[MISC] Macro comments: SEQAN3_HAS_ZLIB

eseiler · eseiler · commit 42beb57a3794 · 2025-02-24T15:18:12.000+01:00
diff --git a/doc/cookbook/compression_threads.cpp b/doc/cookbook/compression_threads.cpp
@@ -24,4 +24,4 @@ int main()
     return 0;
 }
 //![example]
-#endif
+#endif // SEQAN3_HAS_ZLIB
diff --git a/include/seqan3/io/detail/misc_input.hpp b/include/seqan3/io/detail/misc_input.hpp
@@ -123,7 +123,7 @@ inline auto make_secondary_istream(std::basic_istream<char_t> & primary_stream,
         return {new contrib::basic_bgzf_istream<char_t>{primary_stream}, stream_deleter_default};
 #else
         throw file_open_error{"Trying to read from a bgzf file, but no ZLIB available."};
-#endif
+#endif // SEQAN3_HAS_ZLIB
     }
     else if (starts_with(magic_number, gz_compression::magic_header)) // GZIP
     {
@@ -134,7 +134,7 @@ inline auto make_secondary_istream(std::basic_istream<char_t> & primary_stream,
         return {new contrib::basic_gz_istream<char_t>{primary_stream}, stream_deleter_default};
 #else
         throw file_open_error{"Trying to read from a gzipped file, but no ZLIB available."};
-#endif
+#endif // SEQAN3_HAS_ZLIB
     }
     else if (starts_with(magic_number, bz2_compression::magic_header)) // BZip2
     {
diff --git a/include/seqan3/io/detail/misc_output.hpp b/include/seqan3/io/detail/misc_output.hpp
@@ -53,7 +53,7 @@ inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream,
         return {new contrib::basic_gz_ostream<char_t>{primary_stream}, stream_deleter_default};
 #else
         throw file_open_error{"Trying to write a gzipped file, but no ZLIB available."};
-#endif
+#endif // SEQAN3_HAS_ZLIB
     }
     else if ((extension == ".bgzf") || (extension == ".bam"))
     {
@@ -64,7 +64,7 @@ inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream,
         return {new contrib::basic_bgzf_ostream<char_t>{primary_stream}, stream_deleter_default};
 #else
         throw file_open_error{"Trying to write a bgzf'ed file, but no ZLIB available."};
-#endif
+#endif // SEQAN3_HAS_ZLIB
     }
     else if (extension == ".bz2")
     {
diff --git a/test/include/seqan3/test/zlib_skip.hpp b/test/include/seqan3/test/zlib_skip.hpp
@@ -15,7 +15,7 @@
 
 #if SEQAN3_HAS_ZLIB
 #    include <zlib.h>
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 // Some of our tests check the binary compressed output of zlib. This is not guaranteed to be the same for all zlib
 // implementations.
diff --git a/test/performance/io/stream_input_benchmark.cpp b/test/performance/io/stream_input_benchmark.cpp
@@ -15,7 +15,7 @@
 #    include <seqan3/contrib/stream/bgzf_ostream.hpp>
 #    include <seqan3/contrib/stream/gz_istream.hpp>
 #    include <seqan3/contrib/stream/gz_ostream.hpp>
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 // only benchmark BZIP2 if explicitly requested, because slow setup
 #if !defined(SEQAN3_BENCH_BZIP2) && SEQAN3_HAS_BZIP2
@@ -33,7 +33,7 @@
 
