Update to add SPDX

BenBrock · BenBrock · commit e72f60250983 · 2024-09-26T16:14:19.000-07:00
diff --git a/.clang-format b/.clang-format
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 ---
 BasedOnStyle: LLVM
 PointerAlignment: Left
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 name: "CI"
 
 on:
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,6 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
+scripts
+venv
+build
+._*
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 repos:
 
 - repo: https://github.com/pre-commit/mirrors-clang-format
@@ -12,3 +14,8 @@ repos:
     - id: end-of-file-fixer
     - id: mixed-line-ending
     - id: check-added-large-files
+
+- repo: https://github.com/fsfe/reuse-tool
+  rev: v2.1.0
+  hooks:
+  - id: reuse
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 cmake_minimum_required(VERSION 3.5)
 project(binsparse-rc)
 
diff --git a/LICENSES/BSD-3-Clause.txt b/LICENSES/BSD-3-Clause.txt
diff --git a/README.md b/README.md
@@ -1,3 +1,7 @@
+<!--
+SPDX-License-Identifier: BSD-3-Clause
+-->
+
 # Binsparse C Reference Implementation
 
 This library is a reference implementation of the [binsparse Binary Sparse Format Specification](https://github.com/GraphBLAS/binsparse-specification) written using C.
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 function(add_example example_name)
   add_executable(${example_name} ${example_name}.c)
   target_link_libraries(${example_name} binsparse-rc)
@@ -10,6 +12,7 @@ add_example(simple_write)
 add_example(mtx2bsp)
 add_example(bsp2mtx)
 add_example(check_equivalence)
+add_example(check_equivalence_parallel)
 add_example(bsp-ls)
 add_example(benchmark_read)
 add_example(benchmark_read_parallel)
diff --git a/examples/benchmark_read.c b/examples/benchmark_read.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>
diff --git a/examples/benchmark_read_parallel.c b/examples/benchmark_read_parallel.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>
@@ -61,8 +65,9 @@ int main(int argc, char** argv) {
   char* file_name = argv[1];
 
   printf("Opening %s\n", file_name);
+  fflush(stdout);
 
-  const int num_trials = 2;
+  const int num_trials = 10;
 
   int num_threads = 6;
 
@@ -71,11 +76,10 @@ int main(int argc, char** argv) {
   size_t nbytes = 0;
 
   // To flush the filesystem cache before each trial, change to `true`.
-  bool cold_cache = true;
+  bool cold_cache = false;
 
   // If running warm cache experiments, read once to warm cache.
-  if (!cold_cache && false) {
-    printf("Warm cache read...\n");
+  if (!cold_cache) {
     bsp_matrix_t mat = bsp_read_matrix_parallel(file_name, NULL, num_threads);
     bsp_destroy_matrix_t(mat);
   }
@@ -84,6 +88,7 @@ int main(int argc, char** argv) {
     if (cold_cache) {
       flush_cache();
     }
+    fflush(stdout);
     double begin = gettime();
     bsp_matrix_t mat = bsp_read_matrix_parallel(file_name, NULL, num_threads);
     double end = gettime();
@@ -95,6 +100,7 @@ int main(int argc, char** argv) {
     double gbytes = ((double) nbytes) / 1024 / 1024 / 1024;
     double gbytes_s = gbytes / durations[i];
     printf("FORPARSER: %s,%lf,%lf\n", file_name, durations[i], gbytes_s);
+    fflush(stdout);
   }
 
   printf("[");
diff --git a/examples/benchmark_write.c b/examples/benchmark_write.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>
diff --git a/examples/bsp-ls.c b/examples/bsp-ls.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 herr_t visit_group(hid_t loc_id, const char* name, const H5L_info_t* linfo,
diff --git a/examples/bsp2mtx.c b/examples/bsp2mtx.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdio.h>
 
diff --git a/examples/check_equivalence.c b/examples/check_equivalence.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 int check_array_equivalence(bsp_array_t array1, bsp_array_t array2) {
diff --git a/examples/cpp/CMakeLists.txt b/examples/cpp/CMakeLists.txt
@@ -1,3 +1,5 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 function(add_example example_name)
   add_executable(${example_name}-cpp ${example_name}.cpp)
   target_link_libraries(${example_name}-cpp binsparse-rc)
diff --git a/examples/cpp/benchmark_read.cpp b/examples/cpp/benchmark_read.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>
diff --git a/examples/cpp/benchmark_write.cpp b/examples/cpp/benchmark_write.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 #include <stdlib.h>
 #include <time.h>
diff --git a/examples/cpp/bsp-ls.cpp b/examples/cpp/bsp-ls.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 
 herr_t visit_group(hid_t loc_id, const char* name, const H5L_info_t* linfo,
diff --git a/examples/cpp/bsp2mtx.cpp b/examples/cpp/bsp2mtx.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 #include <stdio.h>
 
diff --git a/examples/cpp/check_equivalence.cpp b/examples/cpp/check_equivalence.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 
 int check_array_equivalence(bsp_array_t array1, bsp_array_t array2) {
diff --git a/examples/cpp/mtx2bsp.cpp b/examples/cpp/mtx2bsp.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 #include <stdio.h>
 
