Minor doc cleanups/improvements (#288)

* Remove nav tabs

* Fix tutorial comments

* Add zarr interlinks

* Clean CLI docs

* Add CLi validation to how do page

* Fix attribute access docs

* Clean up wellgroupnotfounderror docs

* Add docs for plate end/start times

Author: dstansby

docs/api/common/well.md

@@ -0,0 +1,3 @@
+# Well
+
+::: ome_zarr_models.common.well

docs/api/index.md

@@ -4,7 +4,7 @@ This package contains a number of classes representing _OME-Zarr groups_.
 Each of these classes represent a single OME-Zarr group.
 
 Each group has a set of associated _metadata attributes_, which provide a listing of the OME-Zarr attributes available for each group.
-To access these, use the `.attributes` property on the group objects.
+To access these, use the `.ome_attributes` property on the group objects.
 
 A listing of the group objects and associated metadata objects is given below for each version of the OME-Zarr specification.
 

docs/cli.md

@@ -1,6 +1,7 @@
 # Command line interface
 
-`ome-zarr-models` has a command line interface.
+`ome-zarr-models` can validate and show metadata using a command line interface.
+
 To see available commands,
 
 ```sh
@@ -34,13 +35,13 @@ ome-zarr-models validate https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/E
 ✅ Valid OME-Zarr
 ```
 
-The group can be specified as any string that can be parsed by **link to zarr.open_group**.
+The group can be specified as any string that can be parsed by [zarr.open_group][].
 
 ## Info
 
 To get information about an OME-Zarr group, pass the path to a group to `ome-zarr-models info`.
 This will print the metadata (see below for an example).
-If you have the `rich` Python package installed, a more readable output will be produced.
+If you have the [`rich`](https://rich.readthedocs.io) Python package installed, a more readable output will be produced.
 
 ```sh
 ome-zarr-models info https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpD_chicken_embryo_MIP.ome.zarr

docs/how-to.md

@@ -2,6 +2,12 @@
 
 ## Validate an OME-Zarr group
 
+### Command line
+
+Use `ome-zarr-models validate <path to group>`.
+
+### Python
+
 If you know what type of group it is, use the `from_zarr()` method on [one of the group objects](api/index.md):
 
 ```python

docs/tutorial.py

@@ -1,6 +1,5 @@
-# # Tutorial
-#
-# This tutorial provides a full worked example of using `ome-zarr-models`
+# This tutorial provides a full worked example of using `ome-zarr-models` in Python
+
 import os
 import tempfile
 
@@ -24,6 +23,7 @@
     "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpD_chicken_embryo_MIP.ome.zarr",
     mode="r",
 )
+
 # If you're not sure what type or OME-Zarr version of data you have, you can
 # use `open_ome_zarr()` to automatically 'guess' the correct group:
 
@@ -75,7 +75,6 @@
 # First, we need to create `ArraySpec` objects, which tell `ome-zarr-models`
 # what the structure of the data arrays will be.
 
-
 array_specs: list[AnyArraySpec] = [
     ArraySpec(
         shape=(100, 100),

mkdocs.yml

@@ -8,7 +8,6 @@ theme:
   icon:
     repo: fontawesome/brands/github
   features:
-    - navigation.tabs
     - navigation.indexes
   palette:
     # Palette toggle for light mode
@@ -48,10 +47,11 @@ plugins:
       handlers:
         python:
           paths: [src]
-          import:
+          inventories:
             - https://docs.python.org/3/objects.inv
             - https://pydantic-zarr.readthedocs.io/stable/objects.inv
             - https://docs.pydantic.dev/latest/objects.inv
+            - https://zarr.readthedocs.io/en/stable/objects.inv
 
           options:
             docstring_style: numpy
@@ -104,6 +104,7 @@ nav:
       - Shared:
           - Base objects: api/common/base.md
           - Validation: api/common/validation.md
+          - Well: api/common/well.md
   - Changelog: changelog.md
   - Contributing: contributing.md
 

src/ome_zarr_models/_v06/hcs.py

@@ -118,7 +118,7 @@ def get_well_group(self, i: int) -> Well:
 
         Raises
         ------
-        WellGroupNotFoundError :
+        WellGroupNotFoundError
             If no Zarr group is found at the well path.
         """
         if self.members is None:

src/ome_zarr_models/common/plate.py

@@ -38,8 +38,12 @@ class Acquisition(BaseAttrs):
         description="Maximum number of fields of view for the acquisition",
     )
     description: str | None = None
-    starttime: int | None = None
-    endtime: int | None = None
+    starttime: int | None = Field(
+        default=None, description="Integer epoch timestamp of acquisition start time"
+    )
+    endtime: int | None = Field(
+        default=None, description="Integer epoch timestamp of acquisition end time"
+    )
 
 
 class WellInPlate(BaseAttrs):

src/ome_zarr_models/v04/hcs.py

@@ -113,7 +113,7 @@ def get_well_group(self, i: int) -> Well:
 
         Raises
         ------
-        WellGroupNotFoundError :
+        WellGroupNotFoundError
             If no Zarr group is found at the well path.
         """
         if self.members is None:

src/ome_zarr_models/v05/hcs.py

@@ -119,7 +119,7 @@ def get_well_group(self, i: int) -> Well:
 
         Raises
         ------
-        WellGroupNotFoundError :
+        WellGroupNotFoundError
             If no Zarr group is found at the well path.
         """
         if self.members is None: