RF: DataLad 0.13 compat fixes - use .save instead of .add for datalad; do not use .repo.repo

There might be one more commit now in the DataLad history but I think it is tollerable

Author: yarikoptic

heudiconv/external/dlad.py

@@ -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/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)