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.

Change Log

Version 0.2.130

  • (#14425) A job’s ‘always run’ state is rendered in the Job and Batch pages. This makes it easier to understand why a job is queued to run when others have failed or been cancelled.

  • (#14437) The billing page now reports users’ spend on the batch service.

Version 0.2.128

  • (#14224) hb.Batch now accepts a default_regions argument which is the default for all jobs in the Batch.

Version 0.2.124

  • (#13681) Fix hailctl batch init and hailctl auth login for new users who have never set up a configuration before.

Version 0.2.123

  • (#13643) Python jobs in Hail Batch that use the default image now support all supported python versions and include the hail python package.

  • (#13614) Fixed a bug that broke the LocalBackend when run inside a Jupyter notebook.

  • (#13200) hailtop.batch will now raise an error by default if a pipeline attempts to read or write files from or two cold storage buckets in GCP.

Version 0.2.122

  • (#13565) Users can now use VEP images from the hailgenetics DockerHub in Hail Batch.

Version 0.2.121

Version 0.2.117

  • (#13007) Memory and storage request strings may now be optionally terminated with a B for bytes.

  • (#13051) Azure Blob Storage https URLs are now supported.

Version 0.2.115

  • (#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.

  • (#12918) Fixed a combinatorial explosion in cancellation calculation in the LocalBackend

  • (#12917) ABS blob URIs in the form of https://<ACCOUNT_NAME><CONTAINER_NAME>/<PATH> are now supported when running in Azure. The hail-az scheme for referencing ABS blobs is now deprecated and will be removed in a future release.

Version 0.2.114

  • (#12780) PythonJobs now handle arguments with resources nested inside dicts and lists.

  • (#12900) Reading data from public blobs is now supported in Azure.

Version 0.2.113

  • (#12780) The LocalBackend now supports always_run jobs. The LocalBackend will no longer immediately error when a job fails, rather now aligns with the ServiceBackend in running all jobs whose parents have succeeded.

  • (#12845) The LocalBackend now sets the working directory for dockerized jobs to the root directory instead of the temp directory. This behavior now matches ServiceBackend jobs.

Version 0.2.111

  • (#12530) Added the ability to update an existing batch with additional jobs by calling more than once. The method Batch.from_batch_id() can be used to construct a Batch from a previously submitted batch.

Version 0.2.110

  • (#12734) now immediately errors when supplied arguments are incompatible with the called function instead of erroring only when the job is run.

  • (#12726) PythonJob now supports intermediate file resources the same as BashJob.

  • (#12684) PythonJob now correctly uses the default region when a specific region for the job is not given.

Version 0.2.103

  • Added a new method Job.regions() as well as a configurable parameter to the ServiceBackend to specify which cloud regions a job can run in. The default value is a job can run in any available region.

Version 0.2.89

  • Support passing an authorization token to the ServiceBackend.

Version 0.2.79

  • The bucket parameter in the ServiceBackend has been deprecated. Use remote_tmpdir instead.

Version 0.2.75

  • Fixed a bug introduced in 0.2.74 where large commands were not interpolated correctly

  • Made resource files be represented as an explicit path in the command rather than using environment variables

  • Fixed Backend.close to be idempotent

  • Fixed BatchPoolExecutor to always cancel all batches on errors

Version 0.2.74

  • Large job commands are now written to GCS to avoid Linux argument length and number limitations.

Version 0.2.72

  • Made failed Python Jobs have non-zero exit codes.

Version 0.2.71

  • Added the ability to set values for Job.cpu, Job.memory,, and Job.timeout to None

Version 0.2.70

  • Made submitting PythonJob faster when using the ServiceBackend

Version 0.2.69

  • Added the option to specify either remote_tmpdir or bucket when using the ServiceBackend

Version 0.2.68

  • Fixed copying a directory from GCS when using the LocalBackend

  • Fixed writing files to GCS when the bucket name starts with a “g” or an “s”

  • Fixed the error “Argument list too long” when using the LocalBackend

  • Fixed an error where memory is set to None when using the LocalBackend

Version 0.2.66

  • Removed the need for the project argument in Batch() unless you are creating a PythonJob

  • Set the default for Job.memory to be ‘standard’

  • Added the cancel_after_n_failures option to Batch()

  • Fixed executing a job with Job.memory set to ‘lowmem’, ‘standard’, and ‘highmem’ when using the LocalBackend

  • Fixed executing a PythonJob when using the LocalBackend

Version 0.2.65

  • Added PythonJob

  • Added new Job.memory inputs lowmem, standard, and highmem corresponding to ~1Gi/core, ~4Gi/core, and ~7Gi/core respectively.

  • is now interpreted as the desired extra storage mounted at /io in addition to the default root filesystem / when using the ServiceBackend. The root filesystem is allocated 5Gi for all jobs except 1.25Gi for 0.25 core jobs and 2.5Gi for 0.5 core jobs.

  • Changed how we bill for storage when using the ServiceBackend by decoupling storage requests from CPU and memory requests.

  • Added new worker types when using the ServiceBackend and automatically select the cheapest worker type based on a job’s CPU and memory requests.

Version 0.2.58

  • Added concatenate and plink_merge functions that use tree aggregation when merging.

  • BatchPoolExecutor now raises an informative error message for a variety of “system” errors, such as missing container images.

Version 0.2.56

  • Fix succeeding when intermediate command fails

Version 0.2.55

  • Attempts are now sorted by attempt time in the Batch Service UI.

Version 0.2.53

  • Implement and document BatchPoolExecutor.

Version 0.2.50

  • Add requester_pays_project as a new parameter on batches.

Version 0.2.43

  • Add support for a user-specified, at-most-once HTTP POST callback when a Batch completes.

Version 0.2.42

  • Fixed the documentation for job memory and storage requests to have default units in bytes.