From 2aace9c7904dda7f7b83b6a1c1fe8be4118dc3f5 Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Thu, 9 Nov 2023 17:57:03 +0100 Subject: [PATCH 1/7] feat: add spdx headers and reuse check --- .github/workflows/ci-msvc.yml | 3 + .github/workflows/ci.yml | 3 + .github/workflows/ci_license_check.yml | 22 ++ .reuse/dep5 | 17 ++ CMakeLists.txt | 9 +- LICENSE | 30 --- LICENSES/Apache-2.0.txt | 73 ++++++ LICENSES/BSD-3-Clause.txt | 11 + LICENSES/BSL-1.0.txt | 7 + LICENSES/CC-BY-4.0.txt | 156 ++++++++++++ LICENSES/CC0-1.0.txt | 121 +++++++++ LICENSES/GPL-3.0-only.txt | 232 ++++++++++++++++++ README.md | 6 + doc/OccTables.drawio.license | 3 + doc/OccTables.png.license | 3 + fmindex_collection-config.cmake | 9 +- lib/cereal-config.cmake | 9 +- src/easyExample/main.cpp | 9 +- src/example/argp.h | 9 +- src/example/main.cpp | 9 +- src/example/utils.h | 9 +- src/example/utils/StopWatch.h | 9 +- src/example/utils/random.h | 9 +- src/example/utils/utils.cpp | 9 +- src/example/utils/utils.h | 9 +- src/fmindex-collection/BiFMIndex.h | 9 +- src/fmindex-collection/BiFMIndexCursor.h | 9 +- src/fmindex-collection/BiFMIndex_32.h | 9 +- src/fmindex-collection/BitStack.h | 9 +- src/fmindex-collection/Bitvector.h | 9 +- src/fmindex-collection/BitvectorCompact.h | 9 +- src/fmindex-collection/CMakeLists.txt | 9 +- src/fmindex-collection/CSA.h | 9 +- src/fmindex-collection/CSA32.h | 9 +- src/fmindex-collection/CSA_32.h | 9 +- src/fmindex-collection/CSA_SAS.h | 9 +- src/fmindex-collection/DenseCSA.h | 9 +- src/fmindex-collection/DenseVector.h | 9 +- src/fmindex-collection/FMIndex.h | 9 +- src/fmindex-collection/FMIndexCursor.h | 9 +- src/fmindex-collection/RBiFMIndex.h | 9 +- src/fmindex-collection/RBiFMIndexCursor.h | 9 +- src/fmindex-collection/ReverseFMIndex.h | 9 +- src/fmindex-collection/ReverseFMIndexCursor.h | 9 +- src/fmindex-collection/builtins.h | 9 +- src/fmindex-collection/cereal_tag.h | 9 +- src/fmindex-collection/concepts.h | 9 +- src/fmindex-collection/fmindex-collection.h | 9 +- src/fmindex-collection/locate.h | 9 +- src/fmindex-collection/occtable/Bitvector.h | 9 +- .../occtable/CompactBitvector.h | 9 +- .../occtable/CompactBitvectorPrefix.h | 9 +- src/fmindex-collection/occtable/DenseEPRV6.h | 9 +- src/fmindex-collection/occtable/EPRV3.h | 9 +- src/fmindex-collection/occtable/EPRV4.h | 9 +- src/fmindex-collection/occtable/EPRV5.h | 9 +- src/fmindex-collection/occtable/EPRV8.h | 9 +- .../occtable/GenericInterleaved.h | 9 +- .../occtable/InterleavedBitvector.h | 9 +- .../occtable/InterleavedEPR.h | 9 +- .../occtable/InterleavedEPRV2.h | 9 +- .../occtable/InterleavedEPRV7.h | 9 +- .../occtable/InterleavedEPRV7_32.h | 9 +- .../occtable/InterleavedEPRV7b.h | 9 +- .../occtable/InterleavedPrefix.h | 9 +- .../occtable/InterleavedWavelet.h | 9 +- .../occtable/InterleavedWavelet32.h | 9 +- src/fmindex-collection/occtable/Naive.h | 9 +- .../occtable/Sdsl_wt_bldc.h | 9 +- src/fmindex-collection/occtable/Sdsl_wt_epr.h | 9 +- src/fmindex-collection/occtable/Wavelet.h | 9 +- src/fmindex-collection/occtable/all.h | 9 +- src/fmindex-collection/occtable/concepts.h | 9 +- src/fmindex-collection/occtable/utils.h | 9 +- src/fmindex-collection/search/Backtracking.h | 9 +- .../search/BacktrackingWithBuffers.h | 9 +- src/fmindex-collection/search/SearchNg12.h | 9 +- src/fmindex-collection/search/SearchNg14.h | 9 +- src/fmindex-collection/search/SearchNg15.h | 9 +- src/fmindex-collection/search/SearchNg16.h | 9 +- src/fmindex-collection/search/SearchNg17.h | 9 +- src/fmindex-collection/search/SearchNg17ea.h | 9 +- src/fmindex-collection/search/SearchNg20.h | 9 +- src/fmindex-collection/search/SearchNg21.h | 9 +- src/fmindex-collection/search/SearchNg21V2.h | 9 +- src/fmindex-collection/search/SearchNg21V3.h | 9 +- src/fmindex-collection/search/SearchNg21V4.h | 9 +- src/fmindex-collection/search/SearchNg21V5.h | 9 +- src/fmindex-collection/search/SearchNg21V6.h | 9 +- src/fmindex-collection/search/SearchNg21V7.h | 9 +- src/fmindex-collection/search/SearchNg21ea.h | 9 +- src/fmindex-collection/search/SearchNg22.h | 9 +- .../search/SearchNoErrors.h | 9 +- .../search/SearchOneError.h | 9 +- src/fmindex-collection/search/SearchPseudo.h | 9 +- src/fmindex-collection/search/SelectCursor.h | 9 +- src/fmindex-collection/search/all.h | 9 +- src/fmindex-collection/utils.h | 9 +- src/run_search_schemes/main.cpp | 9 +- src/search_schemes/CMakeLists.txt | 9 +- src/search_schemes/Scheme.h | 9 +- src/search_schemes/Search.h | 9 +- src/search_schemes/expand.h | 9 +- src/search_schemes/generator/all.h | 9 +- src/search_schemes/generator/backtracking.h | 9 +- src/search_schemes/generator/bestKnown.h | 9 +- src/search_schemes/generator/h2.h | 9 +- src/search_schemes/generator/kianfar.h | 9 +- src/search_schemes/generator/kucherov.h | 9 +- src/search_schemes/generator/optimum.h | 9 +- src/search_schemes/generator/pigeon.h | 9 +- src/search_schemes/generator/suffixFilter.h | 9 +- src/search_schemes/generator/zeroOnesZero.h | 9 +- src/search_schemes/isComplete.h | 9 +- src/search_schemes/isValid.h | 9 +- src/search_schemes/nodeCount.h | 9 +- src/search_schemes/search_schemes.h | 9 +- src/search_schemes/weightedNodeCount.h | 9 +- src/test_fmindex-collection/CMakeLists.txt | 9 +- src/test_fmindex-collection/allTables.h | 9 +- .../checkBiFMIndex.cpp | 9 +- .../checkDenseBiFMIndex.cpp | 9 +- .../checkDenseReverseFMIndex.cpp | 9 +- src/test_fmindex-collection/checkFMIndex.cpp | 9 +- .../checkOccTables.cpp | 9 +- .../checkReverseFMIndex.cpp | 9 +- .../checkReverseIndexSearch.cpp | 9 +- .../checkSearchBacktracking.cpp | 9 +- .../checkSearchPseudo.cpp | 9 +- src/test_fmindex-collection/main.cpp | 9 +- src/test_fmindex-collection/utils.cpp | 9 +- src/test_search_schemes/CMakeLists.txt | 9 +- src/test_search_schemes/checkGenerators.cpp | 9 +- .../checkGeneratorsIsComplete.cpp | 9 +- src/test_search_schemes/expand.cpp | 9 +- src/test_search_schemes/isComplete.cpp | 9 +- src/test_search_schemes/isValid.cpp | 9 +- src/test_search_schemes/main.cpp | 9 +- src/test_search_schemes/nodeCount.cpp | 9 +- 139 files changed, 1032 insertions(+), 780 deletions(-) create mode 100644 .github/workflows/ci_license_check.yml create mode 100644 .reuse/dep5 delete mode 100644 LICENSE create mode 100644 LICENSES/Apache-2.0.txt create mode 100644 LICENSES/BSD-3-Clause.txt create mode 100644 LICENSES/BSL-1.0.txt create mode 100644 LICENSES/CC-BY-4.0.txt create mode 100644 LICENSES/CC0-1.0.txt create mode 100644 LICENSES/GPL-3.0-only.txt create mode 100644 doc/OccTables.drawio.license create mode 100644 doc/OccTables.png.license diff --git a/.github/workflows/ci-msvc.yml b/.github/workflows/ci-msvc.yml index 02811e0b..e3687d2d 100644 --- a/.github/workflows/ci-msvc.yml +++ b/.github/workflows/ci-msvc.yml @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 name: "Windows Server 2022" on: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 476696d8..1fc8b040 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,3 +1,6 @@ +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 name: "Linux and MacOS" on: diff --git a/.github/workflows/ci_license_check.yml b/.github/workflows/ci_license_check.yml new file mode 100644 index 00000000..0e339316 --- /dev/null +++ b/.github/workflows/ci_license_check.yml @@ -0,0 +1,22 @@ +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + +name: REUSE Compliance Check + +on: + push: + branches: + - 'main' + pull_request: + workflow_dispatch: + +jobs: + license_check: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - name: REUSE Compliance Check + uses: fsfe/reuse-action@v2 + with: + args: --suppress-deprecation lint diff --git a/.reuse/dep5 b/.reuse/dep5 new file mode 100644 index 00000000..6064fad1 --- /dev/null +++ b/.reuse/dep5 @@ -0,0 +1,17 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ + +Files: lib/Catch2/* +Copyright: Catch2 Authors +License: BSL-1.0 + +Files: lib/sdsl-lite/* +Copyright: 2007-2014 Simon Gog +License: GPL-3.0-only + +Files: lib/libsais/* +Copyright: 2021-2022 Ilya Grebnov ilya.grebnov@gmail.com +License: Apache-2.0 + +Files: lib/cereal/* +Copyright: 2013-2022, Randolph Voorhies, Shane Grant +License: BSD-3-Clause diff --git a/CMakeLists.txt b/CMakeLists.txt index 42cfac7e..95acf605 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.16) # check if this is the main project diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 70eb996f..00000000 --- a/LICENSE +++ /dev/null @@ -1,30 +0,0 @@ -BSD 3-Clause License - -Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -All rights reserved. - -Redistribution and use in source and binary forms, with or without 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If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . diff --git a/README.md b/README.md index 134faab9..61a5e503 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,9 @@ + + # FMIndex-Collection This Repository implements data structures and algorithms that involve (bidirectional) fm indices and searching. diff --git a/doc/OccTables.drawio.license b/doc/OccTables.drawio.license new file mode 100644 index 00000000..a1ac0ab3 --- /dev/null +++ b/doc/OccTables.drawio.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/doc/OccTables.png.license b/doc/OccTables.png.license new file mode 100644 index 00000000..a1ac0ab3 --- /dev/null +++ b/doc/OccTables.png.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC-BY-4.0 diff --git a/fmindex_collection-config.cmake b/fmindex_collection-config.cmake index 17005839..28034854 100644 --- a/fmindex_collection-config.cmake +++ b/fmindex_collection-config.cmake @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.12) if (TARGET fmindex-collection::fmindex-collection) return() diff --git a/lib/cereal-config.cmake b/lib/cereal-config.cmake index 731f1efa..7f95864e 100644 --- a/lib/cereal-config.cmake +++ b/lib/cereal-config.cmake @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.12) if (TARGET cereal::cereal) diff --git a/src/easyExample/main.cpp b/src/easyExample/main.cpp index bdde2675..387c232e 100644 --- a/src/easyExample/main.cpp +++ b/src/easyExample/main.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include #include diff --git a/src/example/argp.h b/src/example/argp.h index 17612228..7a4bb99e 100644 --- a/src/example/argp.h +++ b/src/example/argp.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/example/main.cpp b/src/example/main.cpp index cd8cfe4b..91ad8bcf 100644 --- a/src/example/main.cpp +++ b/src/example/main.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include "utils.h" #include "argp.h" diff --git a/src/example/utils.h b/src/example/utils.h index 5e85d122..5447d37a 100644 --- a/src/example/utils.h +++ b/src/example/utils.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "utils/utils.h" diff --git a/src/example/utils/StopWatch.h b/src/example/utils/StopWatch.h index 8ca2fc5b..6a047003 100644 --- a/src/example/utils/StopWatch.h +++ b/src/example/utils/StopWatch.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/example/utils/random.h b/src/example/utils/random.h index 88b5bd71..e6c83d42 100644 --- a/src/example/utils/random.h +++ b/src/example/utils/random.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/example/utils/utils.cpp b/src/example/utils/utils.cpp index d3de2d58..f7831951 100644 --- a/src/example/utils/utils.cpp +++ b/src/example/utils/utils.cpp @@ -1,7 +1,4 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include "utils.h" diff --git a/src/example/utils/utils.h b/src/example/utils/utils.h index 2927433a..caa1ac4a 100644 --- a/src/example/utils/utils.h +++ b/src/example/utils/utils.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "StopWatch.h" diff --git a/src/fmindex-collection/BiFMIndex.h b/src/fmindex-collection/BiFMIndex.h index 0fade1c7..60463144 100644 --- a/src/fmindex-collection/BiFMIndex.h +++ b/src/fmindex-collection/BiFMIndex.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "CSA.h" diff --git a/src/fmindex-collection/BiFMIndexCursor.h b/src/fmindex-collection/BiFMIndexCursor.h index 9b9387b5..afd3256a 100644 --- a/src/fmindex-collection/BiFMIndexCursor.h +++ b/src/fmindex-collection/BiFMIndexCursor.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "BiFMIndex.h" diff --git a/src/fmindex-collection/BiFMIndex_32.h b/src/fmindex-collection/BiFMIndex_32.h index fe19d732..0af197a2 100644 --- a/src/fmindex-collection/BiFMIndex_32.h +++ b/src/fmindex-collection/BiFMIndex_32.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "CSA_32.h" diff --git a/src/fmindex-collection/BitStack.h b/src/fmindex-collection/BitStack.h index e262fe26..4cfb962b 100644 --- a/src/fmindex-collection/BitStack.h +++ b/src/fmindex-collection/BitStack.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/fmindex-collection/Bitvector.h b/src/fmindex-collection/Bitvector.h index 67a55d91..92e63e58 100644 --- a/src/fmindex-collection/Bitvector.h +++ b/src/fmindex-collection/Bitvector.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "cereal_tag.h" diff --git a/src/fmindex-collection/BitvectorCompact.h b/src/fmindex-collection/BitvectorCompact.h index 931a76c3..e47bb19b 100644 --- a/src/fmindex-collection/BitvectorCompact.h +++ b/src/fmindex-collection/BitvectorCompact.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "cereal_tag.h" diff --git a/src/fmindex-collection/CMakeLists.txt b/src/fmindex-collection/CMakeLists.txt index 67f575f1..37f70beb 100644 --- a/src/fmindex-collection/CMakeLists.txt +++ b/src/fmindex-collection/CMakeLists.txt @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.8) project(fmindex-collection) diff --git a/src/fmindex-collection/CSA.h b/src/fmindex-collection/CSA.h index f5d5e563..f4e271b8 100644 --- a/src/fmindex-collection/CSA.h +++ b/src/fmindex-collection/CSA.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "BitStack.h" diff --git a/src/fmindex-collection/CSA32.h b/src/fmindex-collection/CSA32.h index 3c05af78..05e3ec41 100644 --- a/src/fmindex-collection/CSA32.h +++ b/src/fmindex-collection/CSA32.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "BitStack.h" diff --git a/src/fmindex-collection/CSA_32.h b/src/fmindex-collection/CSA_32.h index 8b76ab3c..5698a7fa 100644 --- a/src/fmindex-collection/CSA_32.h +++ b/src/fmindex-collection/CSA_32.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "BitStack.h" diff --git a/src/fmindex-collection/CSA_SAS.h b/src/fmindex-collection/CSA_SAS.h index 2b92fc6b..d56d237b 100644 --- a/src/fmindex-collection/CSA_SAS.h +++ b/src/fmindex-collection/CSA_SAS.