sage.repl: Replace use of SAGE_EXTCODE by importlib.resources #31306

mkoeppe · 2021-01-30T18:16:23Z

We eliminate direct reading of files from the package directories of sagelib by using importlib.resources (available since python 3.7)

git grep 'SAGE_EXTCODE' src/sage
git grep '__file__' src/sage

This will help make sagelib zip_safe (https://setuptools.readthedocs.io/en/latest/userguide/miscellaneous.html#setting-the-zip-safe-flag)

In this ticket, we take care of sage.repl, moving data needed by its doctests from SAGE_EXTCODE (= src/sage/ext_data) into the package directory. (Thus, we avoid a dependency on support for resources in namespace packages brought by Python 3.10(?) or the backport package importlib-resources, see python/importlib_resources#196)

Follow-up tickets will deal with other parts of the library. In the end, the directory src/sage/ext_data will be eliminated.

References:

CC: @tobiasdiez @fchapoton @kiwifb @dimpase @soehms @tscrim

Component: refactoring

Author: Matthias Koeppe

Branch/Commit: d925cd2

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/31306

The text was updated successfully, but these errors were encountered:

mkoeppe · 2021-12-06T02:04:11Z

Changed dependencies from #30551 to #30551, #31386

mkoeppe · 2021-12-06T02:57:41Z

Branch: u/mkoeppe/replace_use_of_sage_extcode_by_importlib_resources

mkoeppe · 2021-12-06T03:31:03Z

Commit: b2cb173

mkoeppe · 2021-12-06T03:31:03Z

Last 10 new commits:

`77c957f`	`src/doc/en/developer/packaging_sage_library.rst: Put hierarchy section one level higher`
`9375ef8`	`pkgs/sagemath-standard/tox.ini: Use SAGE_VENV or venv symlink to find wheels`
`c6fc111`	`Prettier diagram`
`7d6a44c`	`Use :mod: as markup for packages/modules`
`f83d424`	`Improve ABC example`
`817a8d0`	`src/doc/en/developer/packaging_sage_library.rst: More :mod: and :class: markup`
`b555735`	`src/doc/en/developer/packaging_sage_library.rst: Link to pypi.org and to documentation of packaging metadata`
`81e9c9a`	`Merge #32899`
`af47b5f`	`Merge #31386`
`b2cb173`	`src/sage/repl/rich_output/: Move example files here from src/sage/ext_data, use importlib.resources`

sagetrac-git · 2021-12-06T03:55:57Z

Branch pushed to git repo; I updated commit sha1. New commits:

`0f63cce`	`src/sage/repl/display/formatter.py: Replace use of SAGE_EXTCODE in doctest by importlib.resources`

sagetrac-git · 2021-12-06T03:55:57Z

Changed commit from b2cb173 to 0f63cce

mkoeppe · 2021-12-06T03:56:45Z

Author: Matthias Koeppe

mkoeppe · 2021-12-06T03:56:45Z

Changed dependencies from #30551, #31386 to #31386

sagetrac-git · 2021-12-12T18:16:57Z

Branch pushed to git repo; I updated commit sha1. New commits:

`09787af`	`Merge tag '9.5.beta8' into t/31306/replace_use_of_sage_extcode_by_importlib_resources`

sagetrac-git · 2021-12-12T18:16:57Z

Changed commit from 0f63cce to 09787af

mkoeppe · 2021-12-17T16:37:02Z

comment:13

The testsuite failures are unrelated

dimpase · 2021-12-18T00:04:01Z

comment:14

lgtm

dimpase · 2021-12-18T00:04:01Z

Reviewer: Dima Pasechnik

mkoeppe · 2021-12-18T00:57:48Z

comment:15

Thanks!

sagetrac-git · 2021-12-23T21:25:29Z

Changed commit from 09787af to 9873958

sagetrac-git · 2021-12-23T21:25:29Z

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

`9873958`	`Merge tag '9.5.beta9' into t/31306/replace_use_of_sage_extcode_by_importlib_resources`

mkoeppe · 2021-12-23T21:25:40Z

comment:17

trivial merge

sagetrac-git · 2022-01-23T01:57:22Z

Branch pushed to git repo; I updated commit sha1 and set ticket back to needs_review. New commits:

`d925cd2`	`Merge tag '9.5.rc3' into t/31306/replace_use_of_sage_extcode_by_importlib_resources`

