From 22571fbccc7c768654d20e52acb4e66a91917f99 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Fri, 13 Oct 2023 16:11:59 +0200 Subject: [PATCH 1/2] [INFRA] Use SPDX License Indentifier --- .clang-format | 4 + .clang-tidy | 4 + .cmake-format.yaml | 4 + .codecov.yml | 4 + .editorconfig | 4 + .github/ISSUE_TEMPLATE/bug_report.yml | 4 + .github/dependabot.yml | 4 + .github/workflows/ci_coverage.yml | 4 + .github/workflows/ci_documentation.yml | 4 + .github/workflows/ci_iwyu.yml | 4 + .github/workflows/ci_lint.yml | 4 + .github/workflows/ci_linux.yml | 4 + .github/workflows/ci_macos.yml | 4 + .github/workflows/ci_misc.yml | 4 + .github/workflows/ci_util.yml | 4 + .github/workflows/readme_snippet.yml | 4 + .github/workflows/scripts/gcov.sh | 5 + .github/workflows/update_cookbook.yml | 4 + .gitmodules | 4 + CHANGELOG.md | 6 + CMakeLists.txt | 9 +- CODE_OF_CONDUCT.md | 6 + CONTRIBUTING.md | 6 + LICENSES/BSD-3-Clause.txt | 11 ++ LICENSES/CC-BY-4.0.txt | 156 ++++++++++++++++++ LICENSES/CC0-1.0.txt | 121 ++++++++++++++ LICENSES/MIT.txt | 9 + README.md | 6 + cmake/configuration.cmake | 9 +- cmake/cpack.cmake | 9 +- cmake/install.cmake | 4 + cmake/version.cmake | 9 +- doc/about/api/index.md | 6 + doc/about/citing/index.md | 6 + doc/about/copyright/bsdl_badge.svg.license | 3 + doc/about/copyright/cc0_badge.svg.license | 3 + doc/about/copyright/ccby_badge.svg.license | 3 + .../copyright/copyfree_badge.svg.license | 3 + doc/cookbook/index.md | 6 + doc/images/hibf.svg.license | 3 + doc/images/hierarchical_dp_init.png.license | 3 + .../hierarchical_dp_recursion.png.license | 3 + doc/main_page.md | 6 + include/hibf/all.hpp | 9 +- include/hibf/build/bin_size_in_bits.hpp | 9 +- include/hibf/build/build_data.hpp | 9 +- include/hibf/build/compute_kmers.hpp | 9 +- include/hibf/build/construct_ibf.hpp | 9 +- include/hibf/build/insert_into_ibf.hpp | 9 +- include/hibf/build/update_parent_kmers.hpp | 9 +- include/hibf/build/update_user_bins.hpp | 9 +- include/hibf/cereal/concepts.hpp | 9 +- include/hibf/cereal/path.hpp | 4 + include/hibf/config.hpp | 9 +- include/hibf/contrib/README.md | 6 + include/hibf/contrib/aligned_allocator.hpp | 9 +- .../hierarchical_interleaved_bloom_filter.hpp | 9 +- include/hibf/interleaved_bloom_filter.hpp | 9 +- .../hibf/layout/compute_fpr_correction.hpp | 4 + include/hibf/layout/compute_layout.hpp | 4 + include/hibf/layout/data_store.hpp | 4 + include/hibf/layout/graph.hpp | 9 +- include/hibf/layout/hierarchical_binning.hpp | 4 + include/hibf/layout/layout.hpp | 4 + include/hibf/layout/prefixes.hpp | 4 + include/hibf/layout/print_matrix.hpp | 4 + include/hibf/layout/simple_binning.hpp | 4 + include/hibf/misc/insert_iterator.hpp | 9 +- include/hibf/misc/next_multiple_of_64.hpp | 4 + include/hibf/misc/print.hpp | 4 + include/hibf/misc/timer.hpp | 9 +- include/hibf/platform.hpp | 9 +- include/hibf/sketch/compute_sketches.hpp | 4 + include/hibf/sketch/estimate_kmer_counts.hpp | 4 + include/hibf/sketch/hyperloglog.hpp | 13 +- include/hibf/sketch/toolbox.hpp | 4 + include/hibf/version.hpp | 9 +- src/CMakeLists.txt | 4 + src/build/compute_kmers.cpp | 9 +- src/build/construct_ibf.cpp | 9 +- src/build/insert_into_ibf.cpp | 9 +- src/config.cpp | 9 +- src/hierarchical_interleaved_bloom_filter.cpp | 9 +- src/interleaved_bloom_filter.cpp | 9 +- src/layout/compute_fpr_correction.cpp | 4 + src/layout/compute_layout.cpp | 4 + src/layout/graph.cpp | 9 +- src/layout/hierarchical_binning.cpp | 4 + src/layout/layout.cpp | 9 +- src/layout/simple_binning.cpp | 4 + src/misc/print.cpp | 9 +- src/sketch/compute_sketches.cpp | 4 + src/sketch/hyperloglog.cpp | 5 + src/sketch/toolbox.cpp | 4 + test/clang_tidy/CMakeLists.txt | 4 + .../diagnostics/list_missing_unit_tests.cmake | 9 +- .../diagnostics/list_unused_snippets.cmake | 9 +- .../diagnostics/list_unused_unit_tests.cmake | 9 +- test/cmake/hibf_add_subdirectories.cmake | 9 +- test/cmake/hibf_generate_snippet.cmake | 9 +- test/cmake/hibf_macro_benchmark.cmake | 9 +- test/cmake/hibf_path_longest_stem.cmake | 9 +- test/cmake/hibf_require_benchmark.cmake | 9 +- test/cmake/hibf_require_ccache.cmake | 9 +- test/cmake/hibf_require_test.cmake | 9 +- test/cmake/hibf_test_component.cmake | 9 +- test/cmake/hibf_test_files.cmake | 9 +- .../add_include_dependencies.cmake | 9 +- .../generate_include_dependencies.cmake | 9 +- test/coverage/CMakeLists.txt | 9 +- test/documentation/.vercel/0_setup.sh | 5 + test/documentation/.vercel/1_build.sh | 5 + test/documentation/.vercel/Notes.md | 6 + test/documentation/.vercel/api/doxysearch.sh | 4 + .../.vercel/powered-by-vercel.svg.license | 2 + .../documentation/.vercel/vercel.json.license | 3 + test/documentation/CMakeLists.txt | 9 +- test/documentation/DoxygenLayout.xml | 7 + test/documentation/README.md | 8 +- test/documentation/api-stability.js | 4 + .../doxygen-awesome-darkmode-toggle.js | 3 + .../doxygen-awesome-fragment-copy-button.js | 3 + .../doxygen-awesome-interactive-toc.js | 3 + .../doxygen-awesome-paragraph-link.js | 3 + .../doxygen-awesome/doxygen-awesome-tabs.js | 3 + .../doxygen-awesome/doxygen-awesome.css | 5 + test/documentation/hibf-doxygen-layout.cmake | 9 +- test/documentation/hibf-doxygen-package.cmake | 9 +- test/documentation/hibf-doxygen.cmake | 9 +- test/documentation/hibf.css | 6 + test/documentation/hibf_doxygen_cfg.in | 4 + test/documentation/hibf_footer.html.in | 6 + test/documentation/hibf_header.html | 6 + test/documentation/seqan_logo.svg.license | 3 + test/header/CMakeLists.txt | 9 +- test/header/generate_header_source.cmake | 4 + test/hibf-test.cmake | 9 +- test/include/hibf/test/bytes.hpp | 9 +- test/include/hibf/test/expect_range_eq.hpp | 9 +- test/include/hibf/test/expect_same_type.hpp | 9 +- test/include/hibf/test/file_access.hpp | 9 +- test/include/hibf/test/sandboxed_path.hpp | 9 +- test/include/hibf/test/seqan3.hpp | 9 +- .../hibf/test/temporary_snippet_file.hpp | 9 +- test/include/hibf/test/tmp_directory.hpp | 9 +- .../include/hibf/test/type_name_as_string.hpp | 9 +- test/iwyu/CMakeLists.txt | 4 + test/iwyu/mappings/gcc.libc.imp | 4 + test/iwyu/mappings/gcc.stl.headers.imp | 4 + test/iwyu/mappings/gcc.symbols.imp | 4 + test/iwyu/mappings/iwyu.imp | 4 + test/iwyu/mappings/libcxx.imp | 4 + test/iwyu/mappings/stl.c.headers.imp | 4 + test/performance/CMakeLists.txt | 9 +- test/performance/example/CMakeLists.txt | 4 + .../performance/example/example_benchmark.cpp | 9 +- test/performance/hibf/CMakeLists.txt | 4 + ...cal_interleaved_bloom_filter_benchmark.cpp | 9 +- test/performance/ibf/CMakeLists.txt | 4 + .../ibf/binning_bitvector_benchmark.cpp | 9 +- .../interleaved_bloom_filter_benchmark.cpp | 9 +- test/scripts/add_snippets_to_cookbook.sh | 11 +- test/scripts/link_check.sh | 11 +- test/scripts/update_copyright.sh | 10 +- test/snippet/CMakeLists.txt | 9 +- test/snippet/compare_snippet_output.cmake | 4 + test/snippet/hibf/config_input_fn_dummy.cpp | 4 + test/snippet/hibf/config_input_fn_file.cpp | 4 + test/snippet/hibf/config_input_fn_vector.cpp | 4 + .../hibf/config_number_of_user_bins.cpp | 4 + test/snippet/hibf/hibf_construction.cpp | 4 + .../hierarchical_interleaved_bloom_filter.cpp | 4 + ...hical_interleaved_bloom_filter.out.license | 3 + test/snippet/ibf/counting_agent.cpp | 4 + test/snippet/ibf/counting_agent.out.license | 3 + .../ibf/counting_agent_construction.cpp | 4 + test/snippet/ibf/counting_vector.cpp | 4 + test/snippet/ibf/counting_vector.out.license | 3 + .../ibf/interleaved_bloom_filter_clear.cpp | 4 + ...interleaved_bloom_filter_clear.out.license | 3 + .../interleaved_bloom_filter_constructor.cpp | 4 + .../ibf/interleaved_bloom_filter_emplace.cpp | 4 + ...ed_bloom_filter_increase_bin_number_to.cpp | 4 + ..._filter_increase_bin_number_to.out.license | 3 + .../ibf/membership_agent_bulk_contains.cpp | 4 + ...membership_agent_bulk_contains.out.license | 3 + .../ibf/membership_agent_construction.cpp | 4 + test/snippet/readme.cpp | 4 + test/snippet/readme.out.license | 3 + test/snippet/snippet_main.cpp | 4 + test/snippet/test/tmp_directory.cpp | 4 + test/unit/CMakeLists.txt | 9 +- test/unit/hibf/CMakeLists.txt | 4 + test/unit/hibf/config_test.cpp | 4 + ...archical_interleaved_bloom_filter_test.cpp | 9 +- .../hibf/interleaved_bloom_filter_test.cpp | 9 +- test/unit/hibf/layout/CMakeLists.txt | 4 + test/unit/hibf/layout/fpr_correction_test.cpp | 4 + test/unit/hibf/layout/graph_test.cpp | 4 + .../hibf/layout/hierarchical_binning_test.cpp | 4 + test/unit/hibf/layout/layout_test.cpp | 4 + test/unit/hibf/layout/simple_binning_test.cpp | 4 + test/unit/hibf/print_test.cpp | 4 + test/unit/hibf/sketch/CMakeLists.txt | 4 + .../hibf/sketch/estimate_kmer_counts_test.cpp | 4 + test/unit/hibf/sketch/hyperloglog_test.cpp | 4 + test/unit/hibf/sketch/toolbox_test.cpp | 4 + test/unit/test/CMakeLists.txt | 4 + test/unit/test/expect_range_eq_test.cpp | 9 +- test/unit/test/expect_same_type_test.cpp | 9 +- test/unit/test/file_access_test.cpp | 9 +- test/unit/test/sandboxed_path_test.cpp | 9 +- .../unit/test/temporary_snippet_file_test.cpp | 9 +- test/unit/test/tmp_directory_test.cpp | 9 +- util/CMakeLists.txt | 9 +- util/fpr_quality.cpp | 9 +- 216 files changed, 1083 insertions(+), 496 deletions(-) create mode 100644 LICENSES/BSD-3-Clause.txt create mode 100644 LICENSES/CC-BY-4.0.txt create mode 100644 LICENSES/CC0-1.0.txt create mode 100644 LICENSES/MIT.txt create mode 100644 doc/about/copyright/bsdl_badge.svg.license create mode 100644 doc/about/copyright/cc0_badge.svg.license create mode 100644 doc/about/copyright/ccby_badge.svg.license create mode 100644 doc/about/copyright/copyfree_badge.svg.license create mode 100644 doc/images/hibf.svg.license create mode 100644 doc/images/hierarchical_dp_init.png.license create mode 100644 doc/images/hierarchical_dp_recursion.png.license create mode 100644 test/documentation/.vercel/powered-by-vercel.svg.license create mode 100644 test/documentation/.vercel/vercel.json.license create mode 100644 test/documentation/seqan_logo.svg.license create mode 100644 test/snippet/hibf/hierarchical_interleaved_bloom_filter.out.license create mode 100644 test/snippet/ibf/counting_agent.out.license create mode 100644 test/snippet/ibf/counting_vector.out.license create mode 100644 test/snippet/ibf/interleaved_bloom_filter_clear.out.license create mode 100644 test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.out.license create mode 100644 test/snippet/ibf/membership_agent_bulk_contains.out.license create mode 100644 test/snippet/readme.out.license diff --git a/.clang-format b/.clang-format index f53fb488..4a1d91d9 100644 --- a/.clang-format +++ b/.clang-format @@ -1,3 +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 + # Format all files in include folder, including std module, excluding contrib module # find . -iname "*.