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "cereal_tag.h" diff --git a/src/fmindex-collection/DenseCSA.h b/src/fmindex-collection/DenseCSA.h index d34dc4c6..7dae1eb8 100644 --- a/src/fmindex-collection/DenseCSA.h +++ b/src/fmindex-collection/DenseCSA.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "BitStack.h" diff --git a/src/fmindex-collection/DenseVector.h b/src/fmindex-collection/DenseVector.h index 44bf79f8..334bf15f 100644 --- a/src/fmindex-collection/DenseVector.h +++ b/src/fmindex-collection/DenseVector.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "cereal_tag.h" diff --git a/src/fmindex-collection/FMIndex.h b/src/fmindex-collection/FMIndex.h index b44a6cb0..c21ed6d0 100644 --- a/src/fmindex-collection/FMIndex.h +++ b/src/fmindex-collection/FMIndex.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "CSA.h" diff --git a/src/fmindex-collection/FMIndexCursor.h b/src/fmindex-collection/FMIndexCursor.h index 5177510a..1e7b9509 100644 --- a/src/fmindex-collection/FMIndexCursor.h +++ b/src/fmindex-collection/FMIndexCursor.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "FMIndex.h" diff --git a/src/fmindex-collection/RBiFMIndex.h b/src/fmindex-collection/RBiFMIndex.h index f7dfe462..93401b4d 100644 --- a/src/fmindex-collection/RBiFMIndex.h +++ b/src/fmindex-collection/RBiFMIndex.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "CSA.h" diff --git a/src/fmindex-collection/RBiFMIndexCursor.h b/src/fmindex-collection/RBiFMIndexCursor.h index b4c883cd..afdc5aa1 100644 --- a/src/fmindex-collection/RBiFMIndexCursor.h +++ b/src/fmindex-collection/RBiFMIndexCursor.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "RBiFMIndex.h" diff --git a/src/fmindex-collection/ReverseFMIndex.h b/src/fmindex-collection/ReverseFMIndex.h index 6fdca009..7ea1917d 100644 --- a/src/fmindex-collection/ReverseFMIndex.h +++ b/src/fmindex-collection/ReverseFMIndex.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "CSA.h" diff --git a/src/fmindex-collection/ReverseFMIndexCursor.h b/src/fmindex-collection/ReverseFMIndexCursor.h index 13d43ba9..918e2236 100644 --- a/src/fmindex-collection/ReverseFMIndexCursor.h +++ b/src/fmindex-collection/ReverseFMIndexCursor.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "ReverseFMIndex.h" diff --git a/src/fmindex-collection/builtins.h b/src/fmindex-collection/builtins.h index e452f0f7..eba273f1 100644 --- a/src/fmindex-collection/builtins.h +++ b/src/fmindex-collection/builtins.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #if _MSC_VER diff --git a/src/fmindex-collection/cereal_tag.h b/src/fmindex-collection/cereal_tag.h index 0b886912..a25f398a 100644 --- a/src/fmindex-collection/cereal_tag.h +++ b/src/fmindex-collection/cereal_tag.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once namespace fmindex_collection { diff --git a/src/fmindex-collection/concepts.h b/src/fmindex-collection/concepts.h index db26352c..5eb3e185 100644 --- a/src/fmindex-collection/concepts.h +++ b/src/fmindex-collection/concepts.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/fmindex-collection/fmindex-collection.h b/src/fmindex-collection/fmindex-collection.h index e4e5568d..92ee2661 100644 --- a/src/fmindex-collection/fmindex-collection.h +++ b/src/fmindex-collection/fmindex-collection.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "FMIndex.h" diff --git a/src/fmindex-collection/locate.h b/src/fmindex-collection/locate.h index 680f9b50..c6297a91 100644 --- a/src/fmindex-collection/locate.h +++ b/src/fmindex-collection/locate.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/fmindex-collection/occtable/Bitvector.h b/src/fmindex-collection/occtable/Bitvector.h index 1d4d02c1..be6f1953 100644 --- a/src/fmindex-collection/occtable/Bitvector.h +++ b/src/fmindex-collection/occtable/Bitvector.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/CompactBitvector.h b/src/fmindex-collection/occtable/CompactBitvector.h index 917ba006..15e73b3f 100644 --- a/src/fmindex-collection/occtable/CompactBitvector.h +++ b/src/fmindex-collection/occtable/CompactBitvector.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/CompactBitvectorPrefix.h b/src/fmindex-collection/occtable/CompactBitvectorPrefix.h index fa3c19dd..0b9f153d 100644 --- a/src/fmindex-collection/occtable/CompactBitvectorPrefix.h +++ b/src/fmindex-collection/occtable/CompactBitvectorPrefix.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/DenseEPRV6.h b/src/fmindex-collection/occtable/DenseEPRV6.h index 59da8933..7618d35a 100644 --- a/src/fmindex-collection/occtable/DenseEPRV6.h +++ b/src/fmindex-collection/occtable/DenseEPRV6.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../DenseVector.h" diff --git a/src/fmindex-collection/occtable/EPRV3.h b/src/fmindex-collection/occtable/EPRV3.h index 7cc6683a..f4f0ead1 100644 --- a/src/fmindex-collection/occtable/EPRV3.h +++ b/src/fmindex-collection/occtable/EPRV3.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/EPRV4.h b/src/fmindex-collection/occtable/EPRV4.h index ae508b7c..a2c25c08 100644 --- a/src/fmindex-collection/occtable/EPRV4.h +++ b/src/fmindex-collection/occtable/EPRV4.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/EPRV5.h b/src/fmindex-collection/occtable/EPRV5.h index 028f8b5f..9fffc44d 100644 --- a/src/fmindex-collection/occtable/EPRV5.h +++ b/src/fmindex-collection/occtable/EPRV5.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/EPRV8.h b/src/fmindex-collection/occtable/EPRV8.h index a481ebef..fd671b87 100644 --- a/src/fmindex-collection/occtable/EPRV8.h +++ b/src/fmindex-collection/occtable/EPRV8.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/GenericInterleaved.h b/src/fmindex-collection/occtable/GenericInterleaved.h index 513138f4..87c638ad 100644 --- a/src/fmindex-collection/occtable/GenericInterleaved.h +++ b/src/fmindex-collection/occtable/GenericInterleaved.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedBitvector.h b/src/fmindex-collection/occtable/InterleavedBitvector.h index 8e8701ea..f956c49e 100644 --- a/src/fmindex-collection/occtable/InterleavedBitvector.h +++ b/src/fmindex-collection/occtable/InterleavedBitvector.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "GenericInterleaved.h" diff --git a/src/fmindex-collection/occtable/InterleavedEPR.h b/src/fmindex-collection/occtable/InterleavedEPR.h index baa23cab..9d0ffd0e 100644 --- a/src/fmindex-collection/occtable/InterleavedEPR.h +++ b/src/fmindex-collection/occtable/InterleavedEPR.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedEPRV2.h b/src/fmindex-collection/occtable/InterleavedEPRV2.h index 8331601e..0545526b 100644 --- a/src/fmindex-collection/occtable/InterleavedEPRV2.h +++ b/src/fmindex-collection/occtable/InterleavedEPRV2.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedEPRV7.h b/src/fmindex-collection/occtable/InterleavedEPRV7.h index 3756449d..773660ee 100644 --- a/src/fmindex-collection/occtable/InterleavedEPRV7.h +++ b/src/fmindex-collection/occtable/InterleavedEPRV7.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedEPRV7_32.h b/src/fmindex-collection/occtable/InterleavedEPRV7_32.h index 44febecb..466b1a39 100644 --- a/src/fmindex-collection/occtable/InterleavedEPRV7_32.h +++ b/src/fmindex-collection/occtable/InterleavedEPRV7_32.