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Merged
eseiler merged 19 commits into from
Feb 26, 2025
Merged

[INFRA] Buildsystem #3337

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e6bb420
[MISC] Always define SEQAN_HAS_{ZLIB,BZIP2}
eseiler Feb 20, 2025
361693c
[MISC] SEQAN_HAS_{ZLIB,BZIP2} are always defined
eseiler Feb 20, 2025
78250df
[MISC] Deprecate and rename SEQAN3_WITH_CEREAL
eseiler Feb 20, 2025
a1bbe3f
[INFRA] Rename SEQAN3_WITH_CEREAL to SEQAN3_HAS_CEREAL
eseiler Feb 20, 2025
421a7d6
[MISC] Do not vendor cereal
eseiler Feb 20, 2025
69b019f
[MISC] Always use zlib/bzip2 if available
eseiler Feb 20, 2025
084e959
[MISC] Streamline package detection
eseiler Feb 20, 2025
c0fe88e
[TEST] Only exclude sdsl from header tests
eseiler Feb 20, 2025
a82b3d5
[INFRA] Fix gcovr
eseiler Feb 20, 2025
93b7aa4
[TEST] Skip compression tests if dependency missing
eseiler Feb 24, 2025
1445e18
[INFRA] Do not fetch cereal if CMAKE_DISABLE_FIND_PACKAGE_cereal is TRUE
eseiler Feb 24, 2025
fc62bdc
[DOC] Add example for force-(de)activating optional dependencies
eseiler Feb 24, 2025
7f72131
[INFRA] Add cron for testing without optional dependencies
eseiler Feb 24, 2025
ed1ad10
[MISC] Add missing includes
eseiler Feb 24, 2025
42beb57
[MISC] Macro comments: SEQAN3_HAS_ZLIB
eseiler Feb 24, 2025
01cbc83
[MISC] Macro comments: SEQAN3_HAS_BZIP2
eseiler Feb 24, 2025
2cbfd77
[MISC] Macro comments: SEQAN3_HAS_CEREAL
eseiler Feb 24, 2025
c27b374
[TEST] Do not check read_mapper output
eseiler Feb 24, 2025
f413686
[INFRA] Simplify platform.hpp combile check
eseiler Feb 26, 2025
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8 changes: 4 additions & 4 deletions doc/tutorial/09_search/search_small_snippets.cpp
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Expand Up @@ -5,11 +5,11 @@
#include "cleanup.hpp"
seqan3::cleanup index_file{"index.file"};

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <fstream>

# include <cereal/archives/binary.hpp>
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL

#include <filesystem>

Expand All @@ -33,7 +33,7 @@ int main()
//![text_collection]
}

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
{
//![store]
# include <fstream> // for writing/reading files
Expand Down Expand Up @@ -61,7 +61,7 @@ int main()
}
//![load]
}
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL

{
//![error_search]
Expand Down
4 changes: 2 additions & 2 deletions doc/tutorial/09_search/search_solution1.cpp
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Expand Up @@ -2,7 +2,7 @@
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL

# include "cleanup.hpp"
seqan3::cleanup index_file{"index.file"};
Expand Down Expand Up @@ -42,4 +42,4 @@ int main()
std::cout << "The indices differ!\n";
}
//![solution]
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL
4 changes: 2 additions & 2 deletions doc/tutorial/11_read_mapper/read_mapper_indexer_step3.cpp
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Expand Up @@ -3,7 +3,7 @@
// SPDX-License-Identifier: CC0-1.0

#include <seqan3/core/platform.hpp>
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
//![complete]
# include <fstream>

Expand Down Expand Up @@ -97,4 +97,4 @@ int main(int argc, char const ** argv)
return 0;
}
//![complete]
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL
4 changes: 2 additions & 2 deletions doc/tutorial/11_read_mapper/read_mapper_step2.cpp
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Expand Up @@ -3,7 +3,7 @@
// SPDX-License-Identifier: CC0-1.0

#include <seqan3/core/platform.hpp>
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
//![complete]
# include <fstream>

Expand Down Expand Up @@ -147,4 +147,4 @@ int main(int argc, char const ** argv)
return 0;
}
//![complete]
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL
4 changes: 2 additions & 2 deletions doc/tutorial/11_read_mapper/read_mapper_step3.cpp
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Expand Up @@ -3,7 +3,7 @@
// SPDX-License-Identifier: CC0-1.0

#include <seqan3/core/platform.hpp>
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
//![complete]
# include <fstream>
# include <span>
Expand Down Expand Up @@ -167,4 +167,4 @@ int main(int argc, char const ** argv)
return 0;
}
//![complete]
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL
4 changes: 2 additions & 2 deletions doc/tutorial/11_read_mapper/read_mapper_step4.cpp
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Expand Up @@ -3,7 +3,7 @@
// SPDX-License-Identifier: CC0-1.0

#include <seqan3/core/platform.hpp>
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
//![complete]
# include <fstream>
# include <span>
Expand Down Expand Up @@ -181,4 +181,4 @@ int main(int argc, char const ** argv)
return 0;
}
//![complete]
#endif //SEQAN3_WITH_CEREAL
#endif //SEQAN3_HAS_CEREAL
4 changes: 2 additions & 2 deletions include/seqan3/alignment/scoring/scoring_scheme_base.hpp
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Expand Up @@ -17,9 +17,9 @@
#include <seqan3/core/detail/strong_type.hpp>
#include <seqan3/utility/concept.hpp>

