Merge branch 'dev' into path

hdmf-dev · Nov 6, 2024 · ebd5950 · ebd5950
2 parents d9fb0c9 + e5c2e9e
commit ebd5950
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Showing 5 changed files with 25 additions and 5 deletions.
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -61,7 +61,7 @@ jobs:
           tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
       - name: Upload distribution as a workspace artifact
         if: ${{ matrix.upload-wheels }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: distributions
           path: dist
@@ -175,7 +175,7 @@ jobs:
           python-version: '3.11'
 
       - name: Download wheel and source distributions from artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: distributions
           path: dist

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,12 +1,16 @@
 # HDMF-ZARR Changelog
 
-## 0.9.0 (Upcoming)
+## 1.0.0 (Upcoming)
+### Enhancements
+* Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212)
+
+## 0.9.0 (September 16, 2024)
 ### Enhancements
 * Added support for appending a dataset of references. @mavaylon1 [#203](https://github.com/hdmf-dev/hdmf-zarr/pull/203)
 * NWBZarrIO load_namespaces=True by default. @mavaylon1 [#204](https://github.com/hdmf-dev/hdmf-zarr/pull/204)
 * Added test for opening file with consolidated metadata from DANDI. @mavaylon1 [#206](https://github.com/hdmf-dev/hdmf-zarr/pull/206)
 * Add dimension labels compatible with xarray. @mavaylon1 [#207](https://github.com/hdmf-dev/hdmf-zarr/pull/207)
-* Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212)
+* Added link_data --> clear_cache relationship to support repacking zarr nwbfiles: [#215](https://github.com/hdmf-dev/hdmf-zarr/pull/215)
 
 ## 0.8.0 (June 4, 2024)
 ### Bug Fixes

diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
@@ -367,6 +367,8 @@ def export(self, **kwargs):
         write_args['export_source'] = src_io.source  # pass export_source=src_io.source to write_builder
         ckwargs = kwargs.copy()
         ckwargs['write_args'] = write_args
+        if not write_args.get('link_data', True):
+            ckwargs['clear_cache'] = True
         super().export(**ckwargs)
         if cache_spec:
             self.__cache_spec()
@@ -1310,6 +1312,13 @@ def __list_fill__(self, parent, name, data, options=None):  # noqa: C901
             except ValueError:
                 for i in range(len(data)):
                     dset[i] = data[i]
+            except TypeError: # If data is an h5py.Dataset with strings, they may need to be decoded
+                for c in np.ndindex(data_shape):
+                    o = data
+                    for i in c:
+                        o = o[i]
+                    # bytes are not JSON serializable
+                    dset[c] = o if not isinstance(o, (bytes, np.bytes_)) else o.decode("utf-8")
         return dset
 
     def __scalar_fill__(self, parent, name, data, options=None):

diff --git a/test_gallery.py b/test_gallery.py
@@ -80,6 +80,10 @@ def _import_from_file(script):
 _deprecation_warning_zarr_store = (
     r"The NestedDirectoryStore is deprecated *"
 )
+_deprecation_warning_numpy = (
+    "__array__ implementation doesn't accept a copy keyword, so passing copy=False failed. "
+    "__array__ must implement 'dtype' and 'copy' keyword arguments."
+)
 
 def run_gallery_tests():
     global TOTAL, FAILURES, ERRORS
@@ -149,6 +153,9 @@ def run_gallery_tests():
                 warnings.filterwarnings(
                     "ignore", message=_deprecation_warning_zarr_store, category=FutureWarning
                 )
+                warnings.filterwarnings(
+                    "ignore", message=_deprecation_warning_numpy, category=DeprecationWarning
+                )
                 _import_from_file(script_abs)
         except Exception:
             print(traceback.format_exc())

diff --git a/tests/unit/test_io_convert.py b/tests/unit/test_io_convert.py
@@ -949,7 +949,7 @@ def __get_data_array(self, foo_container):
 
     def test_maxshape(self):
         """test when maxshape is set for the dataset"""
-        data = H5DataIO(data=list(range(5)), maxshape=(None,))
+        data = H5DataIO(data=list(range(5)), maxshape=(5,))
         self.__roundtrip_data(data=data)
         self.assertContainerEqual(self.out_container, self.read_container, ignore_hdmf_attrs=True)