Ecosyste.ms: Issues

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

GitHub / hail-is/hail issues and pull requests

#13372 - [batch] maybe simplify jobs_after_update

Pull Request - State: closed - Opened by danking about 1 year ago - 13 comments
Labels: migration

#13370 - [Snyk] Security upgrade cryptography from 41.0.2 to 41.0.3

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

#13366 - [Snyk] Security upgrade cryptography from 41.0.2 to 41.0.3

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

#13365 - [Snyk] Security upgrade cryptography from 41.0.2 to 41.0.3

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

#13355 - [compiler] rewrite ExtractIntervalFilters to be more robust

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

#13351 - [query] In Azure, QoB sees elevated rates of weird errors from the Azure Blob Storage SDK

Issue - State: closed - Opened by danking about 1 year ago - 7 comments
Labels: bug, query

#13346 - [query] bad error message when user needs to use array_elements_required=False

Issue - State: closed - Opened by danking about 1 year ago - 2 comments
Labels: bug, query

#13339 - [query] error when annotating a matrix table with a table (joins)

Issue - State: open - Opened by patrick-schultz about 1 year ago - 11 comments
Labels: bug

#13336 - [query] tableaggregate o tableparallelize should be local

Pull Request - State: closed - Opened by danking about 1 year ago - 4 comments

#13333 - [query] allow inteval filters to work with indirect row key

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

#13331 - [ci] Add easier way to add all production developers to a dev namespace

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

#13328 - Batch front-end pods cannot handle large job logs

Issue - State: closed - Opened by daniel-goldstein about 1 year ago
Labels: bug

#13324 - Batch Driver Does not shut down tasks in the correct order

Issue - State: open - Opened by daniel-goldstein about 1 year ago
Labels: bug

#13324 - Batch Driver Does not shut down tasks in the correct order

Issue - State: open - Opened by daniel-goldstein about 1 year ago
Labels: bug

#13324 - Batch Driver Does not shut down tasks in the correct order

Issue - State: open - Opened by daniel-goldstein about 1 year ago
Labels: bug

#13323 - [Snyk] Security upgrade tornado from 6.2 to 6.3.2

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

#13322 - [batch] Stream job logs in the batch front-end

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

#13318 - [batch] Azure preemption rate was too high due to our set point for spot billing prices

Issue - State: closed - Opened by jigold about 1 year ago - 1 comment
Labels: bug

#13317 - [compiler] incremental hashing based on Threefry

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

#13316 - [Snyk] Security upgrade certifi from 2023.5.7 to 2023.7.22

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

#13312 - [query] unexpectedly slow queries in AoU RWB

Issue - State: open - Opened by danking about 1 year ago
Labels: new-feature, query

#13309 - [Snyk] Security upgrade certifi from 2023.5.7 to 2023.7.22

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

#13305 - [Snyk] Security upgrade certifi from 2023.5.7 to 2023.7.22

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

#13304 - [Snyk] Security upgrade certifi from 2023.5.7 to 2023.7.22

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

#13296 - [Snyk] Security upgrade certifi from 2023.5.7 to 2023.7.22

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

#13294 - [Snyk] Security upgrade certifi from 2023.5.7 to 2023.7.22

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

#13287 - [query] bug in group_cols_by

Issue - State: closed - Opened by anh151 about 1 year ago - 5 comments
Labels: bug

#13286 - [Snyk] Security upgrade aiohttp from 3.8.4 to 3.8.5

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

#13285 - [Snyk] Security upgrade aiohttp from 3.8.4 to 3.8.5

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

#13284 - [Snyk] Security upgrade aiohttp from 3.8.4 to 3.8.5

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

#13283 - [Snyk] Security upgrade aiohttp from 3.8.4 to 3.8.5

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

#13282 - [Snyk] Security upgrade aiohttp from 3.8.4 to 3.8.5

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

#13279 - [hailctl] Initialize Hail Environment Interactively

Pull Request - State: closed - Opened by jigold about 1 year ago - 22 comments

#13269 - [batch] Scheduler and autoscaler deadlocked

Issue - State: open - Opened by jigold about 1 year ago
Labels: bug

#13268 - [batch] Fix autoscaler / scheduler deadlock with regions

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

#13268 - [batch] Fix autoscaler / scheduler deadlock with regions

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

#13259 - [security] update scipy pin to 1.11.1

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

#13256 - [auth] deleting a user is broken in the UI

Issue - State: open - Opened by jigold about 1 year ago - 1 comment
Labels: bug

#13256 - [auth] deleting a user is broken in the UI

Issue - State: open - Opened by jigold about 1 year ago - 1 comment
Labels: bug

#13256 - [auth] deleting a user is broken in the UI

Issue - State: open - Opened by jigold about 1 year ago - 3 comments
Labels: bug, batch

#13254 - [ci/ui] fixes 500 when there are no jobs to display

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

#13250 - NormalizeNames at most once

Issue - State: open - Opened by ehigham about 1 year ago
Labels: bug, performance, infrastructure

#13250 - NormalizeNames at most once

Issue - State: open - Opened by ehigham about 1 year ago
Labels: bug, performance, infrastructure

#13249 - [query] gnomAD 2.1.1 sites table VCF is not parseable with Hail

Issue - State: closed - Opened by danking about 1 year ago - 1 comment

#13248 - [query] whole stage codegen fails with exit code 137 on partitions with lots of alleles

Issue - State: open - Opened by danking about 1 year ago - 2 comments
Labels: bug

#13248 - [query] whole stage codegen fails with exit code 137 on partitions with lots of alleles

Issue - State: open - Opened by danking about 1 year ago - 2 comments
Labels: bug

