hail-is/hail issues and pull requests

#14495 - [compiler] delete old binds implementation

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

#14494 - [query] Correct python encoding/decoding of diploid calls

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

#14493 - [docs] Query-on-Batch desperately needs its own tutorial

Issue - State: open - Opened by daniel-goldstein 6 months ago
Labels: documentation, new-feature, query

#14492 - Bump comm from 0.2.1 to 0.2.2 in /hail/python/dev

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

#14491 - Bump types-six from 1.16.21.20240301 to 1.16.21.20240311 in /hail/python

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

#14490 - [ci] hail_curl_image is redundant. kill it.

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

#14489 - Invalid maximum heap size: -Xmx0m

Issue - State: open - Opened by Asppagh 6 months ago
Labels: needs-triage

#14488 - [devdocs] Add dev doc describing gateways configuration

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago

#14487 - [qob] Add metadata server support for JVMJobs and update QoB to use it

Issue - State: open - Opened by daniel-goldstein 6 months ago
Labels: new-feature, query, batch

#14486 - [batch] Complete the transition from GSA key files to the Batch metadata server

Issue - State: open - Opened by daniel-goldstein 6 months ago
Labels: new-feature, Epic, batch

#14485 - [hailtop] The Batch client should warn users when they are using deprecated APIs

Issue - State: closed - Opened by daniel-goldstein 6 months ago
Labels: enhancement, batch, good-first-project

#14484 - Bump jupyter-core from 5.7.1 to 5.7.2 in /hail/python/dev

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

#14483 - Bump jupyterlab-server from 2.25.3 to 2.26.0 in /hail/python

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

#14482 - Bump aiohttp from 3.9.3 to 3.9.4 in /hail/python

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14481 - Bump aiohttp from 3.9.3 to 3.9.4 in /hail/python/dev

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14480 - Bump aiohttp from 3.9.3 to 3.9.4 in /web_common

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14479 - Bump aiohttp from 3.9.3 to 3.9.4 in /gear

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14478 - Bump aiohttp from 3.9.3 to 3.9.4 in /hail/python/hailtop

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14477 - Bump aiohttp from 3.9.3 to 3.9.4 in /batch

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14476 - Revert "[ci] Poll for batch and github changes every 1 minute instead of 5"

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago
Labels: prio:high

#14475 - [compiler] consolidate BindingEnv interface

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

#14474 - [query] Build Hail Wheel With Python build

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

#14473 - Bump zipp from 3.17.0 to 3.18.1 in /hail/python

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#14472 - Bump pyasn1-modules from 0.3.0 to 0.4.0 in /hail/python/dev

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago - 2 comments
Labels: dependencies, python

#14471 - [pip] Update orjson and transitive dependencies

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago

#14463 - [query] Thread `idempotent` flag to `init_spark`

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

#14462 - Hail does not correctly handle spark idempotent initialisation

Issue - State: closed - Opened by ehigham 6 months ago
Labels: bug

#14460 - [batch] Orphaned attempts loop performs full scan of instances table

Issue - State: open - Opened by daniel-goldstein 6 months ago - 1 comment
Labels: performance, batch, good-first-project

#14458 - [batch] Remove remaining locks in read-only billing project queries

Pull Request - State: open - Opened by daniel-goldstein 6 months ago

#14457 - [infra] SOPS-encrypt global.tfvars for Azure deployment

Issue - State: open - Opened by daniel-goldstein 6 months ago
Labels: infrastructure, chore, batch

#14456 - [batch] Remove blob storage read inside Worker job creation endpoint

Issue - State: closed - Opened by daniel-goldstein 6 months ago
Labels: enhancement, batch, good-first-project

#14455 - [compiler] PruneDeadFields simplification

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

#14454 - [release] 0.2.130

Pull Request - State: closed - Opened by ehigham 6 months ago
Labels: prio:high

#14453 - [release] build release wheel with correct `deploy.yaml`

Pull Request - State: closed - Opened by ehigham 6 months ago - 2 comments
Labels: prio:high

