Change Log And Version Policy

Python Version Compatibility Policy

Hail complies with NumPy’s compatibility policy on Python versions. In particular, Hail officially supports:

All minor versions of Python released 42 months prior to the project, and at minimum the two latest minor versions.
All minor versions of numpy released in the 24 months prior to the project, and at minimum the last three minor versions.

Frequently Asked Questions

With a version like 0.x, is Hail ready for use in publications?

Yes. The semantic versioning standard uses 0.x (development) versions to refer to software that is either “buggy” or “partial”. While we don’t view Hail as particularly buggy (especially compared to one-off untested scripts pervasive in bioinformatics!), Hail 0.2 is a partial realization of a larger vision.

What is the difference between the Hail Python library version and the native file format version?

The Hail Python library version, the version you see on PyPI, in pip, or in hl.version() changes every time we release the Python library. The Hail native file format version only changes when we change the format of Hail Table and MatrixTable files. If a version of the Python library introduces a new native file format version, we note that in the change log. All subsequent versions of the Python library can read the new file format version.

The native file format changes much slower than the Python library version. It is not currently possible to view the file format version of a Hail Table or MatrixTable.

What stability is guaranteed?

The Hail file formats and Python API are backwards compatible. This means that a script developed to run on Hail 0.2.5 should continue to work in every subsequent release within the 0.2 major version. This also means any file written by python library versions 0.2.1 through 0.2.5 can be read by 0.2.5.

Forward compatibility of file formats and the Python API is not guaranteed. In particular, a new file format version is only readable by library versions released after the file format. For example, Python library version 0.2.119 introduces a new file format version: 1.7.0. All library versions before 0.2.119, for example 0.2.118, cannot read file format version 1.7.0. All library versions after and including 0.2.119 can read file format version 1.7.0.

Each version of the Hail Python library can only write files using the latest file format version it supports.

The hl.experimental package and other methods marked experimental in the docs are exempt from this policy. Their functionality or even existence may change without notice. Please contact us if you critically depend on experimental functionality.

Version 0.2.133

Released 2024-09-25

New Features

(#14619) Teach hailctl dataproc submit to use the --project argument as an argument to gcloud dataproc rather than the submitted script.

Bug Fixes

(#14673) Fix typo in Interpret rule for TableAggregate.
(#14697) Set QUAL="." to missing rather than htsjdk’s sentinel value.
(#14292) Prevent GCS cold storage check from throwing an error when reading from a public access bucket.
(#14651) Remove jackson string length restriction for all backends.
(#14653) Add --public-ip-address argument to gcloud dataproc start command built by hailctl dataproc start, fixing creation of dataproc 2.2 clusters.

Version 0.2.132

Released 2024-07-08

New Features

(#14572) Added StringExpression.find for finding substrings in a Hail str.

Bug Fixes

(#14574) Fixed TypeError bug when initializing Hail Query with backend='batch'.
(#14571) Fixed a deficiency that caused certain pipelines that construct Hail NDArrays from streams to run out of memory.
(#14579) Fix serialization bug that broke some Query-on-Batch pipelines with many complex expressions.
(#14567) Fix Jackson configuration that broke some Query-on-Batch pipelines with many complex expressions.

Version 0.2.131

Released 2024-05-30

New Features

(#14560) The gvcf import stage of the VDS combiner now preserves the GT of reference blocks. Some datasets have haploid calls on sex chromosomes, and the fact that the reference was haploid should be preserved.

Bug Fixes

(#14563) The version of notebook installed in Hail Dataproc clusters has been upgraded from 6.5.4 to 6.5.6 in order to fix a bug where Jupyter Notebooks wouldn’t start on clusters. The workaround involving creating a cluster with --packages='ipython<8.22' is no longer necessary.

Deprecations

(#14158) Hail now supports and primarily tests against Dataproc 2.2.5, Spark 3.5.0, and Java 11. We strongly recommend updating to Spark 3.5.0 and Java 11. You should also update your GCS connector after installing Hail: curl https://broad.io/install-gcs-connector | python3. Do not try to update before installing Hail 0.2.131.

Version 0.2.130

Released 2024-10-02

0.2.129 contained test configuration artifacts that prevented users from starting dataproc clusters with hailctl. Please upgrade to 0.2.130 if you use dataproc.

New Features

(hail##14447) Added copy_spark_log_on_error initialization flag that when set, copies the hail driver log to the remote tmpdir if query execution raises an exception.

Bug Fixes

(#14452) Fixes a bug that prevents users from starting dataproc clusters with hailctl

Version 0.2.129

Released 2024-04-02

Documentation

(#14321) Removed GOOGLE_APPLICATION_CREDENTIALS from batch docs. Metadata server introduction means users no longer need to explicitly activate service accounts with the gcloud command line tool.
(#14339) Added citations since 2021

New Features

(#14406) Performance improvements for reading structured data from (Matrix)Tables
(#14255) Added Cochran-Hantel-Haenszel test for association (cochran_mantel_haenszel_test). Our thanks to @Will-Tyler for generously contributing this feature.
(#14393) hail depends on protobuf no longer; users may choose their own version of protobuf.
(#14360) Exposed previously internal _num_allele_type as numeric_allele_type and deprecated it. Add new AlleleType enumeration for users to be able to easily use the values returned by numeric_allele_type.
(#14297) vds.sample_gc now uses independent aggregators. Users may now import these functions and use them directly.
(#14405) VariantDataset.validate now checks that all ref blocks are no longer than the ref_block_max_length field, if it exists.

Bug Fixes

(#14420) Fixes a serious, but likely rare, bug in the Table/MatrixTable reader, which has been present since Sep 2020. It manifests as many (around half or more) of the rows being dropped. This could only happen when 1) reading a (matrix)table whose partitioning metadata allows rows with the same key to be split across neighboring partitions, and 2) reading it with a different partitioning than it was written. 1) would likely only happen by reading data keyed by locus and alleles, and rekeying it to only locus before writing. 2) would likely only happen by using the _intervals or _n_partitions arguments to read_(matrix)_table, or possibly repartition. Please reach out to us if you’re concerned you may have been affected by this.
(#14330) Fixes erroneous error in export_vcf with unphased haploid Calls.
(#14303) Fix missingness error when sampling entries from a MatrixTable.
(#14288) Contigs may now be compared for inquality while filtering rows.

Deprecations

(#14386) MatrixTable.make_table is deprecated. Use .localize_entries instead.

Version 0.2.128

Released 2024-02-16

In GCP, the Hail Annotation DB and Datasets API have moved from multi-regional US and EU buckets to regional US-CENTRAL1 and EUROPE-WEST1 buckets. These buckets are requester pays which means unless your cluster is in the US-CENTRAL1 or EUROPE-WEST1 region, you will pay a per-gigabyte rate to read from the Annotation DB or Datasets API. We must make this change because reading from a multi-regional bucket into a regional VM is no longer free. Unfortunately, cost constraints require us to choose only one region per continent and we have chosen US-CENTRAL1 and EUROPE-WEST1.

Documentation

(#14113) Add examples to Table.parallelize, Table.key_by, Table.annotate_globals, Table.select_globals, Table.transmute_globals, Table.transmute, Table.annotate, and Table.filter.
(#14242) Add examples to Table.sample, Table.head, and Table.semi_join.

New Features

(#14206) Introduce hailctl config set http/timeout_in_seconds which Batch and QoB users can use to increase the timeout on their laptops. Laptops tend to have flaky internet connections and a timeout of 300 seconds produces a more robust experience.
(#14178) Reduce VDS Combiner runtime slightly by computing the maximum ref block length without executing the combination pipeline twice.
(#14207) VDS Combiner now verifies that every GVCF path and sample name is unique.

Bug Fixes

(#14300) Require orjson<3.9.12 to avoid a segfault introduced in orjson 3.9.12
(#14071) Use indexed VEP cache files for GRCh38 on both dataproc and QoB.
(#14232) Allow use of large numbers of fields on a table without triggering ClassTooLargeException: Class too large:.
(#14246)(#14245) Fix a bug, introduced in 0.2.114, in which Table.multi_way_zip_join and Table.aggregate_by_key could throw “NoSuchElementException: Ref with name __iruid_...” when one or more of the tables had a number of partitions substantially different from the desired number of output partitions.
(#14202) Support coercing {} (the empty dictionary) into any Struct type (with all missing fields).
(#14239) Remove an erroneous statement from the MatrixTable tutorial.
(#14176) hailtop.fs.ls can now list a bucket, e.g. hailtop.fs.ls("gs://my-bucket").
(#14258) Fix import_avro to not raise NullPointerException in certain rare cases (e.g. when using _key_by_assert_sorted).
(#14285) Fix a broken link in the MatrixTable tutorial.

Deprecations

(#14293) Support for the hail-az:// scheme, deprecated in 0.2.116, is now gone. Please use the standard https://ACCOUNT.blob.core.windows.net/CONTAINER/PATH.

Version 0.2.127

Released 2024-01-12

If you have an Apple M1 laptop, verify that

file $JAVA_HOME/bin/java

returns a message including the phrase “arm64”. If it instead includes the phrase “x86_64” then you must upgrade to a new version of Java. You may find such a version of Java here.

New Features

(#14093) hailctl dataproc now creates clusters using Dataproc version 2.1.33. It previously used version 2.1.2.
(#13617) Query-on-Batch now supports joining two tables keyed by intervals.
(#13795)(#13567) Enable passing a requester pays configuration to hailtop.fs.open.

Bug Fixes

(#14110) Fix hailctl hdinsight start, which has been broken since 0.2.118.
(#14098)(#14090)(#14118) Fix (#14089), which makes hailctl dataproc connect work in Windows Subsystem for Linux.
(#14048) Fix (#13979), affecting Query-on-Batch and manifesting most frequently as “com.github.luben.zstd.ZstdException: Corrupted block detected”.
(#14066) Since 0.2.110, hailctl dataproc set the heap size of the driver JVM dangerously high. It is now set to an appropriate level. This issue manifests in a variety of inscrutable ways including RemoteDisconnectedError and socket closed. See issue (#13960) for details.
(#14057) Fix (#13998) which appeared in 0.2.58 and prevented reading from a networked filesystem mounted within the filesystem of the worker node for certain pipelines (those that did not trigger “lowering”).
(#14006) Fix (#14000). Hail now supports identity_by_descent on Apple M1 and M2 chips; however, your Java installation must be an arm64 installation. Using x86_64 Java with Hail on Apple M1 or M2 will cause SIGILL errors. If you have an Apple M1 or Apple M2 and /usr/libexec/java_home -V does not include (arm64), you must switch to an arm64 version of the JVM.
(#14022) Fix (#13937) caused by faulty library code in the Google Cloud Storage API Java client library.
(#13812) Permit hailctl batch submit to accept relative paths. Fix (#13785).
(#13885) Hail Query-on-Batch previously used Class A Operations for all interaction with blobs. This change ensures that QoB only uses Class A Operations when necessary.
(#14127) hailctl dataproc start ... --dry-run now uses shell escapes such that, after copied and pasted into a shell, the gcloud command works as expected.
(#14062) Fix (#14052) which caused incorrect results for identity by descent in Query-on-Batch.
(#14122) Ensure that stack traces are transmitted from workers to the driver to the client.
(#14105) When a VCF contains missing values in array fields, Hail now suggests using array_elements_required=False.