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <cereal/types/array.hpp>
#endif // SEQAN3_WITH_CEREAL
#endif // SEQAN3_HAS_CEREAL

namespace seqan3
{
Expand Down
2 changes: 1 addition & 1 deletion include/seqan3/alphabet/container/concatenated_sequences.hpp
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Expand Up @@ -19,7 +19,7 @@
#include <seqan3/utility/views/repeat_n.hpp>
#include <seqan3/utility/views/slice.hpp>

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <cereal/types/vector.hpp>
#endif

Expand Down
14 changes: 7 additions & 7 deletions include/seqan3/core/concept/cereal.hpp
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Expand Up @@ -13,7 +13,7 @@

#include <seqan3/core/platform.hpp>

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <cereal/archives/binary.hpp>
# include <cereal/details/traits.hpp>
#endif
Expand All @@ -35,7 +35,7 @@ namespace seqan3
* \see core_concept
*/
//!\cond
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
template <typename t>
concept cereal_output_archive = std::is_base_of_v<cereal::detail::OutputArchiveBase, t>;
#else
Expand All @@ -58,7 +58,7 @@ concept cereal_output_archive = false;
* \see core_concept
*/
//!\cond
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
template <typename t>
concept cereal_input_archive = std::is_base_of_v<cereal::detail::InputArchiveBase, t>;
#else
Expand All @@ -77,7 +77,7 @@ concept cereal_input_archive = false;
* \see core_concept
*/
//!\cond
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
template <typename t>
concept cereal_archive = cereal_output_archive<t> || cereal_input_archive<t>;
#else
Expand All @@ -100,7 +100,7 @@ concept cereal_archive = false;
* \see core_concept
*/
//!\cond
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
template <typename t>
concept cereal_text_archive = std::is_base_of_v<cereal::traits::TextArchive, t>;
#else
Expand Down Expand Up @@ -142,7 +142,7 @@ concept cereal_text_archive = false;
* The cereal library is an optional dependency of SeqAn, if it is not found **no types** satisfy this concept.
*/
//!\cond
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
template <typename value_t,
typename input_archive_t = cereal::BinaryInputArchive,
typename output_archive_t = cereal::BinaryOutputArchive>
Expand All @@ -163,7 +163,7 @@ namespace seqan3::detail
* \details Helpful when defining templatised save/load/serialize functions.
* \ingroup core_concept
*/
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
template <typename type>
using strip_cereal_wrapper_t = typename cereal::traits::strip_minimal<std::decay_t<type>>::type;
#else
Expand Down
4 changes: 2 additions & 2 deletions include/seqan3/utility/container/small_vector.hpp
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Expand Up @@ -12,9 +12,9 @@
#include <array>
#include <type_traits>

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <cereal/types/array.hpp>
#endif // SEQAN3_WITH_CEREAL
#endif // SEQAN3_HAS_CEREAL

#include <seqan3/core/concept/cereal.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
Expand Down
8 changes: 4 additions & 4 deletions test/include/seqan3/test/cereal.hpp
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Expand Up @@ -18,13 +18,13 @@
#include <seqan3/test/tmp_directory.hpp>
#include <seqan3/utility/type_traits/basic.hpp>

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <cereal/archives/binary.hpp>
# include <cereal/archives/json.hpp>
# include <cereal/archives/portable_binary.hpp>
# include <cereal/archives/xml.hpp>
# include <cereal/types/vector.hpp>
#endif // SEQAN3_WITH_CEREAL
#endif // SEQAN3_HAS_CEREAL

namespace seqan3
{
Expand Down Expand Up @@ -70,12 +70,12 @@ void do_cerealisation(value_t && value)
template <typename value_t>
void do_serialisation([[maybe_unused]] value_t && value)
{
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
do_cerealisation<cereal::BinaryInputArchive, cereal::BinaryOutputArchive>(value);
do_cerealisation<cereal::PortableBinaryInputArchive, cereal::PortableBinaryOutputArchive>(value);
do_cerealisation<cereal::JSONInputArchive, cereal::JSONOutputArchive>(value);
do_cerealisation<cereal::XMLInputArchive, cereal::XMLOutputArchive>(value);
#endif // SEQAN3_WITH_CEREAL
#endif // SEQAN3_HAS_CEREAL
}
//!\endcond

Expand Down
2 changes: 1 addition & 1 deletion test/snippet/core/cereal_example.cpp
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Expand Up @@ -2,7 +2,7 @@
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <fstream>
# include <vector>

Expand Down
4 changes: 2 additions & 2 deletions test/unit/core/concept/cereal_test.cpp
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Expand Up @@ -9,15 +9,15 @@

#include <seqan3/core/concept/cereal.hpp>

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL
# include <cereal/archives/binary.hpp>
# include <cereal/archives/json.hpp>
# include <cereal/archives/portable_binary.hpp>
# include <cereal/archives/xml.hpp>
# include <cereal/types/array.hpp>
#endif

#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL

TEST(cereal, cereal_output_archive)
{
Expand Down
2 changes: 1 addition & 1 deletion test/unit/search/fm_index/fm_index_dna4_test.cpp
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Expand Up @@ -21,7 +21,7 @@ TEST(fm_index_test, additional_concepts)

TEST(fm_index_test, cerealisation_errors)
{
#if SEQAN3_WITH_CEREAL
#if SEQAN3_HAS_CEREAL

using seqan3::operator""_dna4;

Expand Down