 #    if SEQAN3_HAS_ZLIB
 #        define SEQAN_HAS_ZLIB 1
-#    endif
+#    endif // SEQAN3_HAS_ZLIB
 
 #    if SEQAN3_HAS_BZIP2
 #        define SEQAN_HAS_BZIP2 1
@@ -96,7 +96,7 @@ std::string const & input_comp<seqan2::GZFile> = input_comp<seqan3::contrib::gz_
 template <>
 std::string const & input_comp<seqan2::BgzfFile> = input_comp<seqan3::contrib::bgzf_istream>;
 #    endif
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 template <>
@@ -169,7 +169,7 @@ void compressed(benchmark::State & state)
 #if SEQAN3_HAS_ZLIB
 BENCHMARK_TEMPLATE(compressed, seqan3::contrib::gz_istream);
 BENCHMARK_TEMPLATE(compressed, seqan3::contrib::bgzf_istream);
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 BENCHMARK_TEMPLATE(compressed, seqan3::contrib::bz2_istream);
@@ -204,7 +204,7 @@ void compressed_type_erased(benchmark::State & state)
 #if SEQAN3_HAS_ZLIB
 BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::gz_istream);
 BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::bgzf_istream);
-#endif
+#endif // SEQAN3_HAS_ZLIB
 #if SEQAN3_HAS_BZIP2
 BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::bz2_istream);
 #endif
@@ -238,7 +238,7 @@ void compressed_type_erased2(benchmark::State & state)
 #if SEQAN3_HAS_ZLIB
 BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::gz_istream);
 BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::bgzf_istream);
-#endif
+#endif // SEQAN3_HAS_ZLIB
 #if SEQAN3_HAS_BZIP2
 BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::bz2_istream);
 #endif
diff --git a/test/performance/io/stream_output_benchmark.cpp b/test/performance/io/stream_output_benchmark.cpp
@@ -11,7 +11,7 @@
 #if SEQAN3_HAS_ZLIB
 #    include <seqan3/contrib/stream/bgzf_ostream.hpp>
 #    include <seqan3/contrib/stream/gz_ostream.hpp>
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 #    include <seqan3/contrib/stream/bz2_ostream.hpp>
@@ -23,7 +23,7 @@
 
 #    if SEQAN3_HAS_ZLIB
 #        define SEQAN_HAS_ZLIB 1
-#    endif
+#    endif // SEQAN3_HAS_ZLIB
 
 #    if SEQAN3_HAS_BZIP2
 #        define SEQAN_HAS_BZIP2 1
@@ -69,7 +69,7 @@ void compressed(benchmark::State & state)
 #if SEQAN3_HAS_ZLIB
 BENCHMARK_TEMPLATE(compressed, seqan3::contrib::gz_ostream);
 BENCHMARK_TEMPLATE(compressed, seqan3::contrib::bgzf_ostream);
-#endif
+#endif // SEQAN3_HAS_ZLIB
 #if SEQAN3_HAS_BZIP2
 BENCHMARK_TEMPLATE(compressed, seqan3::contrib::bz2_ostream);
 #endif
@@ -95,7 +95,7 @@ void compressed_type_erased(benchmark::State & state)
 #if SEQAN3_HAS_ZLIB
 BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::gz_ostream);
 BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::bgzf_ostream);
-#endif
+#endif // SEQAN3_HAS_ZLIB
 #if SEQAN3_HAS_BZIP2
 BENCHMARK_TEMPLATE(compressed_type_erased, seqan3::contrib::bz2_ostream);
 #endif
@@ -121,7 +121,7 @@ void compressed_type_erased2(benchmark::State & state)
 #if SEQAN3_HAS_ZLIB
 BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::gz_ostream);
 BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::bgzf_ostream);
-#endif
+#endif // SEQAN3_HAS_ZLIB
 #if SEQAN3_HAS_BZIP2
 BENCHMARK_TEMPLATE(compressed_type_erased2, seqan3::contrib::bz2_ostream);
 #endif
diff --git a/test/unit/contrib/stream/bgzf_istream_test.cpp b/test/unit/contrib/stream/bgzf_istream_test.cpp
@@ -37,4 +37,4 @@ TEST(bgzf_istream_test, skipped)
     GTEST_SKIP() << "ZLIB is missing. Not running bgzf_istream_test.";
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
diff --git a/test/unit/contrib/stream/bgzf_ostream_test.cpp b/test/unit/contrib/stream/bgzf_ostream_test.cpp
@@ -39,4 +39,4 @@ TEST(bgzf_ostream_test, skipped)
     GTEST_SKIP() << "ZLIB is missing. Not running bgzf_ostream_test.";
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
diff --git a/test/unit/contrib/stream/gz_istream_test.cpp b/test/unit/contrib/stream/gz_istream_test.cpp
@@ -35,4 +35,4 @@ TEST(gz_istream_test, skipped)
     GTEST_SKIP() << "ZLIB is missing. Not running gz_istream_test.";
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
diff --git a/test/unit/contrib/stream/gz_ostream_test.cpp b/test/unit/contrib/stream/gz_ostream_test.cpp
@@ -37,4 +37,4 @@ TEST(gz_ostream_test, skipped)
     GTEST_SKIP() << "ZLIB is missing. Not running gz_ostream_test.";
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
diff --git a/test/unit/io/detail/magic_header_test.cpp b/test/unit/io/detail/magic_header_test.cpp
@@ -19,7 +19,7 @@ TEST(misc, valid_compression_extensions)
     // expect gz and bgzf
     EXPECT_TRUE(std::find(valid_compression.begin(), valid_compression.end(), "gz") != valid_compression.end());
     EXPECT_TRUE(std::find(valid_compression.begin(), valid_compression.end(), "bgzf") != valid_compression.end());
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
     EXPECT_TRUE(std::find(valid_compression.begin(), valid_compression.end(), "bz2") != valid_compression.end());
diff --git a/test/unit/io/detail/misc_output_test.cpp b/test/unit/io/detail/misc_output_test.cpp
@@ -49,7 +49,7 @@ TEST(misc_output, issue2455_bgzf)
 