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedEPRV7b.h b/src/fmindex-collection/occtable/InterleavedEPRV7b.h index 7f81fc06..43bdd9bf 100644 --- a/src/fmindex-collection/occtable/InterleavedEPRV7b.h +++ b/src/fmindex-collection/occtable/InterleavedEPRV7b.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedPrefix.h b/src/fmindex-collection/occtable/InterleavedPrefix.h index 90527fae..2ad4f3cb 100644 --- a/src/fmindex-collection/occtable/InterleavedPrefix.h +++ b/src/fmindex-collection/occtable/InterleavedPrefix.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/InterleavedWavelet.h b/src/fmindex-collection/occtable/InterleavedWavelet.h index 3658b428..7e669515 100644 --- a/src/fmindex-collection/occtable/InterleavedWavelet.h +++ b/src/fmindex-collection/occtable/InterleavedWavelet.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/InterleavedWavelet32.h b/src/fmindex-collection/occtable/InterleavedWavelet32.h index c4509310..0067e769 100644 --- a/src/fmindex-collection/occtable/InterleavedWavelet32.h +++ b/src/fmindex-collection/occtable/InterleavedWavelet32.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../builtins.h" diff --git a/src/fmindex-collection/occtable/Naive.h b/src/fmindex-collection/occtable/Naive.h index 9ec6001f..f2789609 100644 --- a/src/fmindex-collection/occtable/Naive.h +++ b/src/fmindex-collection/occtable/Naive.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/Sdsl_wt_bldc.h b/src/fmindex-collection/occtable/Sdsl_wt_bldc.h index 9bbdc458..d72cde4f 100644 --- a/src/fmindex-collection/occtable/Sdsl_wt_bldc.h +++ b/src/fmindex-collection/occtable/Sdsl_wt_bldc.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/Sdsl_wt_epr.h b/src/fmindex-collection/occtable/Sdsl_wt_epr.h index 12515168..558ade86 100644 --- a/src/fmindex-collection/occtable/Sdsl_wt_epr.h +++ b/src/fmindex-collection/occtable/Sdsl_wt_epr.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/Wavelet.h b/src/fmindex-collection/occtable/Wavelet.h index 71a0ccbf..68eb6c17 100644 --- a/src/fmindex-collection/occtable/Wavelet.h +++ b/src/fmindex-collection/occtable/Wavelet.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/fmindex-collection/occtable/all.h b/src/fmindex-collection/occtable/all.h index 300c04d5..85bcb32b 100644 --- a/src/fmindex-collection/occtable/all.h +++ b/src/fmindex-collection/occtable/all.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Bitvector.h" diff --git a/src/fmindex-collection/occtable/concepts.h b/src/fmindex-collection/occtable/concepts.h index 6334e1d8..d56dd05f 100644 --- a/src/fmindex-collection/occtable/concepts.h +++ b/src/fmindex-collection/occtable/concepts.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../cereal_tag.h" diff --git a/src/fmindex-collection/occtable/utils.h b/src/fmindex-collection/occtable/utils.h index 4f3e55c5..dce4bc31 100644 --- a/src/fmindex-collection/occtable/utils.h +++ b/src/fmindex-collection/occtable/utils.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once namespace fmindex_collection { diff --git a/src/fmindex-collection/search/Backtracking.h b/src/fmindex-collection/search/Backtracking.h index d908dfd2..19fcb666 100644 --- a/src/fmindex-collection/search/Backtracking.h +++ b/src/fmindex-collection/search/Backtracking.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "SelectCursor.h" diff --git a/src/fmindex-collection/search/BacktrackingWithBuffers.h b/src/fmindex-collection/search/BacktrackingWithBuffers.h index ee508b59..45025000 100644 --- a/src/fmindex-collection/search/BacktrackingWithBuffers.h +++ b/src/fmindex-collection/search/BacktrackingWithBuffers.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "SelectCursor.h" diff --git a/src/fmindex-collection/search/SearchNg12.h b/src/fmindex-collection/search/SearchNg12.h index b1fb5054..95919f31 100644 --- a/src/fmindex-collection/search/SearchNg12.h +++ b/src/fmindex-collection/search/SearchNg12.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg14.h b/src/fmindex-collection/search/SearchNg14.h index f59832dd..8e8fb4ef 100644 --- a/src/fmindex-collection/search/SearchNg14.h +++ b/src/fmindex-collection/search/SearchNg14.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg15.h b/src/fmindex-collection/search/SearchNg15.h index 544c4fa0..30966945 100644 --- a/src/fmindex-collection/search/SearchNg15.h +++ b/src/fmindex-collection/search/SearchNg15.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg16.h b/src/fmindex-collection/search/SearchNg16.h index 6ec55071..3bb85eed 100644 --- a/src/fmindex-collection/search/SearchNg16.h +++ b/src/fmindex-collection/search/SearchNg16.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg17.h b/src/fmindex-collection/search/SearchNg17.h index 15394100..93f3103f 100644 --- a/src/fmindex-collection/search/SearchNg17.h +++ b/src/fmindex-collection/search/SearchNg17.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg17ea.h b/src/fmindex-collection/search/SearchNg17ea.h index 60aa2d75..88a77742 100644 --- a/src/fmindex-collection/search/SearchNg17ea.h +++ b/src/fmindex-collection/search/SearchNg17ea.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg20.h b/src/fmindex-collection/search/SearchNg20.h index 20435dac..d38e5718 100644 --- a/src/fmindex-collection/search/SearchNg20.h +++ b/src/fmindex-collection/search/SearchNg20.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21.h b/src/fmindex-collection/search/SearchNg21.h index e7d14d69..23b78588 100644 --- a/src/fmindex-collection/search/SearchNg21.h +++ b/src/fmindex-collection/search/SearchNg21.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21V2.h b/src/fmindex-collection/search/SearchNg21V2.h index 891753f0..15a9168d 100644 --- a/src/fmindex-collection/search/SearchNg21V2.h +++ b/src/fmindex-collection/search/SearchNg21V2.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21V3.h b/src/fmindex-collection/search/SearchNg21V3.h index 95de601c..a998b2d6 100644 --- a/src/fmindex-collection/search/SearchNg21V3.h +++ b/src/fmindex-collection/search/SearchNg21V3.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21V4.h b/src/fmindex-collection/search/SearchNg21V4.h index 85ea3b19..a507cb89 100644 --- a/src/fmindex-collection/search/SearchNg21V4.h +++ b/src/fmindex-collection/search/SearchNg21V4.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21V5.h b/src/fmindex-collection/search/SearchNg21V5.h index 633367b2..46c272b0 100644 --- a/src/fmindex-collection/search/SearchNg21V5.h +++ b/src/fmindex-collection/search/SearchNg21V5.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21V6.h b/src/fmindex-collection/search/SearchNg21V6.h index 81b4ae88..bf1febd8 100644 --- a/src/fmindex-collection/search/SearchNg21V6.h +++ b/src/fmindex-collection/search/SearchNg21V6.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21V7.h b/src/fmindex-collection/search/SearchNg21V7.h index 0a172c8f..2ac5f34e 100644 --- a/src/fmindex-collection/search/SearchNg21V7.h +++ b/src/fmindex-collection/search/SearchNg21V7.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg21ea.h b/src/fmindex-collection/search/SearchNg21ea.h index c4d135e5..6d401f9e 100644 --- a/src/fmindex-collection/search/SearchNg21ea.h +++ b/src/fmindex-collection/search/SearchNg21ea.