ENH: Accept modification of configuration by users

fitlins/cli/run.py

@@ -23,7 +23,7 @@
 
 from .. import __version__
 from ..workflows import init_fitlins_wf
-from ..utils import bids
+from ..utils import bids, config
 from ..viz.reports import build_report_dict, write_full_report
 
 logging.addLevelName(25, 'IMPORTANT')  # Add a new level between INFO and WARNING
@@ -232,12 +232,11 @@ def run_fitlins(argv=None):
         participants=subject_list, base_dir=work_dir,
         smoothing=opts.smoothing, drop_missing=opts.drop_missing,
         )
+    fitlins_wf.config = config.get_fitlins_config()
 
     if opts.work_dir:
         # dump crashes in working directory (non /tmp)
         fitlins_wf.config['execution']['crashdump_dir'] = opts.work_dir
-    # easy to read crashfiles
-    fitlins_wf.config['execution']['crashfile_format'] = 'txt'
     retcode = 0
     if not opts.reports_only:
         try:

fitlins/utils/config.py

@@ -0,0 +1,25 @@
+import os
+from configparser import ConfigParser
+from nipype.utils import config as nuc
+from pkg_resources import resource_filename
+
+
+def get_fitlins_config():
+    """Construct Nipype configuration object with precedence:
+
+    - Local config (``./nipype.cfg``)
+    - Global config (``$HOME/.nipype/nipype.cfg`` or ``$NIPYPE_CONFIG_DIR/nipype.cfg``)
+    - FitLins config (``<fitlins_install_dir>/data/nipype.cfg``)
+    - Nipype default config (defined in ``nipype/utils/config.py``)
+    """
+    config = nuc.NipypeConfig()
+    config.set_default_config()
+
+    fitlins_config_file = resource_filename('fitlins', 'data/nipype.cfg')
+    global_config_file = os.path.join(
+        os.path.expanduser(os.getenv("NIPYPE_CONFIG_DIR", default="~/.nipype")),
+        "nipype.cfg")
+    local_config_file = "nipype.cfg"
+    fitlins_conf = ConfigParser()
+    fitlins_conf.read([fitlins_config_file, global_config_file, local_config_file])
+    config.update_config(fitlins_conf)