[ch]pp" -not -path "./include/hibf/contrib/*" -not -path "./submodules/*" -not -path "./build/*" | xargs clang-format-15 --style=file -i # Staged files: git diff --name-only HEAD --diff-filter=ACMRT | grep -E "(\.cpp|\.hpp)$" | xargs clang-format-15 --style=file -i diff --git a/.clang-tidy b/.clang-tidy index 7aeee1f0..313d4737 100644 --- a/.clang-tidy +++ b/.clang-tidy @@ -1,3 +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 + --- Checks: "bugprone*, performance*, diff --git a/.cmake-format.yaml b/.cmake-format.yaml index d534ef03..3ad587ed 100644 --- a/.cmake-format.yaml +++ b/.cmake-format.yaml @@ -1,3 +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 + _hibf_cmake_format_documentation_only: install: command: diff --git a/.codecov.yml b/.codecov.yml index 20d26664..f581ad3a 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,3 +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 + # See https://docs.codecov.io/docs/codecovyml-reference codecov: token: 8e007bb5-3379-42a3-933a-8e3a0dad27ef diff --git a/.editorconfig b/.editorconfig index 9bbc07ae..69e56e3e 100644 --- a/.editorconfig +++ b/.editorconfig @@ -1,3 +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 + # https://EditorConfig.org # top-most EditorConfig file diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index ff43644d..2e8f3a1a 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -1,3 +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: 🐞 Bug report description: Create a report to help us improve SeqAn3. labels: [bug] diff --git a/.github/dependabot.yml b/.github/dependabot.yml index dcbcb650..9526607e 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,3 +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 + # https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates version: 2 diff --git a/.github/workflows/ci_coverage.yml b/.github/workflows/ci_coverage.yml index 62ccf014..3ea8088c 100644 --- a/.github/workflows/ci_coverage.yml +++ b/.github/workflows/ci_coverage.yml @@ -1,3 +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: Coverage on: diff --git a/.github/workflows/ci_documentation.yml b/.github/workflows/ci_documentation.yml index 86944718..569812a2 100644 --- a/.github/workflows/ci_documentation.yml +++ b/.github/workflows/ci_documentation.yml @@ -1,3 +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: Documentation on: diff --git a/.github/workflows/ci_iwyu.yml b/.github/workflows/ci_iwyu.yml index 8ac4139d..38c8da6a 100644 --- a/.github/workflows/ci_iwyu.yml +++ b/.github/workflows/ci_iwyu.yml @@ -1,3 +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: IWYU on: diff --git a/.github/workflows/ci_lint.yml b/.github/workflows/ci_lint.yml index 7d79e2c2..646a0b69 100644 --- a/.github/workflows/ci_lint.yml +++ b/.github/workflows/ci_lint.yml @@ -1,3 +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: Lint on: diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml index ff235a34..1e4222fc 100644 --- a/.github/workflows/ci_linux.yml +++ b/.github/workflows/ci_linux.yml @@ -1,3 +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: Unit Linux on: diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml index b5cad084..cb20263a 100644 --- a/.github/workflows/ci_macos.yml +++ b/.github/workflows/ci_macos.yml @@ -1,3 +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: Unit macOS on: diff --git a/.github/workflows/ci_misc.yml b/.github/workflows/ci_misc.yml index a4c6dd09..aee78962 100644 --- a/.github/workflows/ci_misc.yml +++ b/.github/workflows/ci_misc.yml @@ -1,3 +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 on: diff --git a/.github/workflows/ci_util.yml b/.github/workflows/ci_util.yml index 392ed653..aa7cf8e2 100644 --- a/.github/workflows/ci_util.yml +++ b/.github/workflows/ci_util.yml @@ -1,3 +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: Util Linux on: diff --git a/.github/workflows/readme_snippet.yml b/.github/workflows/readme_snippet.yml index b7e9c74d..3b86efed 100644 --- a/.github/workflows/readme_snippet.yml +++ b/.github/workflows/readme_snippet.yml @@ -1,3 +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: Readme on: diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh index 5f7c8115..258340d0 100755 --- a/.github/workflows/scripts/gcov.sh +++ b/.github/workflows/scripts/gcov.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# 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 + set -Eeuo pipefail args=${@/--branch-counts/""} diff --git a/.github/workflows/update_cookbook.yml b/.github/workflows/update_cookbook.yml index b000d2db..cafa1ab4 100644 --- a/.github/workflows/update_cookbook.yml +++ b/.github/workflows/update_cookbook.yml @@ -1,3 +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: Cookbook on: diff --git a/.gitmodules b/.gitmodules index 7083bab2..07652b0b 100644 --- a/.gitmodules +++ b/.gitmodules @@ -1,3 +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 + [submodule "submodules/sdsl-lite"] path = submodules/sdsl-lite url = https://github.com/xxsds/sdsl-lite.git diff --git a/CHANGELOG.md b/CHANGELOG.md index 1754cb89..a39d3938 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ + + # Changelog {#about_changelog} [TOC] diff --git a/CMakeLists.txt b/CMakeLists.txt index 79a07cad..bfbe3292 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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.5) diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 9debd10a..bad6f7cb 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,3 +1,9 @@ + + # Code of Conduct {#about_code_of_conduct} The SeqAn project adheres to the [Berlin Code of Conduct](https://berlincodeofconduct.org/). From the code of conduct: diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b3aa0bdf..253eb4de 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -1,3 +1,9 @@ + + # Contributing {#about_contributing} First of all, thanks for wanting to contribute to SeqAn! Community is important to us and we strive to maintain a great diff --git a/LICENSES/BSD-3-Clause.txt b/LICENSES/BSD-3-Clause.txt new file mode 100644 index 00000000..ea890afb --- /dev/null +++ b/LICENSES/BSD-3-Clause.txt @@ -0,0 +1,11 @@ +Copyright (c) . + +Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: + +1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. + +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. + +3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/README.md b/README.md index 6c1cc581..bc4efedf 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,9 @@ + + # HIBF [![build status][1]][2] diff --git a/cmake/configuration.cmake b/cmake/configuration.cmake index 353cad53..f2a172b9 100644 --- a/cmake/configuration.cmake +++ b/cmake/configuration.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.5...3.12) diff --git a/cmake/cpack.cmake b/cmake/cpack.cmake index f565ca50..568b439f 100644 --- a/cmake/cpack.cmake +++ b/cmake/cpack.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 # This file describes how HIBF will be packaged. diff --git a/cmake/install.cmake b/cmake/install.cmake index 6310d77a..cf83b143 100644 --- a/cmake/install.cmake +++ b/cmake/install.cmake @@ -1,3 +1,7 @@ +# 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 + install (TARGETS hibf EXPORT hibf_targets RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} diff --git a/cmake/version.cmake b/cmake/version.cmake index 9558de4c..73f1d404 100644 --- a/cmake/version.cmake +++ b/cmake/version.cmake @@ -1,9 +1,6 @@ -# ------------------------------------------------------------------------------------------------------------ -# Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin -# Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik -# This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License -# shipped with this file and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------- +# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: BSD-3-Clause file (STRINGS "${CMAKE_CURRENT_LIST_DIR}/../include/hibf/version.hpp" HIBF_VERSION_HPP REGEX "#define HIBF_VERSION_(MAJOR|MINOR|PATCH)") diff --git a/doc/about/api/index.md b/doc/about/api/index.md index 1fdf6bbb..7e73caa3 100644 --- a/doc/about/api/index.md +++ b/doc/about/api/index.md @@ -1,3 +1,9 @@ + + # Stability and long-term promises {#about_api} [TOC] diff --git a/doc/about/citing/index.md b/doc/about/citing/index.md index e1f18978..2bc19519 100644 --- a/doc/about/citing/index.md +++ b/doc/about/citing/index.md @@ -1,3 +1,9 @@ + + # Citing {#about_citing} [TOC] diff --git a/doc/about/copyright/bsdl_badge.svg.license b/doc/about/copyright/bsdl_badge.svg.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/doc/about/copyright/bsdl_badge.svg.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: CC0-1.0 diff --git a/doc/about/copyright/cc0_badge.svg.license b/doc/about/copyright/cc0_badge.svg.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/doc/about/copyright/cc0_badge.svg.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: CC0-1.0 diff --git a/doc/about/copyright/ccby_badge.svg.license b/doc/about/copyright/ccby_badge.svg.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/doc/about/copyright/ccby_badge.svg.