Merge branch 'dev' into numpy_2

.github/workflows/project_action.yml

@@ -20,15 +20,15 @@ jobs:
       - name: Add to Developer Board
         env:
           TOKEN: ${{ steps.generate_token.outputs.token }}
-        uses: actions/add-to-project@v0.6.1
+        uses: actions/add-to-project@v1.0.1
         with:
           project-url: https://github.com/orgs/hdmf-dev/projects/7
           github-token: ${{ env.TOKEN }}
 
       - name: Add to Community Board
         env:
           TOKEN: ${{ steps.generate_token.outputs.token }}
-        uses: actions/add-to-project@v0.6.1
+        uses: actions/add-to-project@v1.0.1
         with:
           project-url: https://github.com/orgs/hdmf-dev/projects/8
           github-token: ${{ env.TOKEN }}

pyproject.toml

@@ -36,7 +36,6 @@ dependencies = [
     "pandas>=1.0.5",
     "ruamel.yaml>=0.16",
     "scipy>=1.4",
-    "zarr >= 2.12.0",
     "importlib-resources; python_version < '3.9'",  # TODO: remove when minimum python version is 3.9
 ]
 dynamic = ["version"]

src/hdmf/data_utils.py

@@ -5,7 +5,12 @@
 from warnings import warn
 from typing import Tuple
 from itertools import product, chain
-from zarr import Array as ZarrArray
+
+try:
+    from zarr import Array as ZarrArray
+    ZARR_INSTALLED = True
+except ImportError:
+    ZARR_INSTALLED = False
 
 import h5py
 import numpy as np
@@ -16,9 +21,6 @@ def append_data(data, arg):
     if isinstance(data, (list, DataIO)):
         data.append(arg)
         return data
-    elif isinstance(data, ZarrArray):
-        data.append([arg], axis=0)
-        return data
     elif type(data).__name__ == 'TermSetWrapper': # circular import
         data.append(arg)
         return data
@@ -33,6 +35,9 @@ def append_data(data, arg):
         data.resize(shape)
         data[-1] = arg
         return data
+    elif ZARR_INSTALLED and isinstance(data, ZarrArray):
+        data.append([arg], axis=0)
+        return data
     else:
         msg = "Data cannot append to object of type '%s'" % type(data)
         raise ValueError(msg)

tests/unit/utils_test/test_data_utils.py

@@ -3,9 +3,32 @@
 
 import numpy as np
 from numpy.testing import assert_array_equal
-import zarr
+
+try:
+    import zarr
+    ZARR_INSTALLED = True
+except ImportError:
+    ZARR_INSTALLED = False
+
+
+class MyIterable:
+    def __init__(self, data):
+        self.data = data
+
 
 class TestAppendData(TestCase):
+    def test_append_exception(self):
+        data = MyIterable([1, 2, 3, 4, 5])
+        with self.assertRaises(ValueError):
+            append_data(data, 4)
+
+
+class TestZarrAppendData(TestCase):
+
+    def setUp(self):
+        if not ZARR_INSTALLED:
+            self.skipTest("optional Zarr package is not installed")
+
 
     def test_append_data_zarr(self):
         zarr_array = zarr.array([1,2,3])