Merge pull request #71 from eseiler/infra/spdx

[INFRA] Use SPDX header

.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

.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

.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:

.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

.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:

.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:

.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:

.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
 

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

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. 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. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+This approach simplifies the process of license declaration as it replaces the full license text with a single line
+identifier. The SPDX identifier is a globally recognized standard that allows for easy identification and understanding
+of the license. This means that each file in our project will have a license identifier at the top, making it clear
+under which license the file is provided. For more information about the specific licenses, you can refer to the
+[SPDX License List](https://spdx.org/licenses/).

LICENSES/BSD-3-Clause.txt

@@ -0,0 +1,11 @@
+Copyright (c) <year> <owner>. 
+
+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. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

LICENSES/CC0-1.0.txt

@@ -0,0 +1,121 @@
+Creative Commons Legal Code
+
+CC0 1.0 Universal
+
+    CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
+    LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN
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+    PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM
+    THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED
+    HEREUNDER.
+
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+
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+of copies, and (iv) for any purpose whatsoever, including without
+limitation commercial, advertising or promotional purposes (the
+"License"). The License shall be deemed effective as of the date CC0 was
+applied by Affirmer to the Work. 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. Affirmer offers the Work as-is and makes no representations or
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+ c. Affirmer disclaims responsibility for clearing rights of other persons
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+    consents, permissions or other rights required for any use of the
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+ d. Affirmer understands and acknowledges that Creative Commons is not a
+    party to this document and has no duty or obligation with respect to
+    this CC0 or use of the Work.

LICENSES/MIT.txt

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) <year> <copyright holders>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 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.

README.md

@@ -1,3 +1,9 @@
+<!--
+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
+-->
+
 # SeqAn3 App Template [![build status][1]][2] [![codecov][3]][4]
 <!--
     Above uses reference-style links with numbers.

cmake/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/raptor/blob/main/LICENSE.md
-# --------------------------------------------------------------------------------------------------
+# SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: BSD-3-Clause
 
 cmake_minimum_required (VERSION 3.21)
 

include/configuration.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 <filesystem>

include/fastq_conversion.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 "configuration.hpp"

src/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)
 
 # A interface to reuse common properties.

src/fastq_conversion.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 "fastq_conversion.hpp"
 
 #include <seqan3/io/sequence_file/all.hpp>

src/main.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 <sharg/all.hpp>
 
 #include "fastq_conversion.hpp"

test/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 googletest.

test/api/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 (convert_fastq_test.cpp)

test/api/README.md

@@ -1,3 +1,9 @@
+<!--
+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
+-->
+
 # API Test
 
 Here are test files for API tests, i.e. the internal functions of the app are executed with different input parameters.

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 <gtest/gtest.h>
 
 #include "../app_test.hpp"

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 <gtest/gtest.h>

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)

test/cli/README.md

@@ -1,3 +1,9 @@
+<!--
+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
+-->
+
 # CLI Test
 
 Here are test files for command line interface tests, i.e. the app is executed with defined input files and parameters.