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: CC0-1.0 diff --git a/doc/about/copyright/copyfree_badge.svg.license b/doc/about/copyright/copyfree_badge.svg.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/doc/about/copyright/copyfree_badge.svg.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: CC0-1.0 diff --git a/doc/cookbook/index.md b/doc/cookbook/index.md index f1411073..4b6ebbcd 100644 --- a/doc/cookbook/index.md +++ b/doc/cookbook/index.md @@ -1,3 +1,9 @@ + + # The HIBF Cookbook {#cookbook} [TOC] diff --git a/doc/images/hibf.svg.license b/doc/images/hibf.svg.license new file mode 100644 index 00000000..a1ac0ab3 --- /dev/null +++ b/doc/images/hibf.svg.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/images/hierarchical_dp_init.png.license b/doc/images/hierarchical_dp_init.png.license new file mode 100644 index 00000000..a1ac0ab3 --- /dev/null +++ b/doc/images/hierarchical_dp_init.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/doc/images/hierarchical_dp_recursion.png.license b/doc/images/hierarchical_dp_recursion.png.license new file mode 100644 index 00000000..a1ac0ab3 --- /dev/null +++ b/doc/images/hierarchical_dp_recursion.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/doc/main_page.md b/doc/main_page.md index d253d5b4..ef87c3c7 100644 --- a/doc/main_page.md +++ b/doc/main_page.md @@ -1,3 +1,9 @@ + + # Welcome {#mainpage} Welcome to the documentation. diff --git a/include/hibf/all.hpp b/include/hibf/all.hpp index 306b925b..083f93b3 100644 --- a/include/hibf/all.hpp +++ b/include/hibf/all.hpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 /*!\file * \author Enrico Seiler diff --git a/include/hibf/build/bin_size_in_bits.hpp b/include/hibf/build/bin_size_in_bits.hpp index 45da22e9..610b3849 100644 --- a/include/hibf/build/bin_size_in_bits.hpp +++ b/include/hibf/build/bin_size_in_bits.hpp @@ -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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Implements seqan::hibf::bin_size_in_bits. diff --git a/include/hibf/build/build_data.hpp b/include/hibf/build/build_data.hpp index 825c0375..0331516e 100644 --- a/include/hibf/build/build_data.hpp +++ b/include/hibf/build/build_data.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/build/compute_kmers.hpp b/include/hibf/build/compute_kmers.hpp index d9f1ce16..5411b986 100644 --- a/include/hibf/build/compute_kmers.hpp +++ b/include/hibf/build/compute_kmers.hpp @@ -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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Implements seqan::hibf::compute_kmers. diff --git a/include/hibf/build/construct_ibf.hpp b/include/hibf/build/construct_ibf.hpp index 9ce2c660..fef2ceb9 100644 --- a/include/hibf/build/construct_ibf.hpp +++ b/include/hibf/build/construct_ibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/build/insert_into_ibf.hpp b/include/hibf/build/insert_into_ibf.hpp index 4d6bfb1f..09d95bc8 100644 --- a/include/hibf/build/insert_into_ibf.hpp +++ b/include/hibf/build/insert_into_ibf.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/build/update_parent_kmers.hpp b/include/hibf/build/update_parent_kmers.hpp index eccc615f..7bd84cdc 100644 --- a/include/hibf/build/update_parent_kmers.hpp +++ b/include/hibf/build/update_parent_kmers.hpp @@ -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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Implements seqan::hibf::update_parent_kmers. diff --git a/include/hibf/build/update_user_bins.hpp b/include/hibf/build/update_user_bins.hpp index 2da5a4a3..83ee5216 100644 --- a/include/hibf/build/update_user_bins.hpp +++ b/include/hibf/build/update_user_bins.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/cereal/concepts.hpp b/include/hibf/cereal/concepts.hpp index a803a40e..eebd453a 100644 --- a/include/hibf/cereal/concepts.hpp +++ b/include/hibf/cereal/concepts.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 diff --git a/include/hibf/cereal/path.hpp b/include/hibf/cereal/path.hpp index d4ae0d78..d3472ce7 100644 --- a/include/hibf/cereal/path.hpp +++ b/include/hibf/cereal/path.hpp @@ -1,3 +1,7 @@ +// 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 // for path diff --git a/include/hibf/config.hpp b/include/hibf/config.hpp index 0e0296c0..b99fd377 100644 --- a/include/hibf/config.hpp +++ b/include/hibf/config.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/contrib/README.md b/include/hibf/contrib/README.md index 27373031..65641679 100644 --- a/include/hibf/contrib/README.md +++ b/include/hibf/contrib/README.md @@ -1,3 +1,9 @@ + + The `std` directory is a git subtree and includes the content of https://github.com/seqan/seqan-std. For a general overview regarding `git subtree`, see, for example, https://www.atlassian.com/git/tutorials/git-subtree. diff --git a/include/hibf/contrib/aligned_allocator.hpp b/include/hibf/contrib/aligned_allocator.hpp index 44496e9e..2eb35ce2 100644 --- a/include/hibf/contrib/aligned_allocator.hpp +++ b/include/hibf/contrib/aligned_allocator.hpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 /*!\file * \author Marcel Ehrhardt diff --git a/include/hibf/hierarchical_interleaved_bloom_filter.hpp b/include/hibf/hierarchical_interleaved_bloom_filter.hpp index c826e1e6..bb887402 100644 --- a/include/hibf/hierarchical_interleaved_bloom_filter.hpp +++ b/include/hibf/hierarchical_interleaved_bloom_filter.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/interleaved_bloom_filter.hpp b/include/hibf/interleaved_bloom_filter.hpp index 07076a3a..51c571de 100644 --- a/include/hibf/interleaved_bloom_filter.hpp +++ b/include/hibf/interleaved_bloom_filter.hpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 /*!\file * \author Enrico Seiler diff --git a/include/hibf/layout/compute_fpr_correction.hpp b/include/hibf/layout/compute_fpr_correction.hpp index 460bfb04..9ec10507 100644 --- a/include/hibf/layout/compute_fpr_correction.hpp +++ b/include/hibf/layout/compute_fpr_correction.hpp @@ -1,3 +1,7 @@ +// 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 // for size_t diff --git a/include/hibf/layout/compute_layout.hpp b/include/hibf/layout/compute_layout.hpp index b7ece6d8..2ba637a8 100644 --- a/include/hibf/layout/compute_layout.hpp +++ b/include/hibf/layout/compute_layout.hpp @@ -1,3 +1,7 @@ +// 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 // for size_t diff --git a/include/hibf/layout/data_store.hpp b/include/hibf/layout/data_store.hpp index 31f09209..9d089d0e 100644 --- a/include/hibf/layout/data_store.hpp +++ b/include/hibf/layout/data_store.hpp @@ -1,3 +1,7 @@ +// 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 // for copy, fill_n, max diff --git a/include/hibf/layout/graph.hpp b/include/hibf/layout/graph.hpp index bcceb17b..75c75ffd 100644 --- a/include/hibf/layout/graph.hpp +++ b/include/hibf/layout/graph.hpp @@ -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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Implements seqan::hibf::layout::graph. diff --git a/include/hibf/layout/hierarchical_binning.hpp b/include/hibf/layout/hierarchical_binning.hpp index bce836e7..f53ab659 100644 --- a/include/hibf/layout/hierarchical_binning.hpp +++ b/include/hibf/layout/hierarchical_binning.hpp @@ -1,3 +1,7 @@ +// 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 // for assert diff --git a/include/hibf/layout/layout.hpp b/include/hibf/layout/layout.hpp index 06cde597..ce0ddc6c 100644 --- a/include/hibf/layout/layout.hpp +++ b/include/hibf/layout/layout.hpp @@ -1,3 +1,7 @@ +// 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 // for copy diff --git a/include/hibf/layout/prefixes.hpp b/include/hibf/layout/prefixes.hpp index c529da55..77817ae8 100644 --- a/include/hibf/layout/prefixes.hpp +++ b/include/hibf/layout/prefixes.hpp @@ -1,3 +1,7 @@ +// 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 // for string_view diff --git a/include/hibf/layout/print_matrix.hpp b/include/hibf/layout/print_matrix.hpp index d74608da..4c8ffd5b 100644 --- a/include/hibf/layout/print_matrix.hpp +++ b/include/hibf/layout/print_matrix.hpp @@ -1,3 +1,7 @@ +// 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/include/hibf/layout/simple_binning.hpp b/include/hibf/layout/simple_binning.hpp index fe6d83be..90bf37af 100644 --- a/include/hibf/layout/simple_binning.hpp +++ b/include/hibf/layout/simple_binning.hpp @@ -1,3 +1,7 @@ +// 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 // for assert diff --git a/include/hibf/misc/insert_iterator.hpp b/include/hibf/misc/insert_iterator.hpp index 9fd2c889..e49e9b6e 100644 --- a/include/hibf/misc/insert_iterator.hpp +++ b/include/hibf/misc/insert_iterator.hpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 diff --git a/include/hibf/misc/next_multiple_of_64.hpp b/include/hibf/misc/next_multiple_of_64.hpp index c1deee7b..df8a3b5a 100644 --- a/include/hibf/misc/next_multiple_of_64.hpp +++ b/include/hibf/misc/next_multiple_of_64.hpp @@ -1,3 +1,7 @@ +// 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 // for size_t diff --git a/include/hibf/misc/print.hpp b/include/hibf/misc/print.hpp index 1aaac9da..3a718d5a 100644 --- a/include/hibf/misc/print.hpp +++ b/include/hibf/misc/print.hpp @@ -1,3 +1,7 @@ +// 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 // for int64_t, int16_t, int32_t, int8_t, uint16_t, uint32_t, uint64_t diff --git a/include/hibf/misc/timer.hpp b/include/hibf/misc/timer.hpp index 4e367fd6..4bbe7491 100644 --- a/include/hibf/misc/timer.hpp +++ b/include/hibf/misc/timer.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Provides seqan::hibf::timer. diff --git a/include/hibf/platform.hpp b/include/hibf/platform.hpp index 235798d9..eb112a34 100644 --- a/include/hibf/platform.hpp +++ b/include/hibf/platform.