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Merge pull request #100 from eseiler/infra/init
[INFRA] Init action
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‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"
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ignore:
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- dependency-name: "PuneetMatharu/cmake-format-lint-action"

‎.github/workflows/initialise.yml‎

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# SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
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# SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
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# SPDX-License-Identifier: CC0-1.0
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name: Initialise
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on:
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push:
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workflow_dispatch:
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env:
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TZ: Europe/Berlin
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defaults:
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run:
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shell: bash -Eeuxo pipefail {0}
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jobs:
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init:
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runs-on: ubuntu-latest
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if: github.event_name == 'workflow_dispatch' || (github.event.repository.name != 'app-template' && github.event.created)
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name: Initialise
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permissions:
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contents: write
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Initialise
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run: |
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for file in $(git grep -l '${PROJECT_NAME}'); do sed -i 's/${PROJECT_NAME}/${{ github.event.repository.name }}/g' "${file}"; done
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for file in $(git grep -l 'seqan/app-template'); do sed -i 's@seqan/app-template@${{ github.repository }}@g' "${file}"; done
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for file in $(git grep -l 'app-template'); do sed -i 's/app-template/${{ github.event.repository.name }}/g' "${file}"; done
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sed -i 's/# SeqAn App Template/# ${{ github.event.repository.name }}/' README.md
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sed -i 's/App-Template%20CI/${{ github.event.repository.name }}%20CI/g' README.md
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sed -i '/<!-- InitDelete -->/,/<!-- DeleteInit -->/d' README.md
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git checkout test/data/datasources.cmake
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git checkout .github/workflows/*
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rm .github/workflows/initialise.yml
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rm .github/workflows/ci_cpm.yml
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- name: Commit changes
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uses: EndBug/add-and-commit@v9
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with:
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message: 'Initialise repository'

‎.github/workflows/lint.yml‎

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name: Lint
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runs-on: ubuntu-22.04
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timeout-minutes: 30
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permissions:
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contents: write
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steps:
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- name: Checkout
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uses: actions/checkout@v4

