diff --git a/hail/python/hail/docs/change_log.md b/hail/python/hail/docs/change_log.md index 83f3b79a418..70e87e03db8 100644 --- a/hail/python/hail/docs/change_log.md +++ b/hail/python/hail/docs/change_log.md @@ -52,6 +52,55 @@ supports. policy. Their functionality or even existence may change without notice. Please contact us if you critically depend on experimental functionality.** +## Version 0.2.125 + +Released 2023-10-25 + +### New Features + +- (hail#13682) `hl.export_vcf` now clearly reports all Table or Matrix Table fields which cannot be represented in a VCF. + +- (hail#13355) Improve the Hail compiler to more reliably rewrite `Table.filter` and `MatrixTable.filter_rows` to use `hl.filter_intervals`. Before this change some queries required reading all partitions even though only a small number of partitions match the filter. + +- (hail#13787) Improve speed of reading hail format datasets from disk. Simple pipelines may see as much as a halving in latency. + +- (hail#13849) Fix (hail#13788), improving the error message when `hl.logistic_regression_rows` is provided row or entry annotations for the dependent variable. + +- (hail#13888) `hl.default_reference` can now be passed an argument to change the default reference genome. + +### Bug Fixes + +- (hail#13702) Fix (hail#13699) and (hail#13693). Since 0.2.96, pipelines that combined random functions (e.g. `hl.rand_unif`) with `index(..., all_matches=True)` could fail with a `ClassCastException`. + +- (hail#13707) Fix (hail#13633). `hl.maximum_independent_set` now accepts strings as the names of individuals. It has always accepted structures containing a single string field. + +- (hail#13713) Fix (hail#13704), in which Hail could encounter an IllegalArgumentException if there are too many transient errors. + +- (hail#13730) Fix (hail#133560 and (hail#13409). In QoB pipelines with 10K or more partitions, transient "Corrupted block detected" errors were common. This was caused by incorrect retry logic. That logic has been fixed. + +- (hail#13732) Fix (hail#13721) which manifested with the message "Missing Range header in response". The root cause was a bug in the Google Cloud Storage SDK on which we rely. The fix is to update to a version without this bug. The buggy version of GCS SDK was introduced in 0.2.123. + +- (hail#13759) Since Hail 0.2.123, Hail would hang in Dataproc Notebooks due to (hail#13690). + +- (hail#13755) Ndarray concatenation now works with arrays with size zero dimensions. + +- (hail#13817) Mitigate new transient error from Google Cloud Storage which manifests as `aiohttp.client_exceptions.ClientOSError: [Errno 1] [SSL: SSLV3_ALERT_BAD_RECORD_MAC] sslv3 alert bad record mac (_ssl.c:2548)`. + +- (hail#13715) Fix (hail#13697), a long standing issue with QoB. When a QoB driver or worker fails, the corresponding Batch Job will also appear as failed. + +- (hail#13829) Fix (hail#13828). The Hail combiner now properly imports `PGT` fields from GVCFs. + +- (hail#13805) Fix (hail#13767). `hailctl dataproc submit` now expands `~` in the `--files` and `--pyfiles` arguments. + +- (hail#13797) Fix #13756. Operations that collect large results such as `to_pandas` may require up to 3x less memory. + +- (hail#13826) Fix (hail#13793). Ensure `hailctl describe -u` overrides the `gcs_requester_pays/project` config variable. + +- (hail#13814) Fix (hail#13757). Pipelines that are memory-bound by copious use of `hl.literal`, such as `hl.vds.filter_intervals`, require substantially less memory. + +- (hail#13894) Fix #13837 in which Hail could break a Spark installation if the Hail JAR appears on the classpath before the Scala JARs. + + ## Version 0.2.124 Released 2023-09-21 diff --git a/hail/version.mk b/hail/version.mk index 8a7995f9dc6..56f25007455 100644 --- a/hail/version.mk +++ b/hail/version.mk @@ -16,7 +16,7 @@ endif SCALA_VERSION ?= 2.12.15 SPARK_VERSION ?= 3.3.0 HAIL_MAJOR_MINOR_VERSION := 0.2 -HAIL_PATCH_VERSION := 124 +HAIL_PATCH_VERSION := 125 HAIL_PIP_VERSION := $(HAIL_MAJOR_MINOR_VERSION).$(HAIL_PATCH_VERSION) HAIL_VERSION := $(HAIL_PIP_VERSION)-$(SHORT_REVISION) ELASTIC_MAJOR_VERSION ?= 7