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Provides platform and dependency checks. diff --git a/include/hibf/sketch/compute_sketches.hpp b/include/hibf/sketch/compute_sketches.hpp index bb610bf5..977609e6 100644 --- a/include/hibf/sketch/compute_sketches.hpp +++ b/include/hibf/sketch/compute_sketches.hpp @@ -1,3 +1,7 @@ +// 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 // for size_t diff --git a/include/hibf/sketch/estimate_kmer_counts.hpp b/include/hibf/sketch/estimate_kmer_counts.hpp index 42827b61..0cc76631 100644 --- a/include/hibf/sketch/estimate_kmer_counts.hpp +++ b/include/hibf/sketch/estimate_kmer_counts.hpp @@ -1,3 +1,7 @@ +// 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 // for fill_n, max diff --git a/include/hibf/sketch/hyperloglog.hpp b/include/hibf/sketch/hyperloglog.hpp index aa16f0f1..0b0996a9 100644 --- a/include/hibf/sketch/hyperloglog.hpp +++ b/include/hibf/sketch/hyperloglog.hpp @@ -1,12 +1,7 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- - -// Copyright (c) 2013 Hideaki Ohno -// MIT License: https://github.com/hideo55/cpp-HyperLogLog#license +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-FileCopyrightText: 2013 Hideaki Ohno +// SPDX-License-Identifier: BSD-3-Clause AND MIT /*!\file * \author Felix Droop diff --git a/include/hibf/sketch/toolbox.hpp b/include/hibf/sketch/toolbox.hpp index d318d76e..692da447 100644 --- a/include/hibf/sketch/toolbox.hpp +++ b/include/hibf/sketch/toolbox.hpp @@ -1,3 +1,7 @@ +// 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 // for max diff --git a/include/hibf/version.hpp b/include/hibf/version.hpp index fb341661..b4ca6307 100644 --- a/include/hibf/version.hpp +++ b/include/hibf/version.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 21ade80f..fc8b739f 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + set (HIBF_SOURCE_FILES hierarchical_interleaved_bloom_filter.cpp interleaved_bloom_filter.cpp diff --git a/src/build/compute_kmers.cpp b/src/build/compute_kmers.cpp index a1938c8a..0ccf6fe7 100644 --- a/src/build/compute_kmers.cpp +++ b/src/build/compute_kmers.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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Implements seqan::hibf::compute_kmers. diff --git a/src/build/construct_ibf.cpp b/src/build/construct_ibf.cpp index d60ad273..b241054e 100644 --- a/src/build/construct_ibf.cpp +++ b/src/build/construct_ibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 // for uint64_t #include // for ceil diff --git a/src/build/insert_into_ibf.cpp b/src/build/insert_into_ibf.cpp index 709c7dde..14e6ed9b 100644 --- a/src/build/insert_into_ibf.cpp +++ b/src/build/insert_into_ibf.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 // for assert #include // for uint64_t diff --git a/src/config.cpp b/src/config.cpp index bd31b076..c7c90007 100644 --- a/src/config.cpp +++ b/src/config.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// --------------------------------------------------------------------------------------------------- +// 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 // for assert #include // for ceil, sqrt diff --git a/src/hierarchical_interleaved_bloom_filter.cpp b/src/hierarchical_interleaved_bloom_filter.cpp index d7c8df3b..0ae1a8d0 100644 --- a/src/hierarchical_interleaved_bloom_filter.cpp +++ b/src/hierarchical_interleaved_bloom_filter.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 // for fill_n, max, shuffle #include // for uint64_t, int64_t diff --git a/src/interleaved_bloom_filter.cpp b/src/interleaved_bloom_filter.cpp index 482163d7..c3dcc6d8 100644 --- a/src/interleaved_bloom_filter.cpp +++ b/src/interleaved_bloom_filter.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 // for clamp, max #include // for array diff --git a/src/layout/compute_fpr_correction.cpp b/src/layout/compute_fpr_correction.cpp index 4e758830..78cd694f 100644 --- a/src/layout/compute_fpr_correction.cpp +++ b/src/layout/compute_fpr_correction.cpp @@ -1,3 +1,7 @@ +// 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 // for assert #include // for log1p, exp, log #include // for size_t diff --git a/src/layout/compute_layout.cpp b/src/layout/compute_layout.cpp index c316a315..525d9cc7 100644 --- a/src/layout/compute_layout.cpp +++ b/src/layout/compute_layout.cpp @@ -1,3 +1,7 @@ +// 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 // for __sort_fn, sort #include // for uint64_t #include // for size_t diff --git a/src/layout/graph.cpp b/src/layout/graph.cpp index 38037b92..a00756bd 100644 --- a/src/layout/graph.cpp +++ b/src/layout/graph.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// --------------------------------------------------------------------------------------------------- +// 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 // for max, copy #include // for assert diff --git a/src/layout/hierarchical_binning.cpp b/src/layout/hierarchical_binning.cpp index 646d60a6..8646a16b 100644 --- a/src/layout/hierarchical_binning.cpp +++ b/src/layout/hierarchical_binning.cpp @@ -1,3 +1,7 @@ +// 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 // for max, copy, fill_n, min #include // for assert #include // for log, ceil diff --git a/src/layout/layout.cpp b/src/layout/layout.cpp index a431606a..92a57bd4 100644 --- a/src/layout/layout.cpp +++ b/src/layout/layout.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// --------------------------------------------------------------------------------------------------- +// 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 // for find #include // for assert diff --git a/src/layout/simple_binning.cpp b/src/layout/simple_binning.cpp index 7d4ef1f1..a04c468f 100644 --- a/src/layout/simple_binning.cpp +++ b/src/layout/simple_binning.cpp @@ -1,3 +1,7 @@ +// 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 // for max, copy #include // for assert #include // for size_t diff --git a/src/misc/print.cpp b/src/misc/print.cpp index b94d7fba..a5549b18 100644 --- a/src/misc/print.cpp +++ b/src/misc/print.cpp @@ -1,9 +1,6 @@ -// -------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md -// -------------------------------------------------------------------------------------------------- +// 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 // for uint16_t, int16_t, int64_t, int8_t, uint8_t, int32_t, uint32_t #include // for size_t diff --git a/src/sketch/compute_sketches.cpp b/src/sketch/compute_sketches.cpp index 9e4c4401..75b1c377 100644 --- a/src/sketch/compute_sketches.cpp +++ b/src/sketch/compute_sketches.cpp @@ -1,3 +1,7 @@ +// 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 // for __sort_fn, sort #include // for uint64_t #include // for size_t diff --git a/src/sketch/hyperloglog.cpp b/src/sketch/hyperloglog.cpp index f42fe5bd..e5e95441 100644 --- a/src/sketch/hyperloglog.cpp +++ b/src/sketch/hyperloglog.cpp @@ -1,3 +1,8 @@ +// SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik +// SPDX-FileCopyrightText: 2013 Hideaki Ohno +// SPDX-License-Identifier: BSD-3-Clause AND MIT + #include // for max, fill #include // for array #include // for countl_zero diff --git a/src/sketch/toolbox.cpp b/src/sketch/toolbox.cpp index 9b39c364..15b02667 100644 --- a/src/sketch/toolbox.cpp +++ b/src/sketch/toolbox.cpp @@ -1,3 +1,7 @@ +// 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 // for max, fill_n, sort #include // for assert #include // for uint64_t, int64_t diff --git a/test/clang_tidy/CMakeLists.txt b/test/clang_tidy/CMakeLists.txt index ef435c9f..0de8a468 100644 --- a/test/clang_tidy/CMakeLists.txt +++ b/test/clang_tidy/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + cmake_minimum_required (VERSION 3.10) project (hibf_tidy NONE) diff --git a/test/cmake/diagnostics/list_missing_unit_tests.cmake b/test/cmake/diagnostics/list_missing_unit_tests.cmake index 2d6dbbb1..d47c80f8 100644 --- a/test/cmake/diagnostics/list_missing_unit_tests.cmake +++ b/test/cmake/diagnostics/list_missing_unit_tests.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/diagnostics/list_unused_snippets.cmake b/test/cmake/diagnostics/list_unused_snippets.cmake index 464fdd5b..f2fb4b50 100644 --- a/test/cmake/diagnostics/list_unused_snippets.cmake +++ b/test/cmake/diagnostics/list_unused_snippets.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/diagnostics/list_unused_unit_tests.cmake b/test/cmake/diagnostics/list_unused_unit_tests.cmake index 7a8c5e61..9b128a2b 100644 --- a/test/cmake/diagnostics/list_unused_unit_tests.cmake +++ b/test/cmake/diagnostics/list_unused_unit_tests.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/hibf_add_subdirectories.cmake b/test/cmake/hibf_add_subdirectories.cmake index 08fc5511..5bbd3843 100644 --- a/test/cmake/hibf_add_subdirectories.cmake +++ b/test/cmake/hibf_add_subdirectories.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/hibf_generate_snippet.cmake b/test/cmake/hibf_generate_snippet.cmake index b9762d66..1d613ffb 100644 --- a/test/cmake/hibf_generate_snippet.cmake +++ b/test/cmake/hibf_generate_snippet.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/hibf_macro_benchmark.cmake b/test/cmake/hibf_macro_benchmark.cmake index 9d3d0ab9..0aece455 100644 --- a/test/cmake/hibf_macro_benchmark.cmake +++ b/test/cmake/hibf_macro_benchmark.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/hibf_path_longest_stem.cmake b/test/cmake/hibf_path_longest_stem.cmake index ff0dd5ad..37b1c5b2 100644 --- a/test/cmake/hibf_path_longest_stem.cmake +++ b/test/cmake/hibf_path_longest_stem.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/hibf_require_benchmark.cmake b/test/cmake/hibf_require_benchmark.cmake index 89480828..c7f40143 100644 --- a/test/cmake/hibf_require_benchmark.cmake +++ b/test/cmake/hibf_require_benchmark.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.16) diff --git a/test/cmake/hibf_require_ccache.cmake b/test/cmake/hibf_require_ccache.cmake index 191615de..72e65ef9 100644 --- a/test/cmake/hibf_require_ccache.cmake +++ b/test/cmake/hibf_require_ccache.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.15) diff --git a/test/cmake/hibf_require_test.cmake b/test/cmake/hibf_require_test.cmake index bd69bb2d..efe0c1af 100644 --- a/test/cmake/hibf_require_test.cmake +++ b/test/cmake/hibf_require_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.16) diff --git a/test/cmake/hibf_test_component.cmake b/test/cmake/hibf_test_component.cmake index ae034fe3..0512b83b 100644 --- a/test/cmake/hibf_test_component.cmake +++ b/test/cmake/hibf_test_component.