Handle legacy nested datasets (with tests) (#850)

* Fix #840

* Add legacy tests (See #840)

Each fixture (flat & nested) should have a version
which does not include any new metadata.

* Fix PEP8 issues

* Try dropping editable installs

see: pypa/pip#10573

* Handle case of store being a dict

* Exclude unexpected failure from code coverage

* Add 2.10.2 release notes

Author: joshmoore

.github/workflows/minimal.yml

@@ -24,5 +24,5 @@ jobs:
       shell: "bash -l {0}"
       run: |
         conda activate minimal
-        python -m pip install -e .
+        python -m pip install .
         pytest -svx

.github/workflows/python-package.yml

@@ -57,7 +57,7 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install -U pip setuptools wheel codecov line_profiler
         python -m pip install -rrequirements_dev_minimal.txt numpy${{ matrix.numpy_version}} -rrequirements_dev_optional.txt pymongo redis
-        python -m pip install -e . 
+        python -m pip install .
         python -m pip freeze
     - name: Tests
       shell: "bash -l {0}"

.github/workflows/windows-testing.yml

@@ -39,7 +39,7 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -U pip setuptools wheel
           python -m pip install -r requirements_dev_numpy.txt -r requirements_dev_minimal.txt -r requirements_dev_optional.txt
-          python -m pip install -e .
+          python -m pip install .
           python -m pip freeze
           npm install -g azurite
       - name: Run Tests

docs/release.rst

@@ -6,6 +6,17 @@ Release notes
 Unreleased
 ----------
 
+.. _release_2.10.2:
+
+2.10.2
+------
+
+Bug fixes
+~~~~~~~~~
+
+* Fix NestedDirectoryStore datasets without dimension_separator metadata.
+  By :user:`Josh Moore <joshmoore>`; :issue:`850`.
+
 .. _release_2.10.1:
 
 2.10.1

fixture/flat/.zarray

@@ -10,6 +10,7 @@
         "id": "blosc",
         "shuffle": 1
     },
+    "dimension_separator": ".",
     "dtype": "<i8",
     "fill_value": 0,
     "filters": null,
@@ -19,4 +20,4 @@
         2
     ],
     "zarr_format": 2
-}
+}

fixture/flat_legacy/.zarray

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        2,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        2,
+        2
+    ],
+    "zarr_format": 2
+}

fixture/flat_legacy/0.0

@@ -0,0 +1,22 @@
+{
+    "chunks": [
+        2,
+        2
+    ],
+    "compressor": {
+        "blocksize": 0,
+        "clevel": 5,
+        "cname": "lz4",
+        "id": "blosc",
+        "shuffle": 1
+    },
+    "dtype": "<i8",
+    "fill_value": 0,
+    "filters": null,
+    "order": "C",
+    "shape": [
+        2,
+        2
+    ],
+    "zarr_format": 2
+}

fixture/nested_legacy/.zarray

@@ -195,7 +195,18 @@ def _load_metadata_nosync(self):
             self._dtype = meta['dtype']
             self._fill_value = meta['fill_value']
             self._order = meta['order']
-            self._dimension_separator = meta.get('dimension_separator', '.')
+
+            dimension_separator = meta.get('dimension_separator', None)
+            if dimension_separator is None:
+                try:
+                    dimension_separator = self._store._dimension_separator
+                except (AttributeError, KeyError):
+                    pass
+
+                # Fallback for any stores which do not choose a default
+                if dimension_separator is None:
+                    dimension_separator = "."
+            self._dimension_separator = dimension_separator
 
             # setup compressor
             config = meta['compressor']