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docs: add extensive externally hosted docs (#177)
Signed-off-by: Alex Kanitz <alexander.kanitz@alumni.ethz.ch> Co-authored-by: BIOPZ-Katsantoni Maria <maria.katsantoni@unibas.ch> Co-authored-by: Alex Kanitz <alexander.kanitz@alumni.ethz.ch>
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CITATION.cff

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cff-version: 1.2.0
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message: "If you use this software, please cite it as below."
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title: "ZARP: An automated workflow for processing of RNA-seq data"
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version: 0.3.0
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doi: 10.1101/2021.11.18.469017
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date-released: 2021-11-18
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title: "ZARP: A user-friendly and versatile RNA-seq analysis workflow"
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version: 1.0.0
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doi: 10.12688/f1000research.149237.1
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date-released: 2024-05-24
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url: "https://github.com/zavolanlab/zarp"
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preferred-citation:
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type: article
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- family-names: "Ataman"
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given-names: "Meric"
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orcid: "https://orcid.org/0000-0002-7942-9226"
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- family-names: "Balajti"
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given-names: "Máté"
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orcid: "https://orcid.org/0009-0000-3932-3964"
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- family-names: "Pozzan"
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given-names: "Noè"
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- family-names: "Schlusser"
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given-names: "Niels"
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- family-names: "Moon"
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given-names: "Youngbin"
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orcid: "https://orcid.org/0009-0001-5728-3959"
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- family-names: "Mironov"
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given-names: "Aleksei"
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- family-names: "Boersch"
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given-names: "Anastasiya"
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orcid: "https://orcid.org/0000-0003-3392-5272"
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- family-names: "Kanitz"
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given-names: "Alexander"
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orcid: "https://orcid.org/0000-0002-3468-0652"
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doi: "10.1101/2021.11.18.469017"
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journal: "bioRxiv"
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month: 11
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title: "ZARP: An automated workflow for processing of RNA-seq data"
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year: 2021
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doi: "10.12688/f1000research.149237.1"
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journal: "F1000Research"
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month: 05
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title: "ZARP: A user-friendly and versatile RNA-seq analysis workflow"
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year: 2024

CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the [code owners][contact]. All complaints will be
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reviewed and investigated and will result in a response that is deemed necessary
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and appropriate to the circumstances. The project team is obligated to maintain
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confidentiality with regard to the reporter of an incident. Further details of
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specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at <https://www.contributor-covenant.org/version/1/4/code-of-conduct.html>
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[contact]: <zavolab-biozentrum@unibas.ch>
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[homepage]: <https://www.contributor-covenant.org>

