[MISC] Switch to SPDX headers (#3229)

* patch: introducing spdx headers

* fix: adjusting update_copyright.sh to SPDX headers

* patch: update copyright year number

* feat: add CI for licensing checking

* fix: remove executable bit from files, that shouldn't have it

* fix: minor include order error

* fix: git submodules, thx @eseiler

.clang-format

@@ -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
+
 # Format all files in include folder, including std module, excluding contrib module
 # find . \( -path "./include/seqan3/std/*" -or -iname "*.hpp" \) -and -not -path "./submodules/*" -and -not -path "./build/*" -and -not -path "./include/seqan3/contrib/*" -and -not -path "./test/*" | xargs clang-format-15 --style=file -i
 ---

.cmake-format.yaml

@@ -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
+
 _seqan3_cmake_format_documentation_only:
   install:
     command:

.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

.editorconfig

@@ -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://EditorConfig.org
 
 # top-most EditorConfig file

.github/ISSUE_TEMPLATE/bug_report.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: 🐞 Bug report
 description: Create a report to help us improve SeqAn3.
 labels: [bug]

.github/ISSUE_TEMPLATE/config.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
+
 blank_issues_enabled: true
 contact_links:
   - name: Questions and Answers

.github/ISSUE_TEMPLATE/cron_comment_template.md.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

.github/ISSUE_TEMPLATE/feature_request.md.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

.github/ISSUE_TEMPLATE/question.md.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

.github/ISSUE_TEMPLATE/release-checklist.md.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

.github/ISSUE_TEMPLATE/task.md.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

.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/pull_request_template.md.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

.github/workflows/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: CC-BY-4.0
+-->
+
 # Continuous on Pull Request
 
 ## ci_cmake.yml

.github/workflows/ci_cmake.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: CMake
 
 on:

.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_documentation.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: Documentation
 
 on:

.github/workflows/ci_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:

.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: Unit 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: Unit macOS
 
 on:

.github/workflows/ci_misc.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/cron_api.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: API-Stability
 
 on:

.github/workflows/cron_avx2.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: AVX2
 
 on:

.github/workflows/cron_latest_libraries.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: Latest Libraries
 
 on:

.github/workflows/deploy_documentation.yaml

@@ -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: Deploy documentation (https://docs.seqan.de/)
 
 on:

.github/workflows/hide_comments.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: Hide bot comments
 
 on:

.github/workflows/license_check.yaml

@@ -0,0 +1,22 @@
+# 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: REUSE Compliance Check
+
+on:
+  push:
+    branches:
+      - 'main'
+      - 'master'
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  license_check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: REUSE Compliance Check
+      uses: fsfe/reuse-action@v2
+      with:
+        args: --suppress-deprecation lint

.github/workflows/ram_usage.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: RAM-Usage
 
 on:

.github/workflows/scripts/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: CC-BY-4.0
+-->
+
 ## g++_ram.sh
 
 `VERSION` needs to be replaced with the gcc version. When `DO_TIME` is `0`, this is just a wrapper for gcc that does

.github/workflows/scripts/g++_ram.sh

@@ -1,4 +1,9 @@
 #!/usr/bin/env bash
+
+# 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
+
 GCC="/usr/bin/g++-VERSION"
 DO_TIME=0
 

.github/workflows/scripts/gcov.sh

@@ -1,5 +1,10 @@
 #!/usr/bin/env bash
 
+# 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
+
+
 args=${@/--branch-counts/""}
 args=${args/--branch-probabilities/""}
 

.github/workflows/scripts/process_compiler_error_log.py

@@ -1,10 +1,8 @@
 #!/usr/bin/env python3
-# -----------------------------------------------------------------------------------------------------
-# 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: 2006-2024 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
 #
 # Usage process_compiler_error_log.py <log_file>
 #

.github/workflows/scripts/ram_usage.py

@@ -1,10 +1,8 @@
 #!/usr/bin/env python3
-# -----------------------------------------------------------------------------------------------------
-# 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: 2006-2024 Knut Reinert & Freie Universität Berlin
+# SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+# SPDX-License-Identifier: CC0-1.0
 #
 # Usage ram_usage.py <input_file> <output_file>
 #

.github/workflows/update_cookbook.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: Cookbook
 
 on:

.gitmodules

@@ -1,3 +1,6 @@
+# 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
 [submodule "sdsl-lite"]
 	path = submodules/sdsl-lite
 	url = https://github.com/xxsds/sdsl-lite

.gitpod.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://www.gitpod.io/docs/references/gitpod-yml
 checkoutLocation: "tutorial/seqan3"
 workspaceLocation: "/tutorial"

.travis.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
+
 version: ~> 1.0
 os: linux
 dist: focal

CHANGELOG.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: CC-BY-4.0
+-->
+
 # Changelog {#about_changelog}
 
 [TOC]

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/seqan3/blob/master/LICENSE.md
-# -----------------------------------------------------------------------------------------------------
+# 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
 
 # This file provides functionality common to the different test modules used by
 # SeqAn3. To build tests, run cmake on one of the sub-folders in this directory

CODE_OF_CONDUCT.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: CC-BY-4.0
+-->
+
 # 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:

CONTRIBUTING.md

@@ -1,3 +1,6 @@
+<!-- SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+     SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+     SPDX-License-Identifier: CC-BY-4.0 -->
 # 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

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.