diff --git a/docs/contributing/index.rst b/docs/contributing/index.rst index f47e935b..82897c1c 100644 --- a/docs/contributing/index.rst +++ b/docs/contributing/index.rst @@ -47,6 +47,18 @@ SPRAS contributions: or `10 minutes to pandas `__ + + + 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 + ************************************************* Step 0: Fork the repository and create a branch ************************************************* @@ -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 @@ -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 + ``.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 @@ -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. + + *********************************************************************** General steps for contributing a new pathway reconstruction algorithm ***********************************************************************