Merge pull request #135 from oesteban/fix/test-template-names-early

FIX: Check template identifiers are valid early

MANIFEST.in

@@ -4,4 +4,4 @@ include smriprep/_version.py
 include smriprep/data/reports/*
 include smriprep/data/boilerplate.bib
 include smriprep/data/itkIdentityTransform.txt
-include VERSION
+include smriprep/VERSION

docs/conf.py

@@ -209,9 +209,8 @@
 
 apidoc_module_dir = '../smriprep'
 apidoc_output_dir = 'api'
-apidoc_excluded_paths = ['tests']
+apidoc_excluded_paths = ['conftest.py', '*/tests/*', 'tests/*', 'data/*', 'conf/*']
 apidoc_separate_modules = True
-# apidoc_extra_args = ['--templatedir=_templates/apidoc/', '--no-headings', '--module-first', '-d 1', '-T']
 apidoc_extra_args = ['--module-first', '-d 1', '-T']
 
 # -- Options for intersphinx extension ---------------------------------------

setup.cfg

@@ -51,9 +51,10 @@ doc =
     pydotplus
     sphinx >= 2.1.2
     sphinx-argparse
-    sphinx-versioning @ git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63
     sphinx_rtd_theme
     sphinxcontrib-apidoc ~= 0.3.0
+    sphinxcontrib-napoleon @ git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049785a1026451b3
+    sphinxcontrib-versioning @ git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63
 docs =
     %(doc)s
 duecredit = duecredit

smriprep/__init__.py

@@ -8,9 +8,14 @@
 
 
 """
-
-from .__about__ import (  # noqa
-    __version__,
+from .__about__ import (
     __copyright__,
     __credits__,
+    __version__,
 )
+
+__all__ = [
+    '__copyright__',
+    '__credits__',
+    '__version__',
+]

smriprep/cli/tests/test_utils.py

@@ -0,0 +1,44 @@
+"""Test the output-spaces parser."""
+from collections import OrderedDict
+import pytest
+from .. import utils as u
+
+
+TEST_TEMPLATES = (
+    'MNI152NLin2009cAsym',
+    'MNIInfant',
+    'MNI152NLin6Asym',
+)
+
+
+def test_output_spaces(monkeypatch):
+    """Check the --output-spaces argument parser."""
+    with monkeypatch.context() as m:
+        m.setattr(u, '_TF_TEMPLATES', TEST_TEMPLATES)
+        assert u.output_space('MNI152NLin2009cAsym') == ('MNI152NLin2009cAsym', {})
+        assert u.output_space('MNI152NLin2009cAsym:native') == \
+            ('MNI152NLin2009cAsym', {'native': True})
+        assert u.output_space('MNI152NLin2009cAsym:res-2') == \
+            ('MNI152NLin2009cAsym', {'res': '2'})
+        assert u.output_space('MNIInfant:res-2:cohort-1') == \
+            ('MNIInfant', {'res': '2', 'cohort': '1'})
+
+        with pytest.raises(ValueError):
+            u.output_space('UnkownTemplate')
+
+
+def test_template_parser(monkeypatch):
+    """Check the --output-spaces argument parser."""
+    with monkeypatch.context() as m:
+        m.setattr(u, '_TF_TEMPLATES', TEST_TEMPLATES)
+
+        assert list(u._template(['MNI152NLin2009cAsym']).keys()) == ['MNI152NLin2009cAsym']
+        assert u._template(['MNI152NLin2009cAsym', 'MNI152NLin2009cAsym:res-2']) == \
+            OrderedDict([('MNI152NLin2009cAsym', {})])
+
+        assert u._template(['MNI152NLin2009cAsym', 'MNI152NLin2009cAsym:res-2',
+                            'MNI152NLin6Asym:res-2', 'MNI152NLin6Asym']) == \
+            OrderedDict([('MNI152NLin2009cAsym', {}), ('MNI152NLin6Asym', {'res': '2'})])
+
+        with pytest.raises(ValueError):
+            u._template(['MNI152NLin6Asym:res-2', 'UnkownTemplate:res-2'])

