Merge pull request #289 from yarikoptic/bf-codespell

Minor: codespell run + ignore

.gitignore

@@ -71,3 +71,4 @@ secrets.py
 local_settings.py
 
 *.swp
+.pytest_cache

fitlins/_version.py

@@ -269,7 +269,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = ("unable to parse git-describe output: '%s'"
                                % describe_out)
             return pieces

fitlins/cli/run.py

@@ -75,9 +75,9 @@ def get_parser():
     # optional arguments
     parser.add_argument('--version', action='version', version=verstr)
     parser.add_argument('-v', '--verbose', action='count', default=0,
-                        help="increase log verbosity for each occurence, debug level is -vvv")
+                        help="increase log verbosity for each occurrence, debug level is -vvv")
     parser.add_argument('-q', '--quiet', action='count', default=0,
-                        help="decrease log verbosity for each occurence, debug level is -vvv")
+                        help="decrease log verbosity for each occurrence, debug level is -vvv")
 
     g_bids = parser.add_argument_group('Options for filtering BIDS queries')
     g_bids.add_argument('--participant-label', action='store', nargs='+', default=None,
@@ -101,7 +101,7 @@ def get_parser():
     g_bids.add_argument('--desc-label', action='store', default='preproc',
                         help="use BOLD files with the provided description label")
     g_bids.add_argument('--database-path', action='store', default=None,
-                        help="Path to directory containing SQLite database indicies "
+                        help="Path to directory containing SQLite database indices "
                              "for this BIDS dataset. "
                              "If a value is passed and the file already exists, "
                              "indexing is skipped.")
@@ -208,7 +208,7 @@ def run_fitlins(argv=None):
 
     if opts.estimator != 'afni':
         if opts.error_ts:
-            raise NotImplementedError("Saving the error time series is only implmented for"
+            raise NotImplementedError("Saving the error time series is only implemented for"
                                       " the afni estimator. If this is a feature you want"
                                       f" for {opts.estimator} please let us know on github.")
 

fitlins/interfaces/afni.py

@@ -183,7 +183,7 @@ def _run_interface(self, runtime):
             model_metadata.append({'stat': attr, **out_ents})
             model_maps.append(fname)
 
-        # get pvals and zscore buckets (niftis with heterogenous intent codes)
+        # get pvals and zscore buckets (niftis with heterogeneous intent codes)
         pval = Pval()
         pval.inputs.in_file = reml_res.outputs.out_file
         pval.inputs.out_file = "pval_maps.nii.gz"

fitlins/tests/conftest.py

@@ -21,7 +21,7 @@ def pytest_addoption(parser):
                      help='directory containing reference results for evaluating test results')
     parser.addoption(
         '--database-path', action="append", default=[],
-        help="Path to directory containing SQLite database indicies "
+        help="Path to directory containing SQLite database indices "
              "for this BIDS dataset. "
              "If a value is passed and the file already exists, "
              "indexing is skipped."