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/hibf_test_files.cmake b/test/cmake/hibf_test_files.cmake index 8f0147a2..77ebadd6 100644 --- a/test/cmake/hibf_test_files.cmake +++ b/test/cmake/hibf_test_files.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/include_dependencies/add_include_dependencies.cmake b/test/cmake/include_dependencies/add_include_dependencies.cmake index 30127ad5..458d37fc 100644 --- a/test/cmake/include_dependencies/add_include_dependencies.cmake +++ b/test/cmake/include_dependencies/add_include_dependencies.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/cmake/include_dependencies/generate_include_dependencies.cmake b/test/cmake/include_dependencies/generate_include_dependencies.cmake index aced4004..0464f80b 100644 --- a/test/cmake/include_dependencies/generate_include_dependencies.cmake +++ b/test/cmake/include_dependencies/generate_include_dependencies.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.12) diff --git a/test/coverage/CMakeLists.txt b/test/coverage/CMakeLists.txt index 4cc7ae17..cacd151a 100644 --- a/test/coverage/CMakeLists.txt +++ b/test/coverage/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10...3.22) project (hibf_test_coverage CXX) diff --git a/test/documentation/.vercel/0_setup.sh b/test/documentation/.vercel/0_setup.sh index 9dbbf131..c075021f 100755 --- a/test/documentation/.vercel/0_setup.sh +++ b/test/documentation/.vercel/0_setup.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# 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 + set -euxo pipefail DOXYGEN_VERSION=1.9.8 diff --git a/test/documentation/.vercel/1_build.sh b/test/documentation/.vercel/1_build.sh index d22a188f..9935e6fd 100755 --- a/test/documentation/.vercel/1_build.sh +++ b/test/documentation/.vercel/1_build.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash + +# 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 + set -euxo pipefail WORK_DIR=`pwd` diff --git a/test/documentation/.vercel/Notes.md b/test/documentation/.vercel/Notes.md index 1d7c365a..47a7cd1c 100644 --- a/test/documentation/.vercel/Notes.md +++ b/test/documentation/.vercel/Notes.md @@ -1,3 +1,9 @@ + + * Framekwork: Other * Build Command: ./1_build.sh * Output Directory: ./export/html diff --git a/test/documentation/.vercel/api/doxysearch.sh b/test/documentation/.vercel/api/doxysearch.sh index 8d29de76..1fbad495 100644 --- a/test/documentation/.vercel/api/doxysearch.sh +++ b/test/documentation/.vercel/api/doxysearch.sh @@ -1,3 +1,7 @@ +# 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 + import "querystring@1.3.0" build() { diff --git a/test/documentation/.vercel/powered-by-vercel.svg.license b/test/documentation/.vercel/powered-by-vercel.svg.license new file mode 100644 index 00000000..bba0a398 --- /dev/null +++ b/test/documentation/.vercel/powered-by-vercel.svg.license @@ -0,0 +1,2 @@ +SPDX-FileCopyrightText: 2023 Vercel +SPDX-License-Identifier: MIT diff --git a/test/documentation/.vercel/vercel.json.license b/test/documentation/.vercel/vercel.json.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/documentation/.vercel/vercel.json.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: CC0-1.0 diff --git a/test/documentation/CMakeLists.txt b/test/documentation/CMakeLists.txt index 210121e8..2536289b 100644 --- a/test/documentation/CMakeLists.txt +++ b/test/documentation/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.7) diff --git a/test/documentation/DoxygenLayout.xml b/test/documentation/DoxygenLayout.xml index e0b282af..cc1babb9 100644 --- a/test/documentation/DoxygenLayout.xml +++ b/test/documentation/DoxygenLayout.xml @@ -1,4 +1,11 @@ + + + diff --git a/test/documentation/README.md b/test/documentation/README.md index 6e405ef3..bf266f23 100644 --- a/test/documentation/README.md +++ b/test/documentation/README.md @@ -1,3 +1,9 @@ + + # hibf documentation Currently, we can only build the documentation on *nix systems. @@ -55,7 +61,7 @@ Prerequisites: building the documentation Our installation uses GNU standard installation directories provided by cmake [GNUInstallDirs](https://cmake.org/cmake/help/v3.19/module/GNUInstallDirs.html#module:GNUInstallDirs). -That means the html documentation will be installed to `///html/` where +That means the html documentation will be installed to `///html/` where `` is typically `usr/local` and `` is `share/doc/hibf`. That means our html documentation will be installed to `/usr/local/share/doc/hibf/html`. diff --git a/test/documentation/api-stability.js b/test/documentation/api-stability.js index 6f626b2f..67373d3e 100644 --- a/test/documentation/api-stability.js +++ b/test/documentation/api-stability.js @@ -1,3 +1,7 @@ +// 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 + /* Enrico Seiler (enrico.seiler@fu-berlin.de), 2021 */ $(document).ready(function() diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js b/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js index 40fe2d38..a107a5fe 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-darkmode-toggle.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js b/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js index 86c16fd9..c98a481f 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-fragment-copy-button.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js b/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js index 20a9669d..33a1b95a 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-interactive-toc.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js b/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js index e53d132c..e8c7b1ff 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-paragraph-link.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js b/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js index 8e725b23..061f918b 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js +++ b/test/documentation/doxygen-awesome/doxygen-awesome-tabs.js @@ -1,3 +1,6 @@ +// SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro +// SPDX-License-Identifier: MIT + /** Doxygen Awesome diff --git a/test/documentation/doxygen-awesome/doxygen-awesome.css b/test/documentation/doxygen-awesome/doxygen-awesome.css index e8399cbc..5d6c4138 100644 --- a/test/documentation/doxygen-awesome/doxygen-awesome.css +++ b/test/documentation/doxygen-awesome/doxygen-awesome.css @@ -1,3 +1,8 @@ +/* + * SPDX-FileCopyrightText: 2023 2021 - 2023 jothepro + * SPDX-License-Identifier: MIT + */ + /** Doxygen Awesome diff --git a/test/documentation/hibf-doxygen-layout.cmake b/test/documentation/hibf-doxygen-layout.cmake index 50ed431f..5acc6713 100644 --- a/test/documentation/hibf-doxygen-layout.cmake +++ b/test/documentation/hibf-doxygen-layout.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/documentation/hibf-doxygen-package.cmake b/test/documentation/hibf-doxygen-package.cmake index f2e83f7f..655d3944 100644 --- a/test/documentation/hibf-doxygen-package.cmake +++ b/test/documentation/hibf-doxygen-package.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/documentation/hibf-doxygen.cmake b/test/documentation/hibf-doxygen.cmake index 6898a962..aaf9ece1 100644 --- a/test/documentation/hibf-doxygen.cmake +++ b/test/documentation/hibf-doxygen.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10) diff --git a/test/documentation/hibf.css b/test/documentation/hibf.css index f2c7dd91..b3431aa2 100644 --- a/test/documentation/hibf.css +++ b/test/documentation/hibf.css @@ -1,3 +1,9 @@ +/* + * 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 + */ + /* https://jothepro.github.io/doxygen-awesome-css/md_docs_customization.html */ diff --git a/test/documentation/hibf_doxygen_cfg.in b/test/documentation/hibf_doxygen_cfg.in index 190635e5..aece7f16 100644 --- a/test/documentation/hibf_doxygen_cfg.in +++ b/test/documentation/hibf_doxygen_cfg.in @@ -1,3 +1,7 @@ +# 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 + # Doxyfile 1.9.8 #--------------------------------------------------------------------------- diff --git a/test/documentation/hibf_footer.html.in b/test/documentation/hibf_footer.html.in index c55c8361..e6df2f83 100644 --- a/test/documentation/hibf_footer.html.in +++ b/test/documentation/hibf_footer.html.in @@ -1,3 +1,9 @@ + + diff --git a/test/documentation/hibf_header.html b/test/documentation/hibf_header.html index 9e11917d..fa59fd16 100644 --- a/test/documentation/hibf_header.html +++ b/test/documentation/hibf_header.html @@ -1,3 +1,9 @@ + + diff --git a/test/documentation/seqan_logo.svg.license b/test/documentation/seqan_logo.svg.license new file mode 100644 index 00000000..063ed052 --- /dev/null +++ b/test/documentation/seqan_logo.svg.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: BSD-3-Clause diff --git a/test/header/CMakeLists.txt b/test/header/CMakeLists.txt index be55b0bc..0d991f81 100644 --- a/test/header/CMakeLists.txt +++ b/test/header/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.12...3.22) project (hibf_header_test CXX) diff --git a/test/header/generate_header_source.cmake b/test/header/generate_header_source.cmake index f5699ace..835d0097 100644 --- a/test/header/generate_header_source.cmake +++ b/test/header/generate_header_source.cmake @@ -1,3 +1,7 @@ +# 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 + cmake_minimum_required (VERSION 3.10) option (HEADER_FILE_ABSOLUTE "") diff --git a/test/hibf-test.cmake b/test/hibf-test.cmake index e25dde97..fb69776a 100644 --- a/test/hibf-test.cmake +++ b/test/hibf-test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 # This file provides functionality common to the different test modules used by # HIBF. To build tests, run cmake on one of the sub-folders in this directory diff --git a/test/include/hibf/test/bytes.hpp b/test/include/hibf/test/bytes.hpp index a07cb5f4..7705e658 100644 --- a/test/include/hibf/test/bytes.hpp +++ b/test/include/hibf/test/bytes.