Run codespell on some obvious typos

heudiconv/cli/monitor.py

@@ -79,7 +79,7 @@ def process(paths2process, db, wait=WAIT_TIME, logdir='log'):
 
 def monitor(topdir='/tmp/new_dir', check_ptrn='/20../../..',
             db=None, wait=WAIT_TIME, logdir='log'):
-    # make logdir if not existant
+    # make logdir if not existent
     try:
         os.makedirs(logdir)
     except OSError:

heudiconv/convert.py

@@ -51,7 +51,7 @@ def conversion_info(subject, outdir, info, filegroup, ses):
             continue
         template, outtype = key[0], key[1]
         # So no annotation_classes of any kind!  so if not used -- what was the
-        # intension???? XXX
+        # intention???? XXX
         outpath = outdir
         for idx, itemgroup in enumerate(items):
             if not isinstance(itemgroup, list):
@@ -131,7 +131,7 @@ def prep_conversion(sid, dicoms, outdir, heuristic, converter, anon_sid,
     # ref: https://github.com/nipy/heudiconv/issues/84#issuecomment-330048609
     # for more automagical wishes
     target_heuristic_filename = op.join(idir, 'heuristic.py')
-    # faciliates change - TODO: remove in 1.0
+    # facilitates change - TODO: remove in 1.0
     old_heuristic_filename = op.join(idir, op.basename(heuristic.filename))
     if op.exists(old_heuristic_filename):
         assure_no_file_exists(target_heuristic_filename)

heudiconv/heuristics/reproin.py

@@ -551,7 +551,7 @@ def infotodict(seqinfo):
                                   if isinstance(current_run, int)
                                   else current_run)
         else:
-            # if there is no _run -- no run label addded
+            # if there is no _run -- no run label added
             run_label = None
 
         # yoh: had a wrong assumption

heudiconv/parser.py

@@ -71,7 +71,7 @@ def get_extracted_dicoms(fl):
     #     raise ValueError("some but not all input files are tar files")
 
     # tarfiles already know what they contain, and often the filenames
-    # are unique, or at least in a unqiue subdir per session
+    # are unique, or at least in a unique subdir per session
     # strategy: extract everything in a temp dir and assemble a list
     # of all files in all tarballs
 

heudiconv/queue.py

@@ -91,7 +91,7 @@ def clean_args(hargs, iterarg, iteridx):
     is_iterarg = False
     itercount = 0
 
-    indicies = []
+    indices = []
     cmdargs = hargs[:]
 
     for i, arg in enumerate(hargs):
@@ -100,13 +100,13 @@ def clean_args(hargs, iterarg, iteridx):
             is_iterarg = False
         if is_iterarg:
             if iteridx != itercount:
-                indicies.append(i)
+                indices.append(i)
             itercount += 1
         if arg in iterarg:
             is_iterarg = True
         if arg in queue_args:
-            indicies.extend([i, i+1])
+            indices.extend([i, i+1])
 
-    for j in sorted(indicies, reverse=True):
+    for j in sorted(indices, reverse=True):
         del cmdargs[j]
     return cmdargs

heudiconv/tests/test_heuristics.py

@@ -69,7 +69,7 @@ def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
             runner(args + ['--subjects', 'sub1', 'sub2'])
 
         if heuristic != 'reproin':
-            # if subject is not overriden, raise error
+            # if subject is not overridden, raise error
             with pytest.raises(NotImplementedError):
                 runner(args)
             return
@@ -158,7 +158,7 @@ def test_scout_conversion(tmpdir):
     # Let's do some basic checks on produced files
     j = load_json(sespath / 'fmap/sub-phantom1sid1_ses-localizer_acq-3mm_phasediff.json')
     # We store HeuDiConv version in each produced .json file
-    # TODO: test that we are not somehow overwritting that version in existing
+    # TODO: test that we are not somehow overwriting that version in existing
     # files which we have not produced in a particular run.
     assert j[HEUDICONV_VERSION_JSON_KEY] == __version__