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNg22.h b/src/fmindex-collection/search/SearchNg22.h index a719da06..bb4f7722 100644 --- a/src/fmindex-collection/search/SearchNg22.h +++ b/src/fmindex-collection/search/SearchNg22.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchNoErrors.h b/src/fmindex-collection/search/SearchNoErrors.h index abec4a82..4978af3a 100644 --- a/src/fmindex-collection/search/SearchNoErrors.h +++ b/src/fmindex-collection/search/SearchNoErrors.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../concepts.h" diff --git a/src/fmindex-collection/search/SearchOneError.h b/src/fmindex-collection/search/SearchOneError.h index 37f18225..3643291c 100644 --- a/src/fmindex-collection/search/SearchOneError.h +++ b/src/fmindex-collection/search/SearchOneError.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/SearchPseudo.h b/src/fmindex-collection/search/SearchPseudo.h index f54508f6..f636115c 100644 --- a/src/fmindex-collection/search/SearchPseudo.h +++ b/src/fmindex-collection/search/SearchPseudo.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/fmindex-collection/search/SelectCursor.h b/src/fmindex-collection/search/SelectCursor.h index c9f7cb3b..aa00ecf9 100644 --- a/src/fmindex-collection/search/SelectCursor.h +++ b/src/fmindex-collection/search/SelectCursor.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../BiFMIndexCursor.h" diff --git a/src/fmindex-collection/search/all.h b/src/fmindex-collection/search/all.h index dc8aa423..9ceafa19 100644 --- a/src/fmindex-collection/search/all.h +++ b/src/fmindex-collection/search/all.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Backtracking.h" diff --git a/src/fmindex-collection/utils.h b/src/fmindex-collection/utils.h index c699e3a8..26f532ae 100644 --- a/src/fmindex-collection/utils.h +++ b/src/fmindex-collection/utils.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "concepts.h" diff --git a/src/run_search_schemes/main.cpp b/src/run_search_schemes/main.cpp index 280b48a6..4eef35ca 100644 --- a/src/run_search_schemes/main.cpp +++ b/src/run_search_schemes/main.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #include #include diff --git a/src/search_schemes/CMakeLists.txt b/src/search_schemes/CMakeLists.txt index eff54477..e5be82c2 100644 --- a/src/search_schemes/CMakeLists.txt +++ b/src/search_schemes/CMakeLists.txt @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.8) project(search_schemes) diff --git a/src/search_schemes/Scheme.h b/src/search_schemes/Scheme.h index 5edf15c1..5cd93f25 100644 --- a/src/search_schemes/Scheme.h +++ b/src/search_schemes/Scheme.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Search.h" diff --git a/src/search_schemes/Search.h b/src/search_schemes/Search.h index 4b608622..c428819c 100644 --- a/src/search_schemes/Search.h +++ b/src/search_schemes/Search.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include diff --git a/src/search_schemes/expand.h b/src/search_schemes/expand.h index ecc16e12..2909da1f 100644 --- a/src/search_schemes/expand.h +++ b/src/search_schemes/expand.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Scheme.h" diff --git a/src/search_schemes/generator/all.h b/src/search_schemes/generator/all.h index f888c7fe..27e28a6a 100644 --- a/src/search_schemes/generator/all.h +++ b/src/search_schemes/generator/all.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "backtracking.h" diff --git a/src/search_schemes/generator/backtracking.h b/src/search_schemes/generator/backtracking.h index 2c6238fb..c461a9e5 100644 --- a/src/search_schemes/generator/backtracking.h +++ b/src/search_schemes/generator/backtracking.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/generator/bestKnown.h b/src/search_schemes/generator/bestKnown.h index dcdef0f5..8be08e80 100644 --- a/src/search_schemes/generator/bestKnown.h +++ b/src/search_schemes/generator/bestKnown.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "backtracking.h" diff --git a/src/search_schemes/generator/h2.h b/src/search_schemes/generator/h2.h index 6b55a72d..63884e98 100644 --- a/src/search_schemes/generator/h2.h +++ b/src/search_schemes/generator/h2.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/generator/kianfar.h b/src/search_schemes/generator/kianfar.h index a1dd4965..5fb6193e 100644 --- a/src/search_schemes/generator/kianfar.h +++ b/src/search_schemes/generator/kianfar.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/generator/kucherov.h b/src/search_schemes/generator/kucherov.h index ccd425d1..9f3d6d8c 100644 --- a/src/search_schemes/generator/kucherov.h +++ b/src/search_schemes/generator/kucherov.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/generator/optimum.h b/src/search_schemes/generator/optimum.h index 80724848..9cbf1aaa 100644 --- a/src/search_schemes/generator/optimum.h +++ b/src/search_schemes/generator/optimum.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "backtracking.h" diff --git a/src/search_schemes/generator/pigeon.h b/src/search_schemes/generator/pigeon.h index 144ea2e8..a5ffd8a2 100644 --- a/src/search_schemes/generator/pigeon.h +++ b/src/search_schemes/generator/pigeon.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/generator/suffixFilter.h b/src/search_schemes/generator/suffixFilter.h index acbad55a..f2a51d79 100644 --- a/src/search_schemes/generator/suffixFilter.h +++ b/src/search_schemes/generator/suffixFilter.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/generator/zeroOnesZero.h b/src/search_schemes/generator/zeroOnesZero.h index 9447cd03..501ec8a6 100644 --- a/src/search_schemes/generator/zeroOnesZero.h +++ b/src/search_schemes/generator/zeroOnesZero.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "../Scheme.h" diff --git a/src/search_schemes/isComplete.h b/src/search_schemes/isComplete.h index 415e65b6..4e5d613c 100644 --- a/src/search_schemes/isComplete.h +++ b/src/search_schemes/isComplete.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Scheme.h" diff --git a/src/search_schemes/isValid.h b/src/search_schemes/isValid.h index e8c83f12..ea64ccce 100644 --- a/src/search_schemes/isValid.h +++ b/src/search_schemes/isValid.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Scheme.h" diff --git a/src/search_schemes/nodeCount.h b/src/search_schemes/nodeCount.h index d42e160f..1f5888b2 100644 --- a/src/search_schemes/nodeCount.h +++ b/src/search_schemes/nodeCount.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Scheme.h" diff --git a/src/search_schemes/search_schemes.h b/src/search_schemes/search_schemes.h index 61b84a49..262b8a3c 100644 --- a/src/search_schemes/search_schemes.h +++ b/src/search_schemes/search_schemes.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Scheme.h" diff --git a/src/search_schemes/weightedNodeCount.h b/src/search_schemes/weightedNodeCount.h index 71e6786b..33dc7bd2 100644 --- a/src/search_schemes/weightedNodeCount.h +++ b/src/search_schemes/weightedNodeCount.