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Update README.md
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Included packages in quotation marks
Replaced deprecated contribution instructions with `CONTRIBUTING.md`

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uwcdc authored Oct 11, 2023
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Expand Up @@ -38,7 +38,7 @@ pip install --force-reinstall git+https://github.com/braingeneers/braingeneerspy
If you prefer to install a pre-built wheel due to resource limitations, you can find the latest release on [PyPI](https://pypi.org/project/braingeneers/).

```bash
pip install braingeneerspy.whl
pip download --only-binary :all: --no-deps --dest . --no-cache braingeneers==<version>
```

### Install with Optional Dependencies
Expand All @@ -48,34 +48,20 @@ You can install `braingeneerspy` with specific optional dependencies based on yo
- Install with IoT, analysis, and data access functions (skips machine learning and lab-specific dependencies):

```bash
pip install --force-reinstall git+https://github.com/braingeneers/braingeneerspy.git#egg=braingeneerspy[iot,analysis,data]
pip install --force-reinstall "git+https://github.com/braingeneers/braingeneerspy.git#egg=braingeneerspy[iot,analysis,data]"
```

- Install with all optional dependencies:

```bash
pip install --force-reinstall git+https://github.com/braingeneers/braingeneerspy.git#egg=braingeneerspy[all]
pip install --force-reinstall "git+https://github.com/braingeneers/braingeneerspy.git#egg=braingeneerspy[all]"
```

Please note that macOS users may need to wrap the GitHub URL in quotes if they encounter issues during installation, as shown in the examples above.

## Optional Dependency Groups

Dependencies in `braingeneerspy` are organized into optional groups of requirements. You can install all dependencies with `all`, or you can install a specific set of dependencies. Here are the optional dependency groups:

- *Unspecified*: Minimal packages for data access will be installed.
- `all`: All optional dependencies will be included.
- `iot`: IoT dependencies such as AWS and Redis packages will be installed.
- `analysis`: Dependencies for data analysis routines, plotting tools, math libraries, etc.
- `ml`: Machine learning dependencies such as `torch` will be installed.
- `hengenlab`: Hengenlab data loader-specific packages such as `neuraltoolkit` will be installed.

## Committing Changes to the Repo

If you plan to make changes to the `braingeneerspy` package and publish them on GitHub, please follow these steps:

1. Update the `version` variable in `setup.py`.
2. To receive the updated `braingeneerspy` package on your local machine, run one of the pip install commands mentioned earlier.
To make changes and publish them on GitHub, please refer to the [CONTRIBUTING.md](https://github.com/braingeneers/braingeneerspy/blob/development/.github/CONTRIBUTING.md) file for up-to-date guidelines.

## Modules and Subpackages

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