Merge pull request #6859 from mih/master

Merge `maint`, resolving conflicts between typechange-related PRs

datalad/support/gitrepo.py

@@ -3705,6 +3705,17 @@ def _get_save_status_state(status):
         if state == 'clean':
             # we don't care about clean
             continue
+        if state == 'modified' and props.get('gitshasum') \
+                and props.get('gitshasum') == props.get('prev_gitshasum'):
+            # reported as modified, but with identical shasums -> typechange
+            # a subdataset maybe? do increasingly expensive tests for
+            # speed reasons
+            if props.get('type') != 'dataset' and f.is_dir() \
+                    and GitRepo.is_valid_repo(f):
+                # it was not a dataset, but now there is one.
+                # we declare it untracked to engage the discovery tooling.
+                state = 'untracked'
+                props = dict(type='dataset', state='untracked')
         status_state[state][f] = props
         # The hybrid one to retain the same order as in original status
         if state in ('modified', 'untracked'):

datalad/support/tests/test_repo_save.py

@@ -7,6 +7,7 @@
 # ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
 """Test saveds function"""
 
+import shutil
 
 from datalad.api import create
 from datalad.distribution.dataset import Dataset
@@ -25,7 +26,10 @@
     slow,
     with_tempfile,
 )
-from datalad.utils import rmtree
+from datalad.utils import (
+    on_windows,
+    rmtree,
+)
 
 
 @with_tempfile
@@ -81,6 +85,51 @@ def test_annexrepo_save_all(path=None):
     _test_save_all(path, AnnexRepo)
 
 
+@with_tempfile
+def test_save_typechange(path=None):
+    ckwa = dict(result_renderer='disabled')
+    ds = Dataset(path).create(**ckwa)
+    foo = ds.pathobj / 'foo'
+    # save a file
+    foo.write_text('some')
+    ds.save(**ckwa)
+    # now delete the file and replace with a directory and a file in it
+    foo.unlink()
+    foo.mkdir()
+    bar = foo / 'bar'
+    bar.write_text('foobar')
+    res = ds.save(**ckwa)
+    assert_in_results(res, path=str(bar), action='add', status='ok')
+    assert_repo_status(ds.repo)
+    if not on_windows:
+        # now replace file with subdataset
+        # (this is https://github.com/datalad/datalad/issues/5418)
+        bar.unlink()
+        Dataset(ds.pathobj / 'tmp').create(**ckwa)
+        shutil.move(ds.pathobj / 'tmp', bar)
+        res = ds.save(**ckwa)
+        assert_repo_status(ds.repo)
+        assert len(ds.subdatasets(**ckwa)) == 1
+    # now replace directory with subdataset
+    rmtree(foo)
+    Dataset(ds.pathobj / 'tmp').create(**ckwa)
+    shutil.move(ds.pathobj / 'tmp', foo)
+    # right now a first save() will save the subdataset removal only
+    ds.save(**ckwa)
+    # subdataset is gone
+    assert len(ds.subdatasets(**ckwa)) == 0
+    # but it takes a second save() run to get a valid status report
+    # to understand that there is a new subdataset on a higher level
+    ds.save(**ckwa)
+    assert_repo_status(ds.repo)
+    assert len(ds.subdatasets(**ckwa)) == 1
+    # now replace subdataset with a file
+    rmtree(foo)
+    foo.write_text('some')
+    ds.save(**ckwa)
+    assert_repo_status(ds.repo)
+
+
 @with_tempfile
 def test_save_to_git(path=None):
     ds = Dataset(path).create(result_renderer='disabled')