hdmf-dev/hdmf-zarr issues and pull requests

#224 - [Feature]: improve html representation of Zarr Arrays in NWB

Issue - State: open - Opened by stephprince 17 days ago

#223 - [Feature]: Rework export

Issue - State: open - Opened by mavaylon1 20 days ago

#222 - [Bug]: error when validating ElectricalSeries in NWB Zarr file

Issue - State: open - Opened by stephprince 25 days ago - 2 comments

#221 - [Bug]: validation error on NWB Zarr file

Issue - State: open - Opened by CodyCBakerPhD about 2 months ago - 3 comments
Labels: category: bug, priority: medium

#220 - [Bug]: datetimes in pynwb.validate on NWB Zarr

Issue - State: open - Opened by CodyCBakerPhD about 2 months ago - 1 comment
Labels: category: bug, priority: low

#219 - Writing a name with colon `:` fails in zarr in windows

Issue - State: open - Opened by h-mayorquin 2 months ago - 9 comments
Labels: category: enhancement, priority: medium

#218 - Release 0.9.0

Pull Request - State: closed - Opened by mavaylon1 2 months ago - 1 comment

#217 - Update upload-artifact action to match download-artifact

Pull Request - State: closed - Opened by rly 2 months ago - 1 comment

#216 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: compatability: dependencies, github_actions

#215 - added link_data --> clear_cache relationship to support repacking zarr nwbfiles

Pull Request - State: closed - Opened by pauladkisson 3 months ago - 17 comments

#214 - Numpy 2.0 gallery

Pull Request - State: open - Opened by mavaylon1 3 months ago - 1 comment

#213 - [Bug]: numpy 2.0 causes pynwb ZarrIO tutorial to fail

Issue - State: open - Opened by pauladkisson 3 months ago - 16 comments
Labels: category: bug, priority: high

#212 - Support Pathlib

Pull Request - State: open - Opened by mavaylon1 3 months ago - 3 comments

#211 - [Bug]: NWB Zarr to HDMF export fails

Issue - State: open - Opened by rcpeene 3 months ago - 8 comments
Labels: category: bug, priority: medium

#210 - Numpy 2.0

Pull Request - State: closed - Opened by mavaylon1 3 months ago - 1 comment

#209 - [Feature]: Support numpy 2.0

Issue - State: closed - Opened by rly 4 months ago
Labels: category: enhancement, priority: low

#208 - [Bug]: Reading and exporting Zarr NWB fails to copy over table information

Issue - State: open - Opened by rcpeene 4 months ago - 3 comments
Labels: category: bug, priority: medium

#207 - Xarray Support

Pull Request - State: closed - Opened by mavaylon1 4 months ago - 4 comments

#206 - S3 test

Pull Request - State: closed - Opened by mavaylon1 4 months ago - 1 comment

#205 - [Bug]: `[0.7.0, 0.8.0]` Fails to open file with consolidated metadata from S3

Issue - State: open - Opened by bjhardcastle 4 months ago - 24 comments
Labels: category: bug, priority: medium

#204 - default load_namespace

Pull Request - State: closed - Opened by mavaylon1 4 months ago - 5 comments

#203 - Append References

Pull Request - State: closed - Opened by mavaylon1 5 months ago - 7 comments

#202 - [Feature]: Support zarr-python v3

Issue - State: open - Opened by rly 5 months ago
Labels: category: enhancement

#201 - Limit zarr<3

Pull Request - State: closed - Opened by rly 5 months ago

#200 - [Bug]: Pre-release daily workflows failing with zarr 3.0.0a0

Issue - State: closed - Opened by rly 5 months ago - 2 comments
Labels: category: bug

#199 - Release 0.8.0

Pull Request - State: closed - Opened by mavaylon1 6 months ago - 1 comment

#198 - [Feature]: NWBZarrIO should have load_namespaces=True by default

Issue - State: closed - Opened by rly 6 months ago - 2 comments
Labels: category: enhancement

#197 - [Bug]: Writing NWB with `experimenter` (or any `ArrayLike[str]`) fails

Issue - State: open - Opened by bjhardcastle 6 months ago - 4 comments
Labels: category: bug, priority: low

#196 - [Feature]: Explore use of Zarrita

Issue - State: open - Opened by oruebel 6 months ago - 2 comments
Labels: category: proposal, priority: low

#195 - Update for zarr 2.18.0 and zarr 2.18.1

Pull Request - State: closed - Opened by mavaylon1 6 months ago - 5 comments

#194 - Broken Links when Exporting

Pull Request - State: open - Opened by mavaylon1 6 months ago - 11 comments

#193 - Don't open with consolidated metadata in mode r+

Pull Request - State: closed - Opened by mavaylon1 6 months ago - 2 comments

#192 - [Bug]: Zarr 2.18.0 with Blosc

Issue - State: closed - Opened by CodyCBakerPhD 6 months ago - 5 comments
Labels: category: bug, priority: medium