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Provides literals for unit conversions. diff --git a/test/include/hibf/test/expect_range_eq.hpp b/test/include/hibf/test/expect_range_eq.hpp index 8130b065..687f7d0c 100644 --- a/test/include/hibf/test/expect_range_eq.hpp +++ b/test/include/hibf/test/expect_range_eq.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Provides test utilities for std::ranges::range types. diff --git a/test/include/hibf/test/expect_same_type.hpp b/test/include/hibf/test/expect_same_type.hpp index 24417ea6..441405e8 100644 --- a/test/include/hibf/test/expect_same_type.hpp +++ b/test/include/hibf/test/expect_same_type.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Provides EXPECT_SAME_TYPE. diff --git a/test/include/hibf/test/file_access.hpp b/test/include/hibf/test/file_access.hpp index d1b1af2c..c63e59c0 100644 --- a/test/include/hibf/test/file_access.hpp +++ b/test/include/hibf/test/file_access.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Detects read and write access for a path. diff --git a/test/include/hibf/test/sandboxed_path.hpp b/test/include/hibf/test/sandboxed_path.hpp index 19ed2263..217a3920 100644 --- a/test/include/hibf/test/sandboxed_path.hpp +++ b/test/include/hibf/test/sandboxed_path.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Provides seqan::hibf::test::sandboxed_path and related free functions. diff --git a/test/include/hibf/test/seqan3.hpp b/test/include/hibf/test/seqan3.hpp index 31da1a21..d7149cc5 100755 --- a/test/include/hibf/test/seqan3.hpp +++ b/test/include/hibf/test/seqan3.hpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 /*!\file * \brief Adds seqan3 to the test environment. diff --git a/test/include/hibf/test/temporary_snippet_file.hpp b/test/include/hibf/test/temporary_snippet_file.hpp index 0b55da03..39d86cc1 100644 --- a/test/include/hibf/test/temporary_snippet_file.hpp +++ b/test/include/hibf/test/temporary_snippet_file.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Utility for creating snippet files. diff --git a/test/include/hibf/test/tmp_directory.hpp b/test/include/hibf/test/tmp_directory.hpp index 9a4643f4..fbe5c4c6 100644 --- a/test/include/hibf/test/tmp_directory.hpp +++ b/test/include/hibf/test/tmp_directory.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 diff --git a/test/include/hibf/test/type_name_as_string.hpp b/test/include/hibf/test/type_name_as_string.hpp index ac6f5124..8e1fe8c5 100644 --- a/test/include/hibf/test/type_name_as_string.hpp +++ b/test/include/hibf/test/type_name_as_string.hpp @@ -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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 /*!\file * \brief Provides traits to inspect some information of a type, for example its name. diff --git a/test/iwyu/CMakeLists.txt b/test/iwyu/CMakeLists.txt index 0f354ab1..733cdb81 100644 --- a/test/iwyu/CMakeLists.txt +++ b/test/iwyu/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + cmake_minimum_required (VERSION 3.10) # cmake ../test/iwyu/ -DCMAKE_CXX_COMPILER="clang++-17" -DHIBF_IWYU_DIR=... diff --git a/test/iwyu/mappings/gcc.libc.imp b/test/iwyu/mappings/gcc.libc.imp index 2bfd48a2..d58eea3e 100644 --- a/test/iwyu/mappings/gcc.libc.imp +++ b/test/iwyu/mappings/gcc.libc.imp @@ -1,3 +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 + # Mappings for GNU libc # ( cd /usr/include && grep '^ *# *include' {sys/,net/,}* | perl -nle 'm/^([^:]+).*<([^>]+)>/ && print qq@ { include: [ "<$2>", private, "<$1>", private ] },@' | grep bits/ | sort ) # When I saw more than one mapping for these, I typically picked diff --git a/test/iwyu/mappings/gcc.stl.headers.imp b/test/iwyu/mappings/gcc.stl.headers.imp index f57f33aa..d9811937 100644 --- a/test/iwyu/mappings/gcc.stl.headers.imp +++ b/test/iwyu/mappings/gcc.stl.headers.imp @@ -1,3 +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 + # GCC STL headers [ # Note: make sure to sync this setting with iwyu_include_picker.cc diff --git a/test/iwyu/mappings/gcc.symbols.imp b/test/iwyu/mappings/gcc.symbols.imp index 52be06b9..8b9e0fb8 100644 --- a/test/iwyu/mappings/gcc.symbols.imp +++ b/test/iwyu/mappings/gcc.symbols.imp @@ -1,3 +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 + # For library symbols that can be defined in more than one header # file, maps from symbol-name to legitimate header files. # This list was generated via diff --git a/test/iwyu/mappings/iwyu.imp b/test/iwyu/mappings/iwyu.imp index 7a1869ab..6c6f4c79 100644 --- a/test/iwyu/mappings/iwyu.imp +++ b/test/iwyu/mappings/iwyu.imp @@ -1,3 +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 + # Copied from https://github.com/include-what-you-use/include-what-you-use # Changed mapping in stl.c.headers.imp from public->public to private->public such that CPP-includes are prefered # Adapted other mappings for visibility errors diff --git a/test/iwyu/mappings/libcxx.imp b/test/iwyu/mappings/libcxx.imp index 45306ffb..6a18b0c8 100644 --- a/test/iwyu/mappings/libcxx.imp +++ b/test/iwyu/mappings/libcxx.imp @@ -1,3 +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 + # libc++ headers [ { include: ["<__mutex_base>", private, "", public ] }, diff --git a/test/iwyu/mappings/stl.c.headers.imp b/test/iwyu/mappings/stl.c.headers.imp index 5041adcb..2f41e702 100644 --- a/test/iwyu/mappings/stl.c.headers.imp +++ b/test/iwyu/mappings/stl.c.headers.imp @@ -1,3 +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 + [ { include: [ "", private, "", public ] }, { include: [ "", private, "", public ] }, diff --git a/test/performance/CMakeLists.txt b/test/performance/CMakeLists.txt index f398df84..6e248c5a 100644 --- a/test/performance/CMakeLists.txt +++ b/test/performance/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10...3.22) project (hibf_test_performance CXX) diff --git a/test/performance/example/CMakeLists.txt b/test/performance/example/CMakeLists.txt index fc81ca55..18e44d26 100644 --- a/test/performance/example/CMakeLists.txt +++ b/test/performance/example/CMakeLists.txt @@ -1 +1,5 @@ +# 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 + hibf_benchmark (example_benchmark.cpp) diff --git a/test/performance/example/example_benchmark.cpp b/test/performance/example/example_benchmark.cpp index b281e18b..23d17418 100644 --- a/test/performance/example/example_benchmark.cpp +++ b/test/performance/example/example_benchmark.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 diff --git a/test/performance/hibf/CMakeLists.txt b/test/performance/hibf/CMakeLists.txt index 62259fec..2d70a97f 100644 --- a/test/performance/hibf/CMakeLists.txt +++ b/test/performance/hibf/CMakeLists.txt @@ -1 +1,5 @@ +# 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 + hibf_benchmark (hierarchical_interleaved_bloom_filter_benchmark.cpp) diff --git a/test/performance/hibf/hierarchical_interleaved_bloom_filter_benchmark.cpp b/test/performance/hibf/hierarchical_interleaved_bloom_filter_benchmark.cpp index 5f9b45e3..cdb9e5b1 100644 --- a/test/performance/hibf/hierarchical_interleaved_bloom_filter_benchmark.cpp +++ b/test/performance/hibf/hierarchical_interleaved_bloom_filter_benchmark.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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 // for State, Benchmark, Counter, ClobberMemory, BENCHMARK diff --git a/test/performance/ibf/CMakeLists.txt b/test/performance/ibf/CMakeLists.txt index f5d1e4f6..5d12a74c 100644 --- a/test/performance/ibf/CMakeLists.txt +++ b/test/performance/ibf/CMakeLists.txt @@ -1,2 +1,6 @@ +# 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 + hibf_benchmark (binning_bitvector_benchmark.cpp) hibf_benchmark (interleaved_bloom_filter_benchmark.cpp) diff --git a/test/performance/ibf/binning_bitvector_benchmark.cpp b/test/performance/ibf/binning_bitvector_benchmark.cpp index b38b3ad5..76b5b250 100644 --- a/test/performance/ibf/binning_bitvector_benchmark.cpp +++ b/test/performance/ibf/binning_bitvector_benchmark.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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 // for State, DoNotOptimize, Benchmark, BENCHMARK_DEFINE_F, BENCHMARK_... diff --git a/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp b/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp index 85127df7..799cf5a7 100644 --- a/test/performance/ibf/interleaved_bloom_filter_benchmark.cpp +++ b/test/performance/ibf/interleaved_bloom_filter_benchmark.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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 // for State, Benchmark, Counter, BENCHMARK, ClobberMemory, BEN... diff --git a/test/scripts/add_snippets_to_cookbook.sh b/test/scripts/add_snippets_to_cookbook.sh index 2c74b0bd..2a659f9f 100755 --- a/test/scripts/add_snippets_to_cookbook.sh +++ b/test/scripts/add_snippets_to_cookbook.sh @@ -1,10 +1,9 @@ #!/usr/bin/env bash -# ------------------------------------------------------------------------------------------------------------ -# 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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ + +# 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 + # # Usage: create_all_hpp.sh # Will update the cookbook to include all snippets of the documentation. diff --git a/test/scripts/link_check.sh b/test/scripts/link_check.sh index f1f79d5f..2fb25384 100644 --- a/test/scripts/link_check.sh +++ b/test/scripts/link_check.sh @@ -1,10 +1,9 @@ #!/usr/bin/env bash -# ------------------------------------------------------------------------------------------------------------ -# 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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ + +# 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 + # # Usage: link_check.sh # Will output the status of links in the repository. diff --git a/test/scripts/update_copyright.sh b/test/scripts/update_copyright.sh index be36e90f..5a7082b1 100755 --- a/test/scripts/update_copyright.sh +++ b/test/scripts/update_copyright.sh @@ -1,10 +1,8 @@ #!