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Branch: master
Commits on Jul 18, 2019
  1. Fixed _dump_partitions to correctly transcribe includes* flags (#6676)

    tmwong2003 authored and danking committed Jul 18, 2019
    * Fixed _dump_partitions to correctly transcribe the includes* flag in intervals
    
    * Made dummy commit to trigger CI testing
  2. Extract staged aggregators (#6653)

    catoverdrive authored and danking committed Jul 18, 2019
    * implement Extract and new TableMapRows scan
    
    * remove benchmarking test
    
    * OOPS
    
    * address comments
  3. [notebook] fix bugs. (#6684)

    danking committed Jul 18, 2019
    * fixes
    
    * fix again
  4. Added logging line for ci error (#6685)

    johnc1231 committed Jul 18, 2019
    Overriding CI since it's down.
  5. [batch][ci] tolerate preemptibles (#6664)

    danking committed Jul 18, 2019
    * [batch][ci] tolerate preemptibles
    
    * Update deployment.yaml
    
    * Update deployment.yaml
    
    * fix indentation
  6. No more JVM for URI parsing (#6672)

    johnc1231 authored and danking committed Jul 18, 2019
    * No more JVM for URI parsing
    
    * bump!
  7. [hail][wip] Local ld prune ptype (#6425)

    akotlar authored and danking committed Jul 18, 2019
    * first pass
    
    * add TableValue constructor that takes PType, and make IBD use that
    
    * table constructors
    
    * LoadPlink, use ptypes
    
    * wip
    
    * fix signature
    
    * tests not passing
    
    * wip
    
    * fix
    
    * fix
    
    * reduce # of lines in diff, use tableType.canonicalPType
    
    * fix
    
    * bump
    
    * bump
  8. [notebook] mitigate CVE-2019-11245 (#6678)

    danking committed Jul 18, 2019
    CVE-2019-11245 is a vulnerability in k8s that causes some (all?)
    containers without a runAsUser configuration to run
    as user id 0, i.e. root. Jupyter refuses to start as root.
    This change enables Jupyter to start successfully.
  9. [hail] (PTypes) Extend function registry to support returned PTypes (#…

    tpoterba authored and danking committed Jul 18, 2019
    …6650)
    
    * [hail] (PTypes) Extend function registry to support returned PTypes
    
    * address
  10. List of references (#6671)

    gsarma authored and danking committed Jul 18, 2019
    * 1) New page with list of references
    2) Link from index.md and README.md
    
    * bump
  11. dev deploy dont wait for batch (#6670)

    johnc1231 authored and danking committed Jul 18, 2019
    * Don't wait for batch to run
    
    * Better printing for users
    
    * Quick change just in case it's possible for batch_id = 0
    
    * Debugging information and Jackie's comments
    
    * bump!
    
    * bump!
  12. [hail] Parameterize check on union_rows. Don't check in `split_multi` (

    tpoterba authored and danking committed Jul 18, 2019
    …#6669)
    
    * [hail] Parameterize check on union_rows. Don't check in `split_multi`
    
    When I timed the specific code block we hid behind the flag, it took
    about 1.5 seconds on the benchmark dataset.
    
    * bump!
    
    * bump!
Commits on Jul 17, 2019
  1. [hail] (PTypes) Lift ComparisonOp to use PTypes (#6655)

    tpoterba authored and danking committed Jul 17, 2019
    * [hail] (PTypes) Lift ComparisonOp to use PTypes
    
    * fix
    
    * bump!
  2. rewrite staged aggregator interface (#6652)

    catoverdrive authored and danking committed Jul 17, 2019
    * rewrite staged aggregator interface
    
    * fix test
    
    * unserialize -> deserialize
    
    * more changes
    
    * fix test
    
    * add prints
    
    * fix region test
    
    * bump
    
    * bump
  3. [notebook] Prepare for July 18 workshop (#6668)

    tpoterba authored and danking committed Jul 17, 2019
    * [notebook] Prepare for July 18 workshop
    
    * fix?
    
    * bump
    
    * bump
  4. add worker-image for notebook (#6667)

    akotlar authored and danking committed Jul 17, 2019
  5. Scorecard Readiness Probe (#6661)

    johnc1231 authored and danking committed Jul 17, 2019
    * Scorecard now has readiness probe, which will prevent logging of an error when requests start to rollover from old scorecard on redeploy
    
    * bump!
  6. [hail] only convert row keys into Java objects in PCA (#6666)

    iitalics authored and danking committed Jul 17, 2019
    * RVD.toUnsafeRows
    
    * call Annotation.copy only for the row keys in PCA collectRowKeys()
  7. Dev Deploy profiles live on client side (#6660)

    johnc1231 authored and danking committed Jul 17, 2019
    * Sending the profile along so that it can be changed during development
    
    * Removed old import os
Commits on Jul 16, 2019
  1. allow different region block sizes (#6606)

    catoverdrive authored and danking committed Jul 16, 2019
    * allow regions to have different-sized blocks
    
    * address comments
    
    * fixes
    
    * make constructor private
    
    * fix tests
    
    * refactor test
  2. [deploy] Set object holds on production artifacts (#6590)

    tpoterba authored and danking committed Jul 16, 2019
    * [deploy] Set object holds on production artifacts
    
    * bump!
    
    * bump!
Commits on Jul 15, 2019
  1. [wip] make IBD into a MatrixToTableFunction (#6639)

    iitalics authored and danking committed Jul 15, 2019
    * refactor: lift some logic from IBD.pyApply into IBD.execute method
    
    * phasing out usage of IBD.pyApply on scala side
    
    * python: generate MatrixToTableApply IR in 'identity_by_descent'
    
    * python: MatrixToTableApply.compute_type() for IBD
    
    * scala: add IBD to RelationFunctions.formats (for deserialization)
    
    * scala: delete IBD.pyApply
    
    * python: remove persist() call
  2. Dev Deploy Auth Correction (#6645)

    johnc1231 authored and danking committed Jul 15, 2019
    * WIP
    
    * Returning a response for successful hailctl dev deploy
    
    * Need to await for json()
    
    * Removed extra space
  3. set namespace on admin account (#6638)

    cseed authored and danking committed Jul 15, 2019
  4. Define staged aggregators in Emit (#6535)

    patrick-schultz authored and danking committed Jul 15, 2019
    * extract staged aggs
    
    * fix
    
    * fix
    
    * address comments
    
    * implement emits for staged aggs
    
    * fix
    
    * fixes
    
    * fix
    
    * fix
    
    * fix prev_nonnull
    
    * remove extraction
    
    * write a tests and fix bugs
    
    * cleanup
    
    * more cleanup
    
    * fixes
    
    * bump
    
    * fixes
    
    * bump
    
    * bump
    
    * fix merge
  5. [hail] fix BlockInputBuffer seek assertion (#6633)

    chrisvittal authored and danking committed Jul 15, 2019
    * fix BlockInputBuffer seek assertion
    
    It is currently possible to write a blocked index where the virtual file
    offset is exactly ((REAL_FILE_OFFSET << 16) | BLOCK_SIZE). This is a bug
    and leads to assertion errors when trying to seek to the appropriate row
    because `off == end` for that index.
    
    * Add offset check to `indexOffset` for BlockingOutputBuffer
  6. [batch] fix delete (#6599)

    jigold authored and danking committed Jul 15, 2019
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