Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nadeemlab/spt issues and pull requests

#374 - Record package versions

Pull Request - State: closed - Opened by jimmymathews 19 days ago

#373 - Note on upload to s3

Pull Request - State: closed - Opened by jimmymathews 19 days ago

#372 - Integrate brotli compression feature

Pull Request - State: closed - Opened by jimmymathews 27 days ago - 1 comment

#371 - create_bimodal_vector may return List instead of Series

Issue - State: open - Opened by CarlinLiao about 1 month ago
Labels: bug

#370 - Better logs, and more resilient job queue logic

Pull Request - State: closed - Opened by jimmymathews about 1 month ago - 2 comments

#369 - Database "schemas" consolidation

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

#368 - Better logs

Issue - State: closed - Opened by jimmymathews about 1 month ago
Labels: enhancement

#367 - Release v1.0.0

Pull Request - State: closed - Opened by jimmymathews about 1 month ago - 1 comment

#366 - Docs update

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

#365 - Docs update

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

#364 - Add basic documentation to front page

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

#363 - Adds 8-bit float encoder/decoder

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

#362 - Add computation job queue queries

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

#361 - Slight change to umap preprocessing query

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

#360 - API docs

Pull Request - State: closed - Opened by jimmymathews about 1 month ago - 2 comments

#359 - Dependency updates

Issue - State: open - Opened by jimmymathews about 1 month ago
Labels: refactor

#358 - PostgreSQL schemas (allow simple all-datasets queries)

Issue - State: closed - Opened by jimmymathews about 2 months ago - 4 comments
Labels: refactor

#357 - Adjust import workflow configuration to support S3

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

#356 - Migration from spt-data

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

#355 - Top results on study landing page, solicited from users

Issue - State: open - Opened by jimmymathews about 2 months ago - 2 comments

#354 - Compressed blobs caching

Issue - State: closed - Opened by jimmymathews about 2 months ago

#353 - Some docs

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

#352 - Make large datasets subsettable for UMAP

Issue - State: closed - Opened by jimmymathews 2 months ago - 1 comment
Labels: future

#351 - Issue154

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

#350 - Supply UMAP position information as virtual slide

Pull Request - State: closed - Opened by jimmymathews 3 months ago - 2 comments

#349 - Add findings to study-summary endpoint

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

#348 - Too many null values in computed metrics

Issue - State: closed - Opened by jimmymathews 3 months ago - 1 comment
Labels: bug

#347 - Fold findings endpoint into study summary

Issue - State: closed - Opened by jimmymathews 3 months ago
Labels: refactor

#346 - Fix MIME type header for importance-fraction-plot endpoint

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

#345 - Add nonblocking counts endpoint

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

#344 - Counts endpoint meant for polling

Issue - State: closed - Opened by jimmymathews 3 months ago

#343 - Refine Ripley metric extraction

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

#342 - Fix Ripley metric

Issue - State: closed - Opened by jimmymathews 3 months ago

#341 - Intermittent bug fixes

Pull Request - State: closed - Opened by jimmymathews 3 months ago - 2 comments

#340 - Speed up with C extensions

Issue - State: open - Opened by jimmymathews 3 months ago

#339 - Infinite loop checking for completed metric

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

#338 - Vectorize operations on CellDataArrays

Pull Request - State: closed - Opened by CarlinLiao 4 months ago - 11 comments
Labels: refactor

#337 - Operations over cell data arrays can be vectorized

Issue - State: closed - Opened by CarlinLiao 4 months ago - 3 comments
Labels: refactor

#336 - Partial caching

Issue - State: open - Opened by jimmymathews 4 months ago
Labels: feature

#335 - Fix feature duplication bug

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

#334 - Cache GNN plots

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

#333 - Cache GNN plot

Issue - State: closed - Opened by jimmymathews 5 months ago
Labels: bug

#332 - Findings URLs

Issue - State: closed - Opened by jimmymathews 5 months ago - 1 comment
Labels: feature

#331 - Single-sample computation timeout

Issue - State: closed - Opened by jimmymathews 5 months ago
Labels: bug

#330 - Feature identifier collision

Issue - State: closed - Opened by jimmymathews 5 months ago
Labels: bug

#329 - Bug fix key conflict

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

#328 - Remove unnecessary identifiers, causing concurrency conflicts

Issue - State: closed - Opened by jimmymathews 5 months ago
Labels: bug

#327 - Parallelization refactor

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

#326 - Make ondemand services parallelizable

Issue - State: closed - Opened by jimmymathews 5 months ago - 2 comments
Labels: refactor

#325 - Move plugin repos into this main repo

Pull Request - State: closed - Opened by CarlinLiao 5 months ago - 3 comments
Labels: refactor

#324 - Issue314

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

#323 - Consolidating by bringing in spt plugin repository contents

Issue - State: closed - Opened by jimmymathews 5 months ago
Labels: refactor

#322 - Library dependency updates

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

#321 - Reduce memory footprint with an optimization in cache checking

Pull Request - State: closed - Opened by jimmymathews 6 months ago

#320 - Make GNN plots available as an SPT CLI command and API endpoint

Pull Request - State: closed - Opened by CarlinLiao 6 months ago - 9 comments
Labels: feature

#319 - Make GNN plots available as an SPT CLI command and API endpoint

Issue - State: closed - Opened by CarlinLiao 6 months ago - 7 comments
Labels: feature

