enh: make some init methods classmethods

Author: oesteban

docs/api.rst

@@ -7,7 +7,7 @@ Internal configuration system
 -----------------------------
 
 .. automodule:: fmriprep.config
-   :members: from_dict, load, get, dumps, to_filename, init_layout, init_spaces
+   :members: from_dict, load, get, dumps, to_filename, init_spaces
 
 Workflows
 ---------

fmriprep/cli/parser.py

@@ -308,8 +308,7 @@ def parse_args(args=None, namespace=None):
     opts = parser.parse_args(args, namespace)
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts))
-
-    config.init_loggers()
+    config.loggers.init()
 
     # Retrieve logging level
     build_log = config.loggers.cli
@@ -388,8 +387,8 @@ def parse_args(args=None, namespace=None):
     output_dir.mkdir(exist_ok=True, parents=True)
     work_dir.mkdir(exist_ok=True, parents=True)
 
-    # First check that bids_dir looks like a BIDS folder
-    config.init_layout()
+    # Force initialization of the BIDSLayout
+    config.execution.init()
     all_subjects = config.execution.layout.get_subjects()
     if config.execution.participant_label is None:
         config.execution.participant_label = all_subjects

fmriprep/cli/workflow.py

@@ -42,7 +42,6 @@ def build_workflow(config_file, retval):
         config.execution.bids_description_hash = sha256(desc_content).hexdigest()
 
     # First check that bids_dir looks like a BIDS folder
-    config.init_layout()
     subject_list = collect_participants(
         config.execution.layout,
         participant_label=config.execution.participant_label

fmriprep/config.py

@@ -116,15 +116,11 @@
 ----------------------
 The :py:mod:`config` is responsible for other conveniency actions.
 
-  * Switching Python's ``multiprocessing`` to *forkserver* mode.
+  * Switching Python's :obj:`multiprocessing` to *forkserver* mode.
   * Set up a filter for warnings as early as possible.
-  * Automated I/O magic operations:
-
-    * :obj:`Path` \<-\> :obj:`str` \<-\> :obj:`Path`).
-    * :py:class:`~niworkflows.util.spaces.SpatialReferences` \<-\> :obj:`str` \<-\>
-      :py:class:`~niworkflows.util.spaces.SpatialReferences`
-    * :py:class:`~bids.layout.BIDSLayout` \<-\> :obj:`str` \<-\>
-      :py:class:`~bids.layout.BIDSLayout`
+  * Automated I/O magic operations. Some conversions need to happen in the
+    store/load processes (e.g., from/to :obj:`~pathlib.Path` \<-\> :obj:`str`,
+    :py:class:`~bids.layout.BIDSLayout`, etc.)
 
 """
 from multiprocessing import set_start_method
@@ -229,7 +225,7 @@ def __init__(self):
         raise RuntimeError('Configuration type is not instantiable.')
 
     @classmethod
-    def load(cls, settings):
+    def load(cls, settings, init=True):
         """Store settings from a dictionary."""
         for k, v in settings.items():
             if v is None:
@@ -240,6 +236,12 @@ def load(cls, settings):
             if hasattr(cls, k):
                 setattr(cls, k, v)
 
+        if init:
+            try:
+                cls.init()
+            except AttributeError:
+                pass
+
     @classmethod
     def get(cls):
         """Return defined settings."""
@@ -331,6 +333,32 @@ def get_plugin(cls):
                 out['plugin_args']['memory_gb'] = float(cls.memory_gb)
         return out
 
+    @classmethod
+    def init(cls):
+        """Set NiPype configurations."""
+        from nipype import config as ncfg
+
+        # Configure resource_monitor
+        if cls.resource_monitor:
+            ncfg.update_config({
+                'monitoring': {
+                    'enabled': cls.resource_monitor,
+                    'sample_frequency': '0.5',
+                    'summary_append': True,
+                }
+            })
+            ncfg.enable_resource_monitor()
+
+        # Nipype config (logs and execution)
+        ncfg.update_config({
+            'execution': {
+                'crashdump_dir': str(execution.log_dir),
+                'crashfile_format': cls.crashfile_format,
+                'get_linked_libs': cls.get_linked_libs,
+                'stop_on_first_crash': cls.stop_on_first_crash,
+            }
+        })
+
 
 class execution(_Config):
     """Configure run-level settings."""
@@ -352,8 +380,7 @@ class execution(_Config):
     fs_subjects_dir = None
     """FreeSurfer's subjects directory."""
     layout = None
-    """A py:class:`~bids.layout.BIDSLayout` object, see
-    :py:func:`~fmriprep.config.init_layout`."""
+    """A :py:class:`~bids.layout.BIDSLayout` object, see :py:func:`init`."""
     log_dir = None
     """The path to a directory that contains execution logs."""
     log_level = 25
@@ -397,6 +424,22 @@ class execution(_Config):
         'work_dir',
     )
 
+    @classmethod
+    def init(cls):
+        """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
+        if cls._layout is None:
+            import re
+            from bids.layout import BIDSLayout
+            work_dir = cls.work_dir / 'bids.db'
+            work_dir.mkdir(exist_ok=True, parents=True)
+            cls._layout = BIDSLayout(
+                str(cls.bids_dir),
+                validate=False,
+                # database_path=str(work_dir),
+                ignore=("code", "stimuli", "sourcedata", "models",
+                        "derivatives", re.compile(r'^\.')))
+        cls.layout = cls._layout
+
 
 # These variables are not necessary anymore
 del _fs_license
@@ -467,18 +510,7 @@ class workflow(_Config):
 
 
 class loggers:
-    """
-    Setup loggers, providing access to them across the *fMRIPrep* run.
-
-        * Add new logger levels (25: IMPORTANT, and 15: VERBOSE).
-        * Add a new sub-logger (``cli``).
-        * Logger configuration.
-
-    See also:
-
-      .. autofunction: init_loggers
-
-    """
+    """Keep loggers easily accessible (see :py:func:`init`)."""
 