sagetrac-git · 2022-01-23T01:57:22Z

Changed commit from 9873958 to d925cd2

mkoeppe · 2022-01-23T01:58:05Z

Changed dependencies from #31386 to none

kiwifb · 2022-01-31T08:02:28Z

comment:21

OK, Volker has started merging stuff for 9.6 including this. And I get

$ sage -t --long --random-seed=241985268132368173591124256826068888319 /usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py
too many failed tests, not using stored timings
Running doctests with ID 2022-01-31-20-37-00-111581fe.
Using --optional=pip,sage
Features to be detected: 4ti2,benzene,bliss,buckygen,conway_polynomials,csdp,database_cremona_ellcurve,database_cremona_mini_ellcurve,database_jones_numfield,database_knotinfo,dvipng,graphviz,imagemagick,jupymake,kenzo,latte_int,lrslib,mcqd,meataxe,pandoc,pdf2svg,plantri,pynormaliz,python_igraph,rubiks,sage.combinat,sage.geometry.polyhedron,sage.graphs,sage.groups,sage.plot,sage.rings.number_field,sage.rings.padics,sage.rings.real_double,sage.symbolic,sage_numerical_backends_coin,sagemath_doc_html,sphinx,tdlib
Doctesting 1 file.
sage -t --long --random-seed=241985268132368173591124256826068888319 /usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 248, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputSceneWavefront.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[15]>", line 1, in <module>
        backend.validate(dm.types.OutputSceneWavefront.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_graphics3d.py", line 354, in example
        scene_obj = OutputBuffer.from_file(filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example_wavefront_scene.obj'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 249, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputSceneCanvas3d.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[16]>", line 1, in <module>
        backend.validate(dm.types.OutputSceneCanvas3d.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_graphics3d.py", line 161, in example
        return cls(OutputBuffer.from_file(filename))
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.canvas3d'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 250, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoOgg.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[17]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoOgg.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.ogv'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 251, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoWebM.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[18]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoWebM.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.webm'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 252, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoMp4.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[19]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoMp4.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.mp4'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 253, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoFlash.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[20]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoFlash.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.flv'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 254, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoMatroska.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[21]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoMatroska.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.mkv'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 255, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoAvi.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[22]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoAvi.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.avi'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 256, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoWmv.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[23]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoWmv.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.wmv'
**********************************************************************
File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/backend_doctest.py", line 257, in sage.repl.rich_output.backend_doctest.BackendDoctest.validate
Failed example:
    backend.validate(dm.types.OutputVideoQuicktime.example())
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 694, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/usr/lib/python3.10/site-packages/sage/doctest/forker.py", line 1088, in compile_and_execute
        exec(compiled, globs)
      File "<doctest sage.repl.rich_output.backend_doctest.BackendDoctest.validate[24]>", line 1, in <module>
        backend.validate(dm.types.OutputVideoQuicktime.example())
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py", line 75, in example
        return cls(OutputBuffer.from_file(filename),
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 114, in from_file
        buf._chmod_readonly(buf._filename)
      File "/usr/lib/python3.10/site-packages/sage/repl/rich_output/buffer.py", line 146, in _chmod_readonly
        os.chmod(filename, mode)
    PermissionError: [Errno 1] Operation not permitted: '/usr/lib/python3.10/site-packages/sage/repl/rich_output/example.mov'
**********************************************************************

And it comes down to that block https://github.com/sagemath/sage-prod/blob/develop/src/sage/repl/rich_output/buffer.py#L139 - chmod is not done if the file is in the SAGE_EXTCODE folder but executed otherwise. Of course all those files have been moved out of SAGE_EXTCODE.

kiwifb · 2022-01-31T08:05:36Z

comment:22

I also have

sage -t --long --random-seed=241985268132368173591124256826068888319 /usr/lib/python3.10/site-packages/sage/repl/rich_output/output_graphics3d.py  # 25 doctests failed
sage -t --long --random-seed=241985268132368173591124256826068888319 /usr/lib/python3.10/site-packages/sage/repl/rich_output/output_video.py  # 14 doctests failed

because of the same thing. I guess it doesn't fail on user space build because you can safely chmod anything.

kiwifb · 2022-01-31T09:17:41Z

comment:23

Follow up at #33256.

dimpase · 2022-01-31T12:54:37Z

comment:24

Wow, doctesting of /usr/lib/python3.10/site-packages/sage/...

kiwifb · 2022-01-31T18:37:07Z

comment:25

Replying to @dimpase:

Wow, doctesting of /usr/lib/python3.10/site-packages/sage/...

Is it the python3.10 or the /usr/lib/ that makes you go "wow"? I can do the python3.9 flavor too if you want. I have been doctesting system installed sage and reporting from those tests for the last 10 years so I may be a bit blazé about it.

dimpase · 2022-01-31T21:12:38Z

comment:26

it's about /usr/lib

vbraun · 2022-01-31T23:31:37Z

Changed branch from u/mkoeppe/replace_use_of_sage_extcode_by_importlib_resources to d925cd2

mkoeppe added this to the sage-9.4 milestone Jan 30, 2021

mkoeppe added t: refactoring labels Jan 30, 2021

mkoeppe modified the milestones: sage-9.4, sage-9.5 Jul 19, 2021

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mkoeppe changed the title ~~Replace use of SAGE_EXTCODE by importlib.resources~~ sage.repl: Replace use of SAGE_EXTCODE by importlib.resources Dec 6, 2021

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sagetrac-git mannequin added s: needs review and removed s: positive review labels Dec 23, 2021

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mkoeppe modified the milestones: sage-9.5, sage-9.6 Jan 10, 2022

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vbraun closed this as completed in ddf44d8 Jan 31, 2022

tobiasdiez mentioned this issue Jan 7, 2023

Meta-ticket: Create upstream repositories, pip-installable packages for database packages #30914

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kiwifb mentioned this issue Feb 16, 2022

buffer.py: make files readonly only when possible #33256

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vbraun commented Jan 31, 2022

sage.repl: Replace use of SAGE_EXTCODE by importlib.resources #31306

sage.repl: Replace use of SAGE_EXTCODE by importlib.resources #31306

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