merge #3
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merge #3
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* fix notebook error message if we couldn't connect to the notebook, but it is there, don't say the notebook wasn't found. * refine
* [hail] Do not cache in describe. Holdover from the initial design of something that could aggregate. This just forces evaluation in a bad way. * bump! * bump!
* worksohp callout * wip * faq * cleanup * bump * rename to resources * no new * fix * update * Update resources.html
* add worker service to router deploy * bump
* [batch2] slim down worker image * switch tests to use ubunutu 18.04 * fixes * add curl and gcloud to docker image * get gcloud out of image * add gsutil * actually change the worker image * bump
* NDArrayRef works, passing tests * Caching indices * Testing index out of bounds error * Missingness checks across indices * bump! * bump! * bump!
* [batch2] fix delete_batch2_instances * bump * get rid of bad flag * bump
* worksohp callout * wip * faq * cleanup * bump * rename to resources * no new * fix * update * Update resources.html * workshp header context * fix whitespace * fix whitespace
* print lambda-GC on the plot * add p value to hover Fixes #5567
* [hail] serialize and deserialize SortOrder * bump
* [hail] simplify region value fromBytes code * bump * bump
* do not require a hail context if there are no literals * bump
* [hail] simplify buffer spec parsing * undo removal * remove non-extant parsers * a few more implicits * fix * fix * bump
* [hail] thread execute context through RVD * fixes * fix * fix tests
* improve retry retry in get_userinfo retry on ClientOSError (client connection error) on timeout log errno to diagnose future failures * configure logging in all batch2 test files * add observed exceptions * fix * fix import * fix imports * fix * fix imports * batch2: log info and above in tests
* increase timeout to 2 min * increase timeout to 2 min * aiohttp client timeout * revert kubernetes timeout * log * kube timeout * remove function names * not error * fix * fix * revert
* fixed location of batch2 templates front_end loads them from batch2.front_end * add ui tests * fix typo * bump * fix * bump * fix * fix * fix, debugging * finally? * remove ui tests, cleanup * fix
* [misc] add quantiles to scale test * min/max in quantiles * Update scale-test.py
* worksohp callout * wip * faq * cleanup * bump * rename to resources * no new * fix * update * Update resources.html * workshp header context * fix whitespace * fix whitespace * add resource link * bump * bump * fixes * fix * support attributes * Update rtd_modifications.css
* remove /batch endpoint include_jobs param * fixes * fix * fixes * fix * addressed comments
* optional slash * fix fix better fix * better * wip * gf_server_domain seems unused, reverting. fix bad merge * fix * fix * bump * bump
* Fixed show with no row fields, added a test * Handling empty better
* I want to use _nd module everywhere, planning on nixing _ndarray altogether * Missed 2
* Hail Tables cheatsheet pdf * Addressed Tim's comment, added powerpoint as well * bump!
Add 10 randomly generated VCFs as testing resource
I was going to move it to Python, but it's already there!
* remove legacy job status status is just status returned by worker unify job /log and /status into single job page (batch2 and ci) * fixes * fixes * fix * fix * fix * fixes * fix * fix * fix * fix * address comments * add missing file * fix * fix * fixes * fix unnecessary 404 * fix * fix * more tweaks * fix
* only run input/output if necessary * fix, logging * fix * fixes * fix get log * fix * fix
Delete unnecessary infrastructure.
…re. (#7535) * [hail] Refactor LowerTableIR to use new LoweringPipeline infrastructure. Delete local backend. * fix
* adding visualize_missingness plot function * add to docs
* [testing] Move ExportVCFSuite to Python * add partitions args
* [hail] MT.show() shouldn't use key_by Noticed this while poking around the code for other reasons. This could cause ordering problems. * bump!
* [hail] Thread ExecuteContext through Compile * fix optimize type rules * Fix whitespace * Fix whitespace * bump!
* [hail] Log globs * bump!
* [testing] Move VSMSuite to Python, delete most of `MatrixTable` * bump!
* [ci] expand service account namespace * fix
…ting for scalars to Simplify pass (#7566) * wip * [hail] clean up BlockMatrixMap IRs, delegate broadcasting logic for scalars to Simplify pass * fix bugs * lower before execute * fix broadcase matching in Map2 * more fixes * more fixes, remove ** test * rewrite ** as _apply_map instead of map2, since we don't support ** on two matrices * fixes * more fix * bump
* directly create create_accounts batch job instead of indirectly deploying pod * fix * fix * bump
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