hail-is/hail issues and pull requests

#14583 - [vds/combiner] Deduplicate functions in combiner internals

Pull Request - State: open - Opened by chrisvittal 15 days ago

#14582 - [query] add sparse bm agg tests

Pull Request - State: open - Opened by patrick-schultz 19 days ago - 1 comment

#14581 - [batch] Add internal ssl certs to worker server

Pull Request - State: open - Opened by daniel-goldstein 20 days ago

#14580 - [qob] Batch backend fails to deserialize IR larger than 20MB

Issue - State: open - Opened by daniel-goldstein 20 days ago
Labels: bug, query

#14579 - [query] Fix deserialization of IR function parameter names in QoB

Pull Request - State: open - Opened by daniel-goldstein 20 days ago - 5 comments

#14578 - [compiler] fix BlockMatrixAgg lowering

Pull Request - State: open - Opened by patrick-schultz 20 days ago - 1 comment

#14577 - [vds/combiner] Fix truncation of PL in GVCF import with haploid calls

Pull Request - State: closed - Opened by chrisvittal 21 days ago

#14576 - [hailtop] Prevent event loop RecursionError during highly concurrent file uploads

Pull Request - State: open - Opened by daniel-goldstein 21 days ago - 2 comments

#14575 - [ci] fix mount paths for `start_hail_benchmark` task

Pull Request - State: closed - Opened by ehigham 25 days ago

#14574 - [query] Fix backend arg typecheck in init

Pull Request - State: closed - Opened by chrisvittal 26 days ago

#14573 - Initializing hail with `backend='batch'` fails with `TypeError: Cannot instantiate typing.Literal`.

Issue - State: closed - Opened by chrisvittal 26 days ago - 1 comment
Labels: bug, query

#14572 - [query] add `StringExpression.find`

Pull Request - State: closed - Opened by ehigham 27 days ago - 1 comment

#14571 - [query] Let-Bind Input Collection Parameter In `hl.nd.array`.

Pull Request - State: closed - Opened by ehigham 28 days ago

#14570 - [benchmark] pytestify hail benchmarks

Pull Request - State: closed - Opened by ehigham about 1 month ago

#14569 - [release] v0.2.131

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

#14568 - [infra] Update GCP DB terraform to reflect backup region change

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

#14567 - [query] Remove string length restriction in jackson

Pull Request - State: open - Opened by daniel-goldstein about 1 month ago
Labels: stacked PR

#14566 - Metadata server updates: scopes endpoint and allow omission of trailing slashes

Pull Request - State: closed - Opened by jmarshall about 1 month ago - 1 comment

#14565 - [benchmark] pytest-ify hail benchmarks

Pull Request - State: closed - Opened by ehigham about 1 month ago - 3 comments

#14564 - VDS reference data needs to have ploidy information

Issue - State: closed - Opened by chrisvittal about 1 month ago

#14563 - [dataproc] bumps version of notebook

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

#14562 - [batch] Redesign batch front end pages

Pull Request - State: open - Opened by daniel-goldstein about 1 month ago - 2 comments

#14561 - [internal-gateway] Fix bootstrap invocation

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

#14560 - [vds/combiner] Stop dropping GT in reference data during gvcf import

Pull Request - State: closed - Opened by chrisvittal about 1 month ago - 2 comments
Labels: prio:high

#14559 - MakeNDArray OOM on stream data

Issue - State: closed - Opened by ehigham about 1 month ago - 1 comment
Labels: bug, query

#14558 - [pip] Resolve security vulns in pymysql and requests

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

#14557 - [query] Failures to communicate with the spark/local backend result in cryptic error message

Issue - State: open - Opened by daniel-goldstein about 1 month ago
Labels: enhancement, query, snack

#14556 - Bump pymysql from 1.1.0 to 1.1.1 in /gear

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

#14555 - Bump requests from 2.31.0 to 2.32.0 in /ci

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

#14554 - [compiler] delete old NormalizeNames

Pull Request - State: closed - Opened by patrick-schultz about 2 months ago - 1 comment

