Ecosyste.ms: Issues

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

GitHub / chanzuckerberg/czid-bench issues and pull requests

#64 - Bump certifi from 2023.7.22 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#64 - Bump certifi from 2023.7.22 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#63 - Bump urllib3 from 1.26.18 to 1.26.19

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

#63 - Bump urllib3 from 1.26.18 to 1.26.19

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

#62 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#62 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: open - Opened by dependabot[bot] 9 months ago
Labels: dependencies

#61 - Bump idna from 2.8 to 3.7

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

#61 - Bump idna from 2.8 to 3.7

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

#60 - Bump urllib3 from 1.26.5 to 1.26.18

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

#59 - Bump urllib3 from 1.26.5 to 1.26.17

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

#59 - Bump urllib3 from 1.26.5 to 1.26.17

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

#58 - Bump certifi from 2022.12.7 to 2023.7.22

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

#58 - Bump certifi from 2022.12.7 to 2023.7.22

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

#57 - Add security.md and Code of Conduct

Pull Request - State: closed - Opened by rzlim08 over 1 year ago

#56 - Bump future from 0.17.1 to 0.18.3

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

#55 - Rlim/dsf

Pull Request - State: closed - Opened by rzlim08 over 1 year ago

#55 - Rlim/dsf

Pull Request - State: closed - Opened by rzlim08 over 1 year ago

#54 - Rlim/new pr

Pull Request - State: closed - Opened by rzlim08 over 1 year ago

#54 - Rlim/new pr

Pull Request - State: closed - Opened by rzlim08 over 1 year ago

#53 - Bump scipy from 1.3.1 to 1.10.0

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

#53 - Bump scipy from 1.3.1 to 1.10.0

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

#52 - Bump requests from 2.22.0 to 2.31.0

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

#52 - Bump requests from 2.22.0 to 2.31.0

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

#51 - Bump certifi from 2019.6.16 to 2022.12.7

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

#51 - Bump certifi from 2019.6.16 to 2022.12.7

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

#50 - Bump joblib from 0.13.2 to 1.2.0

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

#50 - Bump joblib from 0.13.2 to 1.2.0

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

#49 - rebranding idseq to czid

Pull Request - State: closed - Opened by rzlim08 over 2 years ago

#49 - rebranding idseq to czid

Pull Request - State: closed - Opened by rzlim08 over 2 years ago

#48 - Bump numpy from 1.17.0 to 1.22.0

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

#48 - Bump numpy from 1.17.0 to 1.22.0

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

#47 - Bump numpy from 1.17.0 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#47 - Bump numpy from 1.17.0 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#46 - Bump urllib3 from 1.25.8 to 1.26.5

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

#46 - Bump urllib3 from 1.25.8 to 1.26.5

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

#45 - Bump urllib3 from 1.25.3 to 1.25.8

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#45 - Bump urllib3 from 1.25.3 to 1.25.8

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#44 - Refer to idseq-workflows instead of idseq-dag

Pull Request - State: closed - Opened by cdebourcy over 4 years ago

#44 - Refer to idseq-workflows instead of idseq-dag

Pull Request - State: closed - Opened by cdebourcy over 4 years ago

#43 - Fix missing @ at start of ID line

Pull Request - State: closed - Opened by tfrcarvalho over 4 years ago
Labels: bug

#43 - Fix missing @ at start of ID line

Pull Request - State: closed - Opened by tfrcarvalho over 4 years ago
Labels: bug

#42 - Relax the version guard for InSilicoSeq

Pull Request - State: closed - Opened by sikuan over 4 years ago - 1 comment

#42 - Relax the version guard for InSilicoSeq

Pull Request - State: closed - Opened by sikuan over 4 years ago - 1 comment

#40 - Time to use GitHub releases?

Issue - State: open - Opened by jmkim over 4 years ago
Labels: enhancement

#40 - Time to use GitHub releases?

Issue - State: open - Opened by jmkim over 4 years ago
Labels: enhancement

#39 - make idseq-bench-score compatible with staging environment

Pull Request - State: closed - Opened by katrinakalantar over 4 years ago

#39 - make idseq-bench-score compatible with staging environment

Pull Request - State: closed - Opened by katrinakalantar over 4 years ago

#38 - enable benchmark scoring with both sfn-wdl and original pipeline

Pull Request - State: closed - Opened by katrinakalantar over 4 years ago

#38 - enable benchmark scoring with both sfn-wdl and original pipeline

Pull Request - State: closed - Opened by katrinakalantar over 4 years ago

#37 - Fix installation: Recursively find packages

Pull Request - State: closed - Opened by tfrcarvalho about 5 years ago

#37 - Fix installation: Recursively find packages

Pull Request - State: closed - Opened by tfrcarvalho about 5 years ago

#36 - Fix filenames to match with pipeline monitor trigger changes

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#36 - Fix filenames to match with pipeline monitor trigger changes

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#35 - Refactor filenames to make them more tightly coupled with benchmark

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago - 1 comment

#35 - Refactor filenames to make them more tightly coupled with benchmark

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago - 1 comment

#34 - Fix AUPR metric as per the Cell paper (optional monotonic adjustment)

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#34 - Fix AUPR metric as per the Cell paper (optional monotonic adjustment)

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#33 - Fix issues with file open and iteration

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#33 - Fix issues with file open and iteration

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#32 - Add more scoring metrics

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#32 - Add more scoring metrics

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#31 - Packaging idseq-bench and move to config files setup

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#31 - Packaging idseq-bench and move to config files setup

Pull Request - State: closed - Opened by tfrcarvalho over 5 years ago

#30 - compare script

Pull Request - State: closed - Opened by yunfangjuan over 6 years ago

#30 - compare script

Pull Request - State: closed - Opened by yunfangjuan over 6 years ago

#29 - minor improvements to scoring

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago - 2 comments

#28 - Boris/disable basis vectors

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#27 - add summary

Pull Request - State: closed - Opened by yunfangjuan over 6 years ago - 1 comment

#26 - standardize capitalization of IDseq to match the portal

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#25 - Boris/taxid annot fasta

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#24 - handle utf8 decode and tally fasta

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#23 - smarter_open and smarter_readline using s3cat

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#22 - count input fastqs

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#21 - update to handle header format change in ISS 1.2.1 and add scorer

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#20 - back to 60k reads

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#19 - todo comment

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#18 - put individual samples into their own subdirectories

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#16 - reduce size for automated daily runs, v5

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#15 - Create LICENSE

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#14 - also generate basis vectors

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#12 - 99.99% of miseq reads fail lzw threshold in idseq

Issue - State: open - Opened by boris-dimitrov over 6 years ago

#11 - reweight abundance by organism

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#10 - Boris/i0

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#9 - add benchmark lineage to read headers

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#8 - fix read IDs for STAR

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#7 - first benchmark run crashed in idseq host filtering

Issue - State: closed - Opened by boris-dimitrov over 6 years ago - 3 comments

#6 - InSilicoSeq generates fewer reads than requested

Issue - State: closed - Opened by boris-dimitrov over 6 years ago - 2 comments

#5 - relative abundance should be per-organism not per-accession

Issue - State: closed - Opened by boris-dimitrov over 6 years ago - 1 comment

#4 - filenames contain options and version info

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#3 - first working version

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#2 - fetch fastas from ncbi

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago

#1 - iterate

Pull Request - State: closed - Opened by boris-dimitrov over 6 years ago