Update to new jzarr 0.4.2

[melissalinkert]

Prompted by ome/ZarrReader#54, see https://github.com/zarr-developers/jzarr.

Discussed briefly with @sbesson. I am not suggesting that we consider this for bioformats2raw 0.7.0, it's more a place to start. Whatever we decide to do here should likely be applied to other repos where we use jzarr (including but not limited to raw2ometiff).

[joshmoore]

These are probably the most relevant missing changes:

+  [gs/master~6] Array nesting: store in .zarray if set
+  [gs/master~7] Array nesting: Handle empty zarr arrays
+  [gs/master~8] Array nesting: Add the ability to use N5-style nested layout

[sbesson]

Following a discussion with @melissalinkert, a few comments:

• the com.bc.zarr:jzarr library should be considered as inactive
• the cleanup of all intermediate repositories and the ability to use Maven Central is really nice
• looking nature of the changes between the 0.3.5 and the 0.4.0 changes bcdev/jzarr@0.3.5...zarr-developers:jzarr:0.4.0, I see nothing of particular concerns:
  • essential metadata got added to the POM like the license 👍
  • a few API additions which could be consumed by the converter e.g. the multi-threaded blosc compression
  • the bump of the jackson dependency which is overriden by a more recent versions from ome:formats-gpl anyways
• at present, https://github.com/zarr-developers/jzarr feels like the best place to discuss & propose new API additions which would be relevant to the needs of this library
• we will likely need to unify the change across all conversion utilities to avoid a mixture of jzarr

Could we update

bioformats2raw/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java

Lines 270 to 273 in b7c5440

	// no getter for DimensionSeparator in ZarrArray
	// check that the correct separator was used by checking
	// that the expected first chunk file exists
	assertTrue(output.resolve("0/0/0/0/0/0/0").toFile().exists());

to use the new dimension separator getter available in the new version?

[sbesson]

👍 maybe let's just remove the outdated test comment and then this should be ready

   // no getter for DimensionSeparator in ZarrArray
    // check that the correct separator was used by checking
    // that the expected first chunk file exists

Next question is whether we want to plan a 0.7.0 release or a release candidate that can be consumed in all the related converter utility PRs adjusting the dependency to use dev.zarr

[melissalinkert]

Test comment updated in 609f092. As discussed separately, this PR should not be merged right now, pending investigation of zarr-developers/jzarr#14.

[sbesson]

Retested the last commit and confirmed that:

• the array metadata of the generated Zarr datasets no longer include the additional numThreads key
• the Zarr datasets can be opened both using the zarr-python implementation and another Java implementation e.g. raw2ometiff

A few recent maintenance issues (zarr-developers/jzarr#17) are further reinforcing my feeling expressed in #203 (review) i.e. the inactive state of com.bc.zarr:jzarr effectively elevates the dev.zarr:jzarr fork as the new reference Java implementation for the Zarr v2 specification.