Ecosyste.ms: Issues

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GitHub / bioio-devs/bioio issues and pull requests

#76 - ubuntu 18.04 support (GLIBC >= 2.28)

Issue - State: open - Opened by toloudis about 2 months ago - 4 comments
Labels: bug

#75 - admin/move-doc-publishing-to-release-cycle

Pull Request - State: closed - Opened by evamaxfield 2 months ago

#74 - Update ome_tiff_writer.py to remove reference to `image_names`

Pull Request - State: closed - Opened by TimMonko 3 months ago

#73 - image_name parameter in OmeTiffWriter should be clearly accessible with BioImage

Issue - State: open - Opened by TimMonko 3 months ago
Labels: enhancement

#72 - unpin zarr max version

Pull Request - State: closed - Opened by joshua-gould 3 months ago - 6 comments

#71 - cannot read file from S3 within parallelized loop

Issue - State: closed - Opened by cfrick13 3 months ago - 11 comments
Labels: bug

#70 - Remove numpy<2.0.0 restriction

Issue - State: open - Opened by pgarrison 3 months ago - 2 comments
Labels: enhancement

#69 - add channel selections to writer

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

#68 - User Warning due to dask dependency discrepancy and ND2File()

Issue - State: closed - Opened by felixS27 3 months ago - 1 comment

#67 - Support public s3 files automatically

Pull Request - State: closed - Opened by SeanLeRoy 3 months ago - 5 comments

#66 - `AttributeError` no `_plugin` with custom `Reader`

Issue - State: closed - Opened by sea-shunned 4 months ago - 2 comments
Labels: bug

#65 - Plans to drop py39 and add py312

Issue - State: closed - Opened by evamaxfield 4 months ago - 3 comments
Labels: enhancement

#64 - bugfix/correct-version-in-doc-builds

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

#63 - feature/reader-surface-info

Pull Request - State: closed - Opened by BrianWhitneyAI 4 months ago

#62 - feature/plugin-registry

Pull Request - State: closed - Opened by BrianWhitneyAI 4 months ago - 3 comments

#61 - Read from public `s3://` paths without authentication, without requiring any code change from users

Issue - State: closed - Opened by pgarrison 4 months ago - 1 comment
Labels: enhancement

#60 - Reader-specific documentation can be hard to discover

Issue - State: closed - Opened by pgarrison 4 months ago - 1 comment
Labels: enhancement

#59 - bugfix/missing-plugin-metadata

Pull Request - State: closed - Opened by BrianWhitneyAI 4 months ago - 2 comments

#58 - generated docs are getting wrong version number

Issue - State: closed - Opened by toloudis 4 months ago - 7 comments
Labels: bug

#57 - Bioio plugin dump unable to report plugins

Issue - State: closed - Opened by BrianWhitneyAI 4 months ago
Labels: bug

#56 - Plugin Reader Metadata Does Not Standardize Supported Suffixes

Issue - State: closed - Opened by evamaxfield 4 months ago - 3 comments
Labels: bug

#55 - bugfix/longest-suffix-wins

Pull Request - State: closed - Opened by evamaxfield 4 months ago - 9 comments

#54 - bioio-tifffile takes precedence over bioio-ome-tiff for ome-tiffs

Issue - State: closed - Opened by evamaxfield 4 months ago - 2 comments
Labels: bug

#53 - remove zarr<2.18.0 constraint

Issue - State: closed - Opened by toloudis 4 months ago - 1 comment
Labels: enhancement

#52 - add resolution_level_dims

Pull Request - State: closed - Opened by BrianWhitneyAI 4 months ago

#51 - Check reader for image typing

Pull Request - State: closed - Opened by BrianWhitneyAI 5 months ago - 2 comments

#50 - Admin: update pre-commit to `ruff`

Issue - State: open - Opened by evamaxfield 5 months ago - 1 comment
Labels: enhancement, admin

#49 - Centralized guess dim order

Issue - State: closed - Opened by BrianWhitneyAI 5 months ago - 2 comments

#48 - Feature/ome zarr writer v2

Pull Request - State: closed - Opened by toloudis 5 months ago - 1 comment

#47 - feature/array-like-reader

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

#46 - Add new ome-zarr-writer

Issue - State: closed - Opened by toloudis 5 months ago
Labels: enhancement

#43 - Update MIGRATION.md

Pull Request - State: closed - Opened by toloudis 7 months ago

#42 - relax the enforce_exists check because it will be done later

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

#41 - HTTP URL for ZARR fails to be validated by `determine_plugin` for bioio-ome-zarr