Deprecations

(#13987) Deprecate default_reference parameter to hl.init, users should use hl.default_reference with an argument to set new default references usually shortly after hl.init.

Version 0.2.126

Released 2023-10-30

Bug Fixes

(#13939) Fix a bug introduced in 0.2.125 which could cause dict literals created in python to be decoded incorrectly, causing runtime errors or, potentially, incorrect results.
(#13751) Correct the broadcasting of ndarrays containing at least one dimension of length zero. This previously produced incorrect results.

Version 0.2.125

Released 2023-10-26

New Features

(#13682) hl.export_vcf now clearly reports all Table or Matrix Table fields which cannot be represented in a VCF.
(#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.
(#13787) Improve speed of reading hail format datasets from disk. Simple pipelines may see as much as a halving in latency.
(#13849) Fix (#13788), improving the error message when hl.logistic_regression_rows is provided row or entry annotations for the dependent variable.
(#13888) hl.default_reference can now be passed an argument to change the default reference genome.

Bug Fixes

(#13702) Fix (#13699) and (#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.
(#13707) Fix (#13633). hl.maximum_independent_set now accepts strings as the names of individuals. It has always accepted structures containing a single string field.
(#13713) Fix (#13704), in which Hail could encounter an IllegalArgumentException if there are too many transient errors.
(#13730) Fix (#13356) and (#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.
(#13732) Fix (#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.
(#13759) Since Hail 0.2.123, Hail would hang in Dataproc Notebooks due to (#13690).
(#13755) Ndarray concatenation now works with arrays with size zero dimensions.
(#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).
(#13715) Fix (#13697), a long standing issue with QoB. When a QoB driver or worker fails, the corresponding Batch Job will also appear as failed.
(#13829) Fix (#13828). The Hail combiner now properly imports PGT fields from GVCFs.
(#13805) Fix (#13767). hailctl dataproc submit now expands ~ in the --files and --pyfiles arguments.
(#13797) Fix (#13756). Operations that collect large results such as to_pandas may require up to 3x less memory.
(#13826) Fix (#13793). Ensure hailctl describe -u overrides the gcs_requester_pays/project config variable.
(#13814) Fix (#13757). Pipelines that are memory-bound by copious use of hl.literal, such as hl.vds.filter_intervals, require substantially less memory.
(#13894) Fix (#13837) in which Hail could break a Spark installation if the Hail JAR appears on the classpath before the Scala JARs.
(#13919) Fix (#13915) which prevented using a glob pattern in hl.import_vcf.

Version 0.2.124

Released 2023-09-21

New Features

(#13608) Change default behavior of hl.ggplot.geom_density to use a new method. The old method is still available using the flag smoothed=True. The new method is typically a much more accurate representation, and works well for any distribution, not just smooth ones.

Version 0.2.123

Released 2023-09-19

New Features

(#13610) Additional setup is no longer required when using hail.plot or hail.ggplot in a Jupyter notebook (calling bokeh.io.output_notebook or hail.plot.output_notebook and/or setting plotly.io.renderers.default = ‘iframe’ is no longer necessary).

Bug Fixes

(#13634) Fix a bug which caused Query-on-Batch pipelines with a large number of partitions (close to 100k) to run out of memory on the driver after all partitions finish.
(#13619) Fix an optimization bug that, on some pipelines, since at least 0.2.58 (commit 23813af), resulted in Hail using essentially unbounded amounts of memory.
(#13609) Fix a bug in hail.ggplot.scale_color_continuous that sometimes caused errors by generating invalid colors.

Version 0.2.122

Released 2023-09-07

New Features

(#13508) The n parameter of MatrixTable.tail is deprecated in favor of a new n_rows parameter.

Bug Fixes

(#13498) Fix a bug where field names can shadow methods on the StructExpression class, e.g. “items”, “keys”, “values”. Now the only way to access such fields is through the getitem syntax, e.g. “some_struct[‘items’]”. It’s possible this could break existing code that uses such field names.
(#13585) Fix bug introduced in 0.2.121 where Query-on-Batch users could not make requests to batch.hail.is without a domain configuration set.

Version 0.2.121

Released 2023-09-06

New Features

(#13385) The VDS combiner now supports arbitrary custom call fields via the call_fields parameter.
(#13224) hailctl config get, set, and unset now support shell auto-completion. Run hailctl --install-completion zsh to install the auto-completion for zsh. You must already have completion enabled for zsh.
(#13279) Add hailctl batch init which helps new users interactively set up hailctl for Query-on-Batch and Batch use.

Bug Fixes

(#13573) Fix (#12936) in which VEP frequently failed (due to Docker not starting up) on clusters with a non-trivial number of workers.
(#13485) Fix (#13479) in which hl.vds.local_to_global could produce invalid values when the LA field is too short. There were and are no issues when the LA field has the correct length.
(#13340) Fix copy_log to correctly copy relative file paths.
(#13364) hl.import_gvcf_interval now treats PGT as a call field.
(#13333) Fix interval filtering regression: filter_rows or filter mentioning the same field twice or using two fields incorrectly read the entire dataset. In 0.2.121, these filters will correctly read only the relevant subset of the data.
(#13368) In Azure, Hail now uses fewer “list blobs” operations. This should reduce cost on pipelines that import many files, export many of files, or use file glob expressions.
(#13414) Resolves (#13407) in which uses of union_rows could reduce parallelism to one partition resulting in severely degraded performance.
(#13405) MatrixTable.aggregate_cols no longer forces a distributed computation. This should be what you want in the majority of cases. In case you know the aggregation is very slow and should be parallelized, use mt.cols().aggregate instead.
(#13460) In Query-on-Spark, restore hl.read_table optimization that avoids reading unnecessary data in pipelines that do not reference row fields.
(#13447) Fix (#13446). In all three submit commands (batch, dataproc, and hdinsight), Hail now allows and encourages the use of – to separate arguments meant for the user script from those meant for hailctl. In hailctl batch submit, option-like arguments, for example “–foo”, are now supported before “–” if and only if they do not conflict with a hailctl option.
(#13422) hailtop.hail_frozenlist.frozenlist now has an eval-able repr.
(#13523) hl.Struct is now pickle-able.
(#13505) Fix bug introduced in 0.2.117 by commit c9de81108 which prevented the passing of keyword arguments to Python jobs. This manifested as “ValueError: too many values to unpack”.
(#13536) Fixed (#13535) which prevented the use of Python jobs when the client (e.g. your laptop) Python version is 3.11 or later.
(#13434) In QoB, Hail’s file systems now correctly list all files in a directory, not just the first 1000. This could manifest in an import_table or import_vcf which used a glob expression. In such a case, only the first 1000 files would have been included in the resulting Table or MatrixTable.
(#13550) hl.utils.range_table(n) now supports all valid 32-bit signed integer values of n.
(#13500) In Query-on-Batch, the client-side Python code will not try to list every job when a QoB batch fails. This could take hours for long-running pipelines or pipelines with many partitions.

Deprecations

(#13275) Hail no longer officially supports Python 3.8.
(#13508) The n parameter of MatrixTable.tail is deprecated in favor of a new n_rows parameter.

Version 0.2.120

Released 2023-07-27

New Features

(#13206) The VDS Combiner now works in Query-on-Batch.

Bug Fixes

(#13313) Fix bug introduced in 0.2.119 which causes a serialization error when using Query-on-Spark to read a VCF which is sorted by locus, with split multi-allelics, in which the records sharing a single locus do not appear in the dictionary ordering of their alternate alleles.
(#13264) Fix bug which ignored the partition_hint of a Table group-by-and-aggregate.
(#13239) Fix bug which ignored the HAIL_BATCH_REGIONS argument when determining in which regions to schedule jobs when using Query-on-Batch.
(#13253) Improve hadoop_ls and hfs.ls to quickly list globbed files in a directory. The speed improvement is proportional to the number of files in the directory.
(#13226) Fix the comparison of an hl.Struct to an hl.struct or field of type tstruct. Resolves (#13045) and (Hail#13046).
(#12995) Fixed bug causing poor performance and memory leaks for MatrixTable.annotate_rows aggregations.

Version 0.2.119

Released 2023-06-28

New Features

(#12081) Hail now uses Zstandard as the default compression algorithm for table and matrix table storage. Reducing file size around 20% in most cases.
(#12988) Arbitrary aggregations can now be used on arrays via ArrayExpression.aggregate. This method is useful for accessing functionality that exists in the aggregator library but not the basic expression library, for instance, call_stats.
(#13166) Add an eigh ndarray method, for finding eigenvalues of symmetric matrices (“h” is for Hermitian, the complex analogue of symmetric).

Bug Fixes

(#13184) The vds.to_dense_mt no longer densifies past the end of contig boundaries. A logic bug in to_dense_mt could lead to reference data toward’s the end of one contig being applied to the following contig up until the first reference block of the contig.
(#13173) Fix globbing in scala blob storage filesystem implementations.

File Format

The native file format version is now 1.7.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.118

Released 2023-06-13

New Features

(#13140) Enable hail-az and Azure Blob Storage https URLs to contain SAS tokens to enable bearer-auth style file access to Azure storage.
(#13129) Allow subnet to be passed through to gcloud in hailctl.

Bug Fixes

(#13126) Query-on-Batch pipelines with one partition are now retried when they encounter transient errors.
(#13113) hail.ggplot.geom_point now displays a legend group for a column even when it has only one value in it.
(#13075) (#13074) Add a new transient error plaguing pipelines in Query-on-Batch in Google: java.net.SocketTimeoutException: connect timed out.
(#12569) The documentation for hail.ggplot.facets is now correctly included in the API reference.

Version 0.2.117

Released 2023-05-22

New Features

(#12875) Parallel export modes now write a manifest file. These manifest files are text files with one filename per line, containing name of each shard written successfully to the directory. These filenames are relative to the export directory.
(#13007) In Query-on-Batch and hailtop.batch, memory and storage request strings may now be optionally terminated with a B for bytes.

Bug Fixes

(#13065) In Azure Query-on-Batch, fix a resource leak that prevented running pipelines with >500 partitions and created flakiness with >250 partitions.
(#13067) In Query-on-Batch, driver and worker logs no longer buffer so messages should arrive in the UI after a fixed delay rather than proportional to the frequency of log messages.
(#13028) Fix crash in hl.vds.filter_intervals when using a table to filter a VDS that stores the max ref block length.
(#13060) Prevent 500 Internal Server Error in Jupyter Notebooks of Dataproc clusters started by hailctl dataproc.
(#13051) In Query-on-Batch and hailtop.batch, Azure Blob Storage https URLs are now supported.
(#13042) In Query-on-Batch, naive_coalesce no longer performs a full write/read of the dataset. It now operates identically to the Query-on-Spark implementation.
(#13031) In hl.ld_prune, an informative error message is raised when a dataset does not contain diploid calls instead of an assertion error.
(#13032) In Query-on-Batch, in Azure, Hail now users a newer version of the Azure blob storage libraries to reduce the frequency of “Stream is already closed” errors.
(#13011) In Query-on-Batch, the driver will use ~1/2 as much memory to read results as it did in 0.2.115.
(#13013) In Query-on-Batch, transient errors while streaming from Google Storage are now automatically retried.