diff --git a/examples/cpp/simple_matrix_read.cpp b/examples/cpp/simple_matrix_read.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/cpp/simple_matrix_write.cpp b/examples/cpp/simple_matrix_write.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/cpp/simple_read.cpp b/examples/cpp/simple_read.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/cpp/simple_write.cpp b/examples/cpp/simple_write.cpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/mtx2bsp.c b/examples/mtx2bsp.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 #include <stdio.h>
 
diff --git a/examples/simple_matrix_read.c b/examples/simple_matrix_read.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/simple_matrix_write.c b/examples/simple_matrix_write.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/simple_read.c b/examples/simple_read.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/examples/simple_write.c b/examples/simple_write.c
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #include <binsparse/binsparse.h>
 
 int main(int argc, char** argv) {
diff --git a/include/CMakeLists.txt b/include/CMakeLists.txt
@@ -1,2 +1,4 @@
+# SPDX-License-Identifier: BSD-3-Clause
+
 add_library(binsparse-rc INTERFACE)
 target_include_directories(binsparse-rc INTERFACE .)
diff --git a/include/binsparse/array.h b/include/binsparse/array.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <assert.h>
diff --git a/include/binsparse/binsparse.h b/include/binsparse/binsparse.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #define BINSPARSE_VERSION "0.1"
diff --git a/include/binsparse/convert_matrix.h b/include/binsparse/convert_matrix.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <assert.h>
diff --git a/include/binsparse/detail/cpp/array.hpp b/include/binsparse/detail/cpp/array.hpp
@@ -1,3 +1,5 @@
+// SPDX-License-Identifier: BSD-3-Clause
+
 #pragma once
 
 #ifdef __cplusplus
diff --git a/include/binsparse/detail/declamp_values.h b/include/binsparse/detail/declamp_values.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <binsparse/matrix.h>
diff --git a/include/binsparse/detail/detail.h b/include/binsparse/detail/detail.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <binsparse/detail/declamp_values.h>
diff --git a/include/binsparse/detail/parse_dataset.h b/include/binsparse/detail/parse_dataset.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <string.h>
diff --git a/include/binsparse/detail/shm_tools.h b/include/binsparse/detail/shm_tools.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <stddef.h>
diff --git a/include/binsparse/generate.h b/include/binsparse/generate.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <binsparse/matrix.h>
diff --git a/include/binsparse/hdf5_wrapper.h b/include/binsparse/hdf5_wrapper.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <assert.h>
diff --git a/include/binsparse/matrix.h b/include/binsparse/matrix.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <binsparse/array.h>
diff --git a/include/binsparse/matrix_formats.h b/include/binsparse/matrix_formats.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <string.h>
diff --git a/include/binsparse/matrix_market/coo_sort_tools.h b/include/binsparse/matrix_market/coo_sort_tools.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <binsparse/array.h>
diff --git a/include/binsparse/matrix_market/matrix_market_inspector.h b/include/binsparse/matrix_market/matrix_market_inspector.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <assert.h>
diff --git a/include/binsparse/matrix_market/matrix_market_read.h b/include/binsparse/matrix_market/matrix_market_read.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <assert.h>
diff --git a/include/binsparse/matrix_market/matrix_market_type_t.h b/include/binsparse/matrix_market/matrix_market_type_t.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 typedef enum bsp_matrix_market_type_t {
diff --git a/include/binsparse/matrix_market/matrix_market_write.h b/include/binsparse/matrix_market/matrix_market_write.h
@@ -1,3 +1,7 @@
+/*
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
 #pragma once
 
 #include <assert.h>
diff --git a/include/binsparse/minimize_values.h b/include/binsparse/minimize_values.h
diff --git a/include/binsparse/read_matrix.h b/include/binsparse/read_matrix.h
diff --git a/include/binsparse/structure.h b/include/binsparse/structure.h
diff --git a/include/binsparse/types.h b/include/binsparse/types.h
diff --git a/include/binsparse/write_matrix.h b/include/binsparse/write_matrix.h
diff --git a/requirements.txt b/requirements.txt
diff --git a/scripts/read_cold_benchmarks.sh b/scripts/read_cold_benchmarks.sh
diff --git a/scripts/read_warm_benchmarks.sh b/scripts/read_warm_benchmarks.sh
diff --git a/scripts/test_fastmm.sh b/scripts/test_fastmm.sh
diff --git a/scripts/test_fastmm_warm.sh b/scripts/test_fastmm_warm.sh
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
diff --git a/test/bash/CMakeLists.txt b/test/bash/CMakeLists.txt
diff --git a/test/bash/test-cpp.sh b/test/bash/test-cpp.sh
diff --git a/test/bash/test.sh b/test/bash/test.sh

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# SPDX-License-Identifier: BSD-3-Clause`
	`2`	`+`
`1`	`3`	`---`
`2`	`4`	`BasedOnStyle: LLVM`
`3`	`5`	`PointerAlignment: Left`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# SPDX-License-Identifier: BSD-3-Clause`
	`2`	`+`
`1`	`3`	`name: "CI"`
`2`	`4`
`3`	`5`	`on:`
-Original file line number
+Diff line change
@@ @@ -0,0 +1,6 @@ @@
 +# SPDX-License-Identifier: BSD-3-Clause
++
 +scripts
 +venv
 +build
 +._*
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+# SPDX-License-Identifier: BSD-3-Clause`
	`2`	`+`
`1`	`3`	`cmake_minimum_required(VERSION 3.5)`
`2`	`4`	`project(binsparse-rc)`
`3`	`5`