Merge pull request #3324 from eseiler/fix/zlib-ng

[FIX,TEST] Do not check zlib output for alternative implementations

Author: eseiler

test/include/seqan3/test/zlib_skip.hpp

@@ -0,0 +1,41 @@
+// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+/*!\file
+ * \brief Provides macros for skipping tests that rely on the binary compressed output of zlib.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <gtest/gtest.h>
+
+#include <seqan3/core/platform.hpp>
+
+#if defined(SEQAN3_HAS_ZLIB)
+#    include <zlib.h>
+#endif
+
+// Some of our tests check the binary compressed output of zlib. This is not guaranteed to be the same for all zlib
+// implementations.
+// This macro should be set to 1 if the zlib implementation is not the standard zlib, for example, zlib-ng.
+// zlib-ng is automatically detected if `zlib.h` resolves to zlib-ng's header.
+#ifndef SEQAN3_TEST_SKIP_ZLIB_DEFLATE
+#    ifdef ZLIBNG_VERSION
+#        define SEQAN3_TEST_SKIP_ZLIB_DEFLATE 1
+#    else
+#        define SEQAN3_TEST_SKIP_ZLIB_DEFLATE 0
+#    endif
+#endif
+
+// Defines a GTEST_SKIP macro if the zlib implementation is not the standard zlib.
+// Otherwise, it does nothing.
+#ifndef SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE
+#    if SEQAN3_TEST_SKIP_ZLIB_DEFLATE
+#        define SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE                                                                    \
+            GTEST_SKIP() << "Not testing binary compressed output for alternative zlib implementations."
+#    else
+#        define SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE
+#    endif
+#endif

test/unit/io/sam_file/sam_file_output_test.cpp

@@ -12,6 +12,7 @@
 #include <seqan3/io/sam_file/input.hpp>
 #include <seqan3/io/sam_file/output.hpp>
 #include <seqan3/test/tmp_directory.hpp>
+#include <seqan3/test/zlib_skip.hpp>
 
 using seqan3::operator""_dna4;
 using seqan3::operator""_dna5;
@@ -702,6 +703,7 @@ TEST(compression, by_filename_gz)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte.
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_gz);
 }
 
@@ -715,6 +717,7 @@ TEST(compression, by_stream_gz)
     }
     std::string buffer = out.str();
     buffer[9] = '\x00'; // zero out OS byte.
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_gz);
 }
 
@@ -725,6 +728,7 @@ TEST(compression, by_filename_bgzf)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte.
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
 
@@ -738,6 +742,7 @@ TEST(compression, by_stream_bgzf)
     }
     std::string buffer = out.str();
     buffer[9] = '\x00'; // zero out OS byte.
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
 #endif

test/unit/io/sequence_file/sequence_file_output_test.cpp

@@ -10,6 +10,7 @@
 #include <seqan3/alphabet/quality/phred42.hpp>
 #include <seqan3/io/sequence_file/output.hpp>
 #include <seqan3/test/tmp_directory.hpp>
+#include <seqan3/test/zlib_skip.hpp>
 #include <seqan3/utility/views/zip.hpp>
 
 using seqan3::operator""_dna5;
@@ -483,6 +484,7 @@ TEST(compression, by_filename_gz)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_gz);
 }
 
@@ -497,6 +499,7 @@ TEST(compression, by_stream_gz)
 
     std::string buffer = out.str();
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_gz);
 }
 
@@ -507,6 +510,7 @@ TEST(compression, by_filename_bgzf)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
 
@@ -521,6 +525,7 @@ TEST(compression, by_stream_bgzf)
 
     std::string buffer = out.str();
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
 

test/unit/io/stream/ostream_test_template.hpp

@@ -11,6 +11,7 @@
 
 #include <seqan3/io/stream/concept.hpp>
 #include <seqan3/test/tmp_directory.hpp>
+#include <seqan3/test/zlib_skip.hpp>
 
 template <typename T>
 class ostream : public ::testing::Test
@@ -41,7 +42,10 @@ TYPED_TEST_P(ostream, output)
     std::string buffer{std::istreambuf_iterator<char>{fi}, std::istreambuf_iterator<char>{}};
 
     if constexpr (TestFixture::zero_out_os_byte)
+    {
         buffer[9] = '\x00'; // zero-out the OS byte.
+        SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
+    }
 
     EXPECT_EQ(buffer, TestFixture::compressed);
 }
@@ -63,7 +67,10 @@ TYPED_TEST_P(ostream, output_type_erased)
     std::string buffer{std::istreambuf_iterator<char>{fi}, std::istreambuf_iterator<char>{}};
 
     if constexpr (TestFixture::zero_out_os_byte)
+    {
         buffer[9] = '\x00'; // zero-out the OS byte.
+        SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
+    }
 
     EXPECT_EQ(buffer, TestFixture::compressed);
 }

test/unit/io/structure_file/structure_file_output_test.cpp

@@ -13,6 +13,7 @@
 #include <seqan3/io/structure_file/input.hpp>
 #include <seqan3/io/structure_file/output.hpp>
 #include <seqan3/test/tmp_directory.hpp>
+#include <seqan3/test/zlib_skip.hpp>
 
 using seqan3::operator""_rna5;
 using seqan3::operator""_wuss51;
@@ -474,6 +475,7 @@ TEST_F(structure_file_output_compression, by_filename_gz)
 
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_gz);
 }
 
@@ -486,6 +488,7 @@ TEST_F(structure_file_output_compression, by_stream_gz)
     }
     std::string buffer = out.str();
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_gz);
 }
 
@@ -495,6 +498,7 @@ TEST_F(structure_file_output_compression, by_filename_bgzf)
     auto filename = tmp.path() / "structure_file_output_test.dbn.bgzf";
     std::string buffer = compression_by_filename_impl(filename);
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
 
@@ -507,6 +511,7 @@ TEST_F(structure_file_output_compression, by_stream_bgzf)
     }
     std::string buffer = out.str();
     buffer[9] = '\x00'; // zero out OS byte
+    SEQAN3_TEST_GTEST_SKIP_ZLIB_DEFLATE;
     EXPECT_EQ(buffer, expected_bgzf);
 }
 #endif