Version 0.2.116

Released 2023-05-08

New Features

(#12917) ABS blob URIs in the format of https://<ACCOUNT_NAME>.blob.core.windows.net/<CONTAINER_NAME>/<PATH> are now supported.
(#12731) Introduced hailtop.fs that makes public a filesystem module that works for local fs, gs, s3 and abs. This is now used as the Backend.fs for hail query but can be used standalone for Hail Batch users by import hailtop.fs as hfs.

Deprecations

(#12929) Hail no longer officially supports Python 3.7.
(#12917) The hail-az scheme for referencing blobs in ABS is now deprecated and will be removed in an upcoming release.

Bug Fixes

(#12913) Fixed bug in hail.ggplot where all legend entries would have the same text if one column had exactly one value for all rows and was mapped to either the shape or the color aesthetic for geom_point.
(#12901) hl.Struct now has a correct and useful implementation of pprint.

Version 0.2.115

Released 2023-04-25

New Features

(#12731) Introduced hailtop.fs that makes public a filesystem module that works for local fs, gs, s3 and abs. This can be used by import hailtop.fs as hfs but has also replaced the underlying implementation of the hl.hadoop_* methods. This means that the hl.hadoop_* methods now support these additional blob storage providers.
(#12917) ABS blob URIs in the form of https://<ACCOUNT_NAME>.blob.core.windows.net/<CONTAINER_NAME>/<PATH> are now supported when running in Azure.

Deprecations

(#12917) The hail-az scheme for referencing ABS blobs in Azure is deprecated in favor of the https scheme and will be removed in a future release.

Bug Fixes

(#12919) An interactive hail session is no longer unusable after hitting CTRL-C during a batch execution in Query-on-Batch
(#12913) Fixed bug in hail.ggplot where all legend entries would have the same text if one column had exactly one value for all rows and was mapped to either the shape or the color aesthetic for geom_point.

Version 0.2.114

Released 2023-04-19

New Features

(#12880) Added hl.vds.store_ref_block_max_len to patch old VDSes to make interval filtering faster.

Bug Fixes

(#12860) Fixed memory leak in shuffles in Query-on-Batch.

Version 0.2.113

Released 2023-04-07

New Features

(#12798) Query-on-Batch now supports BlockMatrix.write(..., stage_locally=True).
(#12793) Query-on-Batch now supports hl.poisson_regression_rows.
(#12801) Hitting CTRL-C while interactively using Query-on-Batch cancels the underlying batch.
(#12810) hl.array can now convert 1-d ndarrays into the equivalent list.
(#12851) hl.variant_qc no longer requires a locus field.
(#12816) In Query-on-Batch, hl.logistic_regression('firth', ...) is now supported.
(#12854) In Query-on-Batch, simple pipelines with large numbers of partitions should be substantially faster.

Bug Fixes

(#12783) Fixed bug where logs were not properly transmitted to Python.
(#12812) Fixed bug where Table/MT._calculate_new_partitions returned unbalanced intervals with whole-stage code generation runtime.
(#12839) Fixed hailctl dataproc jupyter notebooks to be compatible with Spark 3.3, which have been broken since 0.2.110.
(#12855) In Query-on-Batch, allow writing to requester pays buckets, which was broken before this release.

Version 0.2.112

Released 2023-03-15

Bug Fixes

(#12784) Removed an internal caching mechanism in Query on Batch that caused stalls in pipelines with large intermediates

Version 0.2.111

Released 2023-03-13

New Features

(#12581) In Query on Batch, users can specify which regions to have jobs run in.

Bug Fixes

(#12772) Fix hailctl hdinsight submit to pass args to the files

Version 0.2.110

Released 2023-03-08

New Features

(#12643) In Query on Batch, hl.skat(..., logistic=True) is now supported.
(#12643) In Query on Batch, hl.liftover is now supported.
(#12629) In Query on Batch, hl.ibd is now supported.
(#12722) Add hl.simulate_random_mating to generate a population from founders under the assumption of random mating.
(#12701) Query on Spark now officially supports Spark 3.3.0 and Dataproc 2.1.x

Performance Improvements

(#12679) In Query on Batch, hl.balding_nichols_model is slightly faster. Also added hl.utils.genomic_range_table to quickly create a table keyed by locus.

Bug Fixes

(#12711) In Query on Batch, fix null pointer exception (manifesting as scala.MatchError: null) when reading data from requester pays buckets.
(#12739) Fix hl.plot.cdf, hl.plot.pdf, and hl.plot.joint_plot which were broken by changes in Hail and changes in bokeh.
(#12735) Fix (#11738) by allowing user to override default types in to_pandas.
(#12760) Mitigate some JVM bytecode generation errors, particularly those related to too many method parameters.
(#12766) Fix (#12759) by loosening parsimonious dependency pin.
(#12732) In Query on Batch, fix bug that sometimes prevented terminating a pipeline using Control-C.
(#12771) Use a version of jgscm whose version complies with PEP 440.

Version 0.2.109

Released 2023-02-08

New Features

(#12605) Add hl.pgenchisq the cumulative distribution function of the generalized chi-squared distribution.
(#12637) Query-on-Batch now supports hl.skat(..., logistic=False).
(#12645) Added hl.vds.truncate_reference_blocks to transform a VDS to checkpoint reference blocks in order to drastically improve interval filtering performance. Also added hl.vds.merge_reference_blocks to merge adjacent reference blocks according to user criteria to better compress reference data.

Bug Fixes

(#12650) Hail will now throw an exception on hl.export_bgen when there is no GP field, instead of exporting null records.
(#12635) Fix bug where hl.skat did not work on Apple M1 machines.
(#12571) When using Query-on-Batch, hl.hadoop* methods now properly support creation and modification time.
(#12566) Improve error message when combining incompatibly indexed fields in certain operations including array indexing.

Version 0.2.108

Released 2023-1-12

New Features

(#12576) hl.import_bgen and hl.export_bgen now support compression with Zstd.

Bug fixes

(#12585) hail.ggplots that have more than one legend group or facet are now interactive. If such a plot has enough legend entries that the legend would be taller than the plot, the legend will now be scrollable. Legend entries for such plots can be clicked to show/hide traces on the plot, but this does not work and is a known issue that will only be addressed if hail.ggplot is migrated off of plotly.
(#12584) Fixed bug which arose as an assertion error about type mismatches. This was usually triggered when working with tuples.
(#12583) Fixed bug which showed an empty table for ht.col_key.show().
(#12582) Fixed bug where matrix tables with duplicate col keys do not show properly. Also fixed bug where tables and matrix tables with HTML unsafe column headers are rendered wrong in Jupyter.
(#12574) Fixed a memory leak when processing tables. Could trigger unnecessarily high memory use and out of memory errors when there are many rows per partition or large key fields.
(#12565) Fixed a bug that prevented exploding on a field of a Table whose value is a random value.

Version 0.2.107

Released 2022-12-14

Bug fixes

(#12543) Fixed hl.vds.local_to_global error when LA array contains non-ascending allele indices.

Version 0.2.106

Released 2022-12-13

New Features

(#12522) Added hailctl config setting 'batch/backend' to specify the default backend to use in batch scripts when not specified in code.
(#12497) Added support for scales, nrow, and ncol arguments, as well as grouped legends, to hail.ggplot.facet_wrap.
(#12471) Added hailctl batch submit command to run local scripts inside batch jobs.
(#12525) Add support for passing arguments to hailctl batch submit.
(#12465) Batch jobs’ status now contains the region the job ran in. The job itself can access which region it is in through the HAIL_REGION environment variable.
(#12464) When using Query-on-Batch, all jobs for a single hail session are inserted into the same batch instead of one batch per action.
(#12457) pca and hwe_normalized_pca are now supported in Query-on-Batch.
(#12376) Added hail.query_table function for reading tables with indices from Python.
(#12139) Random number generation has been updated, but shouldn’t affect most users. If you need to manually set seeds, see https://hail.is/docs/0.2/functions/random.html for details.
(#11884) Added Job.always_copy_output when using the ServiceBackend. The default behavior is False, which is a breaking change from the previous behavior to always copy output files regardless of the job’s completion state.
(#12139) Brand new random number generation, shouldn’t affect most users. If you need to manually set seeds, see https://hail.is/docs/0.2/functions/random.html for details.

Bug Fixes

(#12487) Fixed a bug causing rare but deterministic job failures deserializing data in Query-on-Batch.
(#12535) QoB will now error if the user reads from and writes to the same path. QoB also now respects the user’s configuration of disable_progress_bar. When disable_progress_bar is unspecified, QoB only disables the progress bar for non-interactive sessions.
(#12517) Fix a performance regression that appears when using hl.split_multi_hts among other methods.

Version 0.2.105

Released 2022-10-31 🎃

New Features

(#12293) Added support for hail.MatrixTables to hail.ggplot.

Bug Fixes

(#12384) Fixed a critical bug that disabled tree aggregation and scan executions in 0.2.104, leading to out-of-memory errors.
(#12265) Fix long-standing bug wherein hl.agg.collect_as_set and hl.agg.counter error when applied to types which, in Python, are unhashable. For example, hl.agg.counter(t.list_of_genes) will not error when t.list_of_genes is a list. Instead, the counter dictionary will use FrozenList keys from the frozenlist package.

Version 0.2.104

Release 2022-10-19

New Features

(#12346): Introduced new progress bars which include total time elapsed and look cool.

Version 0.2.103

Release 2022-10-18

Bug Fixes

(#12305): Fixed a rare crash reading tables/matrixtables with _intervals

Version 0.2.102

Released 2022-10-06

New Features

(#12218) Missing values are now supported in primitive columns in Table.to_pandas.
(#12254) Cross-product-style legends for data groups have been replaced with factored ones (consistent with ggplot2’s implementation) for hail.ggplot.geom_point, and support has been added for custom legend group labels.
(#12268) VariantDataset now implements union_rows for combining datasets with the same samples but disjoint variants.

Bug Fixes

(#12278) Fixed bug made more likely by 0.2.101 in which Hail errors when interacting with a NumPy integer or floating point type.
(#12277) Fixed bug in reading tables/matrixtables with partition intervals that led to error or segfault.

Version 0.2.101

Released 2022-10-04

New Features

(#12218) Support missing values in primitive columns in Table.to_pandas.
(#12195) Add a impute_sex_chr_ploidy_from_interval_coverage to impute sex ploidy directly from a coverage MT.
(#12222) Query-on-Batch pipelines now add worker jobs to the same batch as the driver job instead of producing a new batch per stage.
(#12244) Added support for custom labels for per-group legends to hail.ggplot.geom_point via the legend_format keyword argument

Deprecations

(#12230) The python-dill Batch images in gcr.io/hail-vdc are no longer supported. Use hailgenetics/python-dill instead.

Bug fixes

(#12215) Fix search bar in the Hail Batch documentation.

Version 0.2.100

Released 2022-09-23

New Features

(#12207) Add support for the shape aesthetic to hail.ggplot.geom_point.

