Remove zarr workarounds and update zarr

Author: benjeffery

requirements/CI-tests-complete/requirements.txt

@@ -17,4 +17,4 @@ seaborn==0.11.1
 sortedcontainers==2.3.0
 tqdm==4.60.0
 tskit==0.4.1
-zarr==2.11.1
+zarr==2.11.3

requirements/CI-tests-conda/requirements.txt

@@ -1,5 +1,5 @@
 lmdb==0.9.24
 msprime==1.0.2
 python-lmdb==0.96
-zarr==2.11.1
+zarr==2.11.3
 h5py<3.4

requirements/development.txt

@@ -9,7 +9,7 @@ humanize
 daiquiri
 msprime >= 1.0.0
 tskit >= 0.4.1
-zarr!=2.11.0
+zarr!=2.11.0, !=2.11.1, !=2.11.2
 lmdb
 pytest
 pytest-xdist

setup.py

@@ -83,8 +83,8 @@ def finalize_options(self):
         "daiquiri",
         "tskit>=0.3.7",
         "numcodecs>=0.6",
-        # issues 965 and 967 at zarr-python prevent usage of 2.11.0
-        "zarr>=2.2,!=2.11.0",
+        # issues 965 and 967 at zarr-python prevent usage of 2.11.0 and 2.11.1
+        "zarr>=2.2,!=2.11.0,!=2.11.1,!=2.11.2",
         "lmdb",
         "sortedcontainers",
         "attrs>=19.2.0",

tsinfer/formats.py

@@ -406,7 +406,6 @@ def __init__(
             compressor=self._compressor,
             dtype=object,
             object_codec=self._metadata_codec,
-            fill_value=None,
         )
         provenances_group.create_dataset(
             "record",
@@ -415,7 +414,6 @@ def __init__(
             compressor=self._compressor,
             dtype=object,
             object_codec=self._metadata_codec,
-            fill_value=None,
         )
 
     def __enter__(self):
@@ -949,7 +947,6 @@ def __init__(self, sequence_length=0, **kwargs):
             compressor=self._compressor,
             dtype=object,
             object_codec=self._metadata_codec,
-            fill_value=None,
         )
         populations_group.attrs["metadata_schema"] = None
         self._populations_writer = BufferedItemWriter(
@@ -965,15 +962,13 @@ def __init__(self, sequence_length=0, **kwargs):
             compressor=self._compressor,
             dtype=object,
             object_codec=self._metadata_codec,
-            fill_value=None,
         )
         location = individuals_group.create_dataset(
             "location",
             shape=(0,),
             chunks=chunks,
             compressor=self._compressor,
             dtype="array:f8",
-            fill_value=None,
         )
         time = individuals_group.create_dataset(
             "time",
@@ -1050,7 +1045,6 @@ def __init__(self, sequence_length=0, **kwargs):
             compressor=self._compressor,
             dtype=object,
             object_codec=self._metadata_codec,
-            fill_value=None,
         )
         sites_group.create_dataset(
             "metadata",
@@ -1059,7 +1053,6 @@ def __init__(self, sequence_length=0, **kwargs):
             compressor=self._compressor,
             dtype=object,
             object_codec=self._metadata_codec,
-            fill_value=None,
         )
 
         self._last_position = 0
@@ -2215,15 +2208,13 @@ def __init__(self, sample_data, **kwargs):
             chunks=chunks,
             dtype="array:i4",
             compressor=self._compressor,
-            fill_value=None,
         )
         self.data.create_dataset(
             "ancestors/haplotype",
             shape=(0,),
             chunks=chunks,
             dtype="array:i1",
             compressor=self._compressor,
-            fill_value=None,
         )
 
         self._alloc_ancestor_writer()