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updates contributing
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# Contributing

Welcome to `orca` contributor's guide.
Welcome to `py-orca` contributor's guide.

This document focuses on getting any potential contributor familiarized with
the development processes, but [other kinds of contributions] are also appreciated.
Expand All @@ -16,7 +16,7 @@ behavior guidelines.

## Issue Reports

If you experience bugs or general issues with `orca`, please have a look
If you experience bugs or general issues with `py-orca`, please have a look
on the [issue tracker].
If you don't see anything useful there, please feel free to fire an issue report.

Expand All @@ -34,17 +34,17 @@ you help us to identify the root cause of the issue.

## Documentation Improvements

You can help improve `orca` docs by making them more readable and coherent, or
You can help improve py-`orca` docs by making them more readable and coherent, or
by adding missing information and correcting mistakes.

`orca` documentation uses [Sphinx] as its main documentation compiler.
`py-orca` documentation uses [Sphinx] as its main documentation compiler.
This means that the docs are kept in the same repository as the project code, and
that any documentation update is done in the same way was a code contribution.
The documentation is written using [CommonMark] with [MyST] extensions.

:::{tip}
Please notice that the [GitHub web interface] provides a quick way of
propose changes in `orca`'s files. While this mechanism can
propose changes in `py-orca`'s files. While this mechanism can
be tricky for normal code contributions, it works perfectly fine for
contributing to the docs, and can be quite handy.

Expand Down Expand Up @@ -87,7 +87,7 @@ Before you work on any non-trivial code contribution it's best to first create
a report in the [issue tracker] to start a discussion on the subject.
This often provides additional considerations and avoids unnecessary work.

### Clone the repository
### Development Environment Setup

1. Create an user account on GitHub if you do not already have one.

Expand All @@ -98,18 +98,20 @@ This often provides additional considerations and avoids unnecessary work.

```console
git clone [email protected]:Sage-Bionetworks-Workflows/py-orca.git
cd orca
cd py-orca
```

4. Create an isolated virtual environment containing package dependencies,
including those needed for development (*e.g.* testing, documentation) by running:

```console
./dev_setup.sh 3.10
source py-orca-venv-3.10/bin/activate
./dev_setup.sh <your_supported_python_version>
source py-orca-venv-<your_supported_python_version>/bin/activate
```

**Note:** `py-orca` also supports Python version 3.11.
**Note:**
Ensure that you have a supported Python version installed on your local machine before running `dev_setup.sh`. `py-orca` currently supports Python version 3.10 and 3.11. You can [install](https://github.com/pyenv/pyenv?tab=readme-ov-file#installation) `pyenv`for easy Python version management.


5. Install [pre-commit] hooks:

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