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V0.2.98 upstream3 #222

Merged
merged 25 commits into from
Sep 14, 2022
Merged

V0.2.98 upstream3 #222

merged 25 commits into from
Sep 14, 2022

Commits on Aug 31, 2022

  1. Bump urllib3 from 1.26.9 to 1.26.12 in /hail/python (hail-is#12140)

    Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.9 to 1.26.12.
    - [Release notes](https://github.com/urllib3/urllib3/releases)
    - [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
    - [Commits](urllib3/urllib3@1.26.9...1.26.12)
    
    ---
    updated-dependencies:
    - dependency-name: urllib3
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    
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    dependabot[bot] authored Aug 31, 2022
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  2. [auth] Cache user sessions in memory (hail-is#12122)

    * [auth] Cache user sessions in memory
    
    * fix
    
    * change name
    
    * turn auth decorators into methods on an auth client
    
    * lint
    daniel-goldstein authored Aug 31, 2022
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  4. [query] Table.write_many (hail-is#12091)

    * [query] Table.write_many
    
    CHANGELOG: Teach `Table` to `write_many`, which writes one table per provided field.
    
    * fix
    
    * merge conflict
    danking authored Aug 31, 2022
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  6. Bump importlib-resources from 5.7.1 to 5.9.0 in /hail/python/dev (hai…

    …l-is#12141)
    
    Bumps [importlib-resources](https://github.com/python/importlib_resources) from 5.7.1 to 5.9.0.
    - [Release notes](https://github.com/python/importlib_resources/releases)
    - [Changelog](https://github.com/python/importlib_resources/blob/main/CHANGES.rst)
    - [Commits](python/importlib_resources@v5.7.1...v5.9.0)
    
    ---
    updated-dependencies:
    - dependency-name: importlib-resources
      dependency-type: direct:production
      update-type: version-update:semver-minor
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    
    Signed-off-by: dependabot[bot] <support@github.com>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    dependabot[bot] authored Aug 31, 2022
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Commits on Sep 1, 2022

  1. [batch] Do not retry pulling images from invalid repositories (hail-i…

    …s#12152)
    
    * [batch] Do not retry pulling images from invalid repositories
    
    * better bad repository name
    daniel-goldstein authored Sep 1, 2022
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Commits on Sep 6, 2022

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Commits on Sep 7, 2022

  1. Bump filelock from 3.7.1 to 3.8.0 in /hail/python (hail-is#12157)

    Bumps [filelock](https://github.com/tox-dev/py-filelock) from 3.7.1 to 3.8.0.
    - [Release notes](https://github.com/tox-dev/py-filelock/releases)
    - [Changelog](https://github.com/tox-dev/py-filelock/blob/main/docs/changelog.rst)
    - [Commits](tox-dev/filelock@3.7.1...3.8.0)
    
    ---
    updated-dependencies:
    - dependency-name: filelock
      dependency-type: direct:development
      update-type: version-update:semver-minor
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    
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    dependabot[bot] authored Sep 7, 2022
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  2. [ggplot] make identity color scale continuous (hail-is#12089)

    * [ggplot] make identity color scale continuous
    
    * fix
    patrick-schultz authored Sep 7, 2022
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Commits on Sep 9, 2022

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  3. Bump types-python-dateutil from 2.8.17 to 2.8.19 in /hail/python/dev (h…

    …ail-is#12172)
    
    Bumps [types-python-dateutil](https://github.com/python/typeshed) from 2.8.17 to 2.8.19.
    - [Release notes](https://github.com/python/typeshed/releases)
    - [Commits](https://github.com/python/typeshed/commits)
    
    ---
    updated-dependencies:
    - dependency-name: types-python-dateutil
      dependency-type: direct:production
      update-type: version-update:semver-patch
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    
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    dependabot[bot] authored Sep 9, 2022
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Commits on Sep 10, 2022

  1. [query] Fix handle_randomness for collect_cols_by_key (hail-is#12162)

    CHANGELOG: Fixed crash in `collect_cols_by_key` with preceding random functions
    tpoterba authored Sep 10, 2022
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  2. [query] Stage IndexReader (hail-is#12159)

    * [query] Stage IndexReader
    
    * support matrix tables
    
    * delete the nonsense, woohoo!
    
    * oops
    
    * fixes
    
    * clean up
    
    * clean up
    
    * fixes for upper
    
    * support empty partitions
    
    * fixup
    
    * address
    tpoterba authored Sep 10, 2022
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Commits on Sep 12, 2022

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Commits on Sep 13, 2022

  1. [query] implement bit_count operation (hail-is#12168)

    * [query] implement bit_count operation
    
    * fix test compilation errors
    
    * separate handling for bitcount in interpreter
    
    * pr feedback
    
    * typo
    iris-garden authored Sep 13, 2022
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  3. [query] Fix lowering of aggs to preserve free variables in init args (h…

    …ail-is#12092)
    
    * [query] Fix lowering of aggs to preserve free variables in init args
    
    CHANGELOG: Fixed compiler bug: "NoSuchElementException: Ref with name __iruid_X could not be resolved in env"
    
    This is a bad change to a worse problem. The right solution is to redesign the IR
    so that implicit init eval scopes don't exist -- but the right solution is hard to justify
    going off to do right now.
    
    This change patches the Extract.scala lowering logic to track the variables bound inside a
    lowered IR and find the highest node that provides all necessary free variables. This change
    still makes assumptions about the structure of the IR -- namely, it is still invalid to write
    an IR like:
    
    ```
    MakeTuple
      Let
        initBinding1
        <something>
        ApplyAggOp with ref to initBinding1
      Let
        initBinding2
        <something2>
        ApplyAggOp with ref to initbinding2
    ```
    
    However, this fix resolves the case where init args reference a high single binding chain, as
    in the test added.
    
    * no sharing
    
    * move requiredness
    
    * fix
    
    * fails
    tpoterba authored Sep 13, 2022
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  4. Bump black from 22.3.0 to 22.8.0 in /hail/python/dev (hail-is#12174)

    Bumps [black](https://github.com/psf/black) from 22.3.0 to 22.8.0.
    - [Release notes](https://github.com/psf/black/releases)
    - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
    - [Commits](psf/black@22.3.0...22.8.0)
    
    ---
    updated-dependencies:
    - dependency-name: black
      dependency-type: direct:production
      update-type: version-update:semver-minor
    ...
    
    Signed-off-by: dependabot[bot] <support@github.com>
    
    Signed-off-by: dependabot[bot] <support@github.com>
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    dependabot[bot] authored Sep 13, 2022
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