Merge pull request #272 from dartmouth-pbs/rf-tst-move

RF: move tests under heudiconv/ module

Author: yarikoptic

.coveragerc

@@ -1,4 +1,3 @@
 [run]
-include = tests/*
-          heudiconv/*
+include = heudiconv/*
           setup.py

.travis.yml

@@ -37,7 +37,7 @@ install:
   - git config --global user.name "Travis Almighty"
 
 script:
-  - coverage run `which py.test` -s -v tests heudiconv/heuristics/*.py
+  - coverage run `which py.test` -s -v heudiconv
 
 after_success:
   - codecov

CHANGELOG.md

@@ -14,6 +14,8 @@ TODO Summary
 - Reproin heuristic: `__dup` indices would now be assigned incrementally
   individually per each sequence, so there is a chance to properly treat
   associate for multi-file (e.g. `fmap`) sequences
+- `tests/` moved under `heudiconv/tests` to ease maintenance and facilitate
+  testing of an installed heudiconv
 
 ### Deprecated
 ### Fixed

heudiconv/heuristics/reproin.py

@@ -922,159 +922,3 @@ def fixup_subjectid(subjectid):
         # just filter out possible _- in it
         return re.sub('[-_]', '', subjectid)
     return "sid%06d" % int(reg.groups()[0])
-
-
-def test_filter_files():
-    # Filtering is currently disabled -- any sequence directory is Ok
-    assert(filter_files('/home/mvdoc/dbic/09-run_func_meh/0123432432.dcm'))
-    assert(filter_files('/home/mvdoc/dbic/run_func_meh/012343143.dcm'))
-
-
-def test_md5sum():
-    assert md5sum('cryptonomicon') == '1cd52edfa41af887e14ae71d1db96ad1'
-    assert md5sum('mysecretmessage') == '07989808231a0c6f522f9d8e34695794'
-
-
-def test_fix_canceled_runs():
-    from collections import namedtuple
-    FakeSeqInfo = namedtuple('FakeSeqInfo',
-                             ['accession_number', 'series_id',
-                              'protocol_name', 'series_description'])
-
-    seqinfo = []
-    runname = 'func_run+'
-    for i in range(1, 6):
-        seqinfo.append(
-            FakeSeqInfo('accession1',
-                        '{0:02d}-'.format(i) + runname,
-                        runname, runname)
-        )
-
-    fake_accession2run = {
-        'accession1': ['^01-', '^03-']
-    }
-
-    seqinfo_ = fix_canceled_runs(seqinfo, fake_accession2run)
-
-    for i, s in enumerate(seqinfo_, 1):
-        output = runname
-        if i == 1 or i == 3:
-            output = 'cancelme_' + output
-        for key in ['series_description', 'protocol_name']:
-            value = getattr(s, key)
-            assert(value == output)
-        # check we didn't touch series_id
-        assert(s.series_id == '{0:02d}-'.format(i) + runname)
-
-
-def test_fix_dbic_protocol():
-    from collections import namedtuple
-    FakeSeqInfo = namedtuple('FakeSeqInfo',
-                             ['accession_number', 'study_description',
-                              'field1', 'field2'])
-    accession_number = 'A003'
-    seq1 = FakeSeqInfo(accession_number,
-                       'mystudy',
-                       '02-anat-scout_run+_MPR_sag',
-                       '11-func_run-life2_acq-2mm692')
-    seq2 = FakeSeqInfo(accession_number,
-                       'mystudy',
-                       'nochangeplease',
-                       'nochangeeither')
-
-
-    seqinfos = [seq1, seq2]
-    keys = ['field1']
-    subsdict = {
-        md5sum('mystudy'):
-            [('scout_run\+', 'scout'),
