Remove src/sage/init.py #34187

mkoeppe · 2022-07-15T14:25:03Z

Follow-up from #33011.

Because of the complication described in #33011, we not only remove the file from the source tree but also remove it from site-packages before building sagelib.

Follow-up:

make sagemath-standard, sage-setup depend on sagemath-environment

Depends on #33011

CC: @kwankyu @videlec

Component: refactoring

Author: Matthias Koeppe

Branch: a77b971

Reviewer: Kwankyu Lee

Issue created by migration from https://trac.sagemath.org/ticket/34187

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

mkoeppe · 2022-07-15T14:27:38Z

Dependencies: #33011

kwankyu · 2022-07-15T15:11:24Z

comment:2

If I remove __init__.py from src/sage and pkgs/sagemath-standard/build/lib.macosx-12-x86_64-cpython-39/sage, then sage is built without problem, but doctest fails. Is this expected?

mkoeppe · 2022-07-15T15:37:20Z

Branch: u/mkoeppe/remove_src_sage___init___py

mkoeppe · 2022-07-15T16:10:35Z

Commit: f447a11

mkoeppe · 2022-07-15T16:10:35Z

comment:4

I'm getting

sage -t --random-seed=29572225487268684535188462271558972615 src/sage/misc/sageinspect.py  # 1 doctest failed
sage -t --random-seed=29572225487268684535188462271558972615 src/sage_setup/find.py  # 13 doctests failed
sage -t --random-seed=29572225487268684535188462271558972615 src/sage_setup/clean.py  # 4 doctests failed
sage -t --random-seed=29572225487268684535188462271558972615 src/sage/misc/edit_module.py  # 1 doctest failed

Last 10 new commits:

`1326e17`	`src/sage/numerical/__init__.py: Remove`
`5aebcf3`	`src/sage_docbuild/builders.py: Handle namespace packages`
`bba5284`	`src/sage_setup/find.py: Update doctest output`
`56e9123`	`Merge #28925`
`6a76779`	`Merge #28925`
`bd185b5`	`Merge tag '9.7.beta5' into t/33011/remove___init___py_files_for_packages_designated_to_be_namespace_packages`
`39aa2f1`	`src/sage_setup/command/sage_install.py (sage_clean): Clean __init__.py when installed package was ordinary, source package is namespace`
`d3bdb46`	`Merge #33011`
`7336e9d`	`build/pkgs/sagelib/spkg-install: Remove installed sage/__init__.py`
`f447a11`	`src/sage/__init__.py: Remove`

mkoeppe · 2022-07-15T16:17:08Z

comment:5

> /Users/mkoeppe/s/sage/sage-rebasing/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/sage_setup/find.py(278)_cythonized_dir()
    276         src_dir = Path(src_dir)
    277         sage = import_module('sage')
--> 278         d = Path(sage.__file__).resolve().parent.parent
    279         editable_install = d == src_dir.resolve()
    280     if editable_install:

this use of sage.__file__ now needs to be changed

sagetrac-git · 2022-07-15T16:29:21Z

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

`01f9143`	`src/sage_setup: Fix for namespace package sage`

sagetrac-git · 2022-07-15T16:29:21Z

Changed commit from f447a11 to 01f9143

sagetrac-git · 2022-07-15T16:34:35Z

Changed commit from 01f9143 to 9627219

sagetrac-git · 2022-07-15T16:34:35Z

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

`9627219`	`src/sage/misc/edit_module.py: Update doctest`

sagetrac-git · 2022-07-15T16:39:58Z

Changed commit from 9627219 to e884c9e

sagetrac-git · 2022-07-15T16:39:58Z

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

`e884c9e`	`src/sage/misc/sageinspect.py: Update doctest`

mkoeppe · 2022-07-15T16:40:18Z

Author: Matthias Koeppe

kwankyu · 2022-07-15T22:38:02Z

comment:10

Perhaps we have to respect the deprecation period of isfunction() defined in sage and deprecated by #32479. It ends after two months from now.

sagetrac-git · 2022-07-16T15:14:50Z

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

`7a0ff3f`	`src/sage/all.py: Restore sage.isfunction as a LazyImport`

sagetrac-git · 2022-07-16T15:14:50Z

Changed commit from e884c9e to 7a0ff3f

kwankyu · 2022-07-18T11:08:55Z

comment:14

Sorry for pointing to a minor thing, but the deprecation message is somewhat misleading as the function in sage.misc.sageinspect is is_function_or_cython_function.

sage: isfunction(f)
<ipython-input-3-631f9d828a9a>:1: DeprecationWarning: 
Importing isfunction from here is deprecated. If you need to use it, please import
 it directly from sage.misc.sageinspect
See https://trac.sagemath.org/32479 for details.
  isfunction(f)
True
sage: from sage.misc.sageinspect import isfunction
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-4-53c0fed64cdc> in <module>
----> 1 from sage.misc.sageinspect import isfunction

ImportError: cannot import name 'isfunction' from 'sage.misc.sageinspect' (/Users/kwankyu/GitHub/sage-temp/local/var/lib/sage/venv-python3.9/lib/python3.9/site-packages/sage/misc/sageinspect.py)

kwankyu · 2022-07-18T11:17:43Z

comment:15

Perhaps moving isfunction in sage.__init__.py to sage.all is a solution?

