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update CONTRIBUTION.md [skip-ci]
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oschwengers committed Oct 18, 2024
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Please, have **Git** set up with consistent user information before commiting. Preferably, provide your real name and a working email address.

**Example**:

```bash
git config --global user.name "Your Name Comes Here"
git config --global user.email [email protected]
```

## Make sure that your branch contains clean commits

- Follow the common sense guidelines for writing good commit messages (see below).
- Make separate commits for separate changes. If you cannot describe what the commit does in one sentence, it is probably a mix of changes and should be separated into several commits.
- Do not merge `master` into your branch. Instead use `git rebase`. If you need to resolve merge conflicts or include the latest changes.

## Check your coding style

- Make sure your contributions and changes follow the coding and indentation style of the code surrounding your changes.
- Do not commit commented-out code or files that are no longer needed. Remove the code or the files unless there is a good reason to keep it.

## Guidelines for good commit messages

1. Separate subject from body with a blank line
2. Use the imperative mood in the subject line ("Fix", "Add", "Change" instead of "Fixed", "Added", "Changed")
3. Limit the subject line to 50 characters
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7. Use the body to explain what and why vs. how

Bad:
<pre>

```bash
some changes fixing this and that...
</pre>
```

Good:
<pre>

```bash
fix broken link in reports #123

As foo changed their internal data structure in the last release bar, we need to update our external links accordingly.
</pre>
```

## Helpful Sources

# Helpful Sources
- https://www.atlassian.com/git/tutorials

## Local testing of Bakta

For local tests and debugging of your contributions, you can create a dev Conda/Mamba environment pointing to local source code files:

1. Clone the repository: `git clone https://github.com/oschwengers/bakta.git`
2. Enter the repo: `cd bakta`
3. Set the conda environment with the dependencies: `mamba create -n bakta-dev -c conda-forge -c bioconda bakta`
4. Activate the environment: `mamba activate bakta-dev`
5. Install via pip pointing to the local source code: `python -m pip install -e .`

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