-             ('run-life[0-9]', 'run+_task-life')],
-    }
-
-    seqinfos_ = fix_dbic_protocol(seqinfos, keys=keys, subsdict=subsdict)
-    assert(seqinfos[1] == seqinfos_[1])
-    # field2 shouldn't have changed since I didn't pass it
-    assert(seqinfos_[0] == FakeSeqInfo(accession_number,
-                                       'mystudy',
-                                       '02-anat-scout_MPR_sag',
-                                       seq1.field2))
-
-    # change also field2 please
-    keys = ['field1', 'field2']
-    seqinfos_ = fix_dbic_protocol(seqinfos, keys=keys, subsdict=subsdict)
-    assert(seqinfos[1] == seqinfos_[1])
-    # now everything should have changed
-    assert(seqinfos_[0] == FakeSeqInfo(accession_number,
-                                       'mystudy',
-                                       '02-anat-scout_MPR_sag',
-                                       '11-func_run+_task-life_acq-2mm692'))
-
-
-def test_sanitize_str():
-    assert sanitize_str('[email protected]') == 'superduperfaster'
-    assert sanitize_str('perfect') == 'perfect'
-    assert sanitize_str('never:use:colon:!') == 'neverusecolon'
-
-
-def test_fixupsubjectid():
-    assert fixup_subjectid("abra") == "abra"
-    assert fixup_subjectid("sub") == "sub"
-    assert fixup_subjectid("sid") == "sid"
-    assert fixup_subjectid("sid000030") == "sid000030"
-    assert fixup_subjectid("sid0000030") == "sid000030"
-    assert fixup_subjectid("sid00030") == "sid000030"
-    assert fixup_subjectid("sid30") == "sid000030"
-    assert fixup_subjectid("SID30") == "sid000030"
-
-
-def test_parse_series_spec():
-    pdpn = parse_series_spec
-
-    assert pdpn("nondbic_func-bold") == {}
-    assert pdpn("cancelme_func-bold") == {}
-
-    assert pdpn("bids_func-bold") == \
-           pdpn("func-bold") == \
-           {'seqtype': 'func', 'seqtype_label': 'bold'}
-
-    # pdpn("bids_func_ses+_task-boo_run+") == \
-    # order and PREFIX: should not matter, as well as trailing spaces
-    assert \
-        pdpn(" PREFIX:bids_func_ses+_task-boo_run+  ") == \
-        pdpn("PREFIX:bids_func_ses+_task-boo_run+") == \
-        pdpn("bids_func_ses+_run+_task-boo") == \
-           {
-               'seqtype': 'func',
-               # 'seqtype_label': 'bold',
-               'session': '+',
-               'run': '+',
-               'task': 'boo',
-            }
-
-    # TODO: fix for that
-    assert pdpn("bids_func-pace_ses-1_task-boo_acq-bu_bids-please_run-2__therest") == \
-           pdpn("bids_func-pace_ses-1_run-2_task-boo_acq-bu_bids-please__therest") == \
-           pdpn("func-pace_ses-1_task-boo_acq-bu_bids-please_run-2") == \
-           {
-               'seqtype': 'func', 'seqtype_label': 'pace',
-               'session': '1',
-               'run': '2',
-               'task': 'boo',
-               'acq': 'bu',
-               'bids': 'bids-please'
-           }
-
-    assert pdpn("bids_anat-scout_ses+") == \
-           {
-               'seqtype': 'anat',
-               'seqtype_label': 'scout',
-               'session': '+',
-           }
-
-    assert pdpn("anat_T1w_acq-MPRAGE_run+") == \
-           {
-                'seqtype': 'anat',
-                'run': '+',
-                'acq': 'MPRAGE',
-                'seqtype_label': 'T1w'
-           }

heudiconv/heuristics/test_reproin.py

@@ -2,7 +2,16 @@
 # Tests for reproin.py
 #
 from collections import OrderedDict
-from .reproin import get_dups_marked
+from .reproin import (
+    filter_files,
+    fix_canceled_runs,
+    fix_dbic_protocol,
+    fixup_subjectid,
+    get_dups_marked,
+    md5sum,
+    parse_series_spec,
+    sanitize_str,
+)
 
 
 def test_get_dups_marked():
@@ -37,3 +46,159 @@ def test_get_dups_marked():
             ('smth2',): ['c']
         }
 
+
+
+def test_filter_files():
+    # Filtering is currently disabled -- any sequence directory is Ok
+    assert(filter_files('/home/mvdoc/dbic/09-run_func_meh/0123432432.dcm'))
+    assert(filter_files('/home/mvdoc/dbic/run_func_meh/012343143.dcm'))
+
+
+def test_md5sum():
+    assert md5sum('cryptonomicon') == '1cd52edfa41af887e14ae71d1db96ad1'
+    assert md5sum('mysecretmessage') == '07989808231a0c6f522f9d8e34695794'
+
+
+def test_fix_canceled_runs():
+    from collections import namedtuple
+    FakeSeqInfo = namedtuple('FakeSeqInfo',
+                             ['accession_number', 'series_id',
+                              'protocol_name', 'series_description'])
+
+    seqinfo = []
+    runname = 'func_run+'
+    for i in range(1, 6):
+        seqinfo.append(
+            FakeSeqInfo('accession1',
+                        '{0:02d}-'.format(i) + runname,
+                        runname, runname)
+        )
+
+    fake_accession2run = {
+        'accession1': ['^01-', '^03-']
+    }
+
+    seqinfo_ = fix_canceled_runs(seqinfo, fake_accession2run)
+
+    for i, s in enumerate(seqinfo_, 1):
+        output = runname
+        if i == 1 or i == 3:
+            output = 'cancelme_' + output
+        for key in ['series_description', 'protocol_name']:
+            value = getattr(s, key)
+            assert(value == output)
+        # check we didn't touch series_id
+        assert(s.series_id == '{0:02d}-'.format(i) + runname)
+
+
+def test_fix_dbic_protocol():
+    from collections import namedtuple
+    FakeSeqInfo = namedtuple('FakeSeqInfo',
+                             ['accession_number', 'study_description',
+                              'field1', 'field2'])
+    accession_number = 'A003'
+    seq1 = FakeSeqInfo(accession_number,
+                       'mystudy',
+                       '02-anat-scout_run+_MPR_sag',
+                       '11-func_run-life2_acq-2mm692')
+    seq2 = FakeSeqInfo(accession_number,
+                       'mystudy',
+                       'nochangeplease',
+                       'nochangeeither')
+
+
+    seqinfos = [seq1, seq2]
+    keys = ['field1']
+    subsdict = {
+        md5sum('mystudy'):
+            [('scout_run\+', 'scout'),
+             ('run-life[0-9]', 'run+_task-life')],
+    }
+
+    seqinfos_ = fix_dbic_protocol(seqinfos, keys=keys, subsdict=subsdict)
+    assert(seqinfos[1] == seqinfos_[1])
+    # field2 shouldn't have changed since I didn't pass it
+    assert(seqinfos_[0] == FakeSeqInfo(accession_number,
+                                       'mystudy',
+                                       '02-anat-scout_MPR_sag',
+                                       seq1.field2))
+
+    # change also field2 please
+    keys = ['field1', 'field2']
+    seqinfos_ = fix_dbic_protocol(seqinfos, keys=keys, subsdict=subsdict)
+    assert(seqinfos[1] == seqinfos_[1])
+    # now everything should have changed
+    assert(seqinfos_[0] == FakeSeqInfo(accession_number,
+                                       'mystudy',
+                                       '02-anat-scout_MPR_sag',
+                                       '11-func_run+_task-life_acq-2mm692'))
+
+
+def test_sanitize_str():
+    assert sanitize_str('[email protected]') == 'superduperfaster'
+    assert sanitize_str('perfect') == 'perfect'
+    assert sanitize_str('never:use:colon:!') == 'neverusecolon'
+
+
+def test_fixupsubjectid():
+    assert fixup_subjectid("abra") == "abra"
+    assert fixup_subjectid("sub") == "sub"
+    assert fixup_subjectid("sid") == "sid"
+    assert fixup_subjectid("sid000030") == "sid000030"
+    assert fixup_subjectid("sid0000030") == "sid000030"
+    assert fixup_subjectid("sid00030") == "sid000030"
+    assert fixup_subjectid("sid30") == "sid000030"
+    assert fixup_subjectid("SID30") == "sid000030"
+
+
+def test_parse_series_spec():
+    pdpn = parse_series_spec
+
+    assert pdpn("nondbic_func-bold") == {}
+    assert pdpn("cancelme_func-bold") == {}
+
+    assert pdpn("bids_func-bold") == \
+           pdpn("func-bold") == \
+           {'seqtype': 'func', 'seqtype_label': 'bold'}
+
+    # pdpn("bids_func_ses+_task-boo_run+") == \
+    # order and PREFIX: should not matter, as well as trailing spaces
+    assert \
+        pdpn(" PREFIX:bids_func_ses+_task-boo_run+  ") == \
+        pdpn("PREFIX:bids_func_ses+_task-boo_run+") == \
+        pdpn("bids_func_ses+_run+_task-boo") == \
+           {
+               'seqtype': 'func',
+               # 'seqtype_label': 'bold',
+               'session': '+',
+               'run': '+',
+               'task': 'boo',
+            }
+
+    # TODO: fix for that
+    assert pdpn("bids_func-pace_ses-1_task-boo_acq-bu_bids-please_run-2__therest") == \
+           pdpn("bids_func-pace_ses-1_run-2_task-boo_acq-bu_bids-please__therest") == \
+           pdpn("func-pace_ses-1_task-boo_acq-bu_bids-please_run-2") == \
+           {
+               'seqtype': 'func', 'seqtype_label': 'pace',
+               'session': '1',
+               'run': '2',
+               'task': 'boo',
+               'acq': 'bu',
+               'bids': 'bids-please'
+           }
+
+    assert pdpn("bids_anat-scout_ses+") == \
+           {
+               'seqtype': 'anat',
+               'seqtype_label': 'scout',
+               'session': '+',
+           }
+
+    assert pdpn("anat_T1w_acq-MPRAGE_run+") == \
+           {
+                'seqtype': 'anat',
+                'run': '+',
+                'acq': 'MPRAGE',
+                'seqtype_label': 'T1w'
+           }