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Update testing.rst

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@ -22,11 +22,11 @@ The following is a simple guide to testing RAPIDS. All files necessary for testi
│ └── Snakefile <- The Snakefile for testing only. It contains the rules that you would be testing. │ └── Snakefile <- The Snakefile for testing only. It contains the rules that you would be testing.
│ │
To begin testing RAPIDS place the input data ``csv`` files in the ``tests/data/raw`` directory. The expected output of RAPIDS with the raw input data should be placed in the ``tests/data/processesd``. To begin testing RAPIDS place the input data ``csv`` files in ``tests/data/raw`` and ``data/raw``. The expected output files of RAPIDS after processing the input data should be placed in ``tests/data/processesd``.
Copy all files from ``tests/data/raw`` directory into the ``data/raw`` directory. The rule(s) that are to be tested must be placed in the ``tests/Snakemake`` file. The current ``tests/Snakemake`` is a good example of how to define the rules that are to be tested. The Snakemake rule(s) that are to be tested must be placed in the ``tests/Snakemake`` file. The current ``tests/Snakemake`` is a good example of how to define them.
Store your test scripts in the ``tests/scripts`` directory. Next, you can run all rules in the ``tests/Snakemake`` with: After storing your test scripts in ``tests/scripts``, you can run all rules in the ``tests/Snakemake`` with:
:: ::
@ -38,7 +38,7 @@ Or run a single rule with
snakemake --profile tests/settings -R sms_features snakemake --profile tests/settings -R sms_features
The above example runs the ``sms_features`` rule that is defined in the ``tests/Snakemake`` file. Replace this with the name of the rule you want to test. The ``--profile`` flag is used to run ``Snakemake`` with the ``Snakfile`` and ``confi.yaml`` file stored in ``tests/settings``. The above example runs the ``sms_features`` rule that is defined in the ``tests/Snakemake`` file. Replace this with the name of the rule you want to test. The ``--profile`` flag is used to run Snakemake with the ``Snakfile`` and ``testing_config.yaml`` file stored in ``tests/settings``.
Once RAPIDS has processed the sample data, the next step is to test the output. Testing is implemented using Python's Unittest. To run all the tests scripts stored in the ``tests/scripts`` directory use the following command: Once RAPIDS has processed the sample data, the next step is to test the output. Testing is implemented using Python's Unittest. To run all the tests scripts stored in the ``tests/scripts`` directory use the following command:
@ -46,7 +46,7 @@ Once RAPIDS has processed the sample data, the next step is to test the output.
python -m unittest discover tests/scripts/ -v python -m unittest discover tests/scripts/ -v
The ``discover`` flag finds and runs all of the test scripts within the ``tests/scripts`` directory that start with ``test_``. The name of all test methods in the these scripts should also start with ``test_``. The ``discover`` flag finds and runs all the test scripts within the ``tests/scripts`` directory that start with ``test_``. The name of all test methods in these scripts should also start with ``test_``.
The following is a snippet of the output you should see after running your test. The following is a snippet of the output you should see after running your test.