[ENH] Adds CLI for abagen.get_expression_data functionality

abagen/tests/conftest.py

@@ -1,5 +1,5 @@
 import pytest
-from abagen.datasets import fetch_microarray
+from abagen.datasets import fetch_desikan_killiany, fetch_microarray
 
 
 @pytest.fixture(scope='session')
@@ -14,3 +14,8 @@ def testfiles(testdir):
                              donors=['12876', '15496'],
                              convert=True)
     return files
+
+
+@pytest.fixture(scope='session')
+def atlas():
+    return fetch_desikan_killiany()

abagen/tests/test_cli.py

@@ -0,0 +1,110 @@
+# -*- coding: utf-8 -*-
+"""
+Tests for abagen.cli module
+"""
+
+import os
+from pkg_resources import resource_filename
+import pytest
+
+from abagen import __version__ as version
+from abagen.cli import run
+
+
+def test_run_get_parser(capsys, atlas, testdir):
+    parser = run.get_parser()
+
+    # since we have a positional argument this fails, hard
+    with pytest.raises(SystemExit):
+        parser.parse_args([])
+    assert "following arguments are required: atlas" in capsys.readouterr().err
+
+    # providing the positional succeeds!
+    args = parser.parse_args([atlas['image']])
+    assert args.atlas == atlas['image']
+
+    # some data directories/files need to exist!
+    with pytest.raises(SystemExit):
+        parser.parse_args(['notanatlas.nii.gz'])
+    assert "does not exist" in capsys.readouterr().err
+    with pytest.raises(SystemExit):
+        parser.parse_args(['--data-dir', 'notadir', atlas['image']])
+    assert "does not exist" in capsys.readouterr().err
+    with pytest.raises(SystemExit):
+        parser.parse_args(['--atlas-info', 'notafile', atlas['image']])
+    assert "does not exist" in capsys.readouterr().err
+
+    # does version print correctly?
+    with pytest.raises(SystemExit):
+        parser.parse_args(['--version'])
+    assert 'abagen {}'.format(version) == capsys.readouterr().out.strip()
+
+    # arguments with invalid choices (probe_selection) raise errors
+    with pytest.raises(SystemExit):
+        parser.parse_args(['--probe-selection', 'notamethod', atlas['image']])
+    assert "invalid choice: 'notamethod'" in capsys.readouterr().err
+
+    # just test every option
+    args = parser.parse_args([
+        '-v', '-v', '-v',
+        '--quiet',
+        '--debug',
+        '--atlas-info', atlas['info'],
+        '--donors', '12876', '15496',
+        '--data-dir', testdir,
+        '--inexact',
+        '--tol', '5',
+        '--ibf-threshold', '0.6',
+        '--metric', 'median',
+        '--probe-selection', 'average',
+        '--no-reannotated', '--no-corrected-mni',
+        '--output-file', 'test.csv',
+        '--save-counts', '--save-donors',
+        atlas['image']
+    ])
+
+
+def test_run_main(capsys, atlas, testdir):
+    outputfile = os.path.join(str(testdir), 'abagen_expression.csv')
+
+    # check basic usage
+    run.main([
+        '--data-dir', testdir,
+        '--donors', '12876', '15496',
+        '--output-file', outputfile,
+        atlas['image']
+    ])
+    assert os.path.exists(outputfile)
+
+    # check that save donors/counts outputs desired files
+    run.main([
+        '--data-dir', testdir,
+        '--donors', '12876', '15496',
+        '--output-file', outputfile,
+        '--save-donors', '--save-counts',
+        atlas['image']
+    ])
+    for rep in ['_counts.csv', '_12876.csv', '_15496.csv']:
+        assert os.path.exists(outputfile.replace('.csv', rep))
+
+    # check stdout (BLARGH)
+    run.main([
+        '--data-dir', testdir,
+        '--donors', '12876', '15496',
+        '--output-file', outputfile,
+        '--stdout',
+        atlas['image']
+    ])
+    stdout = capsys.readouterr().out
+    with open(outputfile, 'r') as src:
+        assert stdout == src.read()
+
+
+def test_exec_run_fail():
+    executable = resource_filename('abagen', 'cli/run.py')
+
+    # need to set this otherwise it won't fail
+    __name__ = '__main__'  # noqa
+    with pytest.raises(RuntimeError):
+        with open(executable, 'r') as src:
+            exec(src.read())

docs/cli.rst

@@ -0,0 +1,18 @@
+.. _cli:
+
+------------------
+Command-line usage
+------------------
+
+You can use many of the primary workflows in ``abagen`` from the command line.
+
+.. _cli_abagen:
+
+The ``abagen`` command
+======================
+
+.. argparse::
+   :ref: abagen.cli.run.get_parser
+   :prog: abagen
+   :nodefault:
+   :nodefaultconst:

docs/conf.py

@@ -40,6 +40,7 @@
     'sphinx.ext.mathjax',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
+    'sphinxarg.ext',
 ]
 
 # Generate the API documentation when building

docs/index.rst

@@ -8,5 +8,6 @@ Contents
 
    installation
    changes
+   cli
    usage
    api

docs/requirements.txt

@@ -1,3 +1,4 @@
 -r ../requirements.txt
-sphinx>=1.2
+sphinx>=1.6
+sphinx-argparse
 sphinx_rtd_theme

setup.cfg

@@ -35,7 +35,8 @@ include_package_data = True
 
 [options.extras_require]
 doc =
-    sphinx >=1.2
+    sphinx >=1.6
+    sphinx-argparse
     sphinx_rtd_theme
 io =
     fastparquet
@@ -54,6 +55,10 @@ nibabel =
     tests/data/*
     abagen/data/*
 
+[options.entry_points]
+console_scripts =
+    abagen=abagen.cli.run:main
+
 [coverage:run]
 omit =
     abagen/_version.py