Deprecations

(#12213) The batch_size parameter of vds.new_combiner is deprecated in favor of gvcf_batch_size.

Bug fixes

(#12216) Fix bug that caused make install-on-cluster to fail with a message about sys_platform.
(#12164) Fix bug that caused Query on Batch pipelines to fail on datasets with indexes greater than 2GiB.

Version 0.2.99

Released 2022-09-13

New Features

(#12091) Teach Table to write_many, which writes one table per provided field.
(#12067) Add rand_int32 and rand_int64 for generating random 32-bit and 64-bit integers, respectively.

Performance Improvements

(#12159) Improve performance of MatrixTable reads when using _intervals argument

Bug fixes

(#12179) Fix incorrect composition of interval filters with unordered interval lists that could lead to over- or under-filtering.
(#12162) Fixed crash in collect_cols_by_key with preceding random functions.

Version 0.2.98

Released 2022-08-22

New Features

(#12062) hl.balding_nichols_model now supports an optional boolean parameter, phased, to control the phasedness of the generated genotypes.

Performance improvements

(#12099) Make repeated VCF/PLINK queries much faster by caching compiler data structures.
(#12038) Speed up hl.import_matrix_table by caching header line computation.

Bug fixes

(#12115) When using use_new_shuffle=True, fix a bug when there are more than 2^31 rows
(#12074) Fix bug where hl.init could silently overwrite the global random seed.
(#12079) Fix bug in handling of missing (aka NA) fields in grouped aggregation and distinct by key.
(#12056) Fix hl.export_vcf to actually create tabix files when requested.
(#12020) Fix bug in hl.experimental.densify which manifested as an AssertionError about dtypes.

Version 0.2.97

Released 2022-06-30

New Features

(#11756) hb.BatchPoolExecutor and Python jobs both now also support async functions.

Bug fixes

(#11962) Fix error (logged as (#11891)) in VCF combiner when exactly 10 or 100 files are combined.
(#11969) Fix import_table and import_lines to use multiple partitions when force_bgz is used.
(#11964) Fix erroneous “Bucket is a requester pays bucket but no user project provided.” errors in Google Dataproc by updating to the latest Dataproc image version.

Version 0.2.96

Released 2022-06-21

New Features

(#11833) hl.rand_unif now has default arguments of 0.0 and 1.0

Bug fixes

(#11905) Fix erroneous FileNotFoundError in glob patterns
(#11921) and (#11910) Fix file clobbering during text export with speculative execution.
(#11920) Fix array out of bounds error when tree aggregating a multiple of 50 partitions.
(#11937) Fixed correctness bug in scan order for Table.annotate and MatrixTable.annotate_rows in certain circumstances.
(#11887) Escape VCF description strings when exporting.
(#11886) Fix an error in an example in the docs for hl.split_multi.

Version 0.2.95

Released 2022-05-13

New features

(#11809) Export dtypes_from_pandas in expr.types
(#11807) Teach smoothed_pdf to add a plot to an existing figure.
(#11746) The ServiceBackend, in interactive mode, will print a link to the currently executing driver batch.
(#11759) hl.logistic_regression_rows, hl.poisson_regression_rows, and hl.skat all now support configuration of the maximum number of iterations and the tolerance.
(#11835) Add hl.ggplot.geom_density which renders a plot of an approximation of the probability density function of its argument.

Bug fixes

(#11815) Fix incorrectly missing entries in to_dense_mt at the position of ref block END.
(#11828) Fix hl.init to not ignore its sc argument. This bug was introduced in 0.2.94.
(#11830) Fix an error and relax a timeout which caused hailtop.aiotools.copy to hang.
(#11778) Fix a (different) error which could cause hangs in hailtop.aiotools.copy.

Version 0.2.94

Released 2022-04-26

Deprecation

(#11765) Deprecated and removed linear mixed model functionality.

Beta features

(#11782) hl.import_table is up to twice as fast for small tables.

New features

(#11428) hailtop.batch.build_python_image now accepts a show_docker_output argument to toggle printing docker’s output to the terminal while building container images
(#11725) hl.ggplot now supports facet_wrap
(#11776) hailtop.aiotools.copy will always show a progress bar when --verbose is passed.

`hailctl dataproc`

(#11710) support pass-through arguments to connect

Bug fixes

(#11792) Resolved issue where corrupted tables could be created with whole-stage code generation enabled.

Version 0.2.93

Release 2022-03-27

Beta features

Several issues with the beta version of Hail Query on Hail Batch are addressed in this release.

Version 0.2.92

Release 2022-03-25

New features

(#11613) Add hl.ggplot support for scale_fill_hue, scale_color_hue, and scale_fill_manual, scale_color_manual. This allows for an infinite number of discrete colors.
(#11608) Add all remaining and all versions of extant public gnomAD datasets to the Hail Annotation Database and Datasets API. Current as of March 23rd 2022.
(#11662) Add the weight aesthetic geom_bar.

Beta features

This version of Hail includes all the necessary client-side infrastructure to execute Hail Query pipelines on a Hail Batch cluster. This effectively enables a “serverless” version of Hail Query which is independent of Apache Spark. Broad affiliated users should contact the Hail team for help using Hail Query on Hail Batch. Unaffiliated users should also contact the Hail team to discuss the feasibility of running your own Hail Batch cluster. The Hail team is accessible at both https://hail.zulipchat.com and https://discuss.hail.is .

Version 0.2.91

Release 2022-03-18

Bug fixes

(#11614) Update hail.utils.tutorial.get_movie_lens to use https instead of http. Movie Lens has stopped serving data over insecure HTTP.
(#11563) Fix issue hail-is/hail#11562.
(#11611) Fix a bug that prevents the display of hl.ggplot.geom_hline and hl.ggplot.geom_vline.

Version 0.2.90

Release 2022-03-11

Critical BlockMatrix from_numpy correctness bug

(#11555) BlockMatrix.from_numpy did not work correctly. Version 1.0 of org.scalanlp.breeze, a dependency of Apache Spark that hail also depends on, has a correctness bug that results in BlockMatrices that repeat the top left block of the block matrix for every block. This affected anyone running Spark 3.0.x or 3.1.x.

Bug fixes

(#11556) Fixed assertion error ocassionally being thrown by valid joins where the join key was a prefix of the left key.

Versioning

(#11551) Support Python 3.10.

Version 0.2.89

Release 2022-03-04

(#11452) Fix impute_sex_chromosome_ploidy docs.

Version 0.2.88

Release 2022-03-01

This release addresses the deploy issues in the 0.2.87 release of Hail.

Version 0.2.87

Release 2022-02-28

An error in the deploy process required us to yank this release from PyPI. Please do not use this release.

Bug fixes

(#11401) Fixed bug where from_pandas didn’t support missing strings.

Version 0.2.86

Release 2022-02-25

Bug fixes

(#11374) Fixed bug where certain pipelines that read in PLINK files would give assertion error.
(#11401) Fixed bug where from_pandas didn’t support missing ints.

Performance improvements

(#11306) Newly written tables that have no duplicate keys will be faster to join against.

Version 0.2.85

Release 2022-02-14

Bug fixes

(#11355) Fixed assertion errors being hit relating to RVDPartitioner.
(#11344) Fix error where hail ggplot would mislabel points after more than 10 distinct colors were used.

New features

(#11332) Added geom_ribbon and geom_area to hail ggplot.

Version 0.2.84

Release 2022-02-10

Bug fixes

(#11328) Fix bug where occasionally files written to disk would be unreadable.
(#11331) Fix bug that potentially caused files written to disk to be unreadable.
(#11312) Fix aggregator memory leak.
(#11340) Fix bug where repeatedly annotating same field name could cause failure to compile.
(#11342) Fix to possible issues about having too many open file handles.

New features

(#11300) geom_histogram infers min and max values automatically.
(#11317) Add support for alpha aesthetic and identity position to geom_histogram.

Version 0.2.83

Release 2022-02-01

Bug fixes

(#11268) Fixed log argument in hail.plot.histogram.
(#11276) Fixed log argument in hail.plot.pdf.
(#11256) Fixed memory leak in LD Prune.

New features

(#11274) Added geom_col to hail.ggplot.

hailctl dataproc

(#11280) Updated dataproc image version to one not affected by log4j vulnerabilities.

Version 0.2.82

Release 2022-01-24

Bug fixes

(#11209) Significantly improved usefulness and speed of Table.to_pandas, resolved several bugs with output.

New features

(#11247) Introduces a new experimental plotting interface hail.ggplot, based on R’s ggplot library.
(#11173) Many math functions like hail.sqrt now automatically broadcast over ndarrays.

Performance Improvements

(#11216) Significantly improve performance of parse_locus_interval

Python and Java Support

(#11219) We no longer officially support Python 3.6, though it may continue to work in the short term.
(#11220) We support building hail with Java 11.

File Format

The native file format version is now 1.6.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.81

Release 2021-12-20

hailctl dataproc

(#11182) Updated Dataproc image version to mitigate yet more Log4j vulnerabilities.

Version 0.2.80

Release 2021-12-15

New features

(#11077) hl.experimental.write_matrix_tables now returns the paths of the written matrix tables.

hailctl dataproc

(#11157) Updated Dataproc image version to mitigate the Log4j vulnerability.
(#10900) Added --region parameter to hailctl dataproc submit.
(#11090) Teach hailctl dataproc describe how to read URLs with the protocols s3 (Amazon S3), hail-az (Azure Blob Storage), and file (local file system) in addition to gs (Google Cloud Storage).

Version 0.2.79

Release 2021-11-17

Bug fixes

(#11023) Fixed bug in call decoding that was introduced in version 0.2.78.

New features

(#10993) New function p_value_excess_het.

Version 0.2.78

Release 2021-10-19

Bug fixes

(#10766) Don’t throw out of memory error when broadcasting more than 2^(31) - 1 bytes.
(#10910) Filters on key field won’t be slowed down by uses of MatrixTable.localize_entries or Table.rename.
(#10959) Don’t throw an error in certain situations where some key fields are optimized away.

New features

(#10855) Arbitrary aggregations can be implemented using hl.agg.fold.

Performance Improvements

(#10971) Substantially improve the speed of Table.collect when collecting large amounts of data.

Version 0.2.77

Release 2021-09-21

Bug fixes

(#10888) Fix crash when calling hl.liftover.
(#10883) Fix crash / long compilation times writing matrix tables with many partitions.

Version 0.2.76

Released 2021-09-15

Bug fixes

(#10872) Fix long compile times or method size errors when writing tables with many partitions
(#10878) Fix crash importing or sorting tables with empty data partitions

Version 0.2.75

Released 2021-09-10

Bug fixes

(#10733) Fix a bug in tabix parsing when the size of the list of all sequences is large.
(#10765) Fix rare bug where valid pipelines would fail to compile if intervals were created conditionally.
(#10746) Various compiler improvements, decrease likelihood of ClassTooLarge errors.
(#10829) Fix a bug where hl.missing and CaseBuilder.or_error failed if their type was a struct containing a field starting with a number.

New features

(#10768) Support multiplying StringExpressions to repeat them, as with normal python strings.

Performance improvements

(#10625) Reduced need to copy strings around, pipelines with many string operations should get faster.
(#10775) Improved performance of to_matrix_table_row_major on both BlockMatrix and Table.