/usr/bin/env bash -# ------------------------------------------------------------------------------------------------------------ -# 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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ + +# 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 set -Eeuo pipefail diff --git a/test/snippet/CMakeLists.txt b/test/snippet/CMakeLists.txt index 69753ec9..55b9ee32 100644 --- a/test/snippet/CMakeLists.txt +++ b/test/snippet/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10...3.22) project (hibf_test_snippet CXX) diff --git a/test/snippet/compare_snippet_output.cmake b/test/snippet/compare_snippet_output.cmake index e4a27f57..c0064259 100644 --- a/test/snippet/compare_snippet_output.cmake +++ b/test/snippet/compare_snippet_output.cmake @@ -1,3 +1,7 @@ +# 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 + cmake_minimum_required (VERSION 3.10) include ("${CMAKE_CURRENT_LIST_DIR}/../cmake/hibf_path_longest_stem.cmake") diff --git a/test/snippet/hibf/config_input_fn_dummy.cpp b/test/snippet/hibf/config_input_fn_dummy.cpp index 744b1916..9533307c 100644 --- a/test/snippet/hibf/config_input_fn_dummy.cpp +++ b/test/snippet/hibf/config_input_fn_dummy.cpp @@ -1,3 +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 + #include // for size_t #include // for function diff --git a/test/snippet/hibf/config_input_fn_file.cpp b/test/snippet/hibf/config_input_fn_file.cpp index df25b514..a1cf8d2c 100644 --- a/test/snippet/hibf/config_input_fn_file.cpp +++ b/test/snippet/hibf/config_input_fn_file.cpp @@ -1,3 +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 + #include // for uint64_t #include // for size_t #include // for path diff --git a/test/snippet/hibf/config_input_fn_vector.cpp b/test/snippet/hibf/config_input_fn_vector.cpp index 893c0f5b..fa673438 100644 --- a/test/snippet/hibf/config_input_fn_vector.cpp +++ b/test/snippet/hibf/config_input_fn_vector.cpp @@ -1,3 +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 + #include // for uint64_t #include // for size_t #include // for function diff --git a/test/snippet/hibf/config_number_of_user_bins.cpp b/test/snippet/hibf/config_number_of_user_bins.cpp index 6ddd53fe..753f297a 100644 --- a/test/snippet/hibf/config_number_of_user_bins.cpp +++ b/test/snippet/hibf/config_number_of_user_bins.cpp @@ -1,3 +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 + #include // for size_t #include // for function diff --git a/test/snippet/hibf/hibf_construction.cpp b/test/snippet/hibf/hibf_construction.cpp index 286fea01..6f8994d8 100644 --- a/test/snippet/hibf/hibf_construction.cpp +++ b/test/snippet/hibf/hibf_construction.cpp @@ -1,3 +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 + #include // for size_t #include // for function #include // for vector diff --git a/test/snippet/hibf/hierarchical_interleaved_bloom_filter.cpp b/test/snippet/hibf/hierarchical_interleaved_bloom_filter.cpp index fbf2437a..df3ed221 100644 --- a/test/snippet/hibf/hierarchical_interleaved_bloom_filter.cpp +++ b/test/snippet/hibf/hierarchical_interleaved_bloom_filter.cpp @@ -1,3 +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 + #include // for size_t #include // for function #include // for vector diff --git a/test/snippet/hibf/hierarchical_interleaved_bloom_filter.out.license b/test/snippet/hibf/hierarchical_interleaved_bloom_filter.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/hibf/hierarchical_interleaved_bloom_filter.out.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: CC0-1.0 diff --git a/test/snippet/ibf/counting_agent.cpp b/test/snippet/ibf/counting_agent.cpp index 78bf9934..31a478b3 100644 --- a/test/snippet/ibf/counting_agent.cpp +++ b/test/snippet/ibf/counting_agent.cpp @@ -1,3 +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 + #include // for copy #include // for uint8_t #include // for size_t diff --git a/test/snippet/ibf/counting_agent.out.license b/test/snippet/ibf/counting_agent.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/ibf/counting_agent.out.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: CC0-1.0 diff --git a/test/snippet/ibf/counting_agent_construction.cpp b/test/snippet/ibf/counting_agent_construction.cpp index fd66dddd..ea8df3f2 100644 --- a/test/snippet/ibf/counting_agent_construction.cpp +++ b/test/snippet/ibf/counting_agent_construction.cpp @@ -1,3 +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 + #include int main() diff --git a/test/snippet/ibf/counting_vector.cpp b/test/snippet/ibf/counting_vector.cpp index 46ece370..c2d91a6d 100644 --- a/test/snippet/ibf/counting_vector.cpp +++ b/test/snippet/ibf/counting_vector.cpp @@ -1,3 +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 + #include // for uint16_t #include // for interleaved_bloom_filter, bin_index, counting_vector, bin_count diff --git a/test/snippet/ibf/counting_vector.out.license b/test/snippet/ibf/counting_vector.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/ibf/counting_vector.out.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: CC0-1.0 diff --git a/test/snippet/ibf/interleaved_bloom_filter_clear.cpp b/test/snippet/ibf/interleaved_bloom_filter_clear.cpp index ba4b9839..8f538bfe 100644 --- a/test/snippet/ibf/interleaved_bloom_filter_clear.cpp +++ b/test/snippet/ibf/interleaved_bloom_filter_clear.cpp @@ -1,3 +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 + #include // for iota_view, operator==, _Iota, iota, views #include // for vector diff --git a/test/snippet/ibf/interleaved_bloom_filter_clear.out.license b/test/snippet/ibf/interleaved_bloom_filter_clear.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/ibf/interleaved_bloom_filter_clear.out.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: CC0-1.0 diff --git a/test/snippet/ibf/interleaved_bloom_filter_constructor.cpp b/test/snippet/ibf/interleaved_bloom_filter_constructor.cpp index 02d8ae72..cbe01c96 100644 --- a/test/snippet/ibf/interleaved_bloom_filter_constructor.cpp +++ b/test/snippet/ibf/interleaved_bloom_filter_constructor.cpp @@ -1,3 +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 + #include int main() diff --git a/test/snippet/ibf/interleaved_bloom_filter_emplace.cpp b/test/snippet/ibf/interleaved_bloom_filter_emplace.cpp index 0d5ea0f3..5f610b87 100644 --- a/test/snippet/ibf/interleaved_bloom_filter_emplace.cpp +++ b/test/snippet/ibf/interleaved_bloom_filter_emplace.cpp @@ -1,3 +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 + #include int main() diff --git a/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.cpp b/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.cpp index 826f01f9..bf83f5bc 100644 --- a/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.cpp +++ b/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.cpp @@ -1,3 +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 + #include // for interleaved_bloom_filter, bin_index, bin_count, bin_size #include // for print, print_t diff --git a/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.out.license b/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.out.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: CC0-1.0 diff --git a/test/snippet/ibf/membership_agent_bulk_contains.cpp b/test/snippet/ibf/membership_agent_bulk_contains.cpp index 0b20b990..4569198b 100644 --- a/test/snippet/ibf/membership_agent_bulk_contains.cpp +++ b/test/snippet/ibf/membership_agent_bulk_contains.cpp @@ -1,3 +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 + #include // for interleaved_bloom_filter, bin_index, bin_count, bin_size #include // for print, print_t diff --git a/test/snippet/ibf/membership_agent_bulk_contains.out.license b/test/snippet/ibf/membership_agent_bulk_contains.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/ibf/membership_agent_bulk_contains.out.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: CC0-1.0 diff --git a/test/snippet/ibf/membership_agent_construction.cpp b/test/snippet/ibf/membership_agent_construction.cpp index 13cbc8a8..3058e3c6 100644 --- a/test/snippet/ibf/membership_agent_construction.cpp +++ b/test/snippet/ibf/membership_agent_construction.cpp @@ -1,3 +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 + #include int main() diff --git a/test/snippet/readme.cpp b/test/snippet/readme.cpp index 11f1c11a..fbf24ac0 100644 --- a/test/snippet/readme.cpp +++ b/test/snippet/readme.cpp @@ -1,3 +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 + #include // for copy #include // for uint64_t, int64_t #include // for size_t diff --git a/test/snippet/readme.out.license b/test/snippet/readme.out.license new file mode 100644 index 00000000..7a29e5d1 --- /dev/null +++ b/test/snippet/readme.out.