#318 - Implement a refresh signal for the ondemand containers

Issue - State: closed - Opened by jimmymathews 6 months ago - 2 comments
Labels: wontfix, feature

#317 - Support normalized case for study names

Issue - State: open - Opened by jimmymathews 6 months ago - 1 comment
Labels: feature

#316 - Study sets

Pull Request - State: closed - Opened by jimmymathews 6 months ago

#315 - Implement cell limit for cells data query

Pull Request - State: closed - Opened by jimmymathews 6 months ago

#314 - Stalled backend for large cell data payloads

Issue - State: closed - Opened by jimmymathews 6 months ago - 2 comments
Labels: bug

#313 - scverse ecosystem-package and ADI/SpatialData conversion

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

#312 - Study sets

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

#311 - Update reanalysis scripts

Pull Request - State: closed - Opened by jimmymathews 8 months ago

#310 - More study detail from API service

Pull Request - State: closed - Opened by jimmymathews 8 months ago

#309 - Additional study details

Issue - State: closed - Opened by jimmymathews 8 months ago - 1 comment
Labels: feature

#308 - Failing metric fails to cancel

Issue - State: closed - Opened by jimmymathews 8 months ago - 2 comments
Labels: bug, wontfix

#307 - add graph plugin plot code

Pull Request - State: closed - Opened by CarlinLiao 8 months ago - 14 comments
Labels: enhancement

#306 - Add graph plugin heatmaps

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

#305 - Pin workflow image tag default to current SPT version

Pull Request - State: closed - Opened by CarlinLiao 8 months ago - 3 comments
Labels: refactor

#304 - Upload importance should be generated procedurally in Nextflow workflows

Issue - State: open - Opened by CarlinLiao 8 months ago
Labels: enhancement

#303 - SPT image version isn't pinned

Issue - State: closed - Opened by CarlinLiao 8 months ago - 1 comment
Labels: bug

#302 - Implements sorting by default on most endpoints

Pull Request - State: closed - Opened by jimmymathews 8 months ago

#301 - Include utility for feature deletion

Pull Request - State: closed - Opened by jimmymathews 8 months ago

#300 - Utility to delete one feature

Issue - State: closed - Opened by jimmymathews 8 months ago - 1 comment
Labels: enhancement

#299 - Implement cell-level api endpoint

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

#298 - Cell level data

Issue - State: closed - Opened by jimmymathews 9 months ago - 5 comments
Labels: feature

#297 - add new specifiers to DataAccessor importance

Pull Request - State: closed - Opened by CarlinLiao 9 months ago
Labels: enhancement

#296 - Analysis replication DataAccessor is missing new importance score specifiers

Issue - State: closed - Opened by CarlinLiao 9 months ago
Labels: enhancement

#295 - Counts files to db migration

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

#294 - Quick patch to counts_by_signature to handle if one of positive or negative is empty

Pull Request - State: closed - Opened by CarlinLiao 9 months ago - 1 comment
Labels: bug

#293 - `DataAccessor.counts_by_signature` fails if either no positive or no negative markers are provided

Issue - State: closed - Opened by CarlinLiao 9 months ago
Labels: bug

#292 - Add support for graph-transformer plugin

Pull Request - State: closed - Opened by CarlinLiao 9 months ago - 7 comments
Labels: enhancement

#291 - Modularize workflow Nextflow files

Pull Request - State: closed - Opened by CarlinLiao 10 months ago
Labels: enhancement, refactor

#290 - Balance graph datasets

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

#289 - Modularize graphs workflow

Issue - State: closed - Opened by CarlinLiao 10 months ago
Labels: refactor

#288 - prevent package caching in Docker images

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 1 comment
Labels: enhancement

#287 - Make `spt workflow configure` support both Docker and Singularity

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 20 comments
Labels: enhancement

#286 - Expand workflow configure support for singularity

Issue - State: closed - Opened by CarlinLiao 10 months ago - 1 comment
Labels: enhancement

#285 - No option to show Nextflow logs when running the test suite

Issue - State: closed - Opened by CarlinLiao 10 months ago - 4 comments
Labels: development

#284 - Allow saved graphs to be readable without importing spatialprofilingtoolbox

Issue - State: closed - Opened by CarlinLiao 10 months ago - 1 comment
Labels: refactor

#283 - Convert cggnn/graphs and workflow configure to use config files (redo)

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 17 comments
Labels: refactor

#282 - Dockerize `spt cggnn train` (redo)

Pull Request - State: closed - Opened by CarlinLiao 10 months ago - 1 comment
Labels: enhancement

#281 - Convert cggnn/graphs and workflow configure to use config files

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 8 comments
Labels: refactor

#280 - Save adjacency matrices separately

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 1 comment
Labels: bug

#279 - scipy sparse matrix compatibility issues

Issue - State: closed - Opened by CarlinLiao 11 months ago
Labels: bug

#278 - Refactor `spt workflow configure` to accept a generic configuration file instead of CLI arguments

Issue - State: closed - Opened by CarlinLiao 11 months ago - 1 comment
Labels: refactor

#277 - Rename `cg-gnn` submodule to `graphs`

Issue - State: closed - Opened by CarlinLiao 11 months ago - 4 comments
Labels: duplicate, refactor

#276 - Dockerize `spt cggnn train`

Pull Request - State: closed - Opened by CarlinLiao 11 months ago - 12 comments

#275 - Dockerization of the `cg-gnn` model

Issue - State: closed - Opened by CarlinLiao 11 months ago - 4 comments
Labels: duplicate, refactor