     EXPECT_TRUE(seqan3::detail::bgzf_compression::validate_header(std::span{file_content}));
 }
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 TEST(misc_output, issue2455_bz)
diff --git a/test/unit/io/sam_file/sam_file_input_test.cpp b/test/unit/io/sam_file/sam_file_input_test.cpp
@@ -422,7 +422,7 @@ TEST_F(sam_file_input_f, read_empty_bgzf_file)
     EXPECT_TRUE(fin.begin() == fin.end());
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 std::string input_bz2{
diff --git a/test/unit/io/sam_file/sam_file_output_test.cpp b/test/unit/io/sam_file/sam_file_output_test.cpp
@@ -745,7 +745,7 @@ TEST(compression, by_stream_bgzf)
     SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 std::string expected_bz2{'\x42', '\x5A', '\x68', '\x39', '\x31', '\x41', '\x59', '\x26', '\x53', '\x59', '\xEA',
diff --git a/test/unit/io/sam_file/sam_file_seek_test.cpp b/test/unit/io/sam_file/sam_file_seek_test.cpp
@@ -92,7 +92,7 @@ INSTANTIATE_TEST_SUITE_P(bam_file,
                          sam_file_seek_test,
                          ::testing::Values(sam_file_seek_test_fixture{"simple_three_verbose_reads.bam",
                                                                       {4'915'200, 11'730'944, 23'134'208}}));
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 INSTANTIATE_TEST_SUITE_P(sam_file,
                          sam_file_seek_test,
diff --git a/test/unit/io/sequence_file/sequence_file_input_test.cpp b/test/unit/io/sequence_file/sequence_file_input_test.cpp
@@ -412,7 +412,7 @@ TEST_F(sequence_file_input_f, read_empty_bgzf_file)
 
     EXPECT_TRUE(fin.begin() == fin.end());
 }
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 std::string input_bz2{'\x42', '\x5A', '\x68', '\x39', '\x31', '\x41', '\x59', '\x26', '\x53', '\x59', '\x8D', '\xD7',
diff --git a/test/unit/io/sequence_file/sequence_file_output_test.cpp b/test/unit/io/sequence_file/sequence_file_output_test.cpp
@@ -529,7 +529,7 @@ TEST(compression, by_stream_bgzf)
     EXPECT_EQ(buffer, expected_bgzf);
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 std::string expected_bz2{'\x42', '\x5A', '\x68', '\x39', '\x31', '\x41', '\x59', '\x26', '\x53', '\x59', '\xB4',
diff --git a/test/unit/io/structure_file/structure_file_input_test.cpp b/test/unit/io/structure_file/structure_file_input_test.cpp
@@ -472,7 +472,7 @@ TEST_F(structure_file_input_read, read_empty_bgzf_file)
     EXPECT_TRUE(fin.begin() == fin.end());
 }
 
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 std::string input_bz2{
diff --git a/test/unit/io/structure_file/structure_file_output_test.cpp b/test/unit/io/structure_file/structure_file_output_test.cpp
@@ -514,7 +514,7 @@ TEST_F(structure_file_output_compression, by_stream_bgzf)
     SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
-#endif
+#endif // SEQAN3_HAS_ZLIB
 
