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toward codecs and shards #32

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toward codecs and shards #32

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bd8792a
test: start of partial read benchmarks
bogovicj Aug 16, 2024
591881b
wip(test): method stub for zarr2-zarr3 disambiguation
bogovicj Sep 17, 2024
7879e36
style: N5DatasetDiscoverer code formatting
bogovicj Oct 2, 2024
1a54fe3
fix: ContainerMetadataNode
bogovicj Nov 20, 2024
78b2abf
fix: TranslatedN5Reader / Writer
bogovicj Nov 20, 2024
9e39755
zarr3
normanrz Nov 20, 2024
6a3da69
wip/chore: depend on blosc snapshot
bogovicj Nov 20, 2024
692f400
Merge branch 'main' into wip/codecsShards
bogovicj Nov 20, 2024
3abd6ac
Merge remote-tracking branch 'origin/main' into wip/codecsShards
bogovicj Nov 20, 2024
7fff426
OmeNgffMetadataParser for v0.5
brokkoli71 Nov 21, 2024
ac617f4
Merge pull request #29 from scalableminds/zarr3
bogovicj Nov 21, 2024
c44b8e9
chore: update pom-scijava and dependencies
bogovicj Jan 13, 2025
2beb682
test: demos and a benchmark
bogovicj Jan 13, 2025
8c9a1b7
test: add low level shard writing demos
bogovicj Jan 13, 2025
1b7c14e
test: ShardWritingDemos add midLevelBatch demo
bogovicj Jan 13, 2025
9d682fd
wip: writers override writeShard
bogovicj Jan 14, 2025
21b6400
test: add a shard write benchmark
bogovicj Jan 21, 2025
d1c2d17
benchmark: improve PartialReadBenchmarks
bogovicj Jan 21, 2025
36abed0
wip: implement shard methods
bogovicj Jan 22, 2025
151f945
fix/test: implement zarr v2/v3 disambiguation
bogovicj Jan 22, 2025
0905e52
fix: make sure to close N5Reader in openCompatibleWriter
bogovicj Jan 22, 2025
620a0c6
wip: zarr3 format matches .zarr extension
bogovicj Jan 22, 2025
d453d4f
refactor: renamed Ome-Zarr v0.5 metadata and parser
bogovicj Jan 23, 2025
2c342f8
perf: add OmeNgff v0.5 metadata parser to default list
bogovicj Jan 23, 2025
8110895
fix: need to catch exceptions during group parsing
bogovicj Jan 23, 2025
d84bf75
fix/test: N5Factory behavior changes for zarr3
bogovicj Jan 24, 2025
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31 changes: 24 additions & 7 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>38.0.1</version>
<version>40.0.0</version>
<relativePath />
</parent>

Expand Down Expand Up @@ -111,10 +111,14 @@
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>

<n5.version>3.3.0</n5.version>
<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
<n5-google-cloud.version>4.1.1</n5-google-cloud.version>
<n5-zarr.version>1.3.5</n5-zarr.version>
<n5.version>3.3.2-SNAPSHOT</n5.version>
<n5-aws-s3.version>4.2.2-SNAPSHOT</n5-aws-s3.version>
<n5-blosc.version>1.1.2-SNAPSHOT</n5-blosc.version>
<n5-hdf5.version>2.2.0</n5-hdf5.version>
<n5-imglib2.version>7.0.3-SNAPSHOT</n5-imglib2.version>
<n5-ij.version>4.2.6-SNAPSHOT</n5-ij.version>
<n5-google-cloud.version>4.1.2-SNAPSHOT</n5-google-cloud.version>
<n5-zarr.version>1.4.1-SNAPSHOT</n5-zarr.version>

<jackson-jq.version>1.0.0-preview.20191208</jackson-jq.version>
<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
Expand Down Expand Up @@ -148,6 +152,10 @@
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5-zarr</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
</dependency>
<dependency>
<groupId>net.thisptr</groupId>
<artifactId>jackson-jq</artifactId>
Expand All @@ -161,6 +169,7 @@
<scope>compile</scope>
</dependency>

<!-- Test dependencies -->
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5</artifactId>
Expand Down Expand Up @@ -212,8 +221,6 @@
<version>${commons-io.version}</version>
<scope>test</scope>
</dependency>


<dependency>
<groupId>io.findify</groupId>
<artifactId>s3mock_2.12</artifactId>
Expand All @@ -226,6 +233,16 @@
<version>${jaxb-api.version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.openjdk.jmh</groupId>
<artifactId>jmh-core</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.openjdk.jmh</groupId>
<artifactId>jmh-generator-annprocess</artifactId>
<scope>test</scope>
</dependency>
<!-- include imagej-legacy at test runtime -->
<dependency>
<groupId>net.imagej</groupId>
Expand Down
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