RF: dbic_bids -> reproin

Author: yarikoptic

CHANGELOG.md

@@ -14,6 +14,7 @@ First release after major refactor
 - `Dockerfile` is generated by [neurodocker](https://github.com/kaczmarj/neurodocker)
 - Logging verbosity reduced
 - Increased leniency with missing DICOM fields
+- dbic_bids heuristic renamed into reproin
 ### Removed
 ### Deprecated
 ### Fixed

README.md

@@ -25,7 +25,7 @@ provided to address various use-cases
 
 - the [cmrr_heuristic](heuristics/cmrr_heuristic.py) provides an
   example for a conversion to [BIDS]
-- the [dbic_bids](heuristics/dbic_bids.py) could be used to establish
+- the [reproin](heuristics/reproin.py) could be used to establish
   a complete imaging center wide automation to convert all acquired
   data to [BIDS] following a simple naming
   [convention](https://goo.gl/o0YASC) for studies and sequences

heudiconv/heuristics/dbic_bids_validator.cfg

@@ -1,8 +1,8 @@
 #
-# Tests for dbic_bids.py
+# Tests for reproin.py
 #
 from collections import OrderedDict
-from dbic_bids import get_dups_marked
+from reproin import get_dups_marked
 
 def test_get_dups_marked():
     no_dups = {('some',): [1]}

heudiconv/heuristics/dbic_bids.py renamed to heudiconv/heuristics/reproin.py

@@ -31,16 +31,16 @@ def test_smoke_converall(tmpdir):
     )
 
 
-@pytest.mark.parametrize('heuristic', ['dbic_bids', 'convertall'])
+@pytest.mark.parametrize('heuristic', ['reproin', 'convertall'])
 @pytest.mark.parametrize(
     'invocation', [
         "--files %s" % TESTS_DATA_PATH,    # our new way with automated groupping
         "-d %s/{subject}/* -s 01-fmap_acq-3mm" % TESTS_DATA_PATH # "old" way specifying subject
         # should produce the same results
     ])
 @pytest.mark.skipif(Dataset is None, reason="no datalad")
-def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
-    is_bids = True if heuristic == 'dbic_bids' else False
+def test_reproin_largely_smoke(tmpdir, heuristic, invocation):
+    is_bids = True if heuristic == 'reproin' else False
     arg = "--random-seed 1 -f %s -c dcm2niix -o %s" \
           % (heuristic, tmpdir)
     if is_bids:
@@ -57,7 +57,7 @@ def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
         with pytest.raises(ValueError):
             runner(args + ['--subjects', 'sub1', 'sub2'])
 
-        if heuristic != 'dbic_bids':
+        if heuristic != 'reproin':
             # none other heuristic has mighty infotoids atm
             with pytest.raises(NotImplementedError):
                 runner(args)
@@ -93,8 +93,8 @@ def test_dbic_bids_largely_smoke(tmpdir, heuristic, invocation):
     'invocation', [
         "--files %s" % TESTS_DATA_PATH,    # our new way with automated groupping
     ])
-def test_scans_keys_dbic_bids(tmpdir, invocation):
-    args = "-f dbic_bids -c dcm2niix -o %s -b " % (tmpdir)
+def test_scans_keys_reproin(tmpdir, invocation):
+    args = "-f reproin -c dcm2niix -o %s -b " % (tmpdir)
     args += invocation
     runner(args.split())
     # for now check it exists
@@ -116,7 +116,7 @@ def test_scans_keys_dbic_bids(tmpdir, invocation):
 @patch('sys.stdout', new_callable=StringIO)
 def test_ls(stdout):
     args = (
-            "-f dbic_bids --command ls --files %s"
+            "-f reproin --command ls --files %s"
             % (TESTS_DATA_PATH)
     ).split(' ')
     runner(args)

heudiconv/heuristics/test_dbic_bids.py renamed to heudiconv/heuristics/test_reproin.py

@@ -17,7 +17,7 @@
 
 
 @pytest.mark.parametrize('subject', ['sub-sid000143'])
-@pytest.mark.parametrize('heuristic', ['dbic_bids.py'])
+@pytest.mark.parametrize('heuristic', ['reproin.py'])
 @pytest.mark.skipif(not have_datalad, reason="no datalad")
 def test_conversion(tmpdir, subject, heuristic):
 	tmpdir.chdir()

tests/test_heuristics.py

@@ -30,7 +30,7 @@ function run() {
 
    # just do full conversion
    echo "Running $whichheudiconv with log in $out.log"
-   $RUN heudiconv --random-seed 1 -f $heudiconvdir/heuristics/dbic_bids.py -c dcm2niix -o $out --datalad --bids "$@" >| $out.log 2>&1
+   $RUN heudiconv --random-seed 1 -f $heudiconvdir/heuristics/reproin.py -c dcm2niix -o $out --datalad --bids "$@" >| $out.log 2>&1
 }
 
 run heudiconv rolando "$@"