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The nightly build job failed on Tuesday (2024-07-09) #747

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github-actions bot opened this issue Jul 10, 2024 · 44 comments · Fixed by #756
Closed

The nightly build job failed on Tuesday (2024-07-09) #747

github-actions bot opened this issue Jul 10, 2024 · 44 comments · Fixed by #756
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@Shelnutt2 @ihnorton @jdblischak @awenocur @gspowley
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nightly-failure

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The nightly build job failed on Tuesday (2024-07-09) in run 9867467789
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The nightly build job failed on Wednesday (2024-07-10) in run 9867467789

@jdblischak
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Nightly failure caused by removal of dump functions in TileDB-Inc/TileDB#5026

Other nightlies are also failing for the same reason (TileDB-Inc/conda-forge-nightly-controller#108, https://github.com/jdblischak/centralized-tiledb-nightlies/issues/14)

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The nightly build job failed on Wednesday (2024-07-10) in run 9884769007

@jdblischak
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Still failing due to the dump error

@jdblischak
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Fix pending in TileDB-Inc/TileDB#5179

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The nightly build job failed on Thursday (2024-07-11) in run 9901719476

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The nightly build job failed on Friday (2024-07-12) in run 9916791171

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The nightly build job failed on Saturday (2024-07-13) in run 9924855664

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The nightly build job failed on Monday (2024-07-15) in run 9933055676

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The nightly build job failed on Tuesday (2024-07-16) in run 9950025355

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The nightly build job failed on Wednesday (2024-07-17) in run 9967445139

@jdblischak
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There is a new error now. I think it was caused by the renaming of set_buffer to set_data_buffer in TileDB-Inc/TileDB#5146

/home/runner/work/TileDB-VCF/TileDB-VCF/TileDB-VCF/libtiledbvcf/src/dataset/attribute_buffer_set.cc:705:16: error: ‘class tiledb::Query’ has no member named ‘set_buffer’
  705 |         query->set_buffer(name, buff->data<void>(), 0);
      |                ^~~~~~~~~~

@gspowley
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Yes, VCF is using deprecated APIs that are now being removed from libtiledb.

@jdblischak jdblischak mentioned this issue Jul 17, 2024
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The nightly build job failed on Wednesday (2024-07-17) in run 9984800099

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The nightly build job failed on Friday (2024-07-19) in run 10001849608

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The nightly build job failed on Friday (2024-07-19) in run 10017037575

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The nightly build job failed on Saturday (2024-07-20) in run 10025129401

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The nightly build job failed on Sunday (2024-07-21) in run 10033892381

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The nightly build job failed on Monday (2024-07-22) in run 10051950114

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The nightly build job failed on Tuesday (2024-07-23) in run 10069751383

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The nightly build job failed on Wednesday (2024-07-24) in run 10087413480

@jdblischak
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VCF is using deprecated APIs that are now being removed from libtiledb.

Is there a Shortcut Story to track this?

@gspowley
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https://app.shortcut.com/tiledb-inc/story/45536/vcf-migrate-away-from-deprecated-tiledb-c-apis

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The nightly build job failed on Thursday (2024-07-25) in run 10104974819

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The nightly build job failed on Friday (2024-07-26) in run 10120341663

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The nightly build job failed on Sunday (2024-07-28) in run 10128443495

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The nightly build job failed on Sunday (2024-07-28) in run 10137339331

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The nightly build job failed on Monday (2024-07-29) in run 10155388427

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The nightly build job failed on Tuesday (2024-07-30) in run 10173302227

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github-actions bot commented Aug 1, 2024

The nightly build job failed on Thursday (2024-08-01) in run 10191214289

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github-actions bot commented Aug 2, 2024

The nightly build job failed on Thursday (2024-08-01) in run 10209259984

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github-actions bot commented Aug 3, 2024

The nightly build job failed on Friday (2024-08-02) in run 10224770255

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github-actions bot commented Aug 4, 2024

The nightly build job failed on Saturday (2024-08-03) in run 10232985196

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github-actions bot commented Aug 5, 2024

The nightly build job failed on Sunday (2024-08-04) in run 10241833692

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github-actions bot commented Aug 6, 2024

The nightly build job failed on Monday (2024-08-05) in run 10259517615

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github-actions bot commented Aug 7, 2024

The nightly build job failed on Tuesday (2024-08-06) in run 10277377168

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github-actions bot commented Aug 7, 2024

The nightly build job failed on Wednesday (2024-08-07) in run 10277377168

@gspowley
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gspowley commented Aug 7, 2024

The libtiledb deprecated APIs are resolved. The latest failure happens when building tiledb-py from source.

@jdblischak have you seen this error in other builds?

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github-actions bot commented Aug 8, 2024

The nightly build job failed on Thursday (2024-08-08) in run 10295190928

@jdblischak
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The libtiledb deprecated APIs are resolved.

Awesome! Thanks @awenocur!

xref: #753, #755

The latest failure happens when building tiledb-py from source. have you seen this error in other builds?

@gspowley Yes, this is a known issue, but there is a workaround. I'll investigate. Also, TileDB-Py has migrated to using scikit-build-core, so the nightly script needs updating anyways.

@jdblischak jdblischak mentioned this issue Aug 8, 2024
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@dudoslav
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dudoslav commented Aug 8, 2024

AFAIK this kind of issue happens when you run any code that imports tiledb when you have a folder tiledb in you current directory. I don't understand why it started happening now, but it was an issue even before scikit-build-core rework.

 Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/runner/work/TileDB-VCF/TileDB-VCF/TileDB-Py/tiledb/__init__.py", line 22, in <module>
    from .array_schema import ArraySchema
  File "/Users/runner/work/TileDB-VCF/TileDB-VCF/TileDB-Py/tiledb/array_schema.py", line 10, in <module>
    from .attribute import Attr
  File "/Users/runner/work/TileDB-VCF/TileDB-VCF/TileDB-Py/tiledb/attribute.py", line 9, in <module>
    from .ctx import Ctx, CtxMixin
  File "/Users/runner/work/TileDB-VCF/TileDB-VCF/TileDB-Py/tiledb/ctx.py", line 16, in <module>
    class Config(lt.Config):
AttributeError: module 'tiledb.cc' has no attribute 'Config'

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github-actions bot commented Aug 9, 2024

The nightly build job failed on Thursday (2024-08-08) in run 10312916306

@jdblischak
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AFAIK this kind of issue happens when you run any code that imports tiledb when you have a folder tiledb in you current directory.

@dudoslav thanks! I keep running into this again and again

I don't understand why it started happening now, but it was an issue even before scikit-build-core rework.

Previously I had been using python setup.py develop, which performs an editable install. When I switched to scikit-build-core, I decided to not do an editable install, so that is why the error started happening now.

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The nightly build job failed on Friday (2024-08-09) in run 10328445394

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@Shelnutt2 Shelnutt2

@ihnorton ihnorton

@jdblischak jdblischak

@awenocur awenocur

@gspowley gspowley

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Migrate TileDB-Py to scikit-build-core and don't check for deprecations jdblischak/TileDB-VCF
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@Shelnutt2 @ihnorton @jdblischak @dudoslav @awenocur @gspowley