     _fmt = "%(asctime)s,%(msecs)d %(name)-2s " "%(levelname)-2s:\n\t %(message)s"
     _datefmt = "%y%m%d-%H:%M:%S"
@@ -494,13 +526,41 @@ class loggers:
     utils = nlogging.getLogger('nipype.utils')
     """NiPype's utils logger."""
 
+    @classmethod
+    def init(cls):
+        """
+        Set the log level, initialize all loggers into :py:class:`loggers`.
+
+            * Add new logger levels (25: IMPORTANT, and 15: VERBOSE).
+            * Add a new sub-logger (``cli``).
+            * Logger configuration.
+
+        """
+        from nipype import config as ncfg
+        _handler = logging.StreamHandler(stream=sys.stdout)
+        _handler.setFormatter(
+            logging.Formatter(fmt=cls._fmt, datefmt=cls._datefmt)
+        )
+        cls.cli.addHandler(_handler)
+        cls.default.setLevel(execution.log_level)
+        cls.cli.setLevel(execution.log_level)
+        cls.interface.setLevel(execution.log_level)
+        cls.workflow.setLevel(execution.log_level)
+        cls.utils.setLevel(execution.log_level)
+        ncfg.update_config({
+            'logging': {
+                'log_directory': str(execution.log_dir),
+                'log_to_file': True
+            },
+        })
+
 
 def from_dict(settings):
     """Read settings from a flat dictionary."""
     nipype.load(settings)
     execution.load(settings)
     workflow.load(settings)
-    init_loggers()
+    loggers.init()
 
 
 def load(filename):
@@ -512,10 +572,7 @@ def load(filename):
         if sectionname != 'environment':
             section = getattr(sys.modules[__name__], sectionname)
             section.load(configs)
-    init_nipype()
-    init_loggers()
     init_spaces()
-    init_layout()
 
 
 def get(flat=False):
@@ -546,43 +603,6 @@ def to_filename(filename):
     filename.write_text(dumps())
 
 
-def init_layout():
-    """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
-    if execution._layout is None:
-        import re
-        from bids.layout import BIDSLayout
-        work_dir = execution.work_dir / 'bids.db'
-        work_dir.mkdir(exist_ok=True, parents=True)
-        execution._layout = BIDSLayout(
-            str(execution.bids_dir),
-            validate=False,
-            # database_path=str(work_dir),
-            ignore=("code", "stimuli", "sourcedata", "models",
-                    "derivatives", re.compile(r'^\.')))
-    execution.layout = execution._layout
-
-
-def init_loggers():
-    """Set the current log level to all loggers."""
-    from nipype import config as ncfg
-    _handler = logging.StreamHandler(stream=sys.stdout)
-    _handler.setFormatter(
-        logging.Formatter(fmt=loggers._fmt, datefmt=loggers._datefmt)
-    )
-    loggers.cli.addHandler(_handler)
-    loggers.default.setLevel(execution.log_level)
-    loggers.cli.setLevel(execution.log_level)
-    loggers.interface.setLevel(execution.log_level)
-    loggers.workflow.setLevel(execution.log_level)
-    loggers.utils.setLevel(execution.log_level)
-    ncfg.update_config({
-        'logging': {
-            'log_directory': str(execution.log_dir),
-            'log_to_file': True
-        },
-    })
-
-
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
@@ -624,29 +644,3 @@ def init_spaces(checkpoint=True):
 
     # Make the SpatialReferences object available
     workflow.spaces = spaces
-
-
-def init_nipype():
-    """Set NiPype configurations."""
-    from nipype import config as ncfg
-
-    # Configure resource_monitor
-    if nipype.resource_monitor:
-        ncfg.update_config({
-            'monitoring': {
-                'enabled': nipype.resource_monitor,
-                'sample_frequency': '0.5',
-                'summary_append': True,
-            }
-        })
-        ncfg.enable_resource_monitor()
-
-    # Nipype config (logs and execution)
-    ncfg.update_config({
-        'execution': {
-            'crashdump_dir': str(execution.log_dir),
-            'crashfile_format': nipype.crashfile_format,
-            'get_linked_libs': nipype.get_linked_libs,
-            'stop_on_first_crash': nipype.stop_on_first_crash,
-        }
-    })

fmriprep/tests/test_config.py

@@ -14,8 +14,9 @@ def test_config_spaces():
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
-            section.load(configs)
-    config.init_loggers()
+            section.load(configs, init=False)
+    config.nipype.init()
+    config.loggers.init()
     config.init_spaces()
 
     spaces = config.workflow.spaces

fmriprep/workflows/tests.py

@@ -20,13 +20,14 @@ def mock_config():
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
-            section.load(configs)
-    config.init_loggers()
+            section.load(configs, init=False)
+    config.nipype.init()
+    config.loggers.init()
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())
     config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005')).absolute()
-    config.init_layout()
+    config.execution.init()
 
     yield