add tools test

README.md

@@ -55,16 +55,10 @@ mamba create -n pyclient \
 conda activate pyclient
 ```
 
-- Install all non-conda dependencies via pip
-
-```bash
-pip install -r pip-requirements.txt
-```
-
 - Install `pyclient` (in developer mode)
 
 ```bash
-python setup.py develop
+ pip install --editable .
 ```
 
 - Validate the install via the help message
@@ -79,6 +73,12 @@ client-tools -h
 snakemake --snakefile src/snakemake/hello_world.smk -j 1
 ```
 
+- Run the precommit script (unit tests, linting, code-style, type checking)
+
+```bash
+bash scripts/precommit.sh
+```
+
 [fulcrum-genomics-link]: https://www.fulcrumgenomics.com
 [conda-link]: https://docs.conda.io/projects/conda/en/latest/user-guide/install/
 

src/python/pyclient/tools/tests/__init__.py

@@ -0,0 +1,18 @@
+"""Testing utilities for :module:`~pyclient.tools`"""
+
+import pytest
+
+
+def _to_name(tool) -> str:  # type: ignore
+    """Gives the tool name for a function by taking the function name and replacing
+    underscores with hyphens."""
+    return tool.__name__.replace("_", "-")
+
+
+def test_tool_funcs(tool, main) -> None:  # type: ignore
+    name = _to_name(tool)
+    argv = [name, "-h"]
+    with pytest.raises(SystemExit) as e:
+        main(argv=argv)
+    assert e.type == SystemExit
+    assert e.value.code == 0  # code should be 0 for help

src/python/pyclient/tools/tests/test_main.py

@@ -0,0 +1,31 @@
+"""Tests for :module:`~pyclient.tools.__main__
+Motivation
+~~~~~~~~~~
+The idea is to run help on the main tools method (`-h`) as well as on
+each tool (ex. `tool-name -h`).  This should force :module:`~defopt`
+to parse the docstring for the method.  Since :module:`~defopt` uses
+:module:`~argparse` underneath, `SystemExit`s are raised, which are
+different than regular `Exceptions`.  The exit code returned by help
+(the usage) is 0.  An improperly formatted docstring throws a
+:class:`NotImplementedException`.  We add a few tests below to show
+this.
+"""
+
+import pytest
+from pyclient.tools.__main__ import TOOLS
+from pyclient.tools.__main__ import main
+from pyclient.tools.tests import test_tool_funcs as _test_tool_funcs
+
+
+def test_tools_help() -> None:
+    """Tests that running pyclient-tools with -h exits OK"""
+    argv = ["-h"]
+    with pytest.raises(SystemExit) as e:
+        main(argv=argv)
+    assert e.type == SystemExit
+    assert e.value.code == 0  # code should be 0 for help
+
+
+@pytest.mark.parametrize("tool", TOOLS)
+def test_tool_funcs(tool) -> None:  # type: ignore
+    _test_tool_funcs(tool, main)