diff --git a/.codecov.yml b/.codecov.yml index 2733b79..3271158 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + # See https://docs.codecov.io/docs/codecovyml-reference codecov: require_ci_to_pass: no # codecov reports its results independent of whether CI passed diff --git a/.github/dependabot.yml b/.github/dependabot.yml index dcbcb65..ba5cc58 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 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 66c0ca4..cd123d1 100644 --- a/.github/workflows/ci_coverage.yml +++ b/.github/workflows/ci_coverage.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Coverage on: diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml new file mode 100644 index 0000000..9f4af92 --- /dev/null +++ b/.github/workflows/ci_license.yml @@ -0,0 +1,29 @@ +# SPDX-FileCopyrightText: 2006-2024, Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024, Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + +name: License + +on: + push: + pull_request: + 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 + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: REUSE Compliance Check + uses: fsfe/reuse-action@v2 diff --git a/.github/workflows/ci_linux.yml b/.github/workflows/ci_linux.yml index 6374978..af13384 100644 --- a/.github/workflows/ci_linux.yml +++ b/.github/workflows/ci_linux.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Linux on: diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml index 5f02f1d..b1b593d 100644 --- a/.github/workflows/ci_macos.yml +++ b/.github/workflows/ci_macos.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: macOS on: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index d4ec012..9d3c4a8 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + name: Lint on: diff --git a/.gitignore b/.gitignore index 259148f..12e2843 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + # Prerequisites *.d diff --git a/CMakeLists.txt b/CMakeLists.txt index 3af5223..d179477 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + cmake_minimum_required (VERSION 3.16) ## CUSTOMISE diff --git a/INSTALL.md b/INSTALL.md deleted file mode 100644 index e69de29..0000000 diff --git a/LICENSE.md b/LICENSE.md index c068937..477d1f6 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,29 +1,7 @@ -BSD 3-Clause License +In our project, we have adopted the use of SPDX identifiers to specify the license under which each file is provided. -Copyright (c) 2020, Jörg Winkler -All rights reserved. - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - -1. 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Should any part of the License for any +reason be judged legally invalid or ineffective under applicable law, such +partial invalidity or ineffectiveness shall not invalidate the remainder +of the License, and in such case Affirmer hereby affirms that he or she +will not (i) exercise any of his or her remaining Copyright and Related +Rights in the Work or (ii) assert any associated claims and causes of +action with respect to the Work, in either case contrary to Affirmer's +express Statement of Purpose. + +4. Limitations and Disclaimers. + + a. No trademark or patent rights held by Affirmer are waived, abandoned, + surrendered, licensed or otherwise affected by this document. + b. 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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 8b7156c..1ad6424 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,9 @@ + + # SeqAn3 App Template [![build status][1]][2] [![codecov][3]][4] + # API Test Here are test files for API tests, i.e. the internal functions of the app are executed with different input parameters. diff --git a/test/api/convert_fastq_test.cpp b/test/api/convert_fastq_test.cpp index 5984fac..c63cbe5 100644 --- a/test/api/convert_fastq_test.cpp +++ b/test/api/convert_fastq_test.cpp @@ -1,3 +1,7 @@ +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 + #include #include "../app_test.hpp" diff --git a/test/app_test.hpp b/test/app_test.hpp index b9a8092..726cfb0 100644 --- a/test/app_test.hpp +++ b/test/app_test.hpp @@ -1,3 +1,7 @@ +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 + #pragma once #include diff --git a/test/cli/CMakeLists.txt b/test/cli/CMakeLists.txt index 672855f..c7cdfb1 100644 --- a/test/cli/CMakeLists.txt +++ b/test/cli/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + cmake_minimum_required (VERSION 3.16) add_app_test (fastq_to_fasta_options_test.cpp) diff --git a/test/cli/README.md b/test/cli/README.md index 0d0caa1..fea0b5d 100644 --- a/test/cli/README.md +++ b/test/cli/README.md @@ -1,3 +1,9 @@ + + # CLI Test Here are test files for command line interface tests, i.e. the app is executed with defined input files and parameters. diff --git a/test/cli/fastq_to_fasta_options_test.cpp b/test/cli/fastq_to_fasta_options_test.cpp index 2c1f17f..cc9fe9b 100644 --- a/test/cli/fastq_to_fasta_options_test.cpp +++ b/test/cli/fastq_to_fasta_options_test.cpp @@ -1,3 +1,7 @@ +// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +// SPDX-License-Identifier: CC0-1.0 + #include "../app_test.hpp" // To prevent issues when running multiple CLI tests in parallel, give each CLI test unique names: diff --git a/test/cmake/app_datasources.cmake b/test/cmake/app_datasources.cmake index cb7b425..e64a040 100644 --- a/test/cmake/app_datasources.cmake +++ b/test/cmake/app_datasources.cmake @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + include (ExternalProject) # Example call: diff --git a/test/coverage/CMakeLists.txt b/test/coverage/CMakeLists.txt index 68fb071..075c40b 100644 --- a/test/coverage/CMakeLists.txt +++ b/test/coverage/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + cmake_minimum_required (VERSION 3.16) # Add a custom build type: Coverage diff --git a/test/coverage/README.md b/test/coverage/README.md index 12742ea..f11e41e 100644 --- a/test/coverage/README.md +++ b/test/coverage/README.md @@ -1,3 +1,9 @@ + + # Coverage Test This is the test for the code coverage. diff --git a/test/data/README.md b/test/data/README.md index 305b425..0d4f7aa 100644 --- a/test/data/README.md +++ b/test/data/README.md @@ -1,3 +1,9 @@ + + # Data Directory Store the data here that should be used as input files for the tests. diff --git a/test/data/datasources.cmake b/test/data/datasources.cmake index 46374ed..d7cd6ba 100644 --- a/test/data/datasources.cmake +++ b/test/data/datasources.cmake @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + cmake_minimum_required (VERSION 3.16) include (cmake/app_datasources.cmake) diff --git a/test/data/in.fastq.license b/test/data/in.fastq.license new file mode 100644 index 0000000..b8b3e60 --- /dev/null +++ b/test/data/in.fastq.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC0-1.0 diff --git a/test/data/out.fasta.license b/test/data/out.fasta.license new file mode 100644 index 0000000..b8b3e60 --- /dev/null +++ b/test/data/out.fasta.license @@ -0,0 +1,3 @@ +SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +SPDX-License-Identifier: CC0-1.0 diff --git a/test/header/CMakeLists.txt b/test/header/CMakeLists.txt index 4664ece..31223b2 100644 --- a/test/header/CMakeLists.txt +++ b/test/header/CMakeLists.txt @@ -1,3 +1,7 @@ +# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin +# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik +# SPDX-License-Identifier: CC0-1.0 + cmake_minimum_required (VERSION 3.16) include (seqan3_test_files)