Merge pull request #13 from ome/dependabot/github_actions/actions-a22…

…372143e build(deps): bump codecov/codecov-action from 4.3.0 to 4.5.0 in the actions group
ome · Jul 31, 2024 · 0d93df8 · 0d93df8
2 parents 2d7cb4f + d59787c
commit 0d93df8
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Showing 25 changed files with 338 additions and 282 deletions.
diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -7,7 +7,8 @@ full_name: Josh Moore
 license: BSD
 org: ome
 project_name: ome2024-ngff-challenge
-project_short_description: Tools for converting OME-Zarr data within the ome2024-ngff-challenge
-    (see https://forum.image.sc/t/ome2024-ngff-challenge/97363)
+project_short_description:
+  Tools for converting OME-Zarr data within the ome2024-ngff-challenge (see
+  https://forum.image.sc/t/ome2024-ngff-challenge/97363)
 url: https://github.com/ome/ome2024-ngff-challenge
 vcs: true
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -42,12 +42,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.12"]
-        runs-on: [ubuntu-latest, macos-latest, windows-latest]
-
-        include:
-          - python-version: pypy-3.10
-            runs-on: ubuntu-latest
+        python-version: ["3.10", "3.12"]
+        runs-on: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v4
@@ -68,6 +64,6 @@ jobs:
           --durations=20
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v4.3.0
+        uses: codecov/codecov-action@v4.5.0
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -43,7 +43,7 @@ repos:
     rev: "v0.4.1"
     hooks:
       - id: ruff
-        args: ["--fix", "--show-fixes"]
+        args: ["--fix", "--show-fixes", "--exclude=dev*"]
       - id: ruff-format
 
   # - repo: https://github.com/pre-commit/mirrors-mypy

diff --git a/dev1/convert_zarr_v2_to_v3/convert_zarr_v2_to_v3.py b/dev1/convert_zarr_v2_to_v3/convert_zarr_v2_to_v3.py
@@ -13,8 +13,8 @@
 def convert_zarr_v2_to_v3(input_url, output_url, is_root=True):
     # Uses Zarr v2 for reading, Zarr(ita) v3 for writing
     # reader
-    input_root = zarr.open_group(store=input_url)    # does not seem to support https URLs
-    print(f'Processing {input_root.store.path}')
+    input_root = zarr.open_group(store=input_url)  # does not seem to support https URLs
+    print(f"Processing {input_root.store.path}")
 
     if is_root:
         if input_root:
@@ -24,7 +24,7 @@ def convert_zarr_v2_to_v3(input_url, output_url, is_root=True):
             root = zarrita.Group.create(store=output_url)
             root.update_attributes(update_omezarr_attributes(input_root.attrs.asdict()))
         else:
-            raise FileNotFoundError(f'Error parsing {input_url}')
+            raise FileNotFoundError(f"Error parsing {input_url}")
 
     # writer
     for label in input_root:
@@ -33,29 +33,33 @@ def convert_zarr_v2_to_v3(input_url, output_url, is_root=True):
         output_path = output_url + content.name
         if isinstance(content, zarr.Group):
             # create zarr group
-            zarrita.Group.create(store=output_path,
-                                 attributes=update_omezarr_attributes(content.attrs.asdict()))
+            zarrita.Group.create(
+                store=output_path,
+                attributes=update_omezarr_attributes(content.attrs.asdict()),
+            )
             convert_zarr_v2_to_v3(input_path, output_path, is_root=False)
         elif isinstance(content, zarr.Array):
             codecs = [bytes_codec(), blosc_codec(typesize=4)]
-            output_array = zarrita.Array.create(output_path,
-                                                shape=content.shape,
-                                                chunk_shape=content.chunks,
-                                                dtype=content.dtype,
-                                                codecs=codecs,
-                                                attributes=update_omezarr_attributes(content.attrs.asdict()))
+            output_array = zarrita.Array.create(
+                output_path,
+                shape=content.shape,
+                chunk_shape=content.chunks,
+                dtype=content.dtype,
+                codecs=codecs,
+                attributes=update_omezarr_attributes(content.attrs.asdict()),
+            )
             output_array[:] = content
         else:
-            print(f'Unsupported content {content}')
+            print(f"Unsupported content {content}")
 
 
 def convert_ome_zarr_v2_to_v3(input_url, output_url):
     # Uses Ome-Zarr v2 for reading, Zarr(ita) v3 for writing
-    location = parse_url(input_url)    # supports https URLs*
+    location = parse_url(input_url)  # supports https URLs*
     if location is None:
         # * under particular conditions the URL/zarr is not detected (internal .exists() returns False)
         # caused by OS / PyCharm / version / pytest?
-        raise FileNotFoundError(f'Error parsing {input_url}')
+        raise FileNotFoundError(f"Error parsing {input_url}")
 
     reader = Reader(location)
     input_root_path = os.path.normpath(reader.zarr.path)
@@ -65,34 +69,42 @@ def convert_ome_zarr_v2_to_v3(input_url, output_url):
         shutil.rmtree(output_url)
 