#13248 - [query] whole stage codegen fails with exit code 137 on partitions with lots of alleles

Issue - State: open - Opened by danking about 1 year ago - 3 comments
Labels: bug, query

#13247 - [Snyk] Security upgrade cryptography from 41.0.1 to 41.0.2

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

#13242 - [qob] log4j errors are showing up in JVM container logs

Issue - State: open - Opened by jigold about 1 year ago - 1 comment
Labels: bug

#13242 - [qob] log4j errors are showing up in JVM container logs

Issue - State: open - Opened by jigold about 1 year ago - 2 comments
Labels: bug

#13242 - [qob] log4j errors are showing up in JVM container logs

Issue - State: open - Opened by jigold about 1 year ago - 1 comment
Labels: bug

#13241 - [query] reenable long dormant localize_entries tests

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

#13235 - [lint] runs black on hail/

Pull Request - State: closed - Opened by iris-garden about 1 year ago - 1 comment
Labels: prio:low, WIP

#13228 - Bump scipy from 1.9.3 to 1.11.1 in /hail/python

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies, python

#13224 - [hailctl] Autocomplete for hailctl config {get,set,unset}

Pull Request - State: closed - Opened by jigold over 1 year ago - 7 comments

#13214 - [query] refactor BaseIR so children only exposes iterable interface

Pull Request - State: closed - Opened by patrick-schultz over 1 year ago - 3 comments

#13208 - [infra] Revert GKE metadata workload identity config

Pull Request - State: closed - Opened by daniel-goldstein over 1 year ago
Labels: NIST 800-53

#13201 - [batch/ui] redesigns jobs table

Pull Request - State: open - Opened by iris-garden over 1 year ago
Labels: prio:low, WIP

#13201 - [batch/ui] redesigns jobs table

Pull Request - State: open - Opened by iris-garden over 1 year ago
Labels: prio:low, WIP

#13200 - [batch] restricts operations to GCS buckets using hot storage

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

#13192 - [batch] Add new ResourceGroup items to `_resources_inverse`

Pull Request - State: closed - Opened by jmarshall over 1 year ago - 3 comments

#13191 - ResourceGroup issues modelling writing a bgzipped file and its TBI index via `write_output`

Issue - State: open - Opened by jmarshall over 1 year ago - 10 comments
Labels: new-feature

#13191 - ResourceGroup issues modelling writing a bgzipped file and its TBI index via `write_output`

Issue - State: open - Opened by jmarshall over 1 year ago - 8 comments
Labels: new-feature

#13188 - [WIP] Skeleton of staged interval join implementation

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

#13172 - Revert "[query] Zstdandard (Zstd) compression"

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

#13166 - [query] add eigh method

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

#13162 - [docker] hailgenetics/hail should have tags for each supported Python version

Issue - State: closed - Opened by danking over 1 year ago - 1 comment
Labels: new-feature

#13159 - [Snyk] Security upgrade requests from 2.28.2 to 2.31.0

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

#13158 - [Snyk] Security upgrade requests from 2.28.2 to 2.31.0

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

#13131 - [auth] Allow use of cloud access tokens for hail batch authorization

Pull Request - State: closed - Opened by daniel-goldstein over 1 year ago - 11 comments
Labels: full-deploy, terraform, NIST 800-53

#13107 - [Snyk] Security upgrade requests from 2.28.2 to 2.31.0

Pull Request - State: open - Opened by snyk-bot over 1 year ago

#13106 - [query] Specialize export_blocks into its own writer

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

#13105 - [infra] apply a PDB to kube-dns

Pull Request - State: open - Opened by danking over 1 year ago

#13104 - [qob] retry stream is already closed

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

#13103 - [ci] use buildah

Pull Request - State: open - Opened by danking over 1 year ago

#13102 - Buildah

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

#13101 - [aiotools] Properly close azure storage clients

Pull Request - State: open - Opened by jigold over 1 year ago - 2 comments

#13100 - [Snyk] Security upgrade requests from 2.28.2 to 2.31.0

Pull Request - State: open - Opened by danking over 1 year ago

#13099 - [query] suggest --only-binary=:all: if pip fails to build from source

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

#13098 - [batch] Add resource usage plots for JVM containers

Pull Request - State: open - Opened by jigold over 1 year ago - 3 comments

#13097 - [Snyk] Security upgrade requests from 2.28.2 to 2.31.0

Pull Request - State: open - Opened by snyk-bot over 1 year ago

#13096 - Bump requests from 2.28.2 to 2.31.0 in /ci

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

#13095 - Bump requests from 2.28.2 to 2.31.0 in /auth

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

#13094 - Bump requests from 2.28.2 to 2.31.0 in /gear

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

#13093 - Bump requests from 2.28.2 to 2.31.0 in /hail/python

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

#13092 - Bump requests from 2.28.2 to 2.31.0 in /hail/python/dev

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

#13091 - Bump requests from 2.28.2 to 2.31.0 in /hail/python/hailtop

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

#13090 - [test-dataproc] add subnet

Pull Request - State: closed - Opened by danking over 1 year ago
Labels: prio:high

#13089 - [query] fix requester pays in all Query backends

Pull Request - State: open - Opened by danking over 1 year ago

#13088 - [batch] Exponential backoff of resource usage monitoring

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

#13087 - [docker] Add rsync to hail-ubuntu image

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

#13086 - [batch] Job Groups

Pull Request - State: closed - Opened by jigold over 1 year ago - 3 comments
Labels: WIP, migration

#13085 - [release] 0.2.117

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

#13083 - [batch] Fix attempt resources after update trigger to use deduped resource id

Pull Request - State: open - Opened by jigold over 1 year ago - 1 comment
Labels: WIP, migration