#14452 - `hailctl dataproc start` fails in hail `0.2.129`

Issue - State: closed - Opened by ehigham 6 months ago - 2 comments
Labels: bug

#14451 - [compiler] rewrite FreeVariables to not duplicate binding structure

Pull Request - State: open - Opened by patrick-schultz 6 months ago - 1 comment

#14450 - [terra] Fix terra on azure helm chart and make targets

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

#14449 - [python] Use `importlib.resources` instead of `pkg_resources`

Pull Request - State: open - Opened by ehigham 6 months ago

#14448 - [compiler] Enforce stronger invariants on eval/agg/scan contexts

Pull Request - State: closed - Opened by patrick-schultz 6 months ago

#14447 - [query] Copy spark driver log to remote tmpdir on error

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

#14446 - [query] Remove native llvm experiment

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago

#14445 - [release] dont rely on release.sh being executable

Pull Request - State: closed - Opened by ehigham 6 months ago
Labels: prio:high, do-not-test

#14444 - [ci] Run the test-dataproc jobs on non-preemptible instances

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

#14443 - [batch] Do not lock when querying billing projects

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago

#14442 - [batch] Add websocket endpoint for receiving batch status updates

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago

#14441 - Bump pillow from 10.2.0 to 10.3.0 in /hail/python/dev

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#14440 - Bump pillow from 10.2.0 to 10.3.0 in /hail/python

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#14439 - Bump pillow from 10.2.0 to 10.3.0 in /benchmark/python

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#14438 - [release] split export statements out of desperation more than anything

Pull Request - State: closed - Opened by ehigham 6 months ago - 1 comment
Labels: prio:high

#14437 - [batch] Use spend instead of cost on the billing page

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago
Labels: snack

#14436 - [release] Fix EV syntax in release job for WHEEL variable

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago
Labels: prio:high

#14435 - [ci] Allow GCP g2 test to timeout

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago
Labels: prio:high

#14434 - [release] Retry 0.2.129

Pull Request - State: closed - Opened by ehigham 6 months ago
Labels: prio:high

#14433 - feature request: Java 17 support

Issue - State: open - Opened by pettyalex 6 months ago - 2 comments
Labels: new-feature, query

#14432 - [qob] Use job groups for driver job and worker stages

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

#14431 - [query] Automatically copy logs off spark driver before failure

Issue - State: closed - Opened by patrick-schultz 6 months ago - 1 comment
Labels: enhancement, snack

#14430 - [fs] Add sink write failure in ABS to transient errors

Pull Request - State: closed - Opened by daniel-goldstein 6 months ago

#14429 - fix deploy failure caused by use of relative paths

Pull Request - State: closed - Opened by ehigham 6 months ago
Labels: prio:high

#14428 - [bug] Hail seems to need setuptools at runtime, but does not have it listed as a dependency

Issue - State: open - Opened by pettyalex 6 months ago - 1 comment

#14427 - Bump orjson from 3.9.10 to 3.10.0 in /hail/python

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies, python

#14426 - [release] 0.2.129

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

#14425 - [batch/ui] adds "always run" to job and batch UIs

Pull Request - State: closed - Opened by iris-garden 6 months ago - 5 comments

#14424 - [batch] Some tasks are not properly closed on instance shutdown

Issue - State: open - Opened by daniel-goldstein 6 months ago - 1 comment
Labels: bug, batch, snack

#14423 - [batch] query_billing_projects_with_cost should not lock in share mode

Issue - State: closed - Opened by daniel-goldstein 6 months ago - 1 comment
Labels: batch, snack

#14422 - [infra] CloudSQL backups are happening in multi-regional buckets

Issue - State: closed - Opened by jigold 6 months ago - 1 comment
Labels: batch

#14421 - Remove `auth` from `check-pip-requirements` make target

Pull Request - State: closed - Opened by ehigham 7 months ago

#14420 - [query] fix bad bug in IndexedRVDSpec2

Pull Request - State: closed - Opened by patrick-schultz 7 months ago - 1 comment

#14419 - [ci] Expose `HAIL_CI_STORAGE_URI` as `ci_storage_uri` in CI Steps

Pull Request - State: closed - Opened by ehigham 7 months ago
Labels: full-deploy

