fix(details): address various issues generating docs, running smoke tests, pytest, etc.

Author: oesteban

docs/usage.rst

@@ -31,7 +31,7 @@ Example: ::
 Command-Line Arguments
 ----------------------
 .. argparse::
-   :ref: fmriprep.cli.run.get_parser
+   :ref: fmriprep.cli.parser._build_parser
    :prog: fmriprep
    :nodefault:
    :nodefaultconst:

docs/workflows.rst

@@ -19,8 +19,8 @@ is presented below:
 
     from fmriprep.workflows.tests import mock_config
     from fmriprep.workflows.base import init_single_subject_wf
-    mock_config()
-    wf = init_single_subject_wf()
+    with mock_config():
+        wf = init_single_subject_wf('01')
 
 Preprocessing of structural MRI
 -------------------------------
@@ -54,7 +54,7 @@ single reference template (see `Longitudinal processing`_).
         skull_strip_fixed_seed=False,
     )
 
-See also *sMRIPrep*'s 
+See also *sMRIPrep*'s
 :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`.
 
 .. _t1preproc_steps:
@@ -176,7 +176,7 @@ would be processed by the following command::
         -autorecon1 \
         -noskullstrip
 
-The second phase imports the brainmask calculated in the 
+The second phase imports the brainmask calculated in the
 `Preprocessing of structural MRI`_ sub-workflow.
 The final phase resumes reconstruction, using the T2w image to assist
 in finding the pial surface, if available.
@@ -238,13 +238,12 @@ BOLD preprocessing
     :simple_form: yes
 
     from fmriprep.workflows.tests import mock_config
+    from fmriprep import config
     from fmriprep.workflows.bold.base import init_func_preproc_wf
-    mock_config()
-
-    from collections import namedtuple
-    from niworkflows.utils.spaces import SpatialReferences
-    BIDSLayout = namedtuple('BIDSLayout', ['root'])
-    wf = init_func_preproc_wf('sub-01_task-nback_bold.nii.gz')
+    with mock_config():
+        bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
+            / 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+        wf = init_func_preproc_wf(str(bold_file))
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
 split into multiple sub-workflows described below.
@@ -429,7 +428,7 @@ Resampling BOLD runs onto standard spaces
 This sub-workflow concatenates the transforms calculated upstream (see
 `Head-motion estimation`_, `Susceptibility Distortion Correction (SDC)`_ --if
 fieldmaps are available--, `EPI to T1w registration`_, and an anatomical-to-standard
-transform from `Preprocessing of structural MRI`_) to map the 
+transform from `Preprocessing of structural MRI`_) to map the
 :abbr:`EPI (echo-planar imaging)`
 image to the standard spaces given by the ``--output-spaces`` argument
 (see :ref:`output-spaces`).

fmriprep/cli/tests/test_parser.py

@@ -82,7 +82,7 @@ def test_get_parser_update(monkeypatch, capsys, current, latest):
     def _mock_check_latest(*args, **kwargs):
         return Version(latest)
 
-    monkeypatch.setattr(config.execution, 'version', current)
+    monkeypatch.setattr(config.environment, 'version', current)
     monkeypatch.setattr(_version, 'check_latest', _mock_check_latest)
 
     _build_parser()

fmriprep/config.py

@@ -7,22 +7,27 @@
 
 Example
 -------
->>> from fmriprep import config
->>> config_file = config.execution.work_dir / '.fmriprep.toml'
->>> config.to_filename(config_file)
->>> # Call build_workflow(config_file, retval) in a subprocess
->>> with Manager() as mgr:
->>>     from .workflow import build_workflow
->>>     retval = mgr.dict()
->>>     p = Process(target=build_workflow, args=(str(config_file), retval))
->>>     p.start()
->>>     p.join()
->>> config.load(config_file)
->>> # Access configs from any code section as:
->>> value = config.section.setting
+
+.. code-block:: Python
+
+    >>> from fmriprep import config
+    >>> config_file = config.execution.work_dir / '.fmriprep.toml'
+    >>> config.to_filename(config_file)
+    >>> # Call build_workflow(config_file, retval) in a subprocess
+    >>> with Manager() as mgr:
+    >>>     from .workflow import build_workflow
+    >>>     retval = mgr.dict()
+    >>>     p = Process(target=build_workflow, args=(str(config_file), retval))
+    >>>     p.start()
+    >>>     p.join()
+    >>> config.load(config_file)
+    >>> # Access configs from any code section as:
+    >>> value = config.section.setting
 
 The module also has a :py:func:`to_filename` function to allow writting out
-the settings to hard disk in *ToML* format, which looks like::
+the settings to hard disk in *ToML* format, which looks like
+
+.. code-block:: toml
 
     [environment]
     cpu_count = 8

fmriprep/workflows/base.py

@@ -48,8 +48,8 @@ def init_fmriprep_wf():
 
             from fmriprep.workflows.tests import mock_config
             from fmriprep.workflows.base import init_fmriprep_wf
-            mock_config()
-            wf = init_fmriprep_wf()
+            with mock_config():
+                wf = init_fmriprep_wf()
 
     """
     fmriprep_wf = Workflow(name='fmriprep_wf')
@@ -109,8 +109,8 @@ def init_single_subject_wf(subject_id):
 
             from fmriprep.workflows.tests import mock_config
             from fmriprep.workflows.base import init_single_subject_wf
-            mock_config()
-            wf = init_single_subject_wf('test')
+            with mock_config():
+                wf = init_single_subject_wf('01')
 
     Parameters
     ----------
@@ -222,15 +222,16 @@ def init_single_subject_wf(subject_id):
         freesurfer=config.workflow.run_reconall,
         hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
+        num_t1w=len(subject_data['t1w']),
         omp_nthreads=config.nipype.omp_nthreads,
         output_dir=str(config.execution.output_dir),
         reportlets_dir=reportlets_dir,
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
-        skull_strip_mode='force',
+        # skull_strip_mode='force',
         skull_strip_template=Reference.from_string(
             config.workflow.skull_strip_template)[0],
         spaces=spaces,
-        t1w=subject_data['t1w'],
+        # t1w=subject_data['t1w'],
     )
 
     workflow.connect([

fmriprep/workflows/bold/base.py

@@ -51,9 +51,12 @@ def init_func_preproc_wf(bold_file):
             :simple_form: yes
 
             from fmriprep.workflows.tests import mock_config
+            from fmriprep import config
             from fmriprep.workflows.bold.base import init_func_preproc_wf
-            mock_config()
-            wf = init_func_preproc_wf('sub-01_task-mixedgamblestask_run-01_bold.nii.gz')
+            with mock_config():
+                bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
+                    / 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+                wf = init_func_preproc_wf(str(bold_file))
 
     Parameters
     ----------

fmriprep/workflows/tests.py

@@ -1,13 +1,20 @@
 """Utilities and mocks for testing and documentation building."""
+import os
+from contextlib import contextmanager
 from pathlib import Path
 from pkg_resources import resource_filename as pkgrf
 from toml import loads
 from tempfile import mkdtemp
 
 
+@contextmanager
 def mock_config():
     """Create a mock config for documentation and testing purposes."""
     from .. import config
+    _old_fs = os.getenv('FREESURFER_HOME')
+    if not _old_fs:
+        os.environ['FREESURFER_HOME'] = mkdtemp()
+
     filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
     settings = loads(filename.read_text())
     for sectionname, configs in settings.items():
@@ -18,5 +25,10 @@ def mock_config():
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())
-    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005'))
+    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005')).absolute()
     config.init_layout()
+
+    yield
+
+    if not _old_fs:
+        del os.environ["FREESURFER_HOME"]