CONTRIBUTING.md

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# Guidelines for contributing
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## General workflow
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We are using [Git][git], [GitHub][github] and [Git Flow][git-flow].
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> **Note:** If you are a **beginner** and do not have a lot of experience with
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> this sort of workflow, please do not feel overwhelmed. We will guide you
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> through the process until you feel comfortable using it. And do not worry
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> about mistakes either - everybody does them. Often! Our project layout makes
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> it very very hard for anyone to cause irreversible harm, so relax, try things
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> out, take your time and enjoy the work! :)
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We would kindly ask you to abide by our [Code of Conduct][coc] in all
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interactions with the community when contributing to this project, regardless
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of the type of contribution. We will not accept any offensive or demeaning
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behavior towards others and will take any necessary steps to ensure that
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everyone is treated with respect and dignity.
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## Issue tracker
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Please use each project's GitHub [issue tracker][issue-tracker] to:
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- find issues to work on
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- report bugs
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- propose features
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- discuss future directions
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## Submitting issues
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Please choose a template when submitting an issue: choose the [**bug report**
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template][bug-report] only when reporting bugs; for all other issues,
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choose the [**feature request** template][bug-report]. Please follow the
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instructions in the templates.
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You do not need to worry about adding labels or milestones for an issue, the
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project maintainers will do that for you. However, it is important that all
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issues are written concisely, yet with enough detail and with proper
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references (links, screenshots, etc.) to allow other contributors to start
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working on them. For bug reports, it is essential that they include all
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information required to reproduce the bug.
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Please **do not** use the issue tracker to ask usage questions, installation
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problems etc., unless they appear to be bugs. For these issues, please use
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the [communication channels](#communication) outlined below.
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## Communication
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Send us an [email][contact] if you want to reach out to us
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work on)
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## Code style and testing
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To make it easier for everyone to maintain, read and contribute to the code,
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as well as to ensure that the code base is robust and of high quality, we
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would kindly ask you to stick to the following guidelines for code style and
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testing.
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- Please use a recent version of [Python 3][py] (3.7.4+)
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- Please try to conform to the used code, docstring and commenting style within
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a project to maintain consistency
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- Please use [type hints][py-typing] for all function/method signatures
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(exception: tests)
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- Please use the following linters (see configuration files in repository root
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directory, e.g., `setup.cfg`, for settings):
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- [`flake8`][py-flake8]
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- [`pylint`][py-pylint] (use available [configuration][py-pylint-conf])
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- [`mypy`][py-mypy] OR [`pyright`][py-pyright] to help with type hints
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- Please use the following test suites:
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- [`pytest`][py-pytest]
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- [`coverage`][py-coverage]
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## Commit messages
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In an effort to increase consistency, simplify maintenance and enable automated
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change logs, we would like to kindly ask you to write _semantic commit
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messages_, as described in the [Conventional Commits
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specification][conv-commits].
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The general structure of _Conventional Commits_ is as follows:
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```console
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<type>[optional scope]: <description>
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[optional body]
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[optional footer]
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```
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Depending on the changes, please use one of the following **type** prefixes:
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| Type | Description |
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| --- | --- |
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| build | The build type (formerly known as chore) is used to identify development changes related to the build system (involving scripts, configurations or tools) and package dependencies. |
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| ci | The ci type is used to identify development changes related to the continuous integration and deployment system - involving scripts, configurations or tools. |
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| docs | The docs type is used to identify documentation changes related to the project - whether intended externally for the end users (in case of a library) or internally for the developers. |
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| feat | The feat type is used to identify production changes related to new backward-compatible abilities or functionality. |
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| fix | The fix type is used to identify production changes related to backward-compatible bug fixes. |
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| perf | The perf type is used to identify production changes related to backward-compatible performance improvements. |
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| refactor | The refactor type is used to identify development changes related to modifying the codebase, which neither adds a feature nor fixes a bug - such as removing redundant code, simplifying the code, renaming variables, etc. |
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| revert | For commits that revert one or more previous commits. |
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| style | The style type is used to identify development changes related to styling the codebase, regardless of the meaning - such as indentations, semi-colons, quotes, trailing commas and so on. |
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| test | The test type is used to identify development changes related to tests - such as refactoring existing tests or adding new tests. |
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In order to ensure that the format of your commit messages adheres to the
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Conventional Commits specification and the defined type vocabulary, you can
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use the [dedicated linter][conv-commits-lint]. More information about
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_Conventional Commits_ can also be found in this [blog
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post][conv-commits-blog].
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## Merging your code
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Here is a check list that you can follow to make sure that code merges
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happen smoothly:
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1. [Open an issue](#submitting-issues) _first_ to give other contributors a
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chance to discuss the proposed changes (alternatively: assign yourself
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to one of the existing issues)
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2. Clone the repository, create a feature branch off of the default branch
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(never commit changes to protected branches directly) and implement your
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code changes
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3. If applicable, update relevant sections of the [documentation][docs]
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4. Add or update tests; untested code will not be merged; refer to the
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[guidelines](#code-style-and-testing) above for details
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5. Ensure that your coding style is in line with the
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[guidelines](#code-style-and-testing) described above
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6. Ensure that all tests and linter checks configured in the [Travis
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CI][travis-docs] [continuous integration][ci-cd] (CI) pipeline pass without
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issues
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7. If necessary, clean up excessive commits with `git rebase`; cherry-pick and
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merge commits as you see fit; use concise and descriptive commit messages
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8. Push your clean, tested and documented feature branch to the remote; make
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sure the [Travis CI][travis-docs] [CI][ci-cd] pipeline passes
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9. Issue a pull request against the default branch; follow the instructions in
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the [template][pull-request]; importantly, describe your changes in
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detail, yet with concise language, and do not forget to indicate which
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issue(s) the code changes resolve or refer to; assign a project maintainer
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to review your changes
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## Becoming a co-maintainer
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If you are as interested in the project as we are and have contributed some
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code, suggested some features or bug reports and have taken part in
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discussions on where to go with the project, we will very likely to have you
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on board as a co-maintainer. If you are intersted in that, please let us
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know. You can reach us by [email][contact].
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[bug-report]: .github/ISSUE_TEMPLATE/bug_report.mdrequest.md
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[ci-cd]: <https://en.wikipedia.org/wiki/Continuous_integration>
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[coc]: CODE_OF_CONDUCT.md
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[contact]: <zavolab-biozentrum@unibas.ch>
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[conv-commits]: <https://www.conventionalcommits.org/en/v1.0.0-beta.2/#specification>
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[conv-commits-blog]: <https://nitayneeman.com/posts/understanding-semantic-commit-messages-using-git-and-angular/>
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[conv-commits-lint]: <https://github.com/conventional-changelog/commitlint>
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[docs]: README.md
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[git]: <https://git-scm.com/>
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[git-flow]: <https://nvie.com/posts/a-successful-git-branching-model/>
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[github]: <https://github.com>
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[issue-tracker]: <https://github.com/zavolanlab/zarp/issues>
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[pull-request]: PULL_REQUEST_TEMPLATE.md
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[py]: <https://www.python.org/>
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[py-flake8]: <https://gitlab.com/pycqa/flake8>
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[py-mypy]: <http://mypy-lang.org/>
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[py-pylint]: <https://www.pylint.org/>
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[py-pylint-conf]: pylint.cfg
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[py-pyright]: <https://github.com/microsoft/pyright>
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[py-pytest]: <https://docs.pytest.org/en/latest/>
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[py-coverage]: <https://pypi.org/project/coverage/>
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[py-typing]: <https://docs.python.org/3/library/typing.html>
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[travis-docs]: <https://docs.travis-ci.com/>

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