sagetrac-git · 2022-07-18T17:31:23Z

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

`dc2ddb5`	`src/sage/misc/lazy_import.pyx: Improve deprecation message when as_ is in use`

sagetrac-git · 2022-07-18T17:31:23Z

Changed commit from 7a0ff3f to dc2ddb5

sagetrac-git · 2022-07-18T17:36:35Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`adb89ff`	`src/sage/misc/lazy_import.pyx: Improve deprecation message when as_ is in use`

sagetrac-git · 2022-07-18T17:36:35Z

Changed commit from dc2ddb5 to adb89ff

mkoeppe · 2022-07-18T17:37:45Z

comment:18

I've implemented a more general solution:

sage: from sage import isfunction
sage: isfunction
/Users/mkoeppe/s/sage/sage-rebasing/worktree-gcc11/local/var/lib/sage/venv-python3.8/lib/python3.8/site-packages/sage/repl/display/fancy_repr.py:272: DeprecationWarning: 
Importing isfunction from here is deprecated; please use "from sage.misc.sageinspect import is_function_or_cython_function as isfunction" instead.
See https://trac.sagemath.org/32479 for details.
  output = repr(obj)
<function is_function_or_cython_function at 0x10f957ee0>

kwankyu · 2022-07-18T22:22:40Z

comment:19

That is a right solution. Thanks.

As a side remark, it seems to me that the lazy_import with deprecation capability is misnamed since "lazy import" itself has nothing to do with deprecation. Perhaps LazyImport object can just have a hook to a function, which is called when import happens, and we may have deprecated_import that issues the deprecation warning when import happens. Thus we have deprecated_import separate from the plain lazy_import.

mkoeppe · 2022-07-18T22:49:01Z

comment:20

I don't know, I think it's just an extra feature of lazy_import that is activated by a keyword. I don't see anything wrong with that

kwankyu · 2022-07-19T00:33:42Z

comment:21

Replying to @mkoeppe:

I don't know, I think it's just an extra feature of lazy_import that is activated by a keyword. I don't see anything wrong with that.

a lazy_import with deprecation keyword is to be removed after the deprecation period while a plain lazy_import is to remain. What seems wrong to me is that this distinction is implicitly made by the mere presence of a keyword argument.

Anyway, this ticket looks good to me.

kwankyu · 2022-07-19T03:23:07Z

comment:22

doctest failures due to the changed deprecation message:

sage -t src/sage/functions/other.py  # 1 doctest failed
sage -t src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py  # 1 doctest failed
sage -t src/sage/modular/modform/find_generators.py  # 2 doctests failed
sage -t src/sage/groups/matrix_gps/homset.py  # 1 doctest failed
sage -t src/sage/schemes/hyperelliptic_curves/all.py  # 4 doctests failed
sage -t src/sage/rings/all.py  # 3 doctests failed

mkoeppe · 2022-07-19T03:40:18Z

comment:23

Ah, I forgot about that

sagetrac-git · 2022-07-19T04:25:15Z

Changed commit from adb89ff to a77b971

sagetrac-git · 2022-07-19T04:25:15Z

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

`a77b971`	`Update doctest output for changed lazy_import deprecation warnings`

kwankyu · 2022-07-19T05:45:28Z

Reviewer: Kwankyu Lee

kwankyu · 2022-07-19T05:45:28Z

comment:25

LGTM.

mkoeppe · 2022-07-19T05:51:47Z

comment:26

Thank you!

vbraun · 2022-08-01T20:23:01Z

Changed branch from u/mkoeppe/remove_src_sage___init___py to a77b971

saraedum · 2022-10-07T10:20:52Z

Changed commit from a77b971 to none

saraedum · 2022-10-07T10:20:52Z

comment:28

When building surface-dynamics (a Cython project that builds against sagelib) we are getting

  surface_dynamics/flat_surfaces/origamis/origami_dense.pyx:39:8: 'sage/structure/element.pxd' not found

It seems to me that Cython does not find the .pxd file anymore because the __init__.py in the base directory is missing now.

saraedum · 2022-10-07T10:22:49Z

comment:29

This seems to be cython/cython#2918 essentially.

saraedum · 2022-10-07T10:26:41Z

comment:30

We could patch the cython packaged in conda-forge with cython/cython#4918 but maybe there is some way to fix this that works for unpatched Cythons?

mkoeppe · 2022-10-07T21:50:16Z

comment:31

https://trac.sagemath.org/wiki/ReleaseTours/sage-9.7#Packagessagesage.rings...arenownamespaces

mkoeppe added this to the sage-9.7 milestone Jul 15, 2022

mkoeppe added t: refactoring labels Jul 15, 2022

mkoeppe added the s: needs review label Jul 15, 2022

mkoeppe modified the milestones: sage-9.7, sage-9.8 Jul 16, 2022

mkoeppe modified the milestones: sage-9.8, sage-9.7 Jul 16, 2022

kwankyu added s: positive review and removed s: needs review labels Jul 19, 2022

vbraun removed the s: positive review label Aug 1, 2022

vbraun closed this as completed in aae8d2d Aug 1, 2022

This was referenced Jan 30, 2023

Meta-ticket: Modularize sagelib into separate distributions (pip-installable packages) sagemath-... for Sage 10.x #29705

Open

Remove __init__.py files for subpackages designated to be namespace packages #33011

Closed

Remove src/sage/__init__.py #34187

Remove src/sage/__init__.py #34187

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mkoeppe commented Oct 7, 2022

Remove src/sage/init.py #34187

Remove src/sage/init.py #34187