Version 0.2.74

Released 2021-07-26

Bug fixes

(#10697) Fixed bug in read_table when the table has missing keys and _n_partitions is specified.
(#10695) Fixed bug in hl.experimental.loop causing incorrect results when loop state contained pointers.

Version 0.2.73

Released 2021-07-22

Bug fixes

(#10684) Fixed a rare bug reading arrays from disk where short arrays would have their first elements corrupted and long arrays would cause segfaults.
(#10523) Fixed bug where liftover would fail with “Could not initialize class” errors.

Version 0.2.72

Released 2021-07-19

New Features

(#10655) Revamped many hail error messages to give useful python stack traces.
(#10663) Added DictExpression.items() to mirror python’s dict.items().
(#10657) hl.map now supports mapping over multiple lists like Python’s built-in map.

Bug fixes

(#10662) Fixed partitioning logic in hl.import_plink.
(#10669) NDArrayNumericExpression.sum() now works correctly on ndarrays of booleans.

Version 0.2.71

Released 2021-07-08

New Features

(#10632) Added support for weighted linear regression to hl.linear_regression_rows.
(#10635) Added hl.nd.maximum and hl.nd.minimum.
(#10602) Added hl.starmap.

Bug fixes

(#10038) Fixed crashes when writing/reading matrix tables with 0 partitions.
(#10624) Fixed out of bounds bug with _quantile_from_cdf.

hailctl dataproc

(#10633) Added --scopes parameter to hailctl dataproc start.

Version 0.2.70

Released 2021-06-21

Version 0.2.69

Released 2021-06-14

New Features

(#10592) Added hl.get_hgdp function.
(#10555) Added hl.hadoop_scheme_supported function.
(#10551) Indexing ndarrays now supports ellipses.

Bug fixes

(#10553) Dividing two integers now returns a float64, not a float32.
(#10595) Don’t include nans in lambda_gc_agg.

hailctl dataproc

(#10574) Hail logs will now be stored in /home/hail by default.

Version 0.2.68

Released 2021-05-27

Version 0.2.67

Critical performance fix

Released 2021-05-06

(#10451) Fixed a memory leak / performance bug triggered by hl.literal(...).contains(...)

Version 0.2.66

Released 2021-05-03

New features

(#10398) Added new method BlockMatrix.to_ndarray.
(#10251) Added suport for haploid GT calls to VCF combiner.

Version 0.2.65

Released 2021-04-14

Default Spark Version Change

Starting from version 0.2.65, Hail uses Spark 3.1.1 by default. This will also allow the use of all python versions >= 3.6. By building hail from source, it is still possible to use older versions of Spark.

New features

(#10290) Added hl.nd.solve.
(#10187) Added NDArrayNumericExpression.sum.

Performance improvements

(#10233) Loops created with hl.experimental.loop will now clean up unneeded memory between iterations.

Bug fixes

(#10227) hl.nd.qr now supports ndarrays that have 0 rows or columns.

Version 0.2.64

Released 2021-03-11

New features

(#10164) Add source_file_field parameter to hl.import_table to allow lines to be associated with their original source file.

Bug fixes

(#10182) Fixed serious memory leak in certain uses of filter_intervals.
(#10133) Fix bug where some pipelines incorrectly infer missingness, leading to a type error.
(#10134) Teach hl.king to treat filtered entries as missing values.
(#10158) Fixes hail usage in latest versions of jupyter that rely on asyncio.
(#10174) Fixed bad error message when incorrect return type specified with hl.loop.

Version 0.2.63

Released 2021-03-01

(#10105) Hail will now return frozenset and hail.utils.frozendict instead of normal sets and dicts.

Bug fixes

(#10035) Fix mishandling of NaN values in hl.agg.hist, where they were unintentionally included in the first bin.
(#10007) Improve error message from hadoop_ls when file does not exist.

Performance Improvements

(#10068) Make certain array copies faster.
(#10061) Improve code generation of hl.if_else and hl.coalesce.

Version 0.2.62

Released 2021-02-03

New features

(#9936) Deprecated hl.null in favor of hl.missing for naming consistency.
(#9973) hl.vep now includes a vep_proc_id field to aid in debugging unexpected output.
(#9839) Hail now eagerly deletes temporary files produced by some BlockMatrix operations.
(#9835) hl.any and hl.all now also support a single collection argument and a varargs of Boolean expressions.
(#9816) hl.pc_relate now includes values on the diagonal of kinship, IBD-0, IBD-1, and IBD-2
(#9736) Let NDArrayExpression.reshape take varargs instead of mandating a tuple.
(#9766) hl.export_vcf now warns if INFO field names are invalid according to the VCF 4.3 spec.

Bug fixes

(#9976) Fixed show() representation of Hail dictionaries.

Performance improvements

(#9909) Improved performance of hl.experimental.densify by approximately 35%.

Version 0.2.61

Released 2020-12-03

New features

(#9749) Add or_error method to SwitchBuilder (hl.switch)

Bug fixes

(#9775) Fixed race condition leading to invalid intermediate files in VCF combiner.
(#9751) Fix bug where constructing an array of empty structs causes type error.
(#9731) Fix error and incorrect behavior when using hl.import_matrix_table with int64 data types.

Version 0.2.60

Released 2020-11-16

New features

(#9696) hl.experimental.export_elasticsearch will now support Elasticsearch versions 6.8 - 7.x by default.

Bug fixes

(#9641) Showing hail ndarray data now always prints in correct order.

hailctl dataproc

(#9610) Support interval fields in hailctl dataproc describe

Version 0.2.59

Released 2020-10-22

Datasets / Annotation DB

(#9605) The Datasets API and the Annotation Database now support AWS, and users are required to specify what cloud platform they’re using.

hailctl dataproc

(#9609) Fixed bug where hailctl dataproc modify did not correctly print corresponding gcloud command.

Version 0.2.58

Released 2020-10-08

New features

(#9524) Hail should now be buildable using Spark 3.0.
(#9549) Add ignore_in_sample_frequency flag to hl.de_novo.
(#9501) Configurable cache size for BlockMatrix.to_matrix_table_row_major and BlockMatrix.to_table_row_major.
(#9474) Add ArrayExpression.first and ArrayExpression.last.
(#9459) Add StringExpression.join, an analogue to Python’s str.join.
(#9398) Hail will now throw HailUserErrors if the or_error branch of a CaseBuilder is hit.

Bug fixes

(#9503) NDArrays can now hold arbitrary data types, though only ndarrays of primitives can be collected to Python.
(#9501) Remove memory leak in BlockMatrix.to_matrix_table_row_major and BlockMatrix.to_table_row_major.
(#9424) hl.experimental.writeBlockMatrices didn’t correctly support overwrite flag.

Performance improvements

(#9506) hl.agg.ndarray_sum will now do a tree aggregation.

hailctl dataproc

(#9502) Fix hailctl dataproc modify to install dependencies of the wheel file.
(#9420) Add --debug-mode flag to hailctl dataproc start. This will enable heap dumps on OOM errors.
(#9520) Add support for requester pays buckets to hailctl dataproc describe.

Deprecations

(#9482) ArrayExpression.head has been deprecated in favor of ArrayExpression.first.

Version 0.2.57

Released 2020-09-03

New features

(#9343) Implement the KING method for relationship inference as hl.methods.king.

Version 0.2.56

Released 2020-08-31

New features

(#9308) Add hl.enumerate in favor of hl.zip_with_index, which is now deprecated.
(#9278) Add ArrayExpression.grouped, a function that groups hail arrays into fixed size subarrays.

Performance

(#9373)(#9374) Decrease amount of memory used when slicing or filtering along a single BlockMatrix dimension.

Bug fixes

(#9304) Fix crash in run_combiner caused by inputs where VCF lines and BGZ blocks align.

hailctl dataproc

(#9263) Add support for --expiration-time argument to hailctl dataproc start.
(#9263) Add support for --no-max-idle, no-max-age, --max-age, and --expiration-time to hailctl dataproc --modify.

Version 0.2.55

Released 2020-08-19

Performance

(#9264) Table.checkpoint now uses a faster LZ4 compression scheme.

Bug fixes

(#9250) hailctl dataproc no longer uses deprecated gcloud flags. Consequently, users must update to a recent version of gcloud.
(#9294) The “Python 3” kernel in notebooks in clusters started by hailctl dataproc now features the same Spark monitoring widget found in the “Hail” kernel. There is now no reason to use the “Hail” kernel.

File Format

The native file format version is now 1.5.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.54

Released 2020-08-07

VCF Combiner

(#9224)(#9237) Breaking change: Users are now required to pass a partitioning argument to the command-line interface or run_combiner method. See documentation for details.
(#8963) Improved performance of VCF combiner by ~4x.

New features

(#9209) Add hl.agg.ndarray_sum aggregator.

Bug fixes

(#9206)(#9207) Improved error messages from invalid usages of Hail expressions.
(#9223) Fixed error in bounds checking for NDArray slicing.

Version 0.2.53

Released 2020-07-30

Bug fixes

(#9173) Use less confusing column key behavior in MT.show.
(#9172) Add a missing Python dependency to Hail: google-cloud-storage.
(#9170) Change Hail tree aggregate depth logic to correctly respect the branching factor set in hl.init.

Version 0.2.52

Released 2020-07-29

Bug fixes

(#8944)(#9169) Fixed crash (error 134 or SIGSEGV) in MatrixTable.annotate_cols, hl.sample_qc, and more.

Version 0.2.51

Released 2020-07-28

Bug fixes

(#9161) Fix bug that prevented concatenating ndarrays that are fields of a table.
(#9152) Fix bounds in NDArray slicing.
(#9161) Fix bugs calculating row_id in hl.import_matrix_table.

Version 0.2.50

Released 2020-07-23

Bug fixes

(#9114) CHANGELOG: Fixed crash when using repeated calls to hl.filter_intervals.

New features

(#9101) Add hl.nd.{concat, hstack, vstack} to concatenate ndarrays.
(#9105) Add hl.nd.{eye, identity} to create identity matrix ndarrays.
(#9093) Add hl.nd.inv to invert ndarrays.
(#9063) Add BlockMatrix.tree_matmul to improve matrix multiply performance with a large inner dimension.

Version 0.2.49

Released 2020-07-08

Bug fixes

(#9058) Fixed memory leak affecting Table.aggregate, MatrixTable.annotate_cols aggregations, and hl.sample_qc.

Version 0.2.48

Released 2020-07-07

Bug fixes

(#9029) Fix crash when using hl.agg.linreg with no aggregated data records.
(#9028) Fixed memory leak affecting Table.annotate with scans, hl.experimental.densify, and Table.group_by / aggregate.
(#8978) Fixed aggregation behavior of MatrixTable.{group_rows_by, group_cols_by} to skip filtered entries.

Version 0.2.47

Released 2020-06-23

Bug fixes

(#9009) Fix memory leak when counting per-partition. This caused excessive memory use in BlockMatrix.write_from_entry_expr, and likely in many other places.
(#9006) Fix memory leak in hl.export_bgen.
(#9001) Fix double close error that showed up on Azure Cloud.