     for image_node in reader():
-        print(f'Processing {image_node}')
+        print(f"Processing {image_node}")
         metadata = image_node.metadata
-        axes = metadata.get('axes', [])
-        dimension_order = ''.join([axis.get('name') for axis in axes])
-        output_path = os.path.normpath(image_node.zarr.path).replace(input_root_path, output_url)
+        axes = metadata.get("axes", [])
+        dimension_order = "".join([axis.get("name") for axis in axes])
+        output_path = os.path.normpath(image_node.zarr.path).replace(
+            input_root_path, output_url
+        )
         output_store_path = zarrita.store.make_store_path(output_path)
         # create zarr group
-        output_zarr = zarrita.Group.create(store=output_store_path,
-                                           attributes=update_omezarr_attributes(image_node.zarr.root_attrs))
+        output_zarr = zarrita.Group.create(
+            store=output_store_path,
+            attributes=update_omezarr_attributes(image_node.zarr.root_attrs),
+        )
 
         for level, data in enumerate(image_node.data):
             codecs = [bytes_codec(), blosc_codec(typesize=4)]
             # create zarr array
-            output_array = output_zarr.create_array(str(level),
-                                                    shape=data.shape,
-                                                    chunk_shape=data.chunksize,
-                                                    dtype=data.dtype,
-                                                    codecs=codecs)
-            output_array[:] = np.array(data)    # set only supports ndarray; TODO: wrap inside (dask) chunking?
+            output_array = output_zarr.create_array(
+                str(level),
+                shape=data.shape,
+                chunk_shape=data.chunksize,
+                dtype=data.dtype,
+                codecs=codecs,
+            )
+            output_array[:] = np.array(
+                data
+            )  # set only supports ndarray; TODO: wrap inside (dask) chunking?
 
 
-if __name__ == '__main__':
-    #input_url = 'D:/slides/6001240.zarr'
-    input_url = 'https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr'
-    output_url = 'D:/slides/test/' + os.path.basename(input_url)
+if __name__ == "__main__":
+    # input_url = 'D:/slides/6001240.zarr'
+    input_url = "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
+    output_url = "D:/slides/test/" + os.path.basename(input_url)
 
-    #convert_zarr_v2_to_v3(input_url, output_url)
+    # convert_zarr_v2_to_v3(input_url, output_url)
 
     convert_ome_zarr_v2_to_v3(input_url, output_url)
 
-    print('done')
+    print("done")
diff --git a/dev1/convert_zarr_v2_to_v3/environmentv2_3.yml b/dev1/convert_zarr_v2_to_v3/environmentv2_3.yml
@@ -1,13 +1,13 @@
 name: ome2024-ngff-challenge-v2_3
 channels:
- - ome
- - conda-forge
- - defaults
+  - ome
+  - conda-forge
+  - defaults
 dependencies:
- - python=3.10
- - numpy
- - zarr==2.18
- - ome-zarr==0.9
- - pip
- - pip:
-   - zarrita
+  - python=3.10
+  - numpy
+  - zarr==2.18
+  - ome-zarr==0.9
+  - pip
+  - pip:
+      - zarrita
diff --git a/dev1/convert_zarr_v2_to_v3/util.py b/dev1/convert_zarr_v2_to_v3/util.py
@@ -1,22 +1,30 @@
 def update_omezarr_attributes(attributes):
-    new_attributes = replace_attributes_value(attributes, search_label='version', new_value='0.5-dev1')
+    new_attributes = replace_attributes_value(
+        attributes, search_label="version", new_value="0.5-dev1"
+    )
     return new_attributes
 
 
 def replace_attributes_value(values, search_label, new_value):
     if isinstance(values, dict):
         new_values = {}
         for label, value in values.items():
-            if isinstance(label, str) and not label.startswith('_'):
-                new_values[label] = replace_attributes_value(value, search_label=search_label, new_value=new_value)
+            if isinstance(label, str) and not label.startswith("_"):
+                new_values[label] = replace_attributes_value(
+                    value, search_label=search_label, new_value=new_value
+                )
             else:
                 new_values[label] = value
         if search_label in values:
             new_values[search_label] = new_value
     elif isinstance(values, list):
         new_values = []
         for item in values:
-            new_values.append(replace_attributes_value(item, search_label=search_label, new_value=new_value))
+            new_values.append(
+                replace_attributes_value(
+                    item, search_label=search_label, new_value=new_value
+                )
+            )
     else:
         new_values = values
     return new_values
diff --git a/dev1/environment.yaml b/dev1/environment.yaml
@@ -2,8 +2,8 @@ channels:
   - conda-forge
 dependencies:
   - tensorstore
-  - 'numpy<2'
-  - zarr  # loads dependencies
+  - "numpy<2"
+  - zarr # loads dependencies
   - pip:
       - "--editable=git+https://github.com/will-moore/ome-zarr-py.git@zarr_v3_support#egg=ome-zarr"
       - "--editable=git+https://github.com/zarr-developers/zarr-python.git@v3#egg=zarr"
diff --git a/dev1/environment_windows.yml b/dev1/environment_windows.yml
@@ -4,7 +4,7 @@ channels:
 dependencies:
   - python=3.10
   - numpy<2
-  - zarr  # loads dependencies
+  - zarr # loads dependencies
   - pip
   - pip:
       - tensorstore

