seqan · eseiler · Feb 7, 2024 · Feb 7, 2024
diff --git a/.clang-format b/.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 . \( -iname "*.hpp" -or -iname "*.cpp" \) -and -not -path "./submodules/*" -and -not -path "./build/*" | xargs clang-format-15 --style=file -i
 ---

diff --git a/.cmake-format.yaml b/.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
+
 _sharg_cmake_format_documentation_only:
   install:
     command:

diff --git 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:
   token: b5e588e8-7b85-46f1-bad6-e0a5c19d7d67

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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 Sharg.
 labels: [bug]

diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.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

diff --git a/.github/ISSUE_TEMPLATE/cron_comment_template.md.license b/.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
diff --git a/.github/ISSUE_TEMPLATE/release-checklist.md.license b/.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
diff --git 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/api.yml b/.github/workflows/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: Sharg API-Stability
 
 on:

diff --git a/.github/workflows/ci_cmake.yml b/.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:

diff --git 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_documentation.yml b/.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:

diff --git a/.github/workflows/ci_license.yml b/.github/workflows/ci_license.yml
@@ -0,0 +1,41 @@
+# 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
+
+defaults:
+  run:
+    shell: bash -Eexuo pipefail {0}
+
+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
+
+      - name: Check Markdown files for doxygen
+        run: ${{ github.workspace }}/test/scripts/check_markdown_doxygen.sh ${{ github.workspace }}
diff --git 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: Unit Linux
 
 on:

diff --git 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: Unit macOS
 
 on:

diff --git a/.github/workflows/ci_misc.yml b/.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:

diff --git a/.github/workflows/documentation.yml b/.github/workflows/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: Deploy documentation (https://docs.seqan.de/)
 
 on:

diff --git 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/.github/workflows/readme_snippet.yml b/.github/workflows/readme_snippet.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: Sharg Markdown
 
 on:

diff --git a/.github/workflows/scripts/gcov.sh b/.github/workflows/scripts/gcov.sh
@@ -1,5 +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
+
 args=${@/--branch-counts/""}
 args=${args/--branch-probabilities/""}
 

diff --git a/.github/workflows/update_cookbook.yml b/.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: Sharg lint
 
 on:

diff --git 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/.gitmodules b/.gitmodules
@@ -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
+
 [submodule "submodules/tool_description_lib"]
 	path = submodules/tool_description_lib
 	url = https://github.com/deNBI-cibi/tool_description_lib.git
diff --git a/.gitpod.yml b/.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/sharg-parser"
 workspaceLocation: "/tutorial"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # Changelog {#about_changelog}
 
+<!--
+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
+-->
+
 [TOC]
 
 This changelog contains a top-level entry for each release with sections on new features, API changes and notable

diff --git 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/sharg-parser/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
 
 # This file provides functionality common to the different test modules used by
 # Sharg. To build tests, run cmake on one of the sub-folders in this directory

diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -1,7 +1,13 @@
 # Code of Conduct {#about_code_of_conduct}
 
+<!--
+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
+-->
+
 The Sharg-parser adheres to the [Berlin Code of Conduct](https://berlincodeofconduct.org/). As the Sharg-parser was
-created and is maintained by the SeqAn team, it is part of the SeqAn project. Therefore, SeqAn's Code of Conduct 
-applies to the Sharg-parser as well. Please see 
-[SeqAn's Code of Conduct](http://docs.seqan.de/seqan/3-master-user/about_code_of_conduct.html) for more 
+created and is maintained by the SeqAn team, it is part of the SeqAn project. Therefore, SeqAn's Code of Conduct
+applies to the Sharg-parser as well. Please see
+[SeqAn's Code of Conduct](http://docs.seqan.de/seqan/3-master-user/about_code_of_conduct.html) for more
 information on our Code of Conduct.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,5 +1,11 @@
 # Contributing {#about_contributing}
 
+<!--
+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
+-->
+
 First of all, thanks for wanting to contribute to the SeqAn's Sharg-parser! Community is important to us and we strive
 to maintain a great culture and atmosphere. Please have a look at our [Code of Conduct](\ref about_code_of_conduct).
 

diff --git a/LICENSE.md b/LICENSE.md
@@ -14,8 +14,8 @@ The contents of this repository/directory, in particular the library
 source code of Sharg, are licensed under the following terms:
 
 ```
-Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
-Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+Copyright (c) 2006-2024, Knut Reinert & Freie Universität Berlin
+Copyright (c) 2016-2024, Knut Reinert & MPI für molekulare Genetik
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/LICENSES/BSD-3-Clause.txt b/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.