Version 0.2.46

Released 2020-06-17

Site

(#8955) Natural language documentation search

Bug fixes

(#8981) Fix BlockMatrix OOM triggered by the MatrixWriteBlockMatrix WriteBlocksRDD method

Version 0.2.45

Release 2020-06-15

Bug fixes

(#8948) Fix integer overflow error when reading files >2G with hl.import_plink.
(#8903) Fix Python type annotations for empty collection constructors and hl.shuffle.
(#8942) Refactored VCF combiner to support other GVCF schemas.
(#8941) Fixed hl.import_plink with multiple data partitions.

hailctl dataproc

(#8946) Fix bug when a user specifies packages in hailctl dataproc start that are also dependencies of the Hail package.
(#8939) Support tuples in hailctl dataproc describe.

Version 0.2.44

Release 2020-06-06

New Features

(#8914) hl.export_vcf can now export tables as sites-only VCFs.
(#8894) Added hl.shuffle function to randomly permute arrays.
(#8854) Add composable option to parallel text export for use with gsutil compose.

Bug fixes

(#8883) Fix an issue related to failures in pipelines with force_bgz=True.

Performance

(#8887) Substantially improve the performance of hl.experimental.import_gtf.

Version 0.2.43

Released 2020-05-28

Bug fixes

(#8867) Fix a major correctness bug ocurring when calling BlockMatrix.transpose on sparse, non-symmetric BlockMatrices.
(#8876) Fixed “ChannelClosedException: null” in {Table, MatrixTable}.write.

Version 0.2.42

Released 2020-05-27

New Features

(#8822) Add optional non-centrality parameter to hl.pchisqtail.
(#8861) Add contig_recoding option to hl.experimental.run_combiner.

Bug fixes

(#8863) Fixes VCF combiner to successfully import GVCFs with alleles called as .
(#8845) Fixed issue where accessing an element of an ndarray in a call to Table.transmute would fail.
(#8855) Fix crash in filter_intervals.

Version 0.2.41

Released 2020-05-15

Bug fixes

(#8799)(#8786) Fix ArrayIndexOutOfBoundsException seen in pipelines that reuse a tuple value.

hailctl dataproc

(#8790) Use configured compute zone as default for hailctl dataproc connect and hailctl dataproc modify.

Version 0.2.40

Released 2020-05-12

VCF Combiner

(#8706) Add option to key by both locus and alleles for final output.

Bug fixes

(#8729) Fix assertion error in Table.group_by(...).aggregate(...)
(#8708) Fix assertion error in reading tables and matrix tables with _intervals option.
(#8756) Fix return type of LocusExpression.window to use locus’s reference genome instead of default RG.

Version 0.2.39

Released 2020-04-29

Bug fixes

(#8615) Fix contig ordering in the CanFam3 (dog) reference genome.
(#8622) Fix bug that causes inscrutable JVM Bytecode errors.
(#8645) Ease unnecessarily strict assertion that caused errors when aggregating by key (e.g. hl.experimental.spread).
(#8621) hl.nd.array now supports arrays with no elements (e.g. hl.nd.array([]).reshape((0, 5))) and, consequently, matmul with an inner dimension of zero.

New features

(#8571) hl.init(skip_logging_configuration=True) will skip configuration of Log4j. Users may use this to configure their own logging.
(#8588) Users who manually build Python wheels will experience less unnecessary output when doing so.
(#8572) Add hl.parse_json which converts a string containing JSON into a Hail object.

Performance Improvements

(#8535) Increase speed of import_vcf.
(#8618) Increase speed of Jupyter Notebook file listing and Notebook creation when buckets contain many objects.
(#8613) hl.experimental.export_entries_by_col stages files for improved reliability and performance.

Documentation

(#8619) Improve installation documentation to suggest better performing LAPACK and BLAS libraries.
(#8647) Clarify that a LAPACK or BLAS library is a requirement for a complete Hail installation.
(#8654) Add link to document describing the creation of a Microsoft Azure HDInsight Hail cluster.

Version 0.2.38

Released 2020-04-21

Critical Linreg Aggregator Correctness Bug

(#8575) Fixed a correctness bug in the linear regression aggregator. This was introduced in version 0.2.29. See https://discuss.hail.is/t/possible-incorrect-linreg-aggregator-results-in-0-2-29-0-2-37/1375 for more details.

Performance improvements

(#8558) Make hl.experimental.export_entries_by_col more fault tolerant.

Version 0.2.37

Released 2020-04-14

Bug fixes

(#8487) Fix incorrect handling of badly formatted data for hl.gp_dosage.
(#8497) Fix handling of missingness for hl.hamming.
(#8537) Fix compile-time errror.
(#8539) Fix compiler error in Table.multi_way_zip_join.
(#8488) Fix hl.agg.call_stats to appropriately throw an error for badly-formatted calls.

New features

(#8327) Attempting to write to the same file being read from in a pipeline will now throw an error instead of corrupting data.

Version 0.2.36

Released 2020-04-06

Critical Memory Management Bug Fix

(#8463) Reverted a change (separate to the bug in 0.2.34) that led to a memory leak in version 0.2.35.

Bug fixes

(#8371) Fix runtime error in joins leading to “Cannot set required field missing” error message.
(#8436) Fix compiler bug leading to possibly-invalid generated code.

Version 0.2.35

Released 2020-04-02

Critical Memory Management Bug Fix

(#8412) Fixed a serious per-partition memory leak that causes certain pipelines to run out of memory unexpectedly. Please update from 0.2.34.

New features

(#8404) Added “CanFam3” (a reference genome for dogs) as a bundled reference genome.

Bug fixes

(#8420) Fixed a bug where hl.binom_test’s "lower" and "upper" alternative options were reversed.
(#8377) Fixed “inconsistent agg or scan environments” error.
(#8322) Fixed bug where aggregate_rows did not interact with hl.agg.array_agg correctly.

Performance Improvements

(#8413) Improves internal region memory management, decreasing JVM overhead.
(#8383) Significantly improve GVCF import speed.
(#8358) Fixed memory leak in hl.experimental.export_entries_by_col.
(#8326) Codegen infrastructure improvement resulting in ~3% overall speedup.

hailctl dataproc

(#8399) Enable spark speculation by default.
(#8340) Add new Australia region to --vep.
(#8347) Support all GCP machine types as potential master machines.

Version 0.2.34

Released 2020-03-12

New features

(#8233) StringExpression.matches can now take a hail StringExpression, as opposed to only regular python strings.
(#8198) Improved matrix multiplication interoperation between hail NDArrayExpression and numpy.

Bug fixes

(#8279) Fix a bug where hl.agg.approx_cdf failed inside of a group_cols_by.
(#8275) Fix bad error message coming from mt.make_table() when keys are missing.
(#8274) Fix memory leak in hl.export_bgen.
(#8273) Fix segfault caused by hl.agg.downsample inside of an array_agg or group_by.

hailctl dataproc

(#8253) hailctl dataproc now supports new flags --requester-pays-allow-all and --requester-pays-allow-buckets. This will configure your hail installation to be able to read from requester pays buckets. The charges for reading from these buckets will be billed to the project that the cluster is created in.
(#8268) The data sources for VEP have been moved to gs://hail-us-vep, gs://hail-eu-vep, and gs://hail-uk-vep, which are requester-pays buckets in Google Cloud. hailctl dataproc will automatically infer which of these buckets you should pull data from based on the region your cluster is spun up in. If you are in none of those regions, please contact us on discuss.hail.is.

File Format

The native file format version is now 1.4.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.33

Released 2020-02-27

New features

(#8173) Added new method hl.zeros.

Bug fixes

(#8153) Fixed complier bug causing MatchError in import_bgen.
(#8123) Fixed an issue with multiple Python HailContexts running on the same cluster.
(#8150) Fixed an issue where output from VEP about failures was not reported in error message.
(#8152) Fixed an issue where the row count of a MatrixTable coming from import_matrix_table was incorrect.
(#8175) Fixed a bug where persist did not actually do anything.

`hailctl dataproc`

(#8079) Using connect to open the jupyter notebook browser will no longer crash if your project contains requester-pays buckets.

Version 0.2.32

Released 2020-02-07

Critical performance regression fix

(#7989) Fixed performance regression leading to a large slowdown when hl.variant_qc was run after filtering columns.

Performance

(#7962) Improved performance of hl.pc_relate.
(#8032) Drastically improve performance of pipelines calling hl.variant_qc and hl.sample_qc iteratively.
(#8037) Improve performance of NDArray matrix multiply by using native linear algebra libraries.

Bug fixes

(#7976) Fixed divide-by-zero error in hl.concordance with no overlapping rows or cols.
(#7965) Fixed optimizer error leading to crashes caused by MatrixTable.union_rows.
(#8035) Fix compiler bug in Table.multi_way_zip_join.
(#8021) Fix bug in computing shape after BlockMatrix.filter.
(#7986) Fix error in NDArray matrix/vector multiply.

New features

(#8007) Add hl.nd.diagonal function.

Cheat sheets

(#7940) Added cheat sheet for MatrixTables.
(#7963) Improved Table sheet sheet.

Version 0.2.31

Released 2020-01-22

New features

(#7787) Added transition/transversion information to hl.summarize_variants.
(#7792) Add Python stack trace to array index out of bounds errors in Hail pipelines.
(#7832) Add spark_conf argument to hl.init, permitting configuration of Spark runtime for a Hail session.
(#7823) Added datetime functions hl.experimental.strptime and hl.experimental.strftime.
(#7888) Added hl.nd.array constructor from nested standard arrays.

File size

(#7923) Fixed compression problem since 0.2.23 resulting in larger-than-expected matrix table files for datasets with few entry fields (e.g. GT-only datasets).

Performance

(#7867) Fix performance regression leading to extra scans of data when order_by and key_by appeared close together.
(#7901) Fix performance regression leading to extra scans of data when group_by/aggregate and key_by appeared close together.
(#7830) Improve performance of array arithmetic.

Bug fixes

(#7922) Fix still-not-well-understood serialization error about ApproxCDFCombiner.
(#7906) Fix optimizer error by relaxing unnecessary assertion.
(#7788) Fix possible memory leak in ht.tail and ht.head.
(#7796) Fix bug in ingesting numpy arrays not in row-major orientation.

Version 0.2.30

Released 2019-12-20

Performance

(#7771) Fixed extreme performance regression in scans.
(#7764) Fixed mt.entry_field.take performance regression.

New features

(#7614) Added experimental support for loops with hl.experimental.loop.

Miscellaneous

(#7745) Changed export_vcf to only use scientific notation when necessary.

Version 0.2.29

Released 2019-12-17

Bug fixes

(#7229) Fixed hl.maximal_independent_set tie breaker functionality.
(#7732) Fixed incompatibility with old files leading to incorrect data read when filtering intervals after read_matrix_table.
(#7642) Fixed crash when constant-folding functions that throw errors.
(#7611) Fixed hl.hadoop_ls to handle glob patterns correctly.
(#7653) Fixed crash in ld_prune by unfiltering missing GTs.

Performance improvements

(#7719) Generate more efficient IR for Table.flatten.
(#7740) Method wrapping large let bindings to keep method size down.