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: BSD-3-Clause #pragma once #include "Scheme.h" diff --git a/src/test_fmindex-collection/CMakeLists.txt b/src/test_fmindex-collection/CMakeLists.txt index f7992ce9..04d04abf 100644 --- a/src/test_fmindex-collection/CMakeLists.txt +++ b/src/test_fmindex-collection/CMakeLists.txt @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.8) project(test_fmindex-collection) diff --git a/src/test_fmindex-collection/allTables.h b/src/test_fmindex-collection/allTables.h index 93700444..c4620c25 100644 --- a/src/test_fmindex-collection/allTables.h +++ b/src/test_fmindex-collection/allTables.h @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #pragma once #include diff --git a/src/test_fmindex-collection/checkBiFMIndex.cpp b/src/test_fmindex-collection/checkBiFMIndex.cpp index d3f23b41..4e83f9c9 100644 --- a/src/test_fmindex-collection/checkBiFMIndex.cpp +++ b/src/test_fmindex-collection/checkBiFMIndex.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkDenseBiFMIndex.cpp b/src/test_fmindex-collection/checkDenseBiFMIndex.cpp index e91328b2..80718fde 100644 --- a/src/test_fmindex-collection/checkDenseBiFMIndex.cpp +++ b/src/test_fmindex-collection/checkDenseBiFMIndex.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkDenseReverseFMIndex.cpp b/src/test_fmindex-collection/checkDenseReverseFMIndex.cpp index 47cd0c70..cfa55b0f 100644 --- a/src/test_fmindex-collection/checkDenseReverseFMIndex.cpp +++ b/src/test_fmindex-collection/checkDenseReverseFMIndex.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkFMIndex.cpp b/src/test_fmindex-collection/checkFMIndex.cpp index 30c440c8..d2bbf48b 100644 --- a/src/test_fmindex-collection/checkFMIndex.cpp +++ b/src/test_fmindex-collection/checkFMIndex.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkOccTables.cpp b/src/test_fmindex-collection/checkOccTables.cpp index 89050af4..5a2b9d39 100644 --- a/src/test_fmindex-collection/checkOccTables.cpp +++ b/src/test_fmindex-collection/checkOccTables.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkReverseFMIndex.cpp b/src/test_fmindex-collection/checkReverseFMIndex.cpp index 57ce467c..f4c8f32a 100644 --- a/src/test_fmindex-collection/checkReverseFMIndex.cpp +++ b/src/test_fmindex-collection/checkReverseFMIndex.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkReverseIndexSearch.cpp b/src/test_fmindex-collection/checkReverseIndexSearch.cpp index d146a297..cded630c 100644 --- a/src/test_fmindex-collection/checkReverseIndexSearch.cpp +++ b/src/test_fmindex-collection/checkReverseIndexSearch.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkSearchBacktracking.cpp b/src/test_fmindex-collection/checkSearchBacktracking.cpp index 4c5fd74b..24bdd97d 100644 --- a/src/test_fmindex-collection/checkSearchBacktracking.cpp +++ b/src/test_fmindex-collection/checkSearchBacktracking.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/checkSearchPseudo.cpp b/src/test_fmindex-collection/checkSearchPseudo.cpp index dcc7c938..ceaa71dd 100644 --- a/src/test_fmindex-collection/checkSearchPseudo.cpp +++ b/src/test_fmindex-collection/checkSearchPseudo.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include "allTables.h" #include diff --git a/src/test_fmindex-collection/main.cpp b/src/test_fmindex-collection/main.cpp index ade24161..d2042f2c 100644 --- a/src/test_fmindex-collection/main.cpp +++ b/src/test_fmindex-collection/main.cpp @@ -1,8 +1,5 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #define CATCH_CONFIG_MAIN #include diff --git a/src/test_fmindex-collection/utils.cpp b/src/test_fmindex-collection/utils.cpp index 8ee7f0d6..80616298 100644 --- a/src/test_fmindex-collection/utils.cpp +++ b/src/test_fmindex-collection/utils.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include diff --git a/src/test_search_schemes/CMakeLists.txt b/src/test_search_schemes/CMakeLists.txt index 37d39ad8..9a593f40 100644 --- a/src/test_search_schemes/CMakeLists.txt +++ b/src/test_search_schemes/CMakeLists.txt @@ -1,9 +1,6 @@ -# ----------------------------------------------------------------------------------------------------- -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file. -# ----------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 cmake_minimum_required (VERSION 3.8) project(test_search_schemes) diff --git a/src/test_search_schemes/checkGenerators.cpp b/src/test_search_schemes/checkGenerators.cpp index 5eef4002..175ce2c0 100644 --- a/src/test_search_schemes/checkGenerators.cpp +++ b/src/test_search_schemes/checkGenerators.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include #include diff --git a/src/test_search_schemes/checkGeneratorsIsComplete.cpp b/src/test_search_schemes/checkGeneratorsIsComplete.cpp index 3e97f58c..fab5c950 100644 --- a/src/test_search_schemes/checkGeneratorsIsComplete.cpp +++ b/src/test_search_schemes/checkGeneratorsIsComplete.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include #include diff --git a/src/test_search_schemes/expand.cpp b/src/test_search_schemes/expand.cpp index 171b4eb8..b281fdd9 100644 --- a/src/test_search_schemes/expand.cpp +++ b/src/test_search_schemes/expand.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include #include diff --git a/src/test_search_schemes/isComplete.cpp b/src/test_search_schemes/isComplete.cpp index 31f3f160..3e0bd710 100644 --- a/src/test_search_schemes/isComplete.cpp +++ b/src/test_search_schemes/isComplete.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include diff --git a/src/test_search_schemes/isValid.cpp b/src/test_search_schemes/isValid.cpp index 63290d8d..b7e454ec 100644 --- a/src/test_search_schemes/isValid.cpp +++ b/src/test_search_schemes/isValid.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include diff --git a/src/test_search_schemes/main.cpp b/src/test_search_schemes/main.cpp index ade24161..d2042f2c 100644 --- a/src/test_search_schemes/main.cpp +++ b/src/test_search_schemes/main.cpp @@ -1,8 +1,5 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #define CATCH_CONFIG_MAIN #include diff --git a/src/test_search_schemes/nodeCount.cpp b/src/test_search_schemes/nodeCount.cpp index 26e79c65..ec3035a6 100644 --- a/src/test_search_schemes/nodeCount.cpp +++ b/src/test_search_schemes/nodeCount.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -// shipped with this file. -// ----------------------------------------------------------------------------------------------------- +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 #include #include #include From 87a5a1f612bbfe110b04ae1dfbdb252e93c79ab8 Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Fri, 10 Nov 2023 09:42:03 +0100 Subject: [PATCH 2/7] fix: macos ci update to 12 --- .github/workflows/ci-macos.yml | 99 ++++++++++++++++++++++++++++++++++ .github/workflows/ci.yml | 20 +------ 2 files changed, 100 insertions(+), 19 deletions(-) create mode 100644 .github/workflows/ci-macos.yml diff --git a/.github/workflows/ci-macos.yml b/.github/workflows/ci-macos.yml new file mode 100644 index 00000000..a8c04fb8 --- /dev/null +++ b/.github/workflows/ci-macos.yml @@ -0,0 +1,99 @@ +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 +name: "Linux and MacOS" + +on: + push: + branches: + # Push events to branches matching refs/heads/master + - 'main' + pull_request: + +concurrency: + group: ${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + TZ: Europe/Berlin + +jobs: + build: + name: ${{ matrix.os }} / ${{ matrix.compiler }} + runs-on: macos-12 + timeout-minutes: 120 + strategy: + fail-fast: false + matrix: + osname: ["MacOS 12"] + compiler: ["gcc13 (c++20)", "gcc12 (c++20)", "gcc11 (c++20)", "gcc13 (c++20, Debug)"] + + include: + - osname: "MacOS 12" + os: macos-12 + cmake_flags: "-DFMC_USE_SDSL=NO" + threads: 3 + + - compiler: "gcc13 (c++20)" + cxx: "g++-13" + cc: "gcc-13" + build_type: Release + brew_pkgs: gcc@13 + + - compiler: "gcc12 (c++20)" + cxx: "g++-12" + cc: "gcc-12" + build_type: Release + brew_pkgs: gcc@12 + + - compiler: "gcc11 (c++20)" + cxx: "g++-11" + cc: "gcc-11" + build_type: Release + brew_pkgs: gcc@11 + + - compiler: "gcc13 (c++20, Debug)" + cxx: "g++-13" + cc: "gcc-13" + build_type: Debug + brew_pkgs: gcc@13 + steps: + - name: Checkout Repository + uses: actions/checkout@v3 + with: + path: fmc + fetch-depth: 1 + + - name: Install Tools on Mac + run: | + touch ${HOME}/.activate_brew + brew update-reset + brew install --force-bottle --overwrite fmt boost cmake ${{ matrix.brew_pkgs }} pkg-config + + - name: Tool versions + run: | + source ${HOME}/.activate_brew + cmake --version + ${{ matrix.cxx }} --version + + - name: Configure tests + env: + CXX: ${{ matrix.cxx }} + CC: ${{ matrix.cc }} + run: | + source ${HOME}/.activate_brew + mkdir fmc-build + cd fmc-build + cmake ../fmc -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} ${{ matrix.cmake_flags }} + + - name: Build tests + run: | + source ${HOME}/.activate_brew + cd fmc-build + make -k -j2 + + - name: Run tests + run: | + source ${HOME}/.activate_brew + cd fmc-build + ctest . -j ${{ matrix.threads }} --output-on-failure diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 1fc8b040..f7a2efbe 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -25,7 +25,7 @@ jobs: strategy: fail-fast: false matrix: - osname: ["MacOS 11", "Ubuntu 22.04"] + osname: ["Ubuntu 22.04"] compiler: ["gcc13 (c++20)", "gcc12 (c++20)", "gcc11 (c++20)", "gcc13 (c++20, Debug)", "clang14"] include: @@ -34,11 +34,6 @@ jobs: cmake_flags: "" threads: 2 - - osname: "MacOS 11" - os: macos-11 - cmake_flags: "-DFMC_USE_SDSL=NO" - threads: 3 - - compiler: "gcc13 (c++20)" cxx: "g++-13" cc: "gcc-13" @@ -68,11 +63,6 @@ jobs: cc: "clang-14" build_type: Release brew_pkgs: llvm@14 - - exclude: - - osname: "MacOS 11" - compiler: "clang14" - steps: - name: Checkout Repository uses: actions/checkout@v3 @@ -80,13 +70,6 @@ jobs: path: fmc fetch-depth: 1 - - name: Install Tools on Mac - run: | - touch ${HOME}/.activate_brew - brew update-reset - brew install --force-bottle --overwrite fmt boost cmake ${{ matrix.brew_pkgs }} pkg-config - if: matrix.osname == 'MacOS 11' - - name: Install Tools on Ubuntu run: | NONINTERACTIVE=1 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" @@ -96,7 +79,6 @@ jobs: sudo apt-get install -y build-essential brew install --force-bottle fmt boost cmake ${{ matrix.brew_pkgs }} pkg-config ${{ matrix.cxx }} --version - if: matrix.osname == 'Ubuntu 22.04' - name: Tool versions run: | From 60df9ca22b3ca36d8b708568d9c3ab7140e95f54 Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Fri, 10 Nov 2023 10:11:41 +0100 Subject: [PATCH 3/7] patch: use iv-project action --- .github/workflows/ci-macos.yml | 2 +- .github/workflows/ci.yml | 105 ++++++--------------------------- 2 files changed, 18 insertions(+), 89 deletions(-) diff --git a/.github/workflows/ci-macos.yml b/.github/workflows/ci-macos.yml index a8c04fb8..7bf109fb 100644 --- a/.github/workflows/ci-macos.yml +++ b/.github/workflows/ci-macos.yml @@ -1,7 +1,7 @@ # SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin # SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik # SPDX-License-Identifier: CC0-1.0 -name: "Linux and MacOS" +name: "MacOS" on: push: diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f7a2efbe..a3e98b11 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,12 +1,12 @@ # SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin # SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik # SPDX-License-Identifier: CC0-1.0 -name: "Linux and MacOS" + +name: "Linux" on: push: branches: - # Push events to branches matching refs/heads/master - 'main' pull_request: @@ -14,96 +14,25 @@ concurrency: group: ${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true -env: - TZ: Europe/Berlin - jobs: build: - name: ${{ matrix.os }} / ${{ matrix.compiler }} - runs-on: ${{ matrix.os }} - timeout-minutes: 120 + name: ${{ matrix.compiler }} + runs-on: ubuntu-22.04 + timeout-minutes: 30 strategy: fail-fast: false matrix: - osname: ["Ubuntu 22.04"] - compiler: ["gcc13 (c++20)", "gcc12 (c++20)", "gcc11 (c++20)", "gcc13 (c++20, Debug)", "clang14"] - - include: - - osname: "Ubuntu 22.04" - os: ubuntu-22.04 - cmake_flags: "" - threads: 2 - - - compiler: "gcc13 (c++20)" - cxx: "g++-13" - cc: "gcc-13" - build_type: Release - brew_pkgs: gcc@13 - - - compiler: "gcc12 (c++20)" - cxx: "g++-12" - cc: "gcc-12" - build_type: Release - brew_pkgs: gcc@12 - - - compiler: "gcc11 (c++20)" - cxx: "g++-11" - cc: "gcc-11" - build_type: Release - brew_pkgs: gcc@11 - - - compiler: "gcc13 (c++20, Debug)" - cxx: "g++-13" - cc: "gcc-13" - build_type: Debug - brew_pkgs: gcc@13 - - - compiler: "clang14" - cxx: "clang++-14" - cc: "clang-14" - build_type: Release - brew_pkgs: llvm@14 + compiler: + - "gcc13-cpp20-release" + - "gcc12-cpp20-release" + - "gcc11-cpp20-release" + - "gcc13-cpp20-debug" + - "clang15-cpp20-release" + - "clang16-cpp20-release" steps: - - name: Checkout Repository - uses: actions/checkout@v3 + - name: Standard IV-project testing + uses: iv-project/IVaction/linux-testing@v3 with: - path: fmc - fetch-depth: 1 - - - name: Install Tools on Ubuntu - run: | - NONINTERACTIVE=1 /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" - echo 'eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)"' >> ${HOME}/.activate_brew - eval "$(/home/linuxbrew/.linuxbrew/bin/brew shellenv)" - sudo apt-get update -y - sudo apt-get install -y build-essential - brew install --force-bottle fmt boost cmake ${{ matrix.brew_pkgs }} pkg-config - ${{ matrix.cxx }} --version - - - name: Tool versions - run: | - source ${HOME}/.activate_brew - cmake --version - ${{ matrix.cxx }} --version - - - name: Configure tests - env: - CXX: ${{ matrix.cxx }} - CC: ${{ matrix.cc }} - run: | - source ${HOME}/.activate_brew - mkdir fmc-build - cd fmc-build - cmake ../fmc -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} ${{ matrix.cmake_flags }} - - - name: Build tests - run: | - source ${HOME}/.activate_brew - cd fmc-build - make -k -j2 - - - name: Run tests - run: | - source ${HOME}/.activate_brew - cd fmc-build - ctest . -j ${{ matrix.threads }} --output-on-failure + name: linux-${{ matrix.compiler }} + compiler: ${{ matrix.compiler }} + threads: 2 From d49fb0e5a779544b8a147d671d95a1e6a7c4c13e Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Fri, 10 Nov 2023 10:16:28 +0100 Subject: [PATCH 4/7] patch: rename ci-names --- .github/workflows/{ci.yml => ci_linux.yml} | 7 +++---- .github/workflows/{ci-macos.yml => ci_macos.yml} | 2 +- .github/workflows/{ci-msvc.yml => ci_msvc.yml} | 0 3 files changed, 4 insertions(+), 5 deletions(-) rename .github/workflows/{ci.yml => ci_linux.yml} (80%) rename .github/workflows/{ci-macos.yml => ci_macos.yml} (97%) rename .github/workflows/{ci-msvc.yml => ci_msvc.yml} (100%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci_linux.yml similarity index 80% rename from .github/workflows/ci.yml rename to .github/workflows/ci_linux.yml index a3e98b11..c74f47bf 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci_linux.yml @@ -11,12 +11,12 @@ on: pull_request: concurrency: - group: ${{ github.event.pull_request.number || github.ref }} + group: linux-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true jobs: build: - name: ${{ matrix.compiler }} + name: linux-${{ matrix.compiler }} runs-on: ubuntu-22.04 timeout-minutes: 30 strategy: @@ -31,8 +31,7 @@ jobs: - "clang16-cpp20-release" steps: - name: Standard IV-project testing - uses: iv-project/IVaction/linux-testing@v3 + uses: iv-project/IVaction/linux-testing@feat/simpler_ci with: - name: linux-${{ matrix.compiler }} compiler: ${{ matrix.compiler }} threads: 2 diff --git a/.github/workflows/ci-macos.yml b/.github/workflows/ci_macos.yml similarity index 97% rename from .github/workflows/ci-macos.yml rename to .github/workflows/ci_macos.yml index 7bf109fb..0f1890fd 100644 --- a/.github/workflows/ci-macos.yml +++ b/.github/workflows/ci_macos.yml @@ -11,7 +11,7 @@ on: pull_request: concurrency: - group: ${{ github.event.pull_request.number || github.ref }} + group: macos-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true env: diff --git a/.github/workflows/ci-msvc.yml b/.github/workflows/ci_msvc.yml similarity index 100% rename from .github/workflows/ci-msvc.yml rename to .github/workflows/ci_msvc.yml From 7d4507919e2a38248e5f9c122e7d24a804d1b901 Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Fri, 10 Nov 2023 10:36:27 +0100 Subject: [PATCH 5/7] patch: using modern IVaction macos ci --- .github/workflows/ci_linux.yml | 16 +++--- .github/workflows/ci_macos.yml | 90 ++++++---------------------------- 2 files changed, 22 insertions(+), 84 deletions(-) diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml index c74f47bf..b9a9d22e 100644 --- a/.github/workflows/ci_linux.yml +++ b/.github/workflows/ci_linux.yml @@ -16,22 +16,22 @@ concurrency: jobs: build: - name: linux-${{ matrix.compiler }} + name: ${{ matrix.compiler }} runs-on: ubuntu-22.04 timeout-minutes: 30 strategy: fail-fast: false matrix: compiler: - - "gcc13-cpp20-release" - - "gcc12-cpp20-release" - - "gcc11-cpp20-release" - - "gcc13-cpp20-debug" - - "clang15-cpp20-release" - - "clang16-cpp20-release" + - gcc13-cpp20-release + - gcc12-cpp20-release + - gcc11-cpp20-release + - gcc13-cpp20-debug + - clang15-cpp20-release + - clang16-cpp20-release steps: - name: Standard IV-project testing - uses: iv-project/IVaction/linux-testing@feat/simpler_ci + uses: iv-project/IVaction/linux-testing@feat/macos-testing with: compiler: ${{ matrix.compiler }} threads: 2 diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml index 0f1890fd..b4221a67 100644 --- a/.github/workflows/ci_macos.yml +++ b/.github/workflows/ci_macos.yml @@ -1,12 +1,12 @@ # SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin # SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik # SPDX-License-Identifier: CC0-1.0 + name: "MacOS" on: push: branches: - # Push events to branches matching refs/heads/master - 'main' pull_request: @@ -14,86 +14,24 @@ concurrency: group: macos-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true -env: - TZ: Europe/Berlin - jobs: build: - name: ${{ matrix.os }} / ${{ matrix.compiler }} + name: ${{ matrix.compiler }} runs-on: macos-12 - timeout-minutes: 120 + timeout-minutes: 30 strategy: fail-fast: false matrix: - osname: ["MacOS 12"] - compiler: ["gcc13 (c++20)", "gcc12 (c++20)", "gcc11 (c++20)", "gcc13 (c++20, Debug)"] - - include: - - osname: "MacOS 12" - os: macos-12 - cmake_flags: "-DFMC_USE_SDSL=NO" - threads: 3 - - - compiler: "gcc13 (c++20)" - cxx: "g++-13" - cc: "gcc-13" - build_type: Release - brew_pkgs: gcc@13 - - - compiler: "gcc12 (c++20)" - cxx: "g++-12" - cc: "gcc-12" - build_type: Release - brew_pkgs: gcc@12 - - - compiler: "gcc11 (c++20)" - cxx: "g++-11" - cc: "gcc-11" - build_type: Release - brew_pkgs: gcc@11 - - - compiler: "gcc13 (c++20, Debug)" - cxx: "g++-13" - cc: "gcc-13" - build_type: Debug - brew_pkgs: gcc@13 + compiler: + - gcc13-cpp20-release + - gcc12-cpp20-release + - gcc11-cpp20-release + - gcc13-cpp20-debug + - clang15-cpp20-release + - clang16-cpp20-release steps: - - name: Checkout Repository - uses: actions/checkout@v3 + - name: Standard IV-project testing + uses: iv-project/IVaction/macos-testing@feat/macos-testing with: - path: fmc - fetch-depth: 1 - - - name: Install Tools on Mac - run: | - touch ${HOME}/.activate_brew - brew update-reset - brew install --force-bottle --overwrite fmt boost cmake ${{ matrix.brew_pkgs }} pkg-config - - - name: Tool versions - run: | - source ${HOME}/.activate_brew - cmake --version - ${{ matrix.cxx }} --version - - - name: Configure tests - env: - CXX: ${{ matrix.cxx }} - CC: ${{ matrix.cc }} - run: | - source ${HOME}/.activate_brew - mkdir fmc-build - cd fmc-build - cmake ../fmc -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} ${{ matrix.cmake_flags }} - - - name: Build tests - run: | - source ${HOME}/.activate_brew - cd fmc-build - make -k -j2 - - - name: Run tests - run: | - source ${HOME}/.activate_brew - cd fmc-build - ctest . -j ${{ matrix.threads }} --output-on-failure + compiler: ${{ matrix.compiler }} + threads: 3 From 6e39fc6992b1a0fe6be429e3a07a22c265e8bbc7 Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Fri, 10 Nov 2023 13:24:04 +0100 Subject: [PATCH 6/7] fix: missing include --- src/easyExample/main.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/easyExample/main.cpp b/src/easyExample/main.cpp index 387c232e..91180962 100644 --- a/src/easyExample/main.cpp +++ b/src/easyExample/main.cpp @@ -8,9 +8,10 @@ #include #include +#include #include +#include #include -#include using namespace fmindex_collection; From 311803ee77a76e75fdaeffc541e5b5e1acfaf35a Mon Sep 17 00:00:00 2001 From: Simon Gene Gottlieb Date: Fri, 10 Nov 2023 13:41:35 +0100 Subject: [PATCH 7/7] fix: adjust to proper ivaction version --- .github/workflows/ci_linux.yml | 2 +- .github/workflows/ci_macos.yml | 8 ++------ 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml index b9a9d22e..50ac012c 100644 --- a/.github/workflows/ci_linux.yml +++ b/.github/workflows/ci_linux.yml @@ -31,7 +31,7 @@ jobs: - clang16-cpp20-release steps: - name: Standard IV-project testing - uses: iv-project/IVaction/linux-testing@feat/macos-testing + uses: iv-project/IVaction/linux-testing@v4 with: compiler: ${{ matrix.compiler }} threads: 2 diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml index b4221a67..e433c230 100644 --- a/.github/workflows/ci_macos.yml +++ b/.github/workflows/ci_macos.yml @@ -24,14 +24,10 @@ jobs: matrix: compiler: - gcc13-cpp20-release - - gcc12-cpp20-release - - gcc11-cpp20-release - - gcc13-cpp20-debug - - clang15-cpp20-release - - clang16-cpp20-release steps: - name: Standard IV-project testing - uses: iv-project/IVaction/macos-testing@feat/macos-testing + uses: iv-project/IVaction/macos-testing@v4 with: compiler: ${{ matrix.compiler }} threads: 3 + cmake_flags: "-DFMC_USE_SDSL=NO"