#191 - [Feature]: Use `copy_store` for copying existing zarr data

Issue - State: open - Opened by bjhardcastle 6 months ago - 5 comments
Labels: category: proposal, priority: medium, topic: ZarrIO

#190 - Bump tqdm from 4.66.1 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 2 comments
Labels: compatability: dependencies

#189 - Release 0.7.0

Pull Request - State: closed - Opened by mavaylon1 7 months ago - 1 comment

#188 - Update coverage call, don't install in editable mode in testing

Pull Request - State: closed - Opened by rly 7 months ago - 1 comment

#187 - Update pyproject.toml

Pull Request - State: closed - Opened by mavaylon1 7 months ago - 6 comments
Labels: category: bug

#186 - Zarr datasets info lack compression data

Issue - State: open - Opened by h-mayorquin 7 months ago - 3 comments
Labels: category: bug, priority: low

#185 - [Bug]: Remote read with/without consolidated metadata is not being tested

Issue - State: closed - Opened by oruebel 7 months ago
Labels: category: bug, priority: medium, topic: testing

#184 - Fix bug in ZarrIO.__open_consolidated

Pull Request - State: closed - Opened by oruebel 7 months ago - 2 comments

#183 - Add sdupport for r- read mode to read without consolidated metadata

Pull Request - State: closed - Opened by oruebel 7 months ago - 2 comments

#182 - [Bug]: NWBZarrIO appending

Issue - State: closed - Opened by CodyCBakerPhD 8 months ago - 7 comments
Labels: category: bug, priority: high, topic: storage

#181 - [Feature]: Support pathlib.Path in ZarrIO

Issue - State: open - Opened by CodyCBakerPhD 8 months ago
Labels: category: bug, priority: low

#180 - Clean Up Documentation

Pull Request - State: closed - Opened by mavaylon1 8 months ago - 2 comments

#179 - [Bug]: `export` fails to correctly save units after adding columns

Issue - State: open - Opened by alejoe91 8 months ago - 9 comments
Labels: category: bug, priority: medium, topic: storage

#178 - Update GitHub release checklist

Pull Request - State: closed - Opened by rly 8 months ago - 1 comment

#177 - [Documentation]: `linkable` key has been deprecated

Issue - State: closed - Opened by oruebel 8 months ago - 2 comments

#176 - [Feature]: write `xarray`-compatible Zarr files

Issue - State: closed - Opened by alejoe91 8 months ago - 9 comments
Labels: category: proposal, priority: medium, topic: storage

#175 - Bump black from 23.10.1 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: compatability: dependencies

#174 - kerchunk considerations

Issue - State: closed - Opened by magland 8 months ago - 23 comments

#173 - default object_codec_class -> JSON

Pull Request - State: closed - Opened by magland 9 months ago - 19 comments

#172 - Update to support python 3.12

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 7 comments
Labels: category: enhancement, priority: high

#171 - [Feature]: Write zarr without using pickle

Issue - State: open - Opened by magland 9 months ago - 5 comments
Labels: category: enhancement, priority: low

#170 - Update release.md

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 2 comments

#169 - [Feature]: Refactor tox.ini to match HDMF

Issue - State: open - Opened by mavaylon1 9 months ago
Labels: category: enhancement, priority: low

#168 - Update deploy_release.yml

Pull Request - State: closed - Opened by mavaylon1 9 months ago

#167 - Release 0.6.0

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 1 comment

#166 - [Feature]: support Python 3.12

Issue - State: closed - Opened by bendichter 9 months ago - 4 comments

#165 - Update deprecated actions in deploy and release yaml

Pull Request - State: open - Opened by oruebel 9 months ago - 1 comment

#164 - [Bug]: Deploy and release workflow fails due to unsupported actions

Issue - State: closed - Opened by oruebel 9 months ago

#163 - Update numcodec version in pyproject.toml

Pull Request - State: closed - Opened by oruebel 9 months ago - 1 comment

#162 - Remove strict dependency for numcodecs to support python 3.12

Issue - State: closed - Opened by h-mayorquin 9 months ago - 2 comments

#161 - Add NWB file convert unit test

Pull Request - State: closed - Opened by oruebel 9 months ago - 4 comments
Labels: category: bug, priority: medium

#160 - [Bug]: ValueError when using `export` function (for `subject.date_of_birth`)

Issue - State: closed - Opened by alejoe91 9 months ago - 4 comments
Labels: category: bug, priority: medium

#159 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by rly 10 months ago - 1 comment

#158 - Update CHANGELOG.md

Pull Request - State: closed - Opened by mavaylon1 10 months ago - 1 comment

#157 - Update requirements and fix test gallery failure on pandas pyarrow warning

Pull Request - State: closed - Opened by rly 10 months ago - 1 comment

#156 - [Bug]: Pandas warning causing test gallery errors

Issue - State: closed - Opened by rly 10 months ago
Labels: category: bug, priority: low, topic: testing