‎README.md‎

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`https://img.shields.io/github/workflow/status/` - we do not use GitHub's badges as they are not customisable.
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`/seqan/app-template/` - owner/repository
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`CI%20on%20Linux` - name of the workflow as encoded URL (e.g., whitespace = %20)
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`master` - branch to show
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`main` - branch to show
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`?style=flat&logo=github` - use a GitHub-style badge
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`&label=App-Template%20CI` - text on the badge
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`"Open GitHub actions page"` - this text will be shown on hover
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-->
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[1]: https://img.shields.io/github/actions/workflow/status/seqan/app-template/ci_linux.yml?branch=main&style=flat&logo=github&label=App-Template%20CI "Open GitHub actions page"
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<!--
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This is the CI badge link:
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`https://github.com/seqan/app-template/actions` - actions page of owner(seqan)/repository(app-template)
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`?query=branch%3Amaster` - only show actions that ran on the mater branch
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`https://github.com/seqan/app-template/actions` - actions page of owner/repository
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`?query=branch%3Amain` - only show actions that ran on the mater branch
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-->
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[2]: https://github.com/seqan/app-template/actions?query=branch%3Amain
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<!--
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Copy the image part of the markdown badge here.
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`"Open Codecov page"` - this text will be shown on hover
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-->
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[3]: https://codecov.io/gh/seqan/app-template/branch/master/graph/badge.svg?token=V82JRCXF0K "Open Codecov page"
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[3]: https://codecov.io/gh/seqan/app-template/branch/main/graph/badge.svg "Open Codecov page"
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<!--
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This is the Codecov badge link:
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Codecov offers badges: https://app.codecov.io/gh/seqan/app-template/settings/badge
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If you want to build an app, do the following:
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0. You need to be signed in with a **GitHub account**.
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1. <details><summary>Press the <code>Use this template</code>-Button to create your <b>own repository</b>.</summary><br>
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1. Press the `Use this template`-Button to create your own repository. See [GitHub's documentation](https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/creating-a-repository-from-a-template) for more information.
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2. **Wait** for GitHub actions to create a commit in your new repository. The commit message will be `Initialise repository` and it will placeholders in the code. Afterwards, the README in your repository will be customised to your repository, among other things.
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<!-- InitDelete -->
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---
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### :warning: Important :warning:
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Screenshot TODO
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</details>
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2. **Clone** your repository locally: `git clone git@github.com:max/my-repo-name.git`
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Note: The subsequent steps are not necessary but a recommendation and quick setup.
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3. <details><summary>Adapt the project name in <code>my-repo-name/CMakeLists.txt</code>, e.g., from <code>app-template</code> to <code>MyDragonApp</code></summary><br>
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The project name is defined in these lines:
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```cmake
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project (app-template
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LANGUAGES CXX
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VERSION 1.0.0
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DESCRIPTION "My application description"
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)
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```
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From here on out, follow the instructions in your repository.
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The instructions below are for the template repository and will not work for your repository.
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Change it e.g. to this:
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```cmake
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project (MyDragonApp
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LANGUAGES CXX
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VERSION 1.0.0
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DESCRIPTION "Let dragons fly"
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)
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```
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</details>
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4. <details><summary>Build and test the app (example) </summary><br>
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Next to your local repository clone (e.g. `my-repo-name`), you can do the following to build and test your app:
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---
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<!-- DeleteInit -->
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3. **Clone** your repository locally: `git clone git@github.com:seqan/app-template.git`
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4. <details><summary>Build and test the app (example) </summary>
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In your local repository clone, you can do the following to build and test your app:
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```bash
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mkdir build # create build directory
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cd build # step into build directory
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cmake ../my-repo-name # call cmake on the repository
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make # build the app MyDragonApp
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make check # build and run tests *1
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./bin/MyDragonApp # Execute the app (prints a short help page)
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mkdir build # create build directory
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cd build # step into build directory
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cmake .. # call cmake on the repository
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make # build the app app-template
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make check # build and run tests
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./bin/app-template # Execute the app (prints a short help page)
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```
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</details>
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<!-- 8. optional: publish your tool to the galaxy toolshed, follow the example in https://github.com/SGSSGene/raptor-galaxy -->
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## Instructions for SeqAn3 Tutorial Purposes:
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## Setting up Codecov (optional)
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If you just want some hands-on experience with SeqAn Libraries or a quick setup for our tutorials, do the following:
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1. Go to https://codecov.io/gh/seqan/app-template.
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2. Sign in with your GitHub account.
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3. Go to https://app.codecov.io/gh/seqan/app-template/config/general.
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4. Copy the `Repository Upload Token`.
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5. Go to https://github.com/seqan/app-template/settings/secrets/actions.
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6. Add a `New repository secret` with the name `CODECOV_TOKEN` and the value of the `Repository Upload Token`.
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7. Done! The next push to your repository will create a Codecov report.
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1. Clone this repository: `git clone https://github.com/seqan/app-template.git`
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2. Create a build directory and visit it: `mkdir build && cd build`
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3. Run CMake: `cmake ../app-template`
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4. Build the application: `make`
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5. Try executing the app: `./bin/app-template`
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## Instructions for SeqAn3 Tutorial Purposes:
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You can now start your hands-on experience by looking at or editing the file `src/main.cpp`.
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If you just some quick hands-on experience with SeqAn Libraries, you can also just clone this repository and start editing the `src/main.cpp` file.
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### Adding a new cpp file
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If you want to add a new cpp file (e.g., tutorial1.cpp) that is compiled and linked with the current infrastructure, do the following:
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If you want to add a new cpp file (e.g., `tutorial1.cpp`) that is compiled and linked with the current infrastructure, do the following:
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1. Create a new file `tutorial1.cpp` in the `src/` directory.
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<details><summary>The file content could look like this:</summary><br>
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<details><summary>The file content could look like this:</summary
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```cpp
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#include <seqan3/core/debug_stream.hpp>

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