#14418 - [batch] Close the aiohttp client session used by the gcp WorkerAPI

Pull Request - State: closed - Opened by daniel-goldstein 7 months ago

#14417 - [qob] Remove mount_tokens job spec parameter for worker jobs

Pull Request - State: closed - Opened by daniel-goldstein 7 months ago

#14416 - [batch] Remove hardcoded eastus assert

Pull Request - State: closed - Opened by daniel-goldstein 7 months ago

#14416 - [batch] Remove hardcoded eastus assert

Pull Request - State: closed - Opened by daniel-goldstein 7 months ago

#14415 - [lint] Applies remaining ruff linter changes to hail/ folder

Pull Request - State: closed - Opened by iris-garden 7 months ago

#14415 - [lint] Applies remaining ruff linter changes to hail/ folder

Pull Request - State: open - Opened by iris-garden 7 months ago

#14414 - [chore] Cleanup VEP buckets

Issue - State: open - Opened by jigold 7 months ago
Labels: chore

#14414 - [chore] Cleanup VEP buckets

Issue - State: open - Opened by jigold 7 months ago
Labels: needs-triage, chore

#14413 - [batch] Job groups transient error causing a 400 to the user

Issue - State: open - Opened by jigold 7 months ago
Labels: bug, batch, good-first-project

#14413 - [batch] Job groups transient error causing a 400 to the user

Issue - State: open - Opened by jigold 7 months ago
Labels: needs-triage, batch

#14412 - [batch] Consider rewriting scheduler and canceller queries to be more efficient

Issue - State: open - Opened by jigold 7 months ago
Labels: enhancement, batch

#14412 - [batch] Consider rewriting scheduler and canceller queries to be more efficient

Issue - State: open - Opened by jigold 7 months ago
Labels: needs-triage, batch

#14412 - [batch] Consider rewriting scheduler and canceller queries to be more efficient

Issue - State: open - Opened by jigold 7 months ago
Labels: needs-triage, batch

#14411 - [batch] Explore whether a stored function can be used to check whether a job group is cancelled

Issue - State: open - Opened by jigold 7 months ago
Labels: enhancement, batch

#14410 - [batch] Optimize SQL query generated for listing jobs / batches / job groups

Issue - State: open - Opened by jigold 7 months ago - 1 comment
Labels: needs-triage, batch

#14410 - [batch] Optimize SQL query generated for listing jobs / batches / job groups

Issue - State: open - Opened by jigold 7 months ago - 1 comment
Labels: needs-triage, batch

#14410 - [batch] Optimize SQL query generated for listing jobs / batches / job groups

Issue - State: open - Opened by jigold 7 months ago - 2 comments
Labels: performance, batch

#14409 - [batch] Remove the cancel_batch stored procedure from the database

Issue - State: open - Opened by jigold 7 months ago
Labels: batch, snack

#14408 - [batch] Consider renaming tables and columns for better clarity

Issue - State: open - Opened by jigold 7 months ago
Labels: enhancement, batch

#14408 - [batch] Consider renaming tables and columns for better clarity

Issue - State: open - Opened by jigold 7 months ago
Labels: needs-triage, batch

#14407 - [query] Use RouterFS With LocalBackend

Pull Request - State: open - Opened by ehigham 7 months ago - 1 comment

#14407 - [query] Use RouterFS With LocalBackend

Pull Request - State: open - Opened by ehigham 7 months ago - 3 comments

#14406 - [query] Load each missing byte once during struct decoding.

Pull Request - State: closed - Opened by chrisvittal 7 months ago - 1 comment

#14406 - [query] Load each missing byte once during struct decoding.

Pull Request - State: closed - Opened by chrisvittal 7 months ago - 1 comment

#14405 - [query/vds] Add ref_block_max_length check to VariantDataset.validate

Pull Request - State: closed - Opened by chrisvittal 7 months ago

#14405 - [query/vds] Add ref_block_max_length check to VariantDataset.validate

Pull Request - State: open - Opened by chrisvittal 7 months ago

#14404 - [query, wip] reorganize Binds.scala

Pull Request - State: open - Opened by patrick-schultz 7 months ago

#14404 - [query] reorganize Binds.scala

Pull Request - State: closed - Opened by patrick-schultz 7 months ago - 2 comments

#14403 - [RFC] order-preserving key encoding

Pull Request - State: open - Opened by patrick-schultz 7 months ago

#14403 - [RFC] order-preserving key encoding

Pull Request - State: open - Opened by patrick-schultz 7 months ago - 1 comment
Labels: do-not-test

#14403 - [RFC] order-preserving key encoding

Pull Request - State: open - Opened by patrick-schultz 7 months ago

#14402 - [query] Unify Let and AggLet into new Block node

Pull Request - State: closed - Opened by patrick-schultz 7 months ago - 3 comments

GitHub / hail-is/hail issues and pull requests