diff --git a/dev1/resave.py b/dev1/resave.py
@@ -7,6 +7,7 @@
 import tensorstore as ts
 
 import argparse
+
 parser = argparse.ArgumentParser()
 parser.add_argument("input_path")
 parser.add_argument("output_path")
@@ -22,32 +23,38 @@
 
 
 def convert_array(input_path, output_path):
-    read = ts.open({
-        'driver': 'zarr',
-        'kvstore': {
-            'driver': 'file',
-            'path': input_path,
-        },
-    }).result()
+    read = ts.open(
+        {
+            "driver": "zarr",
+            "kvstore": {
+                "driver": "file",
+                "path": input_path,
+            },
+        }
+    ).result()
 
     shape = read.shape
-    chunks= read.schema.chunk_layout.read_chunk.shape
+    chunks = read.schema.chunk_layout.read_chunk.shape
 
-    write = ts.open({
-        "driver": "zarr3",
-        "kvstore": {
-            "driver": "file",
-            "path": output_path
-        },
-        "metadata": {
-            "shape": shape,
-            "chunk_grid": {"name": "regular", "configuration": {"chunk_shape": chunks}},
-            "chunk_key_encoding": {"name": "default"},
-            "codecs": [{"name": "blosc", "configuration": {"cname": "lz4", "clevel": 5}}],
-            "data_type": read.dtype,
-        },
-        "create": True,
-    }).result()
+    write = ts.open(
+        {
+            "driver": "zarr3",
+            "kvstore": {"driver": "file", "path": output_path},
+            "metadata": {
+                "shape": shape,
+                "chunk_grid": {
+                    "name": "regular",
+                    "configuration": {"chunk_shape": chunks},
+                },
+                "chunk_key_encoding": {"name": "default"},
+                "codecs": [
+                    {"name": "blosc", "configuration": {"cname": "lz4", "clevel": 5}}
+                ],
+                "data_type": read.dtype,
+            },
+            "create": True,
+        }
+    ).result()
 
     future = write.write(read)
     future.result()
@@ -76,6 +83,5 @@ def convert_array(input_path, output_path):
 for ds in multiscales[0]["datasets"]:
     ds_path = ds["path"]
     convert_array(
-        os.path.join(ns.input_path, ds_path),
-        os.path.join(ns.output_path, ds_path)
+        os.path.join(ns.input_path, ds_path), os.path.join(ns.output_path, ds_path)
     )
diff --git a/dev2/.pre-commit-config.yaml b/dev2/.pre-commit-config.yaml
@@ -1,12 +1,11 @@
 ---
 repos:
-
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  # Ruff version.
-  rev: v0.5.5
-  hooks:
-    # Run the linter.
-    - id: ruff
-      args: [ "--fix" ]
-    # Run the formatter.
-    - id: ruff-format
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.5.5
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: ["--fix"]
+      # Run the formatter.
+      - id: ruff-format
diff --git a/dev2/environment.yaml b/dev2/environment.yaml
@@ -3,13 +3,13 @@ channels:
 dependencies:
   - napari
   - pyqt
-  - 'numpy<2'
+  - "numpy<2"
   - tensorstore # loads dependencies
-  - zarr  # loads dependencies
+  - zarr # loads dependencies
   - tqdm
   - pip
   - pip:
       - "--editable=git+https://github.com/will-moore/ome-zarr-py.git@zarr_v3_support#egg=ome-zarr"
       - "--editable=git+https://github.com/zarr-developers/zarr-python.git@v3#egg=zarr"
       - "--editable=git+https://github.com/ome/napari-ome-zarr.git@v3#egg=napari-ome-zarr"
-      - 'tensorstore>=0.1.63'
+      - "tensorstore>=0.1.63"
diff --git a/dev2/resave.py b/dev2/resave.py
@@ -52,7 +52,7 @@ class TSMetrics:
     Instances of this class capture the current tensorstore metrics.
 
     If an existing instance is passed in on creation, it will be stored
-    in order to deduct prevoius values from those measured by this instance.
+    in order to deduct previous values from those measured by this instance.
     """
 
     CHUNK_CACHE_READS = "/tensorstore/cache/chunk_cache/reads"
@@ -217,7 +217,7 @@ def convert_array(
     future.result()
     after = TSMetrics(read_config, write_config, before)
 
-    print(f"""Reencode (tensorstore) {input_path} to {output_path}
+    print(f"""Re-encode (tensorstore) {input_path} to {output_path}
         read: {after.read()}
         write: {after.written()}
         time: {after.elapsed()}