Ecosyste.ms: Issues

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GitHub / vitessce/vitessce-python issues and pull requests

#387 - Example of rendering the image from the SpatialData blobs dataset

Pull Request - State: open - Opened by keller-mark 7 days ago

#386 - Add JsonWrapper class

Pull Request - State: closed - Opened by keller-mark 15 days ago

#385 - `obsSegmentations.json` needs corresponding wrapper class in python

Issue - State: closed - Opened by keller-mark 15 days ago

#384 - Move spatialdata dependency to dev

Pull Request - State: closed - Opened by keller-mark 22 days ago

#383 - Switch to HIDIVE Lab name

Pull Request - State: closed - Opened by keller-mark about 1 month ago

#382 - Refactor wrappers.py

Issue - State: open - Opened by keller-mark about 1 month ago
Labels: tech debt

#381 - Changelog

Issue - State: open - Opened by keller-mark about 1 month ago
Labels: tech debt

#380 - Linting + Formatting

Issue - State: open - Opened by ilan-gold about 1 month ago
Labels: tech debt

#379 - Add python types

Issue - State: open - Opened by ilan-gold about 1 month ago
Labels: tech debt

#378 - SpatialDataWrapper

Pull Request - State: closed - Opened by keller-mark about 1 month ago

#377 - Use `uv` to manage dependencies in development environments, remove conda usage

Issue - State: open - Opened by keller-mark about 1 month ago
Labels: tech debt, devops

#376 - Separate dev dependencies from actual dependencies

Issue - State: closed - Opened by flying-sheep about 1 month ago - 4 comments

#375 - Keller mark/spatial data2

Pull Request - State: closed - Opened by keller-mark about 1 month ago

#374 - SpatialData changes into original SpatialData branch

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

#373 - SpatialDataWrapper v2

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

#372 - Merge. Update spatialdatawrapper

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

#371 - Allow passing artifacts as data in addition to paths, urls, and zarr stores

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

#370 - Keller mark/more exports

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

#369 - Add minimal example notebook that demonstrates multi-obsType segmentations

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

#368 - Added utility functions to update and remove a view

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

#367 - Fix invoke bug

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

#366 - `layout.to_dict()` throwing: `TypeError: unsupported operand type(s) for +: 'NoneType' and 'str'`

Issue - State: open - Opened by ivirshup 2 months ago

#364 - Updated numpy to 2.0.2 and other packages to the latest

Pull Request - State: open - Opened by tkakar 2 months ago - 3 comments

#363 - Fix binder example

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

#362 - Enable `numpy` v2 Support/Unpin `numpy` v1

Issue - State: open - Opened by NickAkhmetov 2 months ago
Labels: tech debt

#361 - Support for H5AD-based AnnData in AnnDataWrapper

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

#360 - Misc: Spatial-query, kerchunk, and OME helper functions

Pull Request - State: closed - Opened by keller-mark 3 months ago

#359 - Command functions should be able to return an updated config

Issue - State: open - Opened by keller-mark 3 months ago - 1 comment
Labels: feature

#358 - Vitessce python on remote jupyter servers do not work

Issue - State: closed - Opened by edwin5588 3 months ago - 3 comments

#357 - Unit test for to_dict output following .add_object(AnnDataWrapper(...))

Pull Request - State: closed - Opened by keller-mark 3 months ago

#356 - Warn if AnnDataWrapper options are empty as it would result in empty list for `vc['datasets']['files']`

Issue - State: open - Opened by falexwolf 3 months ago - 4 comments

#355 - page_mode and page_esm params

Pull Request - State: open - Opened by keller-mark 4 months ago

#354 - Plugin for SpatialQuery

Pull Request - State: closed - Opened by keller-mark 4 months ago

#353 - Update fill_template.py

Pull Request - State: closed - Opened by keller-mark 4 months ago

#352 - NickAkhmetov/Copy `requestInit` when using `from_dict`

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

#351 - Ability to use comparative views + pageMode in a Jupyter notebook

Issue - State: open - Opened by keller-mark 4 months ago
Labels: feature, cell-atlas

#350 - Plugin class

Pull Request - State: closed - Opened by keller-mark 4 months ago

#349 - NickAkhmetov/Cap `numpy` under v2

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

#348 - Support writing plugin_esm using local file with anywidget FileContents

Issue - State: open - Opened by keller-mark 6 months ago
Labels: feature

#347 - Define a plugin class/dataclass to couple on_config_change and anywidget.invoke handlers with plugin_esm

Issue - State: closed - Opened by keller-mark 6 months ago - 1 comment
Labels: feature, cell-atlas

#345 - Adding Vitessce widgets to a visualization dashboard

Issue - State: closed - Opened by georgezakinih 7 months ago - 1 comment

#344 - Notebooks errors (list)

Issue - State: open - Opened by thomcsmits 7 months ago
Labels: bug, docs

#343 - Notebooks environment.yml PackageNotFoundError for starlette==0.14.0

Issue - State: open - Opened by thomcsmits 7 months ago
Labels: bug

#342 - (chore): supported python versions

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

#341 - (chore): Clean up `AnnDataWrapper` API

Pull Request - State: open - Opened by ilan-gold 7 months ago - 2 comments

#340 - Helper function to use adata.uns[obs_set_col + "_colors"] for initial obs set colors

Issue - State: open - Opened by keller-mark 7 months ago
Labels: feature

#339 - Setting colors for obsSets?

