Python updates with openssl300 #996

dhomeier · 2023-02-14T23:46:27Z

The (mostly) current Python versions have not been updated for about a year; upgrading to the current patch/security releases and switching from openssl110 to openssl300. Also fixes a number of utility scripts to use the correct Fink python-pyNN. Builds tested with both pkgconfig and pkgconf; a number of network tests are hanging (as with earlier releases) on 10.14.6; on 13.2 everything building cleanly for arm64 and x86_64.
As 3.10 is also already on the second-to-last regular release