Multiscale labeled images

.pre-commit-config.yaml

@@ -19,7 +19,15 @@ repos:
     rev: v0.782
     hooks:
       - id: mypy
-        files: ome_zarr.py
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.782
+    hooks:
+      - id: mypy
+        args: [
+          --disallow-untyped-defs,
+          --ignore-missing-imports,
+        ]
+        exclude: tests/*|setup.py
   - repo: https://github.com/adrienverge/yamllint.git
     rev: v1.24.2
     hooks:

ome_zarr_cli.py → ome_zarr/cli.py

@@ -3,28 +3,28 @@
 import argparse
 import logging
 
-from ome_zarr import info as zarr_info
-from ome_zarr import download as zarr_download
+from .utils import info as zarr_info
+from .utils import download as zarr_download
 
 
-def config_logging(loglevel, args):
+def config_logging(loglevel: int, args: argparse.Namespace) -> None:
     loglevel = loglevel - (10 * args.verbose) + (10 * args.quiet)
     logging.basicConfig(level=loglevel)
     # DEBUG logging for s3fs so we can track remote calls
     logging.getLogger("s3fs").setLevel(logging.DEBUG)
 
 
-def info(args):
+def info(args: argparse.Namespace) -> None:
     config_logging(logging.INFO, args)
     zarr_info(args.path)
 
 
-def download(args):
+def download(args: argparse.Namespace) -> None:
     config_logging(logging.WARN, args)
     zarr_download(args.path, args.output, args.name)
 
 
-def main():
+def main() -> None:
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "-v",

ome_zarr/napari.py

@@ -0,0 +1,42 @@
+"""
+This module is a napari plugin.
+
+It implements the ``napari_get_reader`` hook specification, (to create
+a reader plugin).
+"""
+
+
+import logging
+
+from typing import Any, Callable, Optional
+from .reader import PathLike, ReaderFunction
+from .utils import parse_url
+
+
+try:
+    from napari_plugin_engine import napari_hook_implementation
+except ImportError:
+
+    def napari_hook_implementation(
+        func: Callable, *args: Any, **kwargs: Any
+    ) -> Callable:
+        return func
+
+
+LOGGER = logging.getLogger("ome_zarr.napari")
+
+
+@napari_hook_implementation
+def napari_get_reader(path: PathLike) -> Optional[ReaderFunction]:
+    """
+    Returns a reader for supported paths that include IDR ID
+
+    - URL of the form: https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/ID.zarr/
+    """
+    if isinstance(path, list):
+        path = path[0]
+    instance = parse_url(path)
+    if instance is not None and instance.is_zarr():
+        return instance.get_reader_function()
+    # Ignoring this path
+    return None