smriprep/cli/utils.py

@@ -2,9 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """CLI Utilities."""
 from argparse import Action
-from templateflow.api import templates as get_templates
-
-TEMPLATES = get_templates()
+from ..conf import TF_TEMPLATES as _TF_TEMPLATES
 
 
 class ParseTemplates(Action):
@@ -15,20 +13,7 @@ def __call__(self, parser, namespace, values, option_string=None):
 
 
 def _template(inlist):
-    """
-    Return an OrderedDict with templates.
-
-    >>> list(_template(['MNI152NLin2009cAsym']).keys())
-    ['MNI152NLin2009cAsym']
-
-    >>> _template(['MNI152NLin2009cAsym', 'MNI152NLin2009cAsym:res-2'])
-    OrderedDict([('MNI152NLin2009cAsym', {})])
-
-    >>> _template(['MNI152NLin2009cAsym', 'MNI152NLin2009cAsym:res-2',
-    ...            'MNI152NLin6Asym:res-2', 'MNI152NLin6Asym'])
-    OrderedDict([('MNI152NLin2009cAsym', {}), ('MNI152NLin6Asym', {'res': '2'})])
-
-    """
+    """Return an OrderedDict with templates."""
     from collections import OrderedDict
     if isinstance(inlist, str):
         inlist = [inlist]
@@ -41,34 +26,15 @@ def _template(inlist):
 
 
 def output_space(value):
-    """
-    Parse one element of ``--output-spaces``.
-
-    >>> output_space('MNI152NLin2009cAsym')
-    ('MNI152NLin2009cAsym', {})
-
-    >>> output_space('MNI152NLin2009cAsym:native')
-    ('MNI152NLin2009cAsym', {'native': True})
-
-    >>> output_space('MNI152NLin2009cAsym:res-2')
-    ('MNI152NLin2009cAsym', {'res': '2'})
-
-    >>> output_space('MNIInfant:res-2:cohort-1') == ('MNIInfant', {'res': '2', 'cohort': '1'})
-    True
-
-    >>> output_space('UnkownTemplate')  # doctest: +IGNORE_EXCEPTION_DETAIL
-    Traceback (most recent call last):
-    ValueError:
-
-    """
+    """Parse one element of ``--output-spaces``."""
     tpl_args = value.split(':')
     template = tpl_args[0]
     spec = {}
     for modifier in tpl_args[1:]:
         mitems = modifier.split('-', 1)
         spec[mitems[0]] = len(mitems) == 1 or mitems[1]
 
-    if template not in TEMPLATES:
+    if template not in _TF_TEMPLATES:
         raise ValueError("""\
 Template identifier "{}" not found. Please, make sure TemplateFlow is \
 correctly installed and contains the given template identifiers.""".format(template))

smriprep/conf/__init__.py

@@ -0,0 +1,4 @@
+"""sMRIPrep settings."""
+from templateflow.api import templates as _get_templates
+
+TF_TEMPLATES = tuple(_get_templates())

smriprep/workflows/__init__.py

@@ -1,6 +0,0 @@
-# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
-# vi: set ft=python sts=4 ts=4 sw=4 et:
-
-from .anatomical import init_anat_preproc_wf
-
-__all__ = ['init_anat_preproc_wf']

smriprep/workflows/norm.py

@@ -7,7 +7,7 @@
 
 from nipype.interfaces.ants.base import Info as ANTsInfo
 
-from templateflow import api as tf
+from templateflow.api import get_metadata
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.ants import ImageMath
 from niworkflows.interfaces.mni import RobustMNINormalization
@@ -103,7 +103,7 @@ def init_anat_norm_wf(
 
     # Append template citations to description
     for template, _ in templates:
-        template_meta = tf.get_metadata(template)
+        template_meta = get_metadata(template)
         template_refs = ['@%s' % template.lower()]
 
         if template_meta.get('RRID', None):