell_qc_metrics.cpp
 )
-
-target_compile_options(libtest PRIVATE -Wall -Werror -Wpedantic -Wextra)
-
-option(CODE_COVERAGE "Enable coverage testing" OFF)
-if(CODE_COVERAGE AND CMAKE_CXX_COMPILER_ID MATCHES "GNU|Clang")
-    target_compile_options(libtest PRIVATE -O0 -g --coverage)
-    target_link_options(libtest PRIVATE --coverage)
-endif()
-
-include(GoogleTest)
-gtest_discover_tests(libtest)
+decorate_executable(cuspartest)
+target_compile_definitions(cuspartest PRIVATE SUBPAR_CUSTOM_PARALLELIZE_RANGE=::subpar::test_parallelize_range)