Merge pull request #464 from dbic/bf-datalad

BF: be compatible with datalad 0.13

Author: yarikoptic

heudiconv/external/dlad.py

@@ -10,7 +10,7 @@
 
 lgr = logging.getLogger(__name__)
 
-MIN_VERSION = '0.12.4'
+from ..info import MIN_DATALAD_VERSION as MIN_VERSION
 
 
 def prepare_datalad(studydir, outdir, sid, session, seqinfo, dicoms, bids):
@@ -105,8 +105,7 @@ def add_to_datalad(topdir, studydir, msg, bids):
             # Previously we did not have it as a submodule, and since no
             # automagic migration is implemented, we just need to check first
             # if any path under .heudiconv is already under git control
-            if any(x[0].startswith('.heudiconv/') for x in
-                   ds.repo.repo.index.entries.keys()):
+            if any(x.startswith('.heudiconv/') for x in ds.repo.get_files()):
                 lgr.warning("%s has .heudiconv not as a submodule from previous"
                             " versions of heudiconv. No automagic migration is "
                             "yet provided", ds)
@@ -119,11 +118,11 @@ def add_to_datalad(topdir, studydir, msg, bids):
         # we place all files under annex and then add
         if create_file_if_missing(op.join(dsh_path, '.gitattributes'),
                                   """* annex.largefiles=anything"""):
-            ds.add('.heudiconv/.gitattributes',
+            ds.save('.heudiconv/.gitattributes',
                    to_git=True,
                    message="Added gitattributes to place all .heudiconv content"
                            " under annex")
-    ds.add('.', recursive=True, save=False,
+    ds.save('.', recursive=True
            # not in effect! ?
            #annex_add_opts=['--include-dotfiles']
            )

heudiconv/external/tests/test_dlad.py

@@ -17,7 +17,7 @@ def test_mark_sensitive(tmpdir):
             'g2': 'd1',
          }
     )
-    ds.add('.')
+    ds.save('.')
     mark_sensitive(ds, 'f*')
     all_meta = dict(ds.repo.get_metadata('.'))
     target_rec = {'distribution-restrictions': ['sensitive']}

heudiconv/info.py

@@ -37,10 +37,11 @@
     'inotify',
 ]
 
+MIN_DATALAD_VERSION = '0.12.4'
 EXTRA_REQUIRES = {
     'tests': TESTS_REQUIRES,
     'extras': [],  # Requires patched version ATM ['dcmstack'],
-    'datalad': ['datalad >=0.12.3']
+    'datalad': ['datalad >=%s' % MIN_DATALAD_VERSION]
 }
 
 # Flatten the lists

heudiconv/tests/test_main.py

@@ -147,7 +147,7 @@ def test_prepare_for_datalad(tmpdir):
     dummy_path = os.path.join(dsh_path, 'dummy.nii.gz')
 
     create_file_if_missing(dummy_path, '')
-    ds.add(dummy_path, message="added a dummy file")
+    ds.save(dummy_path, message="added a dummy file")
     # next call must not fail, should just issue a warning
     add_to_datalad(str(tmpdir), studydir_, None, False)
     ds.repo.is_under_annex(dummy_path)

utils/test-compare-two-versions.sh

@@ -26,6 +26,10 @@ function run() {
    shift
    source $heudiconvdir/venvs/dev3/bin/activate
    whichheudiconv=$(which heudiconv)
+   # to get "reproducible" dataset UUIDs (might be detremental if we had multiple datalad calls
+   # but since we use python API for datalad, should be Ok)
+   export DATALAD_SEED=1
+
 
    if [ ! -e "$out" ]; then
 	  # just do full conversion