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

#277 - Release 1.23.0

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

#276 - Extract clustering from h5ad and delocalize intermediate files to study bucket (SCP-4771)

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

#275 - Fixing bug with slices landing on line ends (SCP-4648)

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

#274 - Release 1.22.0

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

#273 - Integrating `ExpressionWriter` into `IngestPipeline` (SCP-4648)

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

#272 - Release 1.21.0

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

#271 - Handle existing inserts when retrying from dropped MongoDB connection (SCP-4621)

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

#270 - Parallelizing expression matrix processing for Image Pipeline (SCP-4647)

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

#269 - Adding script to generate data for image pipeline (SCP-4584)

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

#268 - Release 1.20.1

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

#267 - Release 1.20.0

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

#266 - Accept additional file extensions for AnnData ingest (SCP-4557)

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

#265 - Distinguish between + and - in sanitized DE filenames (SCP-4533)

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

#264 - Add minimal validation of h5ad files to scp-ingest-pipeline (SCP-4498)

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

#263 - Bump numpy from 1.21.5 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 3 comments
Labels: dependencies

#262 - Release 1.19.2

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

#260 - Fix imprecise name sanitization in DE (SCP-4459)

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

#259 - Release 1.19.1

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

#258 - Fix ingest pipeline user_log.txt delocalization (SCP-4445)

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

#257 - Release 1.19.0

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

#256 - Duplicate gene name handling in DE processing (SCP-4283)

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

#255 - Release 1.18.0

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

#254 - Delocalize DE results to study bucket (SCP-4300)

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

#252 - Release 1.17.2

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

#251 - Enable DE on cluster annotations (SCP-4258)

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#250 - Reverting general try-except (SCP-4279)

Pull Request - State: closed - Opened by devonbush almost 3 years ago - 1 comment

#249 - Release 1.17.1

Pull Request - State: closed - Opened by devonbush almost 3 years ago - 1 comment

#248 - Setting __event_name for unhandled errors, for Mixpanel observability (SCP-4279)

Pull Request - State: closed - Opened by devonbush almost 3 years ago - 1 comment

#247 - Release 1.17.0

Pull Request - State: closed - Opened by devonbush almost 3 years ago - 1 comment

#246 - Add general try-except for better error observability in Sentry (SCP-4279)

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

#245 - Adding a trouble shooting section for setup (SCP-4236)

Pull Request - State: closed - Opened by ehanna4 almost 3 years ago - 1 comment

#244 - Release 1.16.0

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#243 - Extend DE analysis to sparse matrix inputs (SCP-4203)

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#242 - Integration test for pilot DE process (SCP-4204)

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

#241 - Update CircleCI configs to skip problematic tests (SCP-4209)

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#240 - Update pip in docker build to resolve pandas install issue

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

#239 - Release 1.15.0

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#238 - Prototype DE pipeline for dense matrix inputs (SCP-4074)

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

#237 - Release 1.14.2

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#236 - Log ingest pipeline ValueError exceptions to Mixpanel (SCP-4139)

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment
Labels: build failure: false positive

#235 - Release 1.14.1

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

#234 - Store ontology label in BigQuery for synonyms in metadata (SCP-3987)

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

#233 - Release 1.14.0

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

#232 - Adding Mixpanel logging to ingest pipeline expression matrix errors (SCP-4037)

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#231 - Release 1.13.1

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#229 - Release 1.13.0

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#228 - Log ingest annotation validation errors to Mixpanel (SCP-3921)

Pull Request - State: closed - Opened by jlchang almost 3 years ago - 1 comment

#227 - Release 1.12.4

Pull Request - State: closed - Opened by jlchang about 3 years ago - 1 comment

#226 - Handle "Excel drag" ontology ID user error in Ingest Pipeline validation (SCP-3031)

Pull Request - State: closed - Opened by jlchang about 3 years ago - 1 comment

#225 - Validate nonconventional numeric metadata values are numeric (SCP-3876)

Pull Request - State: closed - Opened by jlchang about 3 years ago - 1 comment

#224 - Reject cluster file if coordinate value of NaN detected (SCP-3575)

Pull Request - State: closed - Opened by jlchang about 3 years ago - 1 comment

#222 - Release 1.12.3

Pull Request - State: closed - Opened by jlchang about 3 years ago - 1 comment

#221 - Handle very large group-based metadata annotations in ingest (SCP-3761)

Pull Request - State: closed - Opened by jlchang about 3 years ago - 1 comment

#220 - Improve matrix ingest error reporting (SCP-3832)

Pull Request - State: closed - Opened by jlchang about 3 years ago

#219 - Release 1.12.2

Pull Request - State: closed - Opened by jlchang over 3 years ago - 1 comment

#218 - Allow Exact Synonyms in metadata validation (SCP-3631)

Pull Request - State: closed - Opened by jlchang over 3 years ago - 2 comments
Labels: build failure: false positive

#217 - Release 1.12.1

Pull Request - State: closed - Opened by jlchang over 3 years ago

#216 - Relocate IngestPipeline method about metadata convention to CellMetadata Class (SCP-3631)

Pull Request - State: closed - Opened by jlchang over 3 years ago - 1 comment

#215 - Release 1.12.0

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

#214 - PyMongo batch operations error handling (SCP-3703)

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

#213 - Updating setup.py for 1.11.0 release (SCP-3414)

Pull Request - State: closed - Opened by bistline over 3 years ago

#212 - Release 1.11.0

Pull Request - State: closed - Opened by bistline over 3 years ago - 3 comments

#211 - Relaxing ontology label matching (SCP-3370)

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

#175 - * SCP-2900 Add comments from peer review

Pull Request - State: closed - Opened by knapii-developments about 4 years ago - 1 comment

#174 - * SCP-2900 Resolve "not enough values to unpack (expected 3, got 1)"

Pull Request - State: closed - Opened by knapii-developments about 4 years ago - 2 comments

#172 - * SCP-2893 Fix bug blocking release

Pull Request - State: closed - Opened by knapii-developments about 4 years ago - 1 comment

#167 - * SCP-2891 Add extra validations for gzipped files

Pull Request - State: closed - Opened by knapii-developments about 4 years ago

#161 - * SCP-2761 Measure the number of unsorted/sorted mtx uploads via Mixpanel

Pull Request - State: closed - Opened by knapii-developments about 4 years ago - 1 comment