Test using zarr-dev to potentially catch regressions.

.github/workflows/build.yml

@@ -25,6 +25,8 @@ jobs:
           channels: conda-forge,ome
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
+        env:
+          ACTIONS_ALLOW_UNSECURE_COMMANDS: true
 
       - name: Run tests
         shell: bash -l {0}

.github/workflows/zarr-dev.yml

@@ -0,0 +1,38 @@
+---
+name: Build with Zarr dev
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    name: ${{ matrix.platform }} ${{ matrix.python-version }}
+    runs-on: ${{ matrix.platform }}
+
+    strategy:
+      fail-fast: true
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [3.7]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,ome
+          environment-file: environment.yml
+          python-version: ${{ matrix.python-version }}
+        env:
+          ACTIONS_ALLOW_UNSECURE_COMMANDS: true
+
+      - name: Install zarr dev
+        shell: bash -l {0}
+        run: |
+          python -m pip install git+https://github.com/zarr-developers/zarr-python.git@master
+
+      - name: Run tests
+        shell: bash -l {0}
+        run: make

environment.yml

@@ -5,7 +5,7 @@ dependencies:
   - openjdk
   - maven
   - make
-  - z5py
+  - z5py >= 2.0.8
   - python == 3.7.9
   - scikit-image
   - pytest

generate_data/generate_z5py.py

@@ -5,28 +5,32 @@
 CHUNKS = (100, 100, 1)
 
 # options for the different compressors
-COMPRESSION_OPTIONS = {'blosc': {'filter_id': 'lz4'}}
+COMPRESSION_OPTIONS = {"blosc": {"codec": "lz4"}}
 
 
 # TODO support more compressors:
 # - more compressors in numcodecs
 # - more blosc codecs
 def generate_zarr_format(compressors=['gzip', 'blosc', 'zlib', 'raw']):
-    path = '../data/z5py.zr'
+    path = 'data/z5py.zr'
     im = astronaut()
 
-    f = z5py.File(path)
+    f = z5py.File(path, mode='w')
     for compressor in compressors:
         copts = COMPRESSION_OPTIONS.get(compressor, {})
-        name = compressor if compressor != 'blosc' else '%s/%s' % (compressor, copts.get('filter_id'))
+        name = (
+            compressor
+            if compressor != "blosc"
+            else "%s/%s" % (compressor, copts.get("codec"))
+        )
         f.create_dataset(name, data=im, compression=compressor, chunks=CHUNKS, **copts)
 
 
 def generate_n5_format(compressors=['gzip', 'raw']):
-    path = '../data/z5py.n5'
+    path = 'data/z5py.n5'
     im = astronaut()
 
-    f = z5py.File(path)
+    f = z5py.File(path, mode='w')
     for compressor in compressors:
         name = compressor
         f.create_dataset(name, data=im, chunks=CHUNKS, compression=compressor)

generate_data/generate_zarr.py

@@ -4,40 +4,41 @@
 
 # choose chunks s.t. we do have overhanging edge-chunks
 CHUNKS = (100, 100, 1)
-STR_TO_COMPRESSOR = {'gzip': numcodecs.GZip,
-                     'blosc': numcodecs.Blosc,
-                     'zlib': numcodecs.Zlib}
-COMPRESSION_OPTIONS = {'blosc': {'filter_id': 'lz4'}}
+STR_TO_COMPRESSOR = {
+    "gzip": numcodecs.GZip,
+    "blosc": numcodecs.Blosc,
+    "zlib": numcodecs.Zlib,
+}
+COMPRESSION_OPTIONS = {"blosc": {"cname": "lz4"}}
 
 
 # TODO use more compressors from numcodecs and more blosc filter_ids
 def generate_zarr_format(compressors=['gzip', 'blosc', 'zlib', None]):
-    path = '../data/zarr.zr'
+    path = 'data/zarr.zr'
     im = astronaut()
 
-    f = zarr.open(path)
+    f = zarr.open(path, mode='w')
     for compressor in compressors:
         copts = COMPRESSION_OPTIONS.get(compressor, {})
         if compressor is None:
-            name = 'taw'
-        elif compressor == 'blosc':
-            name = '%s/%s' % (compressor, copts.get('filter_id'))
+            name = "raw"
+        elif compressor == "blosc":
+            name = "%s/%s" % (compressor, copts.get("cname"))
         else:
             name = compressor
         compressor_impl = STR_TO_COMPRESSOR[compressor](**copts) if compressor is not None else None
         f.create_dataset(name, data=im, chunks=CHUNKS,
                          compressor=compressor_impl)
 
 
-# this needs PR https://github.com/zarr-developers/zarr/pull/309
 def generate_n5_format(compressors=['gzip', None]):
-    path = '../data/zarr.n5'
+    path = 'data/zarr.n5'
     im = astronaut()
 
-    f = zarr.open(path)
+    f = zarr.open(path, mode='w')
     for compressor in compressors:
         name = compressor if compressor is not None else 'raw'
-        compressor_impl = STR_TO_COMPRESSOR[compressor] if compressor is not None else None
+        compressor_impl = STR_TO_COMPRESSOR[compressor]() if compressor is not None else None
         f.create_dataset(name, data=im, chunks=CHUNKS,
                          compressor=compressor_impl)
 

test/test_read_all.py

@@ -40,6 +40,8 @@
 
 def read_with_zarr(fpath, ds_name):
     import zarr
+    if ds_name == "blosc":
+        ds_name = "blosc/lz4"
     return zarr.open(os.fspath(fpath))[ds_name][:]
 
 
@@ -50,6 +52,8 @@ def read_with_pyn5(fpath, ds_name):
 
 def read_with_z5py(fpath, ds_name):
     import z5py
+    if ds_name == "blosc":
+        ds_name = "blosc/lz4"
     return z5py.File(fpath)[ds_name][:]