Ecosyste.ms: Issues

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GitHub / vitessce/vitessce-python issues and pull requests

#298 - Convert spatialdata-plot plotting tree to Vitessce config

Issue - State: open - Opened by keller-mark over 1 year ago - 1 comment
Labels: feature

#297 - Demos for SquidPy example datasets

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: data_utils, demo

#296 - Snakemake pipeline for 10x Genomics Multiome outputs

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: data_utils

#295 - Bump version

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

#294 - Convert flattened multi-level coordination JSON back to nested dict for `to_python`

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: feature, cell-atlas

#293 - Support emObject

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: data_utils

#292 - Support RDS files

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: data_utils

#291 - Support Spatial CUT&tag and spatial ATAC formats

Issue - State: open - Opened by keller-mark almost 2 years ago
Labels: data_utils

#290 - Support Vizgen example formats

Issue - State: open - Opened by keller-mark almost 2 years ago
Labels: data_utils

#289 - Support Nanostring example formats

Issue - State: open - Opened by keller-mark almost 2 years ago
Labels: data_utils

#288 - Support cellranger outputs

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: data_utils

#287 - Support SpatialTis

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: data_utils

#286 - Support SpatialData

Issue - State: open - Opened by keller-mark about 2 years ago - 3 comments
Labels: data_utils

#285 - Support spateo formats

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: data_utils

#284 - Support MuData objects

Issue - State: open - Opened by keller-mark about 2 years ago - 1 comment
Labels: data_utils

#283 - Support bento formats

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: data_utils

#282 - Support writing pyramidal OME-TIFF and OME-NGFF

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: data_utils

#281 - Support 10X genomics HDF5 files

Issue - State: open - Opened by keller-mark about 4 years ago
Labels: data_utils

#280 - Support Seurat data objects

Issue - State: open - Opened by keller-mark about 4 years ago
Labels: data_utils

#279 - Support Starfish data objects

Issue - State: open - Opened by keller-mark about 4 years ago - 4 comments
Labels: data_utils

#278 - Support BiocPy SingleCellExperiment

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: data_utils

#277 - Refactor data_utils

Pull Request - State: open - Opened by keller-mark over 1 year ago

#276 - Refactor data_utils and extras_require

Issue - State: open - Opened by keller-mark over 1 year ago - 1 comment
Labels: data_utils

#275 - Release 3.0.7

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

#272 - NickAkhmetov/Add support for `obs_labels_names` and `obs_labels_paths` arrays

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

#270 - Update `FileType` enum to match JS API values

Issue - State: closed - Opened by NickAkhmetov over 1 year ago - 1 comment

#269 - Support `uid` field in VitessceConfig constructor

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: feature, cell-atlas

#268 - Release

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

#267 - Upgrade dynamic-import package version to fix bug

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

#266 - Complex coordination port

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

#265 - Revert removal of data_type argument for VitessceConfigDatasetFile

Issue - State: open - Opened by keller-mark over 1 year ago
Labels: enhancement

#264 - Keller mark/issue 1228 pr

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

#260 - MultiImageWrapper with ome-zarr

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

#258 - Update README.md

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

#257 - Figure out why omero metadata might be within multiscales[0] rather than at root level of .zattrs

Issue - State: open - Opened by keller-mark over 1 year ago - 2 comments
Labels: investigation

#256 - Figure out how to surface JS errors in Python

Issue - State: open - Opened by keller-mark over 1 year ago - 1 comment
Labels: feature, investigation

#255 - Ensure widget works in Jupyter running in VSCode

Issue - State: closed - Opened by keller-mark over 1 year ago - 8 comments
Labels: feature, investigation, devops

#254 - error with UJSONResponse with Starlette v0.28.0

Issue - State: open - Opened by keller-mark over 1 year ago - 1 comment
Labels: possibly-outdated, tech debt

#253 - Release v3.0.5

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

#252 - Create data_options.rst

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

#251 - Add page describing data location options

Issue - State: closed - Opened by keller-mark over 1 year ago

#250 - Update anndata.py

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

#249 - Validate configs on python side using `@vitessce/json-schema` NPM package

Issue - State: open - Opened by keller-mark over 1 year ago - 1 comment
Labels: feature

#248 - JS v3

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

#246 - Anywidget cleanup function

Issue - State: closed - Opened by keller-mark over 1 year ago

#245 - Spatial view coordinates flipped.

