ENH: Test calling the scripts

pyproject.toml

@@ -38,6 +38,7 @@ doc = [
 test = [
     "coverage",
     "pytest",
+    "pytest-console-scripts",
 ]
 
 [project.urls]

tract_querier/tests/datasets.py

@@ -2,33 +2,29 @@
 import os
 from os import path
 import tempfile
-from six.moves import urllib
-
-import unittest
+import urllib.request
 
 
 FILES = {
     'tract_file': (
-        'http://midas.kitware.com/bitstream/view/17631',
+        'https://osf.io/download/aq3cu/',
         'IIT3mean_left_hemisphere_small.trk',
-        '\xe7\xec\xfd+\xd2n\xff\x96\xae\xb4\xdf+\x194\xdf\x81'
+        b'\xe7\xec\xfd+\xd2n\xff\x96\xae\xb4\xdf+\x194\xdf\x81'
     ),
     'atlas_file': (
-        'http://midas.kitware.com/bitstream/view/17622',
+        'https://osf.io/download/rk7a5/',
         'IIT3mean_desikan_2009.nii.gz',
-        'vx\x13\xbaE\x1dR\t\xcd\xc9EF\x17\xa66\xb7'
+        b'vx\x13\xbaE\x1dR\t\xcd\xc9EF\x17\xa66\xb7'
     ),
     'query_uf_file': (
-        'http://midas.kitware.com/bitstream/view/17627',
+        'https://osf.io/download/3zj5h/',
         'wmql_2_uf.qry',
-        '\\+R\x8c<B#\xea\xfc\x9aE\xbd\xb0(\xbdn'
+        b'\\+R\x8c<B#\xea\xfc\x9aE\xbd\xb0(\xbdn'
     )
 }
 
 
-class TestDataSet(unittest.TestCase):
-
-    @unittest.skip("temporarily disabled")
+class TestDataSet:
     def __init__(self):
         self.dirname = path.join(
             tempfile.gettempdir(),
@@ -40,25 +36,29 @@ def __init__(self):
         if not path.exists(self.dirname):
             os.mkdir(self.dirname)
 
-        for k, v in FILES.items():
-            dst_filename = path.join(self.dirname, v[1])
-
+        for k, (url, filename, md5) in FILES.items():
+            dst_filename = path.join(self.dirname, filename)
             if (
                 not path.exists(dst_filename) or
-                hashlib.md5(open(dst_filename).read()).digest() != v[2]
+                hashlib.md5(open(dst_filename, "rb").read()).digest() != md5
             ):
-                dl_file = urllib.request.urlopen(v[0])
-                dst_file = open(dst_filename, 'wb')
-                dst_file.write(dl_file.read())
-                dst_file.close()
-
+                request = urllib.request.Request(url)
+                try:
+                    response = urllib.request.urlopen(request)
+                except urllib.error.HTTPError as e:
+                    if e.status not in (307, 308):
+                        raise
+                    redirected_url = urllib.parse.urljoin(url, e.headers['Location'])
+                    response = urllib.request.urlopen(redirected_url)
+                with open(dst_filename, 'wb') as out_file:
+                    while True:
+                        chunk = response.read(8192)  # Read 8 KB at a time
+                        if not chunk:
+                            break
+                        out_file.write(chunk)
             if (
-                hashlib.md5(open(dst_filename).read()).digest() != v[2]
+                hashlib.md5(open(dst_filename, "rb").read()).digest() != md5
             ):
-                raise IOError('File %s url %s was not properly downloaded' % (v[1], v[0]))
+                raise IOError('File %s url %s was not properly downloaded' % (filename, url))
 
             self.files[k] = dst_filename
-
-
-
-

tract_querier/tests/test_tract_math.py

@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import re
+
+from tract_querier.tests import datasets
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run(["tract_math", "--help"])
+    assert ret.success
+
+
+def test_tract_math_count(script_runner):
+    test_data = datasets.TestDataSet()
+    tract_file = test_data.files["tract_file"]
+    ret = script_runner.run(["tract_math", tract_file, "count"])
+    assert re.search('[^0-9]6783[^0-9]', ret.stdout) is not None
+    assert ret.success

tract_querier/tests/test_tract_querier.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+from os import path
+
+from tract_querier.tests import datasets
+
+
+def test_help_option(script_runner):
+    ret = script_runner.run(["tract_querier", "--help"])
+    assert ret.success
+
+
+def test_tract_querier_query(script_runner):
+    test_data = datasets.TestDataSet()
+    atlas_file = test_data.files["atlas_file"]
+    query_uf_file = test_data.files["query_uf_file"]
+    tract_file = test_data.files["tract_file"]
+    output_prefix = test_data.dirname + "/test"
+
+    ret = script_runner.run(["tract_querier", "-a", atlas_file,"-t", tract_file, "-q", query_uf_file, "-o", output_prefix])
+    tract_fname_end = "_uncinate.left.trk"
+    assert "uncinate.left: 000102" in ret.stdout
+    assert "uncinate.right: 000000" in ret.stdout
+    assert path.exists(output_prefix + tract_fname_end)
+    assert ret.success
+    if path.exists(output_prefix + tract_fname_end):
+        os.remove(output_prefix + tract_fname_end)

tract_querier/tract_math/decorator.py

@@ -100,7 +100,7 @@ def wrapper(*input_args):
             args, options_dict = find_optional_args(input_args)
 
             total_args = len(args)
-            argspec = inspect.getargspec(func)
+            argspec = inspect.getfullargspec(func)
             # Subtract 1 for implicit options_dict
             func_total_args = len(argspec.args) - 1
 
@@ -196,7 +196,7 @@ def process_output(output, file_output=None):
             header = dict(zip(writer.fieldnames, writer.fieldnames))
             writer.writerow(header)
 
-        first_value = output.values()[0]
+        first_value = next(iter(output.values()))
         if (
             not isinstance(first_value, str) and
             isinstance(first_value, Iterable)