diff --git a/docs/contributing/index.rst b/docs/contributing/index.rst index f47e935b0..2b1e6650c 100644 --- a/docs/contributing/index.rst +++ b/docs/contributing/index.rst @@ -47,6 +47,20 @@ 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 + python -c "import spras; print('SPRAS import successful')" + +If the commands above run without errors, your environment is ready. + ************************************************* Step 0: Fork the repository and create a branch ************************************************* @@ -202,8 +216,9 @@ 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 @@ -331,6 +346,13 @@ its contents before rerunning the Snakemake command. Step 5: Add Local Neighborhood to the tests ********************************************* +.. note:: + + These tests modify files in ``.github/workflows/``. If you push over + HTTPS using a Personal Access Token, make sure the token has + permission to modify GitHub Actions workflows. Otherwise, GitHub may + reject the push. SSH push works without this restriction. + Add test functions to the test file ``test/test_ln.py``. This file already has existing tests to test the correctness of the Local Neighborhood implementation that was added to the Docker image. The new