Issue - State: open - Opened by srivarra 7 months ago - 2 comments

#337 - Create module for plugin JS

Pull Request - State: closed - Opened by keller-mark 7 months ago

#336 - Release v3.2.5

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

#335 - NickAkhmetov/Add `requestInit` param to `MultivecZarrWrapper`

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

#334 - Support using JSX for writing plugin views

Issue - State: closed - Opened by keller-mark 7 months ago
Labels: feature

#333 - (feat): `SpatialData` wrapper

Pull Request - State: closed - Opened by ilan-gold 7 months ago - 10 comments

#332 - Bump version

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

#331 - Support automatic instantiation of Wrapper objects

Issue - State: open - Opened by keller-mark 8 months ago - 2 comments
Labels: feature

#330 - (chore): update linting/formatting + pre-commits

Pull Request - State: open - Opened by giovp 8 months ago - 1 comment

#329 - Use anywidget-based IPC for zarr gets which do not require serving data on localhost

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

#328 - Versions of anndata, anywidget, JS package

Pull Request - State: closed - Opened by keller-mark 8 months ago

#327 - Bumping supported Anndata Version?

Issue - State: closed - Opened by srivarra 8 months ago - 1 comment

#326 - Update adata_to_multivec

Pull Request - State: closed - Opened by keller-mark 8 months ago

#325 - Support scope_prefix parameter in link_views_by_dict

Pull Request - State: closed - Opened by keller-mark 9 months ago

#324 - Support for plugins

Pull Request - State: closed - Opened by keller-mark 9 months ago

#323 - Proof of concept for spatial-query plugin view

Pull Request - State: closed - Opened by keller-mark 9 months ago

#322 - Add option for widget to communicate directly with Zarr store (no local HTTP server)

Issue - State: open - Opened by keller-mark 9 months ago - 2 comments
Labels: feature

#321 - >1 million cell datasets for demos

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

#320 - Additional improvements to adata_to_multivec_zarr function

Issue - State: open - Opened by keller-mark 9 months ago
Labels: feature

#319 - Split interval conversion logic from the rest of multivec

Pull Request - State: open - Opened by NickAkhmetov 9 months ago

#318 - ValueError: data too large for non-BigTIFF file

Issue - State: closed - Opened by J-Yash 10 months ago - 4 comments

#317 - bump js 3.3.3

Pull Request - State: closed - Opened by keller-mark 10 months ago

#316 - Release

Pull Request - State: closed - Opened by keller-mark 10 months ago

#315 - Upgrade ome-zarr package

Pull Request - State: closed - Opened by keller-mark 10 months ago

#314 - Keller mark/mini dataset

Pull Request - State: open - Opened by keller-mark 10 months ago

#313 - Support additional parameters for imaging wrapper classes to support …

Pull Request - State: closed - Opened by keller-mark 10 months ago

#312 - Support obsSpots and obsPoints

Pull Request - State: closed - Opened by keller-mark 10 months ago

#311 - Adding scale bar to spatial view image

Issue - State: open - Opened by J-Yash 10 months ago

#310 - Minimal example for obsSegmentations.json for visualizing polygons in Spatial View

Issue - State: open - Opened by J-Yash 10 months ago - 2 comments

#309 - OmeTiffWrapper - support coordinationValues and fileType: "image.ome-tiff"

Issue - State: closed - Opened by keller-mark 10 months ago

#308 - AnnDataWrapper - support for obsSpots, obsPoints, etc.

Issue - State: closed - Opened by keller-mark 10 months ago

#307 - Example using 10x Space Ranger outputs

Pull Request - State: open - Opened by keller-mark 12 months ago

#306 - Publish a Vitessce notebook on Posit Connect

Issue - State: closed - Opened by georgezakinih about 1 year ago - 11 comments

#305 - Failed to load model class "Anymodel"

Issue - State: closed - Opened by CReihsmann about 1 year ago - 2 comments

#304 - Matt scott68/unzip

Pull Request - State: open - Opened by mattscott68 about 1 year ago

#303 - Use v3.3.0

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

#302 - Fix use_coordination function

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

#301 - Version bump

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

#300 - Bump js package version

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

#299 - Add file extensions

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

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

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

#297 - Demos for SquidPy example datasets

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

#296 - Snakemake pipeline for 10x Genomics Multiome outputs

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

#295 - Bump version

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

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

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

#290 - Support Vizgen example formats

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

#289 - Support Nanostring example formats

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

#288 - Support cellranger outputs

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

#287 - Support SpatialTis

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

#286 - Support SpatialData

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

#285 - Support spateo formats

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