failed fix(ds005): ensure that spaces are being correctly read

it seems that the std_targets iterable of the workflow resampling ciftis
is not properly being filled in - apparently the spec is being dropped.

@mgxd - are there any changes in your side to niworkflows/spaces that
might have affected that particular?

The parameterized folders of nipype are like ``templatename.``, so it
seems the specs are not being honored.

Author: oesteban

fmriprep/cli/run.py

@@ -62,6 +62,17 @@ def main():
     # Clean up master process before running workflow, which may create forks
     gc.collect()
 
+    # Configure resource_monitor
+    if config.nipype.resource_monitor:
+        ncfg.update_config({
+            'monitoring': {
+                'enabled': config.nipype.resource_monitor,
+                'sample_frequency': '0.5',
+                'summary_append': True,
+            }
+        })
+        ncfg.enable_resource_monitor()
+
     # Nipype config (logs and execution)
     ncfg.update_config({
         'logging': {
@@ -70,20 +81,12 @@ def main():
         },
         'execution': {
             'crashdump_dir': str(config.execution.log_dir),
-            'crashfile_format': 'txt',
-            'get_linked_libs': False,
+            'crashfile_format': config.nipype.crashfile_format,
+            'get_linked_libs': config.nipype.get_linked_libs,
             'stop_on_first_crash': config.nipype.stop_on_first_crash,
-        },
-        'monitoring': {
-            'enabled': config.nipype.resource_monitor,
-            'sample_frequency': '0.5',
-            'summary_append': True,
         }
     })
 
-    if config.nipype.resource_monitor:
-        ncfg.enable_resource_monitor()
-
     # Sentry tracking
     if sentry_sdk is not None:
         with sentry_sdk.configure_scope() as scope:
@@ -92,10 +95,10 @@ def main():
         sentry_sdk.add_breadcrumb(message='fMRIPrep started', level='info')
         sentry_sdk.capture_message('fMRIPrep started', level='info')
 
-    config.loggers.workflow.log(25, 'fMRIPrep started!')
     config.loggers.workflow.log(15, '\n'.join(
         ['fMRIPrep config:'] + ['\t\t%s' % s for s in config.dumps().splitlines()])
     )
+    config.loggers.workflow.log(25, 'fMRIPrep started!')
     errno = 1  # Default is error exit unless otherwise set
     try:
         fmriprep_wf.run(**config.nipype.get_plugin())

fmriprep/tests/__init__.py

@@ -0,0 +1,28 @@
+"""Check the configuration module and file."""
+from pathlib import Path
+from pkg_resources import resource_filename as pkgrf
+from toml import loads
+from niworkflows.utils.spaces import format_reference
+
+from .. import config
+
+
+def test_config_spaces():
+    """Check that all necessary spaces are recorded in the config."""
+    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
+    settings = loads(filename.read_text())
+    for sectionname, configs in settings.items():
+        if sectionname != 'environment':
+            section = getattr(config, sectionname)
+            section.load(configs)
+    config.set_logger_level()
+    config.init_spaces()
+
+    spaces = config.workflow.spaces
+    assert "MNI152NLin6Asym:res-2" in [
+        str(s) for s in spaces.get_standard(full_spec=True)]
+
+    assert "MNI152NLin6Asym_res-2" in [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references if s.standard and s.dim == 3
+    ]