#155 - Fix bug when exporting HDF5 datasets with unlimited dimension

Pull Request - State: closed - Opened by oruebel 10 months ago - 1 comment

#154 - [Bug]: Converting HDF5 to Zarr with unlimted dimensions fails

Issue - State: closed - Opened by oruebel 10 months ago - 1 comment
Labels: category: bug, priority: high

#153 - Preserve h5py.Dataset filter settings on export

Pull Request - State: closed - Opened by oruebel 11 months ago - 8 comments
Labels: category: enhancement

#152 - [Feature]: Preserve HDF5 dataset filter settings on export to Zarr if possible

Issue - State: closed - Opened by oruebel 11 months ago - 1 comment
Labels: category: enhancement, priority: medium, topic: storage

#151 - [CI]: Compare vs. last commit in black CI action

Pull Request - State: open - Opened by sneakers-the-rat 11 months ago - 3 comments

#150 - Playing with Workflows (Others should ignore)

Pull Request - State: closed - Opened by mavaylon1 11 months ago - 2 comments

#149 - Write references in compound datasets at the end

Pull Request - State: closed - Opened by mavaylon1 11 months ago - 14 comments

#148 - [Feature]: Test without consolidate metadata

Issue - State: open - Opened by mavaylon1 11 months ago - 2 comments
Labels: category: enhancement, priority: low

#147 - Release 0.5.0

Pull Request - State: closed - Opened by mavaylon1 12 months ago - 1 comment

#146 - Write references in compound datasets as an array

Pull Request - State: closed - Opened by sneakers-the-rat 12 months ago - 23 comments
Labels: category: enhancement

#145 - [Bug]: Extension namespaces not exported from HDF5 NWB

Issue - State: open - Opened by sneakers-the-rat 12 months ago - 5 comments
Labels: category: bug, priority: medium

#144 - [Bug]: Iterative write for compound reference datasets takes 5ever

Issue - State: closed - Opened by sneakers-the-rat 12 months ago - 1 comment
Labels: category: bug, category: enhancement, priority: medium

#143 - Update pyproject.toml and remove setup.py

Pull Request - State: closed - Opened by mavaylon1 12 months ago - 8 comments

#142 - Consolidate Metadata

Pull Request - State: closed - Opened by mavaylon1 12 months ago - 9 comments

#141 - [Bug]: reading unit table arrays via string keys much slower than reading as properties

Issue - State: open - Opened by dyf about 1 year ago - 3 comments
Labels: category: enhancement, priority: low

#140 - [Documentation]: Add tutorial for S3 streaming

Issue - State: open - Opened by oruebel about 1 year ago - 1 comment
Labels: priority: medium, topic: docs

#139 - [Feature]: Always consolidate store structure

Issue - State: closed - Opened by CodyCBakerPhD about 1 year ago - 3 comments

#138 - Fix linking for FSSpec

Pull Request - State: closed - Opened by alejoe91 about 1 year ago - 8 comments

#137 - [Feature]: Expose `mode` to NWBZarrIO

Issue - State: open - Opened by CodyCBakerPhD about 1 year ago - 4 comments
Labels: category: enhancement, priority: medium

#136 - Create HDMF_dev.yaml

Pull Request - State: closed - Opened by mavaylon1 about 1 year ago - 7 comments

#135 - [Feature]: Create an example NWB Zarr dataset

Issue - State: open - Opened by rly about 1 year ago - 5 comments
Labels: category: enhancement, priority: low

#134 - [Feature]: S3 streaming support via fsspec

Issue - State: closed - Opened by oruebel about 1 year ago - 1 comment
Labels: category: enhancement, priority: high

#133 - Update description in overview.rst

Pull Request - State: closed - Opened by oruebel about 1 year ago - 1 comment

#132 - Update deploy_release.yml

Pull Request - State: closed - Opened by mavaylon1 about 1 year ago - 1 comment

#131 - Update deploy_release.yml

Pull Request - State: closed - Opened by mavaylon1 about 1 year ago

#130 - Release 0.4.0

Pull Request - State: closed - Opened by mavaylon1 about 1 year ago - 1 comment

#129 - Workflows

Pull Request - State: closed - Opened by mavaylon1 about 1 year ago - 4 comments

#128 - Fix #127 update paralle write test to set table ids

Pull Request - State: closed - Opened by oruebel about 1 year ago - 4 comments

#127 - [Bug]: Test for parallel write failing with HDMF dev

Issue - State: closed - Opened by oruebel about 1 year ago

#126 - [Feature]: Run tests again dev branch of HDMF

Issue - State: closed - Opened by oruebel about 1 year ago - 3 comments

#125 - Update CHANGELOG for upcoming release

Pull Request - State: closed - Opened by oruebel about 1 year ago - 1 comment

GitHub / hdmf-dev/hdmf-zarr issues and pull requests