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: CC0-1.0 diff --git a/test/snippet/snippet_main.cpp b/test/snippet/snippet_main.cpp index 905869df..4f739c93 100644 --- a/test/snippet/snippet_main.cpp +++ b/test/snippet/snippet_main.cpp @@ -1,3 +1,7 @@ +// 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 + int main() { return 0; diff --git a/test/snippet/test/tmp_directory.cpp b/test/snippet/test/tmp_directory.cpp index 4d9afcb8..9d593aa8 100644 --- a/test/snippet/test/tmp_directory.cpp +++ b/test/snippet/test/tmp_directory.cpp @@ -1,3 +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 + #include // for Test, AssertionResult, TestInfo, EXPECT_TRUE, Message, TEST, TestPar... #include // for remove diff --git a/test/unit/CMakeLists.txt b/test/unit/CMakeLists.txt index 89cb2eaf..5e30e0e0 100644 --- a/test/unit/CMakeLists.txt +++ b/test/unit/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10...3.22) project (hibf_test_unit CXX) diff --git a/test/unit/hibf/CMakeLists.txt b/test/unit/hibf/CMakeLists.txt index a3e1cc2b..cac2b2ba 100644 --- a/test/unit/hibf/CMakeLists.txt +++ b/test/unit/hibf/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + add_subdirectories () hibf_test (config_test.cpp) diff --git a/test/unit/hibf/config_test.cpp b/test/unit/hibf/config_test.cpp index cb54d461..78fd93a5 100644 --- a/test/unit/hibf/config_test.cpp +++ b/test/unit/hibf/config_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Message, TestPartResult, AssertionResult, Test, EXPECT_EQ, CaptureStderr, GetCapt... #include // for size_t diff --git a/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp b/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp index fb717950..ce67fa13 100644 --- a/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp +++ b/test/unit/hibf/hierarchical_interleaved_bloom_filter_test.cpp @@ -1,9 +1,6 @@ -// ----------------------------------------------------------------------------------------------------- -// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin -// Copyright (c) 2016-2022, 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 and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md -// ----------------------------------------------------------------------------------------------------- +// 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 // for Test, Message, TestInfo, TestPartResult, EXPECT_EQ diff --git a/test/unit/hibf/interleaved_bloom_filter_test.cpp b/test/unit/hibf/interleaved_bloom_filter_test.cpp index e0c7018b..4b267e62 100644 --- a/test/unit/hibf/interleaved_bloom_filter_test.cpp +++ b/test/unit/hibf/interleaved_bloom_filter_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for Message, TestPartResult, AssertionResult, EXPECT_EQ, TYPED_TEST diff --git a/test/unit/hibf/layout/CMakeLists.txt b/test/unit/hibf/layout/CMakeLists.txt index 2b8e5801..4a252c78 100644 --- a/test/unit/hibf/layout/CMakeLists.txt +++ b/test/unit/hibf/layout/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + hibf_test (hierarchical_binning_test.cpp) hibf_test (simple_binning_test.cpp) hibf_test (layout_test.cpp) diff --git a/test/unit/hibf/layout/fpr_correction_test.cpp b/test/unit/hibf/layout/fpr_correction_test.cpp index 0bfebaa6..420e22df 100644 --- a/test/unit/hibf/layout/fpr_correction_test.cpp +++ b/test/unit/hibf/layout/fpr_correction_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Test, Message, TestPartResult, EXPECT_NEAR, TestInfo #include // for size_t diff --git a/test/unit/hibf/layout/graph_test.cpp b/test/unit/hibf/layout/graph_test.cpp index c562ee74..eef6c098 100644 --- a/test/unit/hibf/layout/graph_test.cpp +++ b/test/unit/hibf/layout/graph_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Message, TestPartResult, EXPECT_EQ, Test, ASSERT_EQ, TestInfo, TEST #include // for size_t diff --git a/test/unit/hibf/layout/hierarchical_binning_test.cpp b/test/unit/hibf/layout/hierarchical_binning_test.cpp index 5024c5fe..9610d37c 100644 --- a/test/unit/hibf/layout/hierarchical_binning_test.cpp +++ b/test/unit/hibf/layout/hierarchical_binning_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Test, Message, TestPartResult, TestInfo, EXPECT_EQ #include // for size_t diff --git a/test/unit/hibf/layout/layout_test.cpp b/test/unit/hibf/layout/layout_test.cpp index f90d7852..d1e1cc67 100644 --- a/test/unit/hibf/layout/layout_test.cpp +++ b/test/unit/hibf/layout/layout_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Test, EXPECT_EQ, Message, TestPartResult, TestInfo, TEST #include // for size_t diff --git a/test/unit/hibf/layout/simple_binning_test.cpp b/test/unit/hibf/layout/simple_binning_test.cpp index ca68db9f..2689a43c 100644 --- a/test/unit/hibf/layout/simple_binning_test.cpp +++ b/test/unit/hibf/layout/simple_binning_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Test, TestInfo, Message, TestPartResult, TEST, EXPECT_EQ #include // for size_t diff --git a/test/unit/hibf/print_test.cpp b/test/unit/hibf/print_test.cpp index 2ed9816e..7b69b391 100644 --- a/test/unit/hibf/print_test.cpp +++ b/test/unit/hibf/print_test.cpp @@ -1,3 +1,7 @@ +// 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 // for EXPECT_EQ, GetCapturedStderr, GetCapturedStdout, Message, TestP... #include // for int64_t, int16_t, int32_t, int8_t, uint16_t, uint32_t, uint64_t diff --git a/test/unit/hibf/sketch/CMakeLists.txt b/test/unit/hibf/sketch/CMakeLists.txt index be98985e..4706cb7c 100644 --- a/test/unit/hibf/sketch/CMakeLists.txt +++ b/test/unit/hibf/sketch/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + hibf_test (estimate_kmer_counts_test.cpp) hibf_test (hyperloglog_test.cpp) hibf_test (toolbox_test.cpp) diff --git a/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp b/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp index b336bbf4..aea4fdad 100644 --- a/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp +++ b/test/unit/hibf/sketch/estimate_kmer_counts_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Test, Message, TestPartResult, EXPECT_EQ, TestInfo #include // for uint8_t diff --git a/test/unit/hibf/sketch/hyperloglog_test.cpp b/test/unit/hibf/sketch/hyperloglog_test.cpp index d9e1ab11..f4ca33ed 100644 --- a/test/unit/hibf/sketch/hyperloglog_test.cpp +++ b/test/unit/hibf/sketch/hyperloglog_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Test, TestInfo, Message, TestPartResult, TEST, EXPECT_EQ, EXPE... #include // for uint8_t diff --git a/test/unit/hibf/sketch/toolbox_test.cpp b/test/unit/hibf/sketch/toolbox_test.cpp index 844b9949..7eb702fc 100644 --- a/test/unit/hibf/sketch/toolbox_test.cpp +++ b/test/unit/hibf/sketch/toolbox_test.cpp @@ -1,3 +1,7 @@ +// 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 // for Message, TestPartResult, EXPECT_EQ, TestInfo, TEST_F, Test #include // for uint64_t diff --git a/test/unit/test/CMakeLists.txt b/test/unit/test/CMakeLists.txt index f89ff05b..6a8322ab 100644 --- a/test/unit/test/CMakeLists.txt +++ b/test/unit/test/CMakeLists.txt @@ -1,3 +1,7 @@ +# 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 + hibf_test (expect_range_eq_test.cpp) hibf_test (expect_same_type_test.cpp) hibf_test (file_access_test.cpp) diff --git a/test/unit/test/expect_range_eq_test.cpp b/test/unit/test/expect_range_eq_test.cpp index 8e8e2048..32345e7b 100644 --- a/test/unit/test/expect_range_eq_test.cpp +++ b/test/unit/test/expect_range_eq_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for EXPECT_NONFATAL_FAILURE #include // for Test, AssertionResult, Message, TestPartResult, TestInfo, TEST, EXP... diff --git a/test/unit/test/expect_same_type_test.cpp b/test/unit/test/expect_same_type_test.cpp index 066da4d6..8021d743 100644 --- a/test/unit/test/expect_same_type_test.cpp +++ b/test/unit/test/expect_same_type_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for EXPECT_NONFATAL_FAILURE #include // for Test, AssertionResult, Message, TestPartResult, TestInfo, TEST diff --git a/test/unit/test/file_access_test.cpp b/test/unit/test/file_access_test.cpp index bf9684e7..aa4eabf5 100644 --- a/test/unit/test/file_access_test.cpp +++ b/test/unit/test/file_access_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for AssertionResult, TestInfo, Message, TEST_F, TestPartResult, EXPECT_EQ diff --git a/test/unit/test/sandboxed_path_test.cpp b/test/unit/test/sandboxed_path_test.cpp index 17d3a54e..d48803df 100644 --- a/test/unit/test/sandboxed_path_test.cpp +++ b/test/unit/test/sandboxed_path_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for Test, Message, TestPartResult, EXPECT_EQ, TestInfo, EXPECT_NO_THROW diff --git a/test/unit/test/temporary_snippet_file_test.cpp b/test/unit/test/temporary_snippet_file_test.cpp index 21b9c7ed..afdbc3e8 100644 --- a/test/unit/test/temporary_snippet_file_test.cpp +++ b/test/unit/test/temporary_snippet_file_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for Test, AssertionResult, Message, TestInfo, TestPartResult diff --git a/test/unit/test/tmp_directory_test.cpp b/test/unit/test/tmp_directory_test.cpp index 66d6c6a5..6298c7cb 100644 --- a/test/unit/test/tmp_directory_test.cpp +++ b/test/unit/test/tmp_directory_test.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 // for AssertionResult, Test, Message, TestPartResult, EXPECT_TRUE, CmpHelp... diff --git a/util/CMakeLists.txt b/util/CMakeLists.txt index 860c3927..00d94f1b 100644 --- a/util/CMakeLists.txt +++ b/util/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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -# ------------------------------------------------------------------------------------------------------------ +# 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 cmake_minimum_required (VERSION 3.10...3.22) project (hibf_util CXX) diff --git a/util/fpr_quality.cpp b/util/fpr_quality.cpp index 7646b12d..a3ad3cc7 100644 --- a/util/fpr_quality.cpp +++ b/util/fpr_quality.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 and also available at: https://github.com/seqan/hibf/blob/main/LICENSE.md -// ------------------------------------------------------------------------------------------------------------ +// 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 From 9a91b43cba3417ae3b8775192e9827a3fdfe5b76 Mon Sep 17 00:00:00 2001 From: Enrico Seiler Date: Fri, 13 Oct 2023 16:16:30 +0200 Subject: [PATCH 2/2] [INFRA] Add CI --- .github/workflows/ci_license.yml | 34 ++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 .github/workflows/ci_license.yml diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml new file mode 100644 index 00000000..77c9193e --- /dev/null +++ b/.github/workflows/ci_license.yml @@ -0,0 +1,34 @@ +# 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: License + +on: + push: + branches: + - 'main' + pull_request: + types: + - unlabeled + workflow_dispatch: + +concurrency: + group: license-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: ${{ github.event_name != 'push' }} + +env: + TZ: Europe/Berlin + +jobs: + check: + name: REUSE Compliance + runs-on: ubuntu-22.04 + timeout-minutes: 120 + if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: REUSE Compliance Check + uses: fsfe/reuse-action@v2