ENH: Test the CLI scripts

Test the CLI scripts:
- Adapt and transfer the contents of the `test_scripts.py` test script
  to a more modern and compact approach that uses the `pytest`
  `pytest-console-script` plugin and that does not require fiddling
  with the location of the files. This allows to test that the CLI
  scripts are installed appropriately/called using the names defined in
  the `pyproject.toml` `project.scripts` section.
- Split the tests into two different files following the scripts being
  tested: `tract_math` and `tract_querier`.
- Remove the `test_scripts.py` file.

Add the `pytest-console-script` dependency so that the scripts can be
called when executing `pytest`.

Convert the `output.values()` ordered dictionary values to a list prior
to slicing in `decorator.py`. Fixes:
```
"/src/tract_querier/scripts/cli_tract_math.py",
 line 109, in main\n    operations[args.operation]
(\n  File "/src/tract_querier/tract_querier/tract_math/decorator.py",
 line 148, in wrapper\n    process_output(func(*option_and_args))\n
  File "/src/tract_querier/tract_querier/tract_math/decorator.py",
 line 199, in process_output\n
    first_value = output.values()[0]\n
TypeError: \'odict_values\' object is not subscriptable\n')
```

raised locally when running the script tests.

pyproject.toml

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

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

@@ -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 = list(output.values())[0]
         if (
             not isinstance(first_value, str) and
             isinstance(first_value, Iterable)