Issue - State: open - Opened by lee-t over 1 year ago
Labels: investigation

#244 - Add support for obsLabels with AnnData

Pull Request - State: closed - Opened by keller-mark almost 2 years ago

#243 - Use base_dir and OOP api in `demos`

Issue - State: open - Opened by keller-mark almost 2 years ago
Labels: docs, tech debt, demo

#242 - Creating a configuration with multiple OME-Zarr using `MultiImageWrapper` fails

Issue - State: open - Opened by NHPatterson almost 2 years ago - 2 comments
Labels: bug

#241 - Document how to install latest version or particular branch from github

Issue - State: open - Opened by keller-mark almost 2 years ago
Labels: docs

#240 - base_dir mode

Pull Request - State: closed - Opened by keller-mark almost 2 years ago

#239 - Base_dir mode

Issue - State: closed - Opened by keller-mark almost 2 years ago - 1 comment
Labels: enhancement

#238 - Refactor genomic profiles code

Pull Request - State: closed - Opened by keller-mark almost 2 years ago

#237 - Add VitessceConfig.display

Pull Request - State: closed - Opened by keller-mark almost 2 years ago

#236 - Proxy parameter for vc.web_app

Issue - State: closed - Opened by keller-mark almost 2 years ago

#235 - Debug mode

Issue - State: open - Opened by keller-mark almost 2 years ago
Labels: enhancement

#234 - Upgrade anywidget

Pull Request - State: closed - Opened by keller-mark almost 2 years ago

#233 - Check adata.obs and adata.var column dtypes in optimize_adata

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: feature, data_utils

#232 - Perform validation of data (local only?) passed to wrapper classes, with parameter to opt out

Issue - State: open - Opened by keller-mark about 2 years ago - 1 comment
Labels: enhancement

#231 - Can't load figures

Issue - State: closed - Opened by Irisapo about 2 years ago - 10 comments

#229 - Fix `feature_labels_path` bug in AnnDataWrapper class

Issue - State: closed - Opened by keller-mark about 2 years ago - 1 comment
Labels: bug

#228 - Add JS CDN fallback urls

Issue - State: open - Opened by keller-mark about 2 years ago - 3 comments
Labels: feature

#227 - Remove usage of temp directory in AbstractWrapper

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: enhancement

#226 - Move `coordination_values` parameter to AbstractWrapper class

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: enhancement

#224 - Add parameters for linkage()

Pull Request - State: open - Opened by keller-mark about 2 years ago

#223 - Error if `out_dir` exists and is not empty in export_to_files (with option to ignore)

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: enhancement

#222 - Include file extensions in UIDs for cleaner exports

Issue - State: closed - Opened by keller-mark about 2 years ago
Labels: feature, cell-atlas

#221 - Render notebooks into docs

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: docs, feature, devops

#220 - Support writing pyramidal OME-TIFF and OME-NGFF in `vitessce.data_utils.ome`

Issue - State: open - Opened by keller-mark about 2 years ago
Labels: enhancement

#218 - Create smaller easier-to-solve CI env

Pull Request - State: closed - Opened by keller-mark about 2 years ago

#217 - Less copying of local data

Pull Request - State: closed - Opened by keller-mark about 2 years ago

#216 - Copy less data

Issue - State: closed - Opened by keller-mark about 2 years ago
Labels: enhancement

#215 - Update config api

Pull Request - State: closed - Opened by keller-mark about 2 years ago - 1 comment

#214 - Try to fix github pages deployment

Pull Request - State: closed - Opened by keller-mark about 2 years ago - 3 comments

#213 - (chore): release

Pull Request - State: closed - Opened by ilan-gold about 2 years ago

#212 - Vitessce 1.2.2

Pull Request - State: closed - Opened by ilan-gold about 2 years ago - 1 comment

#211 - Use More Dynamic Gene Loading

Pull Request - State: closed - Opened by ilan-gold about 2 years ago

#210 - vitessce (js) v2.x

Pull Request - State: closed - Opened by keller-mark about 2 years ago - 2 comments

#209 - upgrade vitessce version?

Issue - State: closed - Opened by tmchartrand about 2 years ago - 4 comments

#208 - widget fails to load "vitessce-jupyter.js:1 Failed to load resource: the server responded with a status of 404 (Not Found)"

Issue - State: open - Opened by lee-t over 2 years ago - 5 comments
Labels: bug, possibly-outdated

#205 - Pin ipywidgets dependency version

Pull Request - State: closed - Opened by keller-mark over 2 years ago

#204 - No longer installable in google colab?

Issue - State: closed - Opened by mccalluc over 2 years ago - 4 comments

#203 - Start from raw data rather than intermediate data

Pull Request - State: closed - Opened by keller-mark over 2 years ago

#202 - Data processing utils

Pull Request - State: closed - Opened by keller-mark over 2 years ago

#201 - Demo data processing

Pull Request - State: closed - Opened by keller-mark over 2 years ago - 3 comments

#198 - "Exception opening new comm"

Issue - State: open - Opened by mccalluc over 2 years ago - 6 comments
Labels: bug, possibly-outdated

#197 - Sort components in JSON serialization

Issue - State: open - Opened by mccalluc over 2 years ago
Labels: feature

#196 - Add TiffWrapper and OmeZarrWrapper classes

Issue - State: closed - Opened by keller-mark over 2 years ago

#195 - Keep the JS version number in just one place

Pull Request - State: closed - Opened by mccalluc over 2 years ago - 1 comment