Merge pull request #416 from eseiler/misc/license

[DOC] SPDX Licenses

.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/test folder, including std module, excluding contrib module
 # find . \( -iname "*.cpp" -or -iname "*.hpp" \) -and -not -path "./lib/*" -and -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

.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
+
 # find . \( -iname CMakeLists.txt -o -iname *.cmake \) -a -not -path "./lib/*" -a -not -path "./build/*" | xargs cmake-format -c .cmake-format.yaml -i
 _help_parse: Options affecting listfile parsing
 parse:

.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:
   token: 493cd34e-2543-4e61-b7a8-da2c0bc62fb9

.gitattributes

@@ -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
+
 doc/** linguist-documentation
 test/util/** linguist-documentation
 test/benchmark/parse.py linguist-documentation

.github/ISSUE_TEMPLATE/bug_report.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
+-->
+
 ---
 name: Bug report
 about: Create a report to help us improve Raptor

.github/ISSUE_TEMPLATE/feature_request.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
+-->
+
 ---
 name: Feature request
 about: Request a new feature that you would like to see in Raptor

.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_codeql.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: CodeQL
 
 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_fortify.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: Fortify
 
 on:

.github/workflows/ci_license.yml

@@ -0,0 +1,34 @@
+# 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:
+    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@v3

.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: 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/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: Misc
 
 on:

.github/workflows/ci_sanitizer.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: Sanitizer
 
 on:

.github/workflows/ci_utility.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: Utility
 
 on:

.github/workflows/ci_workflows.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: Workflows
 
 on:

.github/workflows/scripts/gcov.sh

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
-# SPDX-FileCopyrightText: 2006-2023, Knut Reinert & Freie Universität Berlin
-# SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
+# 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
 
 set -Eeuo pipefail

.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
 

.reuse/dep5

@@ -0,0 +1,11 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Raptor
+Upstream-Contact: Enrico Seiler <enrico.seiler@fu-berlin.de>
+Source: https://github.com/seqan/raptor/
+
+Files: test/data/*
+       workflow/galaxy/test-data/*
+       workflow/nextflow/data/*
+Copyright: 2006-2024, Knut Reinert & Freie Universität Berlin
+           2016-2024, Knut Reinert & MPI für molekulare Genetik
+License: CC0-1.0

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
+-->
+
 # 2.0.0
 
 ## Features

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/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 3.25)
 

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
 
 The SeqAn project adheres to the [Berlin Code of Conduct](https://berlincodeofconduct.org/). From the code of conduct:

LICENSE.md

@@ -1,30 +1,9 @@
-BSD 3-Clause License
+In Raptor, we have adopted the use of SPDX identifiers to specify the license under which each file is provided.
 
-Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
-Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
-All rights reserved.
+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/).
 
-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.
+For the purpose of referring to a singular license, Raptor is licensed under BSD-3-Clause.

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.