#14553 - [query] fix lowered blockmatrix densify

Pull Request - State: closed - Opened by patrick-schultz about 2 months ago - 1 comment

#14552 - Merge upstream HEAD(b7bde56d5, 2024-05-14) Stop writing to V2 tables

Pull Request - State: closed - Opened by milo-hyben about 2 months ago

#14551 - [query] reenable test_tree_matmul_splits

Pull Request - State: open - Opened by patrick-schultz about 2 months ago - 1 comment

#14550 - [query] disable test_tree_matmul_splits

Pull Request - State: closed - Opened by patrick-schultz about 2 months ago - 1 comment

#14549 - [ci] Fix query for deployed services when filtering to live namespaces

Pull Request - State: closed - Opened by daniel-goldstein about 2 months ago - 1 comment
Labels: prio:high

#14548 - [batch] Prevent double close of the async worker pool by the canceller

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

#14547 - [compiler] add newtype for bound names in IR

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

#14546 - [query] Cleanup following 'PArray implements PArrayBackedContainer'

Pull Request - State: closed - Opened by chrisvittal about 2 months ago

#14545 - [hailtop] Dont assume exact error message match for ClientPayloadError retrying

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

#14544 - Allow os.PathLike paths for Batch.read_input()/read_input_group()

Pull Request - State: closed - Opened by jmarshall about 2 months ago - 3 comments

#14543 - [batch] Use more precise terminology around instance cost, price and revenue

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

#14542 - add a2 machine into batch

Pull Request - State: closed - Opened by sjparsa about 2 months ago

#14541 - [qob] Always send the git revision from the python service backend instead of jar_url

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

#14540 - Machine Memory Calculations in Hail Batch

Issue - State: open - Opened by sjparsa about 2 months ago - 1 comment
Labels: bug, batch

#14539 - [hailctl] QoB job specs should always use the git revision and never jar_url

Issue - State: closed - Opened by daniel-goldstein about 2 months ago
Labels: bug, query, batch

#14538 - [query] Expand EStructOfArrays to all primitive types

Pull Request - State: closed - Opened by chrisvittal about 2 months ago

#14537 - RuntimeException: IR is.hail.expr.ir.StreamFlatMap of type stream<struct{oldContext: str, nRows: int64, nCols: int64}> is not realizable

Issue - State: closed - Opened by ehigham about 2 months ago
Labels: query

#14536 - Memory refactor

Pull Request - State: closed - Opened by sjparsa about 2 months ago

#14535 - [docker] Fix pip pin

Pull Request - State: closed - Opened by daniel-goldstein about 2 months ago
Labels: prio:high

#14534 - [query] Ensure Table group_by + aggregate can't clobber global fields

Pull Request - State: closed - Opened by chrisvittal about 2 months ago

#14533 - [compiler] lift relational lets first in lowering pipeline

Pull Request - State: closed - Opened by patrick-schultz about 2 months ago - 1 comment

#14532 - [pip] Update jinja to avoid 3.1.3 vulnerability

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

#14531 - [ci] Remove past members

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

#14530 - from_pandas is super low for a pd.DataFrame with shape 35000*67

Issue - State: closed - Opened by Zhiwen-Owen-Jiang about 2 months ago - 1 comment

#14529 - [query] filter intervals causing a failed partitioner assertion

Issue - State: open - Opened by patrick-schultz about 2 months ago
Labels: bug

#14528 - Bump jinja2 from 3.1.3 to 3.1.4 in /hail/python

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

#14527 - Bump jinja2 from 3.1.3 to 3.1.4 in /web_common

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

#14526 - Bump jinja2 from 3.1.3 to 3.1.4 in /hail/python/dev

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

#14525 - A2 dev

Pull Request - State: closed - Opened by sjparsa about 2 months ago

#14524 - [ci] Add tests for generating envoy xds configs

Pull Request - State: closed - Opened by daniel-goldstein about 2 months ago - 2 comments
Labels: prio:high

