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Patch/copyrightyear update #3229

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merged 7 commits into from
Jan 30, 2024
+7,364 −5,641
Merged

Patch/copyrightyear update #3229

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0498a80
patch: introducing spdx headers
SGSSGene Jan 30, 2024
a294dd4
fix: adjusting update_copyright.sh to SPDX headers
SGSSGene Jan 30, 2024
2de2758
patch: update copyright year number
SGSSGene Jan 30, 2024
b98e2f7
feat: add CI for licensing checking
SGSSGene Jan 30, 2024
3fbacd1
fix: remove executable bit from files, that shouldn't have it
SGSSGene Jan 30, 2024
c0cb991
fix: minor include order error
SGSSGene Jan 30, 2024
182a7d3
fix: git subodules, thx @eseiler
SGSSGene Jan 30, 2024
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4 changes: 4 additions & 0 deletions .clang-format
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# 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
---
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4 changes: 4 additions & 0 deletions .cmake-format.yaml
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# 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:
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4 changes: 4 additions & 0 deletions .codecov.yml
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# 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
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4 changes: 4 additions & 0 deletions .editorconfig
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# 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
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4 changes: 4 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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# 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]
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4 changes: 4 additions & 0 deletions .github/ISSUE_TEMPLATE/config.yml
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# 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
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3 changes: 3 additions & 0 deletions .github/ISSUE_TEMPLATE/cron_comment_template.md.license
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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
3 changes: 3 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md.license
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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
3 changes: 3 additions & 0 deletions .github/ISSUE_TEMPLATE/question.md.license
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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
3 changes: 3 additions & 0 deletions .github/ISSUE_TEMPLATE/release-checklist.md.license
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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
3 changes: 3 additions & 0 deletions .github/ISSUE_TEMPLATE/task.md.license
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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
4 changes: 4 additions & 0 deletions .github/dependabot.yml
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# 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
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3 changes: 3 additions & 0 deletions .github/pull_request_template.md.license
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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
6 changes: 6 additions & 0 deletions .github/workflows/README.md
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<!--
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
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4 changes: 4 additions & 0 deletions .github/workflows/ci_cmake.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/ci_coverage.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/ci_documentation.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/ci_lint.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/ci_linux.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/ci_macos.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/ci_misc.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/cron_api.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/cron_avx2.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/cron_latest_libraries.yml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/deploy_documentation.yaml
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# 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:
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4 changes: 4 additions & 0 deletions .github/workflows/hide_comments.yml
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# 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:
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22 changes: 22 additions & 0 deletions .github/workflows/license_check.yaml
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# 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
4 changes: 4 additions & 0 deletions .github/workflows/ram_usage.yml
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# 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:
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6 changes: 6 additions & 0 deletions .github/workflows/scripts/README.md
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<!--
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
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5 changes: 5 additions & 0 deletions .github/workflows/scripts/g++_ram.sh
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#!/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

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5 changes: 5 additions & 0 deletions .github/workflows/scripts/gcov.sh
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#!/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/""}

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10 changes: 4 additions & 6 deletions .github/workflows/scripts/process_compiler_error_log.py
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#!/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>
#
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10 changes: 4 additions & 6 deletions .github/workflows/scripts/ram_usage.py
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#!/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>
#
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4 changes: 4 additions & 0 deletions .github/workflows/update_cookbook.yml
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# 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:
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3 changes: 3 additions & 0 deletions .gitmodules
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# 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
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Does this need a new line? The submodules aren't checked out in the ci

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Yeah, this doesn't seem to work like this at all :/ added a .gitmodules.license

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Looks like some commit removed the submodules/* directories. I tried readding them

[submodule "sdsl-lite"]
path = submodules/sdsl-lite
url = https://github.com/xxsds/sdsl-lite
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4 changes: 4 additions & 0 deletions .gitpod.yml
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# 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"
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4 changes: 4 additions & 0 deletions .travis.yml
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# 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
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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<!--
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]
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9 changes: 3 additions & 6 deletions CMakeLists.txt
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# -----------------------------------------------------------------------------------------------------
# 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
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6 changes: 6 additions & 0 deletions CODE_OF_CONDUCT.md
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<!--
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:
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3 changes: 3 additions & 0 deletions CONTRIBUTING.md
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<!-- 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
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11 changes: 11 additions & 0 deletions LICENSES/BSD-3-Clause.txt
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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.
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