 #if SEQAN3_HAS_BZIP2
 std::string expected_bz2{

Original file line number	Diff line number	Diff line change
`@@ -24,4 +24,4 @@ int main()`
`24`	`24`	`return 0;`
`25`	`25`	`}`
`26`	`26`	`//![example]`
`27`		`-#endif`
	`27`	`+#endif // SEQAN3_HAS_ZLIB`
Original file line number	Diff line number	Diff line change
`@@ -123,7 +123,7 @@ inline auto make_secondary_istream(std::basic_istream<char_t> & primary_stream,`
`123`	`123`	`return {new contrib::basic_bgzf_istream<char_t>{primary_stream}, stream_deleter_default};`
`124`	`124`	`#else`
`125`	`125`	`throw file_open_error{"Trying to read from a bgzf file, but no ZLIB available."};`
`126`		`-#endif`
	`126`	`+#endif // SEQAN3_HAS_ZLIB`
`127`	`127`	`}`
`128`	`128`	`else if (starts_with(magic_number, gz_compression::magic_header)) // GZIP`
`129`	`129`	`{`
`@@ -134,7 +134,7 @@ inline auto make_secondary_istream(std::basic_istream<char_t> & primary_stream,`
`134`	`134`	`return {new contrib::basic_gz_istream<char_t>{primary_stream}, stream_deleter_default};`
`135`	`135`	`#else`
`136`	`136`	`throw file_open_error{"Trying to read from a gzipped file, but no ZLIB available."};`
`137`		`-#endif`
	`137`	`+#endif // SEQAN3_HAS_ZLIB`
`138`	`138`	`}`
`139`	`139`	`else if (starts_with(magic_number, bz2_compression::magic_header)) // BZip2`
`140`	`140`	`{`
Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,7 @@ inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream,`
`53`	`53`	`return {new contrib::basic_gz_ostream<char_t>{primary_stream}, stream_deleter_default};`
`54`	`54`	`#else`
`55`	`55`	`throw file_open_error{"Trying to write a gzipped file, but no ZLIB available."};`
`56`		`-#endif`
	`56`	`+#endif // SEQAN3_HAS_ZLIB`
`57`	`57`	`}`
`58`	`58`	`else if ((extension == ".bgzf") \|\| (extension == ".bam"))`
`59`	`59`	`{`
`@@ -64,7 +64,7 @@ inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream,`
`64`	`64`	`return {new contrib::basic_bgzf_ostream<char_t>{primary_stream}, stream_deleter_default};`
`65`	`65`	`#else`
`66`	`66`	`throw file_open_error{"Trying to write a bgzf'ed file, but no ZLIB available."};`
`67`		`-#endif`
	`67`	`+#endif // SEQAN3_HAS_ZLIB`
`68`	`68`	`}`
`69`	`69`	`else if (extension == ".bz2")`
`70`	`70`	`{`
Original file line number	Diff line number	Diff line change
`@@ -37,4 +37,4 @@ TEST(bgzf_istream_test, skipped)`
`37`	`37`	`GTEST_SKIP() << "ZLIB is missing. Not running bgzf_istream_test.";`
`38`	`38`	`}`
`39`	`39`
`40`		`-#endif`
	`40`	`+#endif // SEQAN3_HAS_ZLIB`
Original file line number	Diff line number	Diff line change
`@@ -39,4 +39,4 @@ TEST(bgzf_ostream_test, skipped)`
`39`	`39`	`GTEST_SKIP() << "ZLIB is missing. Not running bgzf_ostream_test.";`
`40`	`40`	`}`
`41`	`41`
`42`		`-#endif`
	`42`	`+#endif // SEQAN3_HAS_ZLIB`
Original file line number	Diff line number	Diff line change
`@@ -35,4 +35,4 @@ TEST(gz_istream_test, skipped)`
`35`	`35`	`GTEST_SKIP() << "ZLIB is missing. Not running gz_istream_test.";`
`36`	`36`	`}`
`37`	`37`
`38`		`-#endif`
	`38`	`+#endif // SEQAN3_HAS_ZLIB`
Original file line number	Diff line number	Diff line change
`@@ -37,4 +37,4 @@ TEST(gz_ostream_test, skipped)`
`37`	`37`	`GTEST_SKIP() << "ZLIB is missing. Not running gz_ostream_test.";`
`38`	`38`	`}`
`39`	`39`
`40`		`-#endif`
	`40`	`+#endif // SEQAN3_HAS_ZLIB`