hail-is/hail issues and pull requests

#13082 - [batch] Fix Python to add correct deduped resource id

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

#13081 - [vds] Compute max reference block length in the VDS combiner

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

#13080 - [batch] Fix and reset migrations to dedup resource ids in billing tables

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

#13079 - [query] warn about force=True in hl.import_vcf

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

#13078 - [nd] docs should use \ge not \gte

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

#13077 - rapid compilation

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

#13076 - More parallelism

Pull Request - State: open - Opened by danking over 1 year ago - 10 comments

#13075 - [qob] novel transient error

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

#13074 - [QoB] new transient error: java.net.SocketTimeoutException: connect timed out

Issue - State: closed - Opened by danking over 1 year ago
Labels: bug

#13073 - [batch] Remove unnecessary get_compute_client method on CloudWorkerAPI

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

#13072 - [Snyk] Security upgrade tornado from 6.2 to 6.3.2

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

#13071 - [batch] Dont use the authorization header for worker tokens to the driver

Pull Request - State: closed - Opened by daniel-goldstein over 1 year ago - 5 comments

#13070 - [build.yaml] Remove failing dedup_bp_user_resources migration

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

#13069 - [batch] Fix dedup billing project user resources audit

Pull Request - State: closed - Opened by jigold over 1 year ago - 2 comments
Labels: prio:high, migration

#13068 - [batch] Delete unused batch user code ssl config

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

#13067 - [qob] immediateFlush=true for QoB logger

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

#13066 - [Snyk] Security upgrade tornado from 6.2 to 6.3.2

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

#13065 - [qob] remove resource leak in readNoCompression

Pull Request - State: closed - Opened by danking over 1 year ago - 3 comments
Labels: prio:high

#13064 - QoB should start a new Batch after a keyboard interrupt.

Issue - State: closed - Opened by danking over 1 year ago - 2 comments
Labels: bug

#13063 - QoB should include some cluster statistics in the terminal output

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

#13062 - QoB's job URL should use ?last_job_id to send us to the page containing the current driver.

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

#13061 - In Query-on-Batch in Azure, a 1500 partition VCF fails to import

Issue - State: closed - Opened by danking over 1 year ago
Labels: bug

#13060 - [hailctl] fix init_notebook.py requirements to be compatible with Hail

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

#13059 - 500 inside notebook of hailctl dataproc start cluster

Issue - State: closed - Opened by danking over 1 year ago

#13058 - Azure-redeploy-fixes-upstream

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

#13057 - [gar-cleaner]

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

#13056 - [batch] Let worker control job deploy-config instead of using k8s secret

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

#13055 - [batch] Dont schedule on instances that dont match the current instance version

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

#13054 - Bump sphinx from 6.2.1 to 7.0.1 in /hail/python/dev

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

#13053 - [batch] include instance name in labels and label disks

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

#13052 - hailtop.fs `ReadableStream` does not support seeking on streams from blob storage

Issue - State: open - Opened by daniel-goldstein over 1 year ago - 1 comment
Labels: help wanted, new-feature, fs

#13051 - [hailctl] Fix validation for remote_tmpdir to allow azure https scheme

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

#13050 - Hail is missing deploys 0.2.114 and 0.2.115 in Azure

Issue - State: open - Opened by danking over 1 year ago - 5 comments
Labels: bug

#13049 - https:// is considered invalid by hailctl config set batch/remote_tmpdir

Issue - State: closed - Opened by danking over 1 year ago

#13048 - [query] Split up matrix randomness test

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

#13047 - Correct the 0.2.116 release date [very minor]

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

#13046 - ClassCastException when comparing hl.Locus to row key

Issue - State: open - Opened by danking over 1 year ago
Labels: bug

#13045 - Hail Locus (and other Python data types) in eq, etc. should check if the RHS is a Hail Expression and delegate to the expression instead.

Issue - State: open - Opened by danking over 1 year ago
Labels: bug

#13044 - [query] minor performance improvement

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

#13043 - [transient-errors] will it ever end?

Pull Request - State: closed - Opened by danking over 1 year ago - 2 comments
Labels: prio:high

#13042 - [qob] actually do a naive_coalsece

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

#13041 - [infra] fix workload_identity_config

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

#13040 - [qob] only use highmem for one test

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

#13039 - [benchmark] Make benchmarks run in Google Artifact Repository

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

#13038 - [ci] Remove redundancies between the two build_hail steps

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

#13037 - [query] eliminate irrelevant META-INF.services

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

#13036 - [batch] Allow private job network traffic to internal IPs

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

#13035 - [batch] Give cloud-specific API implementations more control over container registry credentials

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

#13034 - Bump types-chardet from 5.0.4.5 to 5.0.4.6 in /hail/python/dev

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

#13033 - [batch] no wget

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

#13032 - [services] update azure-storage-blob 12.22.0 to mitigate "Stream is already closed"

Pull Request - State: closed - Opened by danking over 1 year ago - 5 comments
Labels: prio:high

#13031 - [query] Better message for LocalLDPrune only taking diploid calls

Pull Request - State: closed - Opened by chrisvittal over 1 year ago
Labels: tiny PR

#13030 - [ci] Create a test MySQL server in test and dev namespaces

Pull Request - State: closed - Opened by daniel-goldstein over 1 year ago - 2 comments
Labels: prio:high

#13029 - [services] reliably retry all requests

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

#13028 - [vds] Fix bug in vds.filter_intervals with reference block max len

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

#13023 - [services] restore logging

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

#13022 - [ci] Add CreateDatabase2Step for in-namespace test and dev databases

Pull Request - State: closed - Opened by daniel-goldstein over 1 year ago - 1 comment
Labels: prio:high

#13021 - [services] retry five times instead of once

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

#13020 - [batch] without auto-create subnetworks, you must specify a subnet

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

#13019 - [docs] fix minor doc bug

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

#13018 - [services] update azure-storage-blob 12.22.0 to mitigate "Stream is already closed"

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

#13017 - [infra][gke] disable gce metadata enable gke metadata

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

#13016 - [infra] create subnetworks manually

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

#13015 - [infra] use uniform bucket level access

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

#13014 - [ci] Dont use in-pipeline images for cleanup jobs

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

#13013 - [qob] maybe retry GSFS reads

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

#13012 - [services] retry five times instead of once

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

#13011 - [compiler] ensure CDA result Array[Array[Byte]] can be GCed after dec…

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

#13010 - [admin-pod] Fix admin-pod Makefile and deployment.yaml

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

#13009 - Hail datasets API and annotation database need to move to regional rather than multi-regional buckets

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

#13008 - [ci] Use the ci-utils image from the new branch for db creation

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

#13007 - [batch] Allow optional byte suffix for memory and storage requests

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

#13006 - [git] ignore .metals and .bloop

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

#13005 - [query] struct pprint tests

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

#13004 - [ci] Run service backend tests on non-preemptibles

Pull Request - State: closed - Opened by daniel-goldstein over 1 year ago - 2 comments
Labels: prio:high

#13003 - Before execution, Hail Batch and Hail Query should assert that no referenced buckets have storage classes with elevated read costs.

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

GitHub / hail-is/hail issues and pull requests