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Improve contributing tutorial documentation #486

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29 changes: 27 additions & 2 deletions docs/contributing/index.rst
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Expand Up @@ -47,6 +47,18 @@ SPRAS contributions:
or `10 minutes to pandas
<https://pandas.pydata.org/pandas-docs/stable/user_guide/10min.html>`__



Before getting started, verify your environment is ready with these checks:

.. code:: bash

docker --version
docker run hello-world
docker login
conda --version
git --version

@ntalluri ntalluri Jun 15, 2026

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should we also add a check to make sure SPRAS conda env is ready?

@ntalluri ntalluri Jun 15, 2026

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python -c "import spras; print('SPRAS import successful')" is what is in the spras tutorial.

*************************************************
Step 0: Fork the repository and create a branch
*************************************************
Expand Down Expand Up @@ -202,8 +214,9 @@ and explore the nodes and interactome.
.. code:: python

> from spras.dataset import Dataset
> dataset_dict = {'label': 'data0', 'node_files': ['node-prizes.txt', 'sources.txt', 'targets.txt'], 'edge_files': ['network.txt'], 'other_files': [], 'data_dir': 'input'}
> data = Dataset(dataset_dict)
> from spras.config.dataset import DatasetSchema
> dataset_schema = DatasetSchema(label='data0', node_files=['node-prizes.txt', 'sources.txt', 'targets.txt'], edge_files=['network.txt'], other_files=[], data_dir='input')
> data = Dataset(dataset_schema)
> data.node_table.head()
NODEID prize active sources targets
0 C 5.7 True NaN True
Expand Down Expand Up @@ -416,6 +429,16 @@ branch and create a pull request. Make sure to commit all of the new and
modified files and push them to the ``local-neighborhood`` branch on
your fork.


.. note::

If you are using HTTPS to push and your commit touches files in

@ntalluri ntalluri Jun 15, 2026

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Can we just explicitly say for developers to use SSH to push to SPRAS in the contributing guide? And then add a warning that if you use https the issues you mentioned will happen.

``.github/workflows/``, your PAT must have both ``repo`` and
``workflow`` scopes. A PAT with ``repo`` scope only will be rejected
with a non-obvious error. SSH push works without this restriction.



The SPRAS maintainers will review the pull request and provide feedback
and suggested changes. If you are not already in communication with
them, you can open a `GitHub issue
Expand All @@ -425,6 +448,8 @@ feedback. However, once the pull request has been approved, it will
``main`` branch of the fork stays synchronized with the ``main`` branch
of the main SPRAS repository.


@ntalluri ntalluri Jun 15, 2026

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Can we remove these new white space lines?


***********************************************************************
General steps for contributing a new pathway reconstruction algorithm
***********************************************************************
Expand Down