Issue - State: closed - Opened by pgarrison 7 months ago - 6 comments
Labels: bug

#40 - Support ZARRs via https

Pull Request - State: closed - Opened by pgarrison 7 months ago

#39 - Add ArrayLikeReader

Issue - State: closed - Opened by toloudis 8 months ago
Labels: enhancement

#38 - bioio-tifffile and bioio-ome-tiff parse ome-tiff metadata differently

Issue - State: closed - Opened by TimMonko 8 months ago - 2 comments
Labels: bug

#37 - ci(dependabot): bump extractions/setup-just from 1 to 2

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#36 - writer compression parameter

Issue - State: open - Opened by toloudis 9 months ago - 1 comment
Labels: enhancement

#35 - read physical time metadata

Issue - State: open - Opened by toloudis 10 months ago - 1 comment
Labels: enhancement

#34 - ci(dependabot): bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#33 - reader chunk_dims are too coarse-grained for dask

Issue - State: open - Opened by toloudis 10 months ago
Labels: enhancement

#32 - ci(dependabot): bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#31 - Unable to open czi line-scan kymographs - missing raw frame(t) pixel data

Issue - State: open - Opened by cudmore 12 months ago - 1 comment
Labels: bug

#30 - add resolution levels implementation

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

#29 - can't instantiate BioImage in v1.0

Issue - State: closed - Opened by toloudis 12 months ago - 3 comments
Labels: bug

#27 - Improve error message on UnsupportedFileFormatError

Issue - State: closed - Opened by tlambert03 12 months ago - 7 comments
Labels: enhancement

#26 - Surface more information during reader/plugin selection

Issue - State: closed - Opened by SeanLeRoy about 1 year ago - 7 comments
Labels: enhancement

#25 - Add units to PhysicalPixelSizes

Issue - State: open - Opened by SeanLeRoy about 1 year ago
Labels: enhancement

#24 - Anaconda Distribution

Issue - State: open - Opened by SeanLeRoy about 1 year ago - 1 comment
Labels: admin

#23 - Allow '.' in plugin ext prefix

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

#22 - Auto retrieve plugins + adjust caching

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 3 comments

#21 - Report plugin in repr

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

#20 - improve error string

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

#19 - use correct package name for bioio-base

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

#18 - Features / Bugs / Eva Notes

Issue - State: open - Opened by evamaxfield about 1 year ago - 6 comments
Labels: bug, enhancement

#17 - Consider a public plugin registry

Issue - State: closed - Opened by toloudis about 1 year ago - 5 comments
Labels: admin

#16 - Upgrade docs

Pull Request - State: closed - Opened by SeanLeRoy about 1 year ago - 3 comments

#15 - ci(dependabot): bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago
Labels: dependencies

#14 - Update CI and add CODEOWNERS

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

#13 - Migrate python versions

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago - 2 comments

#12 - Plan to keep up with aicsimageio maintenance updates

Issue - State: closed - Opened by toloudis over 1 year ago - 4 comments
Labels: admin

#11 - Full documentation

Issue - State: closed - Opened by toloudis over 1 year ago - 2 comments
Labels: admin

#10 - timeseries writer tests break in actual use

Issue - State: open - Opened by SeanLeRoy over 1 year ago
Labels: bug

#9 - Feature/add writers

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago

#8 - feature/add bioimage

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago

#7 - feature/require minimum bioio-base for plugins

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago

#6 - admin/fix-ci-and-upgrade-lint-dependencies

Pull Request - State: closed - Opened by SeanLeRoy over 1 year ago

#5 - Migration document from aicsimageio

Issue - State: closed - Opened by toloudis over 1 year ago - 1 comment
Labels: admin

#4 - Add AICSImage

Issue - State: closed - Opened by SeanLeRoy over 1 year ago
Labels: enhancement

#3 - Add writers

Issue - State: closed - Opened by SeanLeRoy over 1 year ago
Labels: enhancement

#2 - Modify Plug-in Search Capabilities

Issue - State: closed - Opened by SeanLeRoy over 1 year ago
Labels: enhancement

#1 - feature/integrate-with-types

Pull Request - State: closed - Opened by evamaxfield about 2 years ago
Labels: documentation, enhancement