Ecosyste.ms: Issues

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

GitHub / broadinstitute/scp-ingest-pipeline issues and pull requests

#377 - Fixing Github ref for minify ontology commits (SCP-5881)

Pull Request - State: open - Opened by bistline about 1 month ago - 1 comment

#376 - adding debug logging

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

#375 - Release 1.38.0

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

#374 - Enable pairwise DE in ingest pipeline (SCP-5766)

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

#373 - Release 1.37.1

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

#372 - Show gene name in DE table for CELLxGENE-style AnnData files (SCP-5859)

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

#371 - Release 1.37.0

Pull Request - State: closed - Opened by eweitz 3 months ago
Labels: review exception: deferred

#370 - Add secondary data check for Ensembl gene ID index (SCP-5853)

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

#369 - Release 1.36.1

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

#368 - Coerce boolean data to categorical annotations (SCP-5850)

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

#367 - Release 1.36.0

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

#366 - Harmonizing default Mixpanel properties across Rails & ingest (SCP-5798)

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

#365 - Refine ontology cache, for fast metadata validation (SCP-5790)

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

#364 - Minify ontologies and keep them fresh, for fast metadata validation (SCP-5719)

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

#363 - Release 1.35.0

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

#362 - Extending differential expression analysis to AnnData files (SCP-5764)

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

#361 - Release 1.34.0

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

#359 - Ingest raw count cells for AnnData files (SCP-5103)

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

#358 - Renaming master branch to main (SCP-3346)

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

#357 - Release 1.33.0

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

#356 - Replacing vault with GSM for local development (SCP-5716)

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

#355 - Fix cluster query during AnnData subsampling (SCP-5140)

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

#354 - Enable merging cell types from CAS into AnnData via CLI (SCP-5732)

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

#353 - Cell Annotation Service: proof of concept

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

#352 - Bump sentry-sdk from 1.14.0 to 2.8.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 1 comment
Labels: dependencies

#351 - Remove all subsample thresholds below 100K (SCP-5702)

Pull Request - State: closed - Opened by bistline 6 months ago - 1 comment
Labels: build failure: false positive

#350 - Release 1.31.0

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

#349 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#348 - Transform `has_<modality>` to boolean for BigQuery (SCP-5566)

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

#347 - Canonicalize study publications, for better scientific context (SCP-5641)

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

#346 - Generate matrix data from exon + intron count files (SCP-5558)

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

#343 - Bump pymongo from 3.12.0 to 4.6.3

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#342 - Release 1.30.0

Pull Request - State: closed - Opened by eweitz 10 months ago

#341 - Enable friendly gene search for CELLxGENE AnnData (SCP-5571)

Pull Request - State: closed - Opened by eweitz 10 months ago - 3 comments

#340 - Release 1.29.0

Pull Request - State: closed - Opened by jlchang 10 months ago - 2 comments

#339 - Bump black from 19.3b0 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#338 - Update alexandria metadata convention for BRAIN RF1 (SCP-5549)

Pull Request - State: closed - Opened by jlchang 10 months ago

#336 - Create metadata file for BRAIN RF1 in traditional SCP format (SCP-5502)

Pull Request - State: closed - Opened by jlchang 11 months ago - 1 comment

#335 - Bump grpcio from 1.53.0 to 1.53.2

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#334 - Rank genes in study by relevance (SCP-5399)

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

#333 - Release 1.28.4

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

#332 - Increasing maximum number of MongoDB retries, jitter for backoff (SCP-5429)

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

#331 - Increase server timeout, decrease DataArray batch to 500 (SCP-5429)

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

#330 - Release 1.28.3

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

#329 - Fix gene names with slashes in expression writer (SCP-5341)

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

#328 - Release 1.28.2

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

#327 - Fix issue with non-standard `fileLocation` URLs (SCP-5419)

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

#326 - Restore curl in Docker image; removed in upstream dependency (SCP-5359)

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

#325 - Release 1.28.1

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

#324 - Fix breaking changes related to upstream OLS4 update (SCP-5359)