New features

(#7686) Added comment argument to import_matrix_table, allowing lines with certain prefixes to be ignored.
(#7688) Added experimental support for NDArrayExpressions in new hl.nd module.
(#7608) hl.grep now has a show argument that allows users to either print the results (default) or return a dictionary of the results.

`hailctl dataproc`

(#7717) Throw error when mispelling arguments instead of silently quitting.

Version 0.2.28

Released 2019-11-22

Critical correctness bug fix

(#7588) Fixes a bug where filtering old matrix tables in newer versions of hail did not work as expected. Please update from 0.2.27.

Bug fixes

(#7571) Don’t set GQ to missing if PL is missing in split_multi_hts.
(#7577) Fixed an optimizer bug.

New Features

(#7561) Added hl.plot.visualize_missingness() to plot missingness patterns for MatrixTables.
(#7575) Added hl.version() to quickly check hail version.

`hailctl dataproc`

(#7586) hailctl dataproc now supports --gcloud_configuration option.

Documentation

(#7570) Hail has a cheatsheet for Tables now.

Version 0.2.27

Released 2019-11-15

New Features

(#7379) Add delimiter argument to hl.import_matrix_table
(#7389) Add force and force_bgz arguments to hl.experimental.import_gtf
(#7386)(#7394) Add {Table, MatrixTable}.tail.
(#7467) Added hl.if_else as an alias for hl.cond; deprecated hl.cond.
(#7453) Add hl.parse_int{32, 64} and hl.parse_float{32, 64}, which can parse strings to numbers and return missing on failure.
(#7475) Add row_join_type argument to MatrixTable.union_cols to support outer joins on rows.

Bug fixes

(#7479)(#7368)(#7402) Fix optimizer bugs.
(#7506) Updated to latest htsjdk to resolve VCF parsing problems.

`hailctl dataproc`

(#7460) The Spark monitor widget now automatically collapses after a job completes.

Version 0.2.26

Released 2019-10-24

New Features

(#7325) Add string.reverse function.
(#7328) Add string.translate function.
(#7344) Add hl.reverse_complement function.
(#7306) Teach the VCF combiner to handle allele specific (AS_*) fields.
(#7346) Add hl.agg.approx_median function.

Bug Fixes

(#7361) Fix AD calculation in sparse_split_multi.

Performance Improvements

(#7355) Improve performance of IR copying.

File Format

The native file format version is now 1.3.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.25

Released 2019-10-14

New features

(#7240) Add interactive schema widget to {MatrixTable, Table}.describe. Use this by passing the argument widget=True.
(#7250) {Table, MatrixTable, Expression}.summarize() now summarizes elements of collections (arrays, sets, dicts).
(#7271) Improve hl.plot.qq by increasing point size, adding the unscaled p-value to hover data, and printing lambda-GC on the plot.
(#7280) Add HTML output for {Table, MatrixTable, Expression}.summarize().
(#7294) Add HTML output for hl.summarize_variants().

Bug fixes

(#7200) Fix VCF parsing with missingness inside arrays of floating-point values in the FORMAT field.
(#7219) Fix crash due to invalid optimizer rule.

Performance improvements

(#7187) Dramatically improve performance of chained BlockMatrix multiplies without checkpoints in between.
(#7195)(#7194) Improve performance of group[_rows]_by / aggregate.
(#7201) Permit code generation of larger aggregation pipelines.

File Format

The native file format version is now 1.2.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.24

Released 2019-10-03

`hailctl dataproc`

(#7185) Resolve issue in dependencies that led to a Jupyter update breaking cluster creation.

New features

(#7071) Add permit_shuffle flag to hl.{split_multi, split_multi_hts} to allow processing of datasets with both multiallelics and duplciate loci.
(#7121) Add hl.contig_length function.
(#7130) Add window method on LocusExpression, which creates an interval around a locus.
(#7172) Permit hl.init(sc=sc) with pip-installed packages, given the right configuration options.

Bug fixes

(#7070) Fix unintentionally strict type error in MatrixTable.union_rows.
(#7170) Fix issues created downstream of BlockMatrix.T.
(#7146) Fix bad handling of edge cases in BlockMatrix.filter.
(#7182) Fix problem parsing VCFs where lines end in an INFO field of type flag.

Version 0.2.23

Released 2019-09-23

`hailctl dataproc`

(#7087) Added back progress bar to notebooks, with links to the correct Spark UI url.
(#7104) Increased disk requested when using --vep to address the “colony collapse” cluster error mode.

Bug fixes

(#7066) Fixed generated code when methods from multiple reference genomes appear together.
(#7077) Fixed crash in hl.agg.group_by.

New features

(#7009) Introduced analysis pass in Python that mostly obviates the hl.bind and hl.rbind operators; idiomatic Python that generates Hail expressions will perform much better.
(#7076) Improved memory management in generated code, add additional log statements about allocated memory to improve debugging.
(#7085) Warn only once about schema mismatches during JSON import (used in VEP, Nirvana, and sometimes import_table.
(#7106) hl.agg.call_stats can now accept a number of alleles for its alleles parameter, useful when dealing with biallelic calls without the alleles array at hand.

Performance

(#7086) Improved performance of JSON import.
(#6981) Improved performance of Hail min/max/mean operators. Improved performance of split_multi_hts by an additional 33%.
(#7082)(#7096)(#7098) Improved performance of large pipelines involving many annotate calls.

Version 0.2.22

Released 2019-09-12

New features

(#7013) Added contig_recoding to import_bed and import_locus_intervals.

Performance

(#6969) Improved performance of hl.agg.mean, hl.agg.stats, and hl.agg.corr.
(#6987) Improved performance of import_matrix_table.
(#7033)(#7049) Various improvements leading to overall 10-15% improvement.

`hailctl dataproc`

(#7003) Pass through extra arguments for hailctl dataproc list and hailctl dataproc stop.

Version 0.2.21

Released 2019-09-03

Bug fixes

(#6945) Fixed expand_types to preserve ordering by key, also affects to_pandas and to_spark.
(#6958) Fixed stack overflow errors when counting the result of a Table.union.

New features

(#6856) Teach hl.agg.counter to weigh each value differently.
(#6903) Teach hl.range to treat a single argument as 0..N.
(#6903) Teach BlockMatrix how to checkpoint.

Performance

(#6895) Improved performance of hl.import_bgen(...).count().
(#6948) Fixed performance bug in BlockMatrix filtering functions.
(#6943) Improved scaling of Table.union.
(#6980) Reduced compute time for split_multi_hts by as much as 40%.

`hailctl dataproc`

(#6904) Added --dry-run option to submit.
(#6951) Fixed --max-idle and --max-age arguments to start.
(#6919) Added --update-hail-version to modify.

Version 0.2.20

Released 2019-08-19

Critical memory management fix

(#6824) Fixed memory management inside annotate_cols with aggregations. This was causing memory leaks and segfaults.

Bug fixes

(#6769) Fixed non-functional hl.lambda_gc method.
(#6847) Fixed bug in handling of NaN in hl.agg.min and hl.agg.max. These will now properly ignore NaN (the intended semantics). Note that hl.min and hl.max propagate NaN; use hl.nanmin and hl.nanmax to ignore NaN.

New features

(#6847) Added hl.nanmin and hl.nanmax functions.

Version 0.2.19

Released 2019-08-01

Critical performance bug fix

(#6629) Fixed a critical performance bug introduced in (#6266). This bug led to long hang times when reading in Hail tables and matrix tables written in version 0.2.18.

Bug fixes

(#6757) Fixed correctness bug in optimizations applied to the combination of Table.order_by with hl.desc arguments and show(), leading to tables sorted in ascending, not descending order.
(#6770) Fixed assertion error caused by Table.expand_types(), which was used by Table.to_spark and Table.to_pandas.

Performance Improvements

(#6666) Slightly improve performance of hl.pca and hl.hwe_normalized_pca.
(#6669) Improve performance of hl.split_multi and hl.split_multi_hts.
(#6644) Optimize core code generation primitives, leading to across-the-board performance improvements.
(#6775) Fixed a major performance problem related to reading block matrices.

`hailctl dataproc`

(#6760) Fixed the address pointed at by ui in connect, after Google changed proxy settings that rendered the UI URL incorrect. Also added new address hist/spark-history.

Version 0.2.18

Released 2019-07-12

Critical performance bug fix

(#6605) Resolved code generation issue leading a performance regression of 1-3 orders of magnitude in Hail pipelines using constant strings or literals. This includes almost every pipeline! This issue has exists in versions 0.2.15, 0.2.16, and 0.2.17, and any users on those versions should update as soon as possible.

Bug fixes

(#6598) Fixed code generated by MatrixTable.unfilter_entries to improve performance. This will slightly improve the performance of hwe_normalized_pca and relatedness computation methods, which use unfilter_entries internally.

Version 0.2.17

Released 2019-07-10

New features

(#6349) Added compression parameter to export_block_matrices, which can be 'gz' or 'bgz'.
(#6405) When a matrix table has string column-keys, matrixtable.show uses the column key as the column name.
(#6345) Added an improved scan implementation, which reduces the memory load on master.
(#6462) Added export_bgen method.
(#6473) Improved performance of hl.agg.array_sum by about 50%.
(#6498) Added method hl.lambda_gc to calculate the genomic control inflation factor.
(#6456) Dramatically improved performance of pipelines containing long chains of calls to Table.annotate, or MatrixTable equivalents.
(#6506) Improved the performance of the generated code for the Table.annotate(**thing) pattern.

Bug fixes

(#6404) Added n_rows and n_cols parameters to Expression.show for consistency with other show methods.
(#6408)(#6419) Fixed an issue where the filter_intervals optimization could make scans return incorrect results.
(#6459)(#6458) Fixed rare correctness bug in the filter_intervals optimization which could result too many rows being kept.
(#6496) Fixed html output of show methods to truncate long field contents.
(#6478) Fixed the broken documentation for the experimental approx_cdf and approx_quantiles aggregators.
(#6504) Fix Table.show collecting data twice while running in Jupyter notebooks.
(#6571) Fixed the message printed in hl.concordance to print the number of overlapping samples, not the full list of overlapping sample IDs.
(#6583) Fixed hl.plot.manhattan for non-default reference genomes.

Experimental

(#6488) Exposed table.multi_way_zip_join. This takes a list of tables of identical types, and zips them together into one table.

File Format

The native file format version is now 1.1.0. Older versions of Hail will not be able to read tables or matrix tables written by this version of Hail.

Version 0.2.16

Released 2019-06-19

`hailctl`

(#6357) Accommodated Google Dataproc bug causing cluster creation failures.

Bug fixes

(#6378) Fixed problem in how entry_float_type was being handled in import_vcf.

Version 0.2.15

Released 2019-06-14

After some infrastructural changes to our development process, we should be getting back to frequent releases.

`hailctl`

Starting in 0.2.15, pip installations of Hail come bundled with a command- line tool, hailctl. This tool subsumes the functionality of cloudtools, which is now deprecated. See the release thread on the forum for more information.

