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Update CONTRIBUTING.md to include dev packages
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jhiemstrawisc committed Oct 10, 2023
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Expand Up @@ -169,8 +169,7 @@ After completing this step, try running the Local Neighborhood algorithm through
```bash
snakemake --cores 1 --configfile config/config.yaml
```
Make sure to run the command inside the `spras` conda environment. If installing via `pip` instead of using conda, install with the `-e` flag (the full command to run from the repo root is
`python -m pip install -e .`) so that Python picks up any changes you make. Omitting the `-e` flag will prevent your changes from being reflected unless you force re-install.
Make sure to run the command inside the `spras` conda environment. If installing via `pip` instead of using conda, install with the `-e .[dev]` options (the full command to run from the repo root is `python -m pip install -e .[dev] .`) so that Python picks up any changes you make and installs all optional development packages. Omitting the `-e` flag will prevent your changes from being reflected unless you force re-install, and omitting `.[dev]` will prevent pip from installing `pre-commit` and `pytest`.

As a workflow manager, Snakemake will consider the work described in the configuration file to be completed once the necessary output files have been written to the relevant output directory (`output` in the `config/config.yaml` configuration).
That means that if you change your code and rerun the Snakemake command above, nothing may happen if the output files already exist.
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