Pull Request - State: closed - Opened by eweitz about 1 year ago - 2 comments

#323 - Release 1.28.0

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

#322 - Author DE: support Seurat and other formats, fix numerical groups (SCP-5296)

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

#321 - Parameterize size and significance metrics, improve robustness (SCP-5241)

Pull Request - State: closed - Opened by eweitz over 1 year ago - 4 comments

#320 - Release 1.27.4

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

#319 - Author DE: Fix pairwise columns, support TSV (SCP-5292)

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

#318 - Author DE maintainability: refactor, add automated test (SCP-5241)

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

#317 - Release 1.27.3

Pull Request - State: closed - Opened by eweitz over 1 year ago - 1 comment
Labels: review exception: deferred, review exception: post-merge approved

#316 - Bump grpcio from 1.48.2 to 1.53.0

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

#315 - Release 1.27.2

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

#314 - Fix sorting in pairwise output filenames for author DE (SCP-5204)

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

#313 - Release 1.27.1

Pull Request - State: closed - Opened by ehanna4 over 1 year ago

#312 - Bugfix for AnnData file upload with 3D clustering (SCP-5191)

Pull Request - State: closed - Opened by ehanna4 over 1 year ago

#311 - Release 1.27.0

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

#310 - Integrate author DE into Ingest Pipeline (SCP-5086)

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

#309 - Add author DE manifest and one-vs-rest support (SCP-5087)

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

#308 - Bump requests from 2.28.2 to 2.31.0

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

#307 - Verify and parse author DE files (SCP-5087)

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

#306 - Release 1.26.1

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

#305 - Update ingest to extract processed gene expression as mtx (SCP-5127)

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

#304 - Release 1.26.0

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

#303 - Extract processed expression matrix data from AnnData (SCP-4911)

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

#302 - Update SCP ingest to use AnnData 0.9.1 (SCP-5097)

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

#301 - Refine mtx error messaging for transposed matrices (SCP-5073)

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

#300 - Release 1.25.1

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

#299 - Restore missing symlink to python in docker image (SCP-4547)

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

#298 - Release 1.25.0

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

#297 - Add synthetic example (SCP-4980)

Pull Request - State: closed - Opened by michelle-vel almost 2 years ago - 3 comments

#296 - Bump sentry-sdk from 0.16.1 to 1.14.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#295 - Added notebook to create example metadata image (SCP-4963)

Pull Request - State: closed - Opened by michelle-vel almost 2 years ago - 1 comment

#294 - Update ingest to use python3.10 (SCP-4547, SCP-4208)

Pull Request - State: closed - Opened by jlchang almost 2 years ago - 1 comment

#293 - Update ingest to use python3.8 (SCP-4547, SCP-4208)

Pull Request - State: closed - Opened by jlchang almost 2 years ago - 3 comments

#292 - Add pairwise DE testing (SCP-4958)

Pull Request - State: closed - Opened by michelle-vel almost 2 years ago - 1 comment

#291 - Update sparse and dense matrix examples (SCP-4883)

Pull Request - State: closed - Opened by michelle-vel almost 2 years ago - 1 comment

#290 - Enable local development via Docker compose (SCP-4883)

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

#289 - Release 1.24.0

Pull Request - State: closed - Opened by ehanna4 about 2 years ago

#288 - Adding test coverage for metadata extraction (SCP-4863)

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

#286 - Release 1.23.3

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

#285 - Adding test coverage for `AnnDataIngestor` (SCP-4825)

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

#284 - Make "cell type (custom)" test data more correct (SCP-4835, SCP-4836)

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

#282 - Release 1.23.2

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

#281 - Remove cell_type requirement for cell_type__custom (SCP-4835)

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

#280 - Check that "extract cluster" argument is True (SCP-4842)

Pull Request - State: closed - Opened by ehanna4 about 2 years ago - 1 comment

#279 - Release 1.23.1

Pull Request - State: closed - Opened by ehanna4 about 2 years ago

#278 - Allow clustering_dimension for 2 dimensions (SCP-4828)

Pull Request - State: closed - Opened by ehanna4 about 2 years ago - 1 comment