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[ENH] Update instructions for CLI dev environment setup #145

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merged 4 commits into from
Dec 14, 2023
Merged

[ENH] Update instructions for CLI dev environment setup #145

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22bba6a
update instructions for dev environment setup
alyssadai Dec 8, 2023
d33908b
recommend installing pre-commit hooks
alyssadai Dec 14, 2023
58827d7
clarify dev env setup
alyssadai Dec 14, 2023
d51950b
grammar fix
alyssadai Dec 14, 2023
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44 changes: 39 additions & 5 deletions docs/cli.md
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Expand Up @@ -152,11 +152,45 @@ Neurobagel is under active, early development and future releases of the CLI may
_If you have already created `.jsonld` files for your Neurobagel graph database using the CLI_,
they can be quickly re-generated under the new data model by following the instructions [here](updating_dataset.md#following-a-change-in-the-neurobagel-data-model) so that they will not conflict with dataset `.jsonld` files generated using the latest CLI version.


## Development environment

To set up a development environment, please run
To ensure that our Docker images are built in a predictable way,
we use `requirements.txt` as a lock-file.
That is, `requirements.txt` includes the entire dependency tree of our tool,
with pinned versions for every dependency (for more information, see [https://pip.pypa.io/en/latest/topics/repeatable-installs/#repeatability](https://pip.pypa.io/en/latest/topics/repeatable-installs/#repeatability)).

### Setting up a local development environment
We suggest that you create a development environment
that is as close as possible to the environment we run in production.

To do so, we first need to install the dependencies from our lockfile (`dev_requirements.txt`):

```bash
git clone https://github.com/neurobagel/bagel-cli.git
cd bagel-cli
pip install -e '.[all]'
```
pip install -r dev_requirements.txt
```

And then we install the CLI without touching the dependencies

```bash
pip install --no-deps -e .
```

Finally, to run the test suite we need to install the `bids-examples` and `neurobagel_examples` submodules:
```bash
git submodule init
git submodule update
```
Confirm that everything works well by running a test:
`pytest .`
(no tests should fail).


#### Setting up code formatting and linting (recommended)

[pre-commit](https://pre-commit.com/) is configured in the development environment for this repository, and can be set up to automatically run a number of code linters and formatters on any commit you make according to the consistent code style set for this project.

Run the following from the repository root to install the configured pre-commit "hooks" for your local clone of the repo:
```bash
pre-commit install
```