New features

(#5932)(#6115) hl.import_bed abd hl.import_locus_intervals now accept keyword arguments to pass through to hl.import_table, which is used internally. This permits parameters like min_partitions to be set.
(#5980) Added log option to hl.plot.histogram2d.
(#5937) Added all_matches parameter to Table.index and MatrixTable.index_{rows, cols, entries}, which produces an array of all rows in the indexed object matching the index key. This makes it possible to, for example, annotate all intervals overlapping a locus.
(#5913) Added functionality that makes arrays of structs easier to work with.
(#6089) Added HTML output to Expression.show when running in a notebook.
(#6172) hl.split_multi_hts now uses the original GQ value if the PL is missing.
(#6123) Added hl.binary_search to search sorted numeric arrays.
(#6224) Moved implementation of hl.concordance from backend to Python. Performance directly from read() is slightly worse, but inside larger pipelines this function will be optimized much better than before, and it will benefit improvements to general infrastructure.
(#6214) Updated Hail Python dependencies.
(#5979) Added optimizer pass to rewrite filter expressions on keys as interval filters where possible, leading to massive speedups for point queries. See the blog post for examples.

Bug fixes

(#5895) Fixed crash caused by -0.0 floating-point values in hl.agg.hist.
(#6013) Turned off feature in HTSJDK that caused crashes in hl.import_vcf due to header fields being overwritten with different types, if the field had a different type than the type in the VCF 4.2 spec.
(#6117) Fixed problem causing Table.flatten() to be quadratic in the size of the schema.
(#6228)(#5993) Fixed MatrixTable.union_rows() to join distinct keys on the right, preventing an unintentional cartesian product.
(#6235) Fixed an issue related to aggregation inside MatrixTable.filter_cols.
(#6226) Restored lost behavior where Table.show(x < 0) shows the entire table.
(#6267) Fixed cryptic crashes related to hl.split_multi and MatrixTable.entries() with duplicate row keys.

Version 0.2.14

Released 2019-04-24

A back-incompatible patch update to PySpark, 2.4.2, has broken fresh pip installs of Hail 0.2.13. To fix this, either downgrade PySpark to 2.4.1 or upgrade to the latest version of Hail.

New features

(#5915) Added hl.cite_hail and hl.cite_hail_bibtex functions to generate appropriate citations.
(#5872) Fixed hl.init when the idempotent parameter is True.

Version 0.2.13

Released 2019-04-18

Hail is now using Spark 2.4.x by default. If you build hail from source, you will need to acquire this version of Spark and update your build invocations accordingly.

New features

(#5828) Remove dependency on htsjdk for VCF INFO parsing, enabling faster import of some VCFs.
(#5860) Improve performance of some column annotation pipelines.
(#5858) Add unify option to Table.union which allows unification of tables with different fields or field orderings.
(#5799) mt.entries() is four times faster.
(#5756) Hail now uses Spark 2.4.x by default.
(#5677) MatrixTable now also supports show.
(#5793)(#5701) Add array.index(x) which find the first index of array whose value is equal to x.
(#5790) Add array.head() which returns the first element of the array, or missing if the array is empty.
(#5690) Improve performance of ld_matrix.
(#5743) mt.compute_entry_filter_stats computes statistics about the number of filtered entries in a matrix table.
(#5758) failure to parse an interval will now produce a much more detailed error message.
(#5723) hl.import_matrix_table can now import a matrix table with no columns.
(#5724) hl.rand_norm2d samples from a two dimensional random normal.

Bug fixes

(#5885) Fix Table.to_spark in the presence of fields of tuples.
(#5882)(#5886) Fix BlockMatrix conversion methods to correctly handle filtered entries.
(#5884)(#4874) Fix longstanding crash when reading Hail data files under certain conditions.
(#5855)(#5786) Fix hl.mendel_errors incorrectly reporting children counts in the presence of entry filtering.
(#5830)(#5835) Fix Nirvana support
(#5773) Fix hl.sample_qc to use correct number of total rows when calculating call rate.
(#5763)(#5764) Fix hl.agg.array_agg to work inside mt.annotate_rows and similar functions.
(#5770) Hail now uses the correct unicode string encoding which resolves a number of issues when a Table or MatrixTable has a key field containing unicode characters.
(#5692) When keyed is True, hl.maximal_independent_set now does not produce duplicates.
(#5725) Docs now consistently refer to hl.agg not agg.
(#5730)(#5782) Taught import_bgen to optimize its variants argument.

Experimental

(#5732) The hl.agg.approx_quantiles aggregate computes an approximation of the quantiles of an expression.
(#5693)(#5396) Table._multi_way_zip_join now correctly handles keys that have been truncated.

Version 0.2.12

Released 2019-03-28

New features

(#5614) Add support for multiple missing values in hl.import_table.
(#5666) Produce HTML table output for Table.show() when running in Jupyter notebook.

Bug fixes

(#5603)(#5697) Fixed issue where min_partitions on hl.import_table was non-functional.
(#5611) Fix hl.nirvana crash.

Experimental

(#5524) Add summarize functions to Table, MatrixTable, and Expression.
(#5570) Add hl.agg.approx_cdf aggregator for approximate density calculation.
(#5571) Add log parameter to hl.plot.histogram.
(#5601) Add hl.plot.joint_plot, extend functionality of hl.plot.scatter.
(#5608) Add LD score simulation framework.
(#5628) Add hl.experimental.full_outer_join_mt for full outer joins on MatrixTables.

Version 0.2.11

Released 2019-03-06

New features

(#5374) Add default arguments to hl.add_sequence for running on GCP.
(#5481) Added sample_cols method to MatrixTable.
(#5501) Exposed MatrixTable.unfilter_entries. See filter_entries documentation for more information.
(#5480) Added n_cols argument to MatrixTable.head.
(#5529) Added Table.{semi_join, anti_join} and MatrixTable.{semi_join_rows, semi_join_cols, anti_join_rows, anti_join_cols}.
(#5528) Added {MatrixTable, Table}.checkpoint methods as wrappers around write / read_{matrix_table, table}.

Bug fixes

(#5416) Resolved issue wherein VEP and certain regressions were recomputed on each use, rather than once.
(#5419) Resolved issue with import_vcf force_bgz and file size checks.
(#5427) Resolved issue with Table.show and dictionary field types.
(#5468) Resolved ordering problem with Expression.show on key fields that are not the first key.
(#5492) Fixed hl.agg.collect crashing when collecting float32 values.
(#5525) Fixed hl.trio_matrix crashing when complete_trios is False.

Version 0.2.10

Released 2019-02-15

New features

(#5272) Added a new ‘delimiter’ option to Table.export.
(#5251) Add utility aliases to hl.plot for output_notebook and show.
(#5249) Add histogram2d function to hl.plot module.
(#5247) Expose MatrixTable.localize_entries method for converting to a Table with an entries array.
(#5300) Add new filter and find_replace arguments to hl.import_table and hl.import_vcf to apply regex and substitutions to text input.

Performance improvements

(#5298) Reduce size of exported VCF files by exporting missing genotypes without trailing fields.

Bug fixes

(#5306) Fix ReferenceGenome.add_sequence causing a crash.
(#5268) Fix Table.export writing a file called ‘None’ in the current directory.
(#5265) Fix hl.get_reference raising an exception when called before hl.init().
(#5250) Fix crash in pc_relate when called on a MatrixTable field other than ‘GT’.
(#5278) Fix crash in Table.order_by when sorting by fields whose names are not valid Python identifiers.
(#5294) Fix crash in hl.trio_matrix when sample IDs are missing.
(#5295) Fix crash in Table.index related to key field incompatibilities.

Version 0.2.9

Released 2019-01-30

New features

(#5149) Added bitwise transformation functions: hl.bit_{and, or, xor, not, lshift, rshift}.
(#5154) Added hl.rbind function, which is similar to hl.bind but expects a function as the last argument instead of the first.

Performance improvements

(#5107) Hail’s Python interface generates tighter intermediate code, which should result in moderate performance improvements in many pipelines.
(#5172) Fix unintentional performance deoptimization related to Table.show introduced in 0.2.8.
(#5078) Improve performance of hl.ld_prune by up to 30x.

Bug fixes

(#5144) Fix crash caused by hl.index_bgen (since 0.2.7)
(#5177) Fix bug causing Table.repartition(n, shuffle=True) to fail to increase partitioning for unkeyed tables.
(#5173) Fix bug causing Table.show to throw an error when the table is empty (since 0.2.8).
(#5210) Fix bug causing Table.show to always print types, regardless of types argument (since 0.2.8).
(#5211) Fix bug causing MatrixTable.make_table to unintentionally discard non-key row fields (since 0.2.8).

Version 0.2.8

Released 2019-01-15

New features

(#5072) Added multi-phenotype option to hl.logistic_regression_rows
(#5077) Added support for importing VCF floating-point FORMAT fields as float32 as well as float64.

Performance improvements

(#5068) Improved optimization of MatrixTable.count_cols.
(#5131) Fixed performance bug related to hl.literal on large values with missingness

Bug fixes

(#5088) Fixed name separator in MatrixTable.make_table.
(#5104) Fixed optimizer bug related to experimental functionality.
(#5122) Fixed error constructing Table or MatrixTable objects with fields with certain character patterns like $.

Version 0.2.7

Released 2019-01-03

New features

(#5046)(experimental) Added option to BlockMatrix.export_rectangles to export as NumPy-compatible binary.

Performance improvements

(#5050) Short-circuit iteration in logistic_regression_rows and poisson_regression_rows if NaNs appear.

Version 0.2.6

Released 2018-12-17

New features

(#4962) Expanded comparison operators (==, !=, <, <=, >, >=) to support expressions of every type.
(#4927) Expanded functionality of Table.order_by to support ordering by arbitrary expressions, instead of just top-level fields.
(#4926) Expanded default GRCh38 contig recoding behavior in import_plink.

Performance improvements

(#4952) Resolved lingering issues related to (#4909).

Bug fixes

(#4941) Fixed variable scoping error in regression methods.
(#4857) Fixed bug in maximal_independent_set appearing when nodes were named something other than i and j.
(#4932) Fixed possible error in export_plink related to tolerance of writer process failure.
(#4920) Fixed bad error message in Table.order_by.

Version 0.2.5

Released 2018-12-07

New features

(#4845) The or_error method in hl.case and hl.switch statements now takes a string expression rather than a string literal, allowing more informative messages for errors and assertions.
(#4865) We use this new or_error functionality in methods that require biallelic variants to include an offending variant in the error message.
(#4820) Added hl.reversed for reversing arrays and strings.
(#4895) Added include_strand option to the hl.liftover function.

Performance improvements

(#4907)(#4911) Addressed one aspect of bad scaling in enormous literal values (triggered by a list of 300,000 sample IDs) related to logging.
(#4909)(#4914) Fixed a check in Table/MatrixTable initialization that scaled O(n^2) with the total number of fields.

Bug fixes

(#4754)(#4799) Fixed optimizer assertion errors related to certain types of pipelines using group_rows_by.
(#4888) Fixed assertion error in BlockMatrix.sum.
(#4871) Fixed possible error in locally sorting nested collections.
(#4889) Fixed break in compatibility with extremely old MatrixTable/Table files.
(#4527)(#4761) Fixed optimizer assertion error sometimes encountered with hl.split_multi[_hts].

Version 0.2.4: Beginning of history!

We didn’t start manually curating information about user-facing changes until version 0.2.4.

The full commit history is available here.