#14523 - [query] run `scalafix` on test sources

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

#14522 - [batch] Azure storage requirements beyond tempdisk for standing worker result in NotImplementedError

Issue - State: open - Opened by jeremiahwander 2 months ago - 1 comment
Labels: bug, batch

#14521 - [query] PArray implements PArrayBackedContainer

Pull Request - State: closed - Opened by chrisvittal 2 months ago - 1 comment

#14520 - [query] Always use _assert_type after read(..., _n_partitions)

Pull Request - State: closed - Opened by chrisvittal 2 months ago

#14519 - Add Full G2 Machine Family into Batch

Pull Request - State: closed - Opened by sjparsa 2 months ago

#14518 - [misc] adds script for exporting posts from discourse to github issues

Pull Request - State: open - Opened by iris-garden 2 months ago
Labels: do-not-test

#14517 - [compiler] refactor types in bindings

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

#14516 - [query] Add more transient error handling

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

#14515 - [query] add string find() function

Issue - State: closed - Opened by patrick-schultz 2 months ago
Labels: new-feature, snack

#14514 - [compiler] simplify NormalizeNames

Pull Request - State: closed - Opened by patrick-schultz 2 months ago - 1 comment

#14513 - VEP is being incorrectly initialised in australia-southeast1 region

Issue - State: closed - Opened by mgeaghan 2 months ago - 4 comments
Labels: bug, query

#14512 - [query] Batch Backend Job Creation Contract Tests

Pull Request - State: closed - Opened by ehigham 2 months ago - 1 comment

#14511 - [batch] Remove unused cost_from_msec_mcpu code

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

#14510 - Bump google-auth-oauthlib from 0.8.0 to 1.2.0 in /hail/python/dev

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

#14509 - [compiler] simplify PruneDeadFields

Pull Request - State: closed - Opened by patrick-schultz 2 months ago - 1 comment

#14508 - [docs] Change input/output bucket warning to recommend regional buckets

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

#14507 - Bump pytest-asyncio from 0.21.1 to 0.23.6 in /hail/python

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

#14506 - [query] global field name clash in GroupedTable

Issue - State: closed - Opened by konradjk 2 months ago
Labels: bug, query

#14505 - [batch] Batch charges for private instance creation that fails with exhausted resource errors.

Issue - State: open - Opened by cseed 2 months ago
Labels: bug, batch

#14504 - [dependabot] Remove dependabot automatic PRs

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

#14503 - [pip] Use `uv` for generating lockfiles

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

#14502 - Bump sphinx-rtd-theme from 1.3.0 to 2.0.0 in /hail/python/dev

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies, python

#14501 - Bump types-six from 1.16.21.20240301 to 1.16.21.20240425 in /hail/python

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies, python

#14500 - [batch] Properly expose and document "job-private instances"

Issue - State: open - Opened by daniel-goldstein 2 months ago
Labels: documentation, new-feature, batch

#14499 - [query/vds] Actually use `ref_block_max_length` in `to_dense_mt`

Issue - State: open - Opened by chrisvittal 2 months ago

#14498 - [batch] fix g2 machine memory calculation

Pull Request - State: closed - Opened by sjparsa 2 months ago

#14497 - [query] Cleanup Code-Duplication around `parallelizeAndComputeWithIndex`

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

#14496 - [compiler] declarative `Bindings`

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

#14495 - [compiler] delete old binds implementation

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

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

Pull Request - State: closed - Opened by chrisvittal 2 months ago

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

Issue - State: open - Opened by daniel-goldstein 2 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] 2 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] 2 months ago - 1 comment
Labels: dependencies, python

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

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

#14489 - Invalid maximum heap size: -Xmx0m

Issue - State: open - Opened by Asppagh 2 months ago
Labels: needs-triage

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

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

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

Issue - State: open - Opened by daniel-goldstein 2 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 2 months ago
Labels: new-feature, Epic, batch

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

Issue - State: open - Opened by daniel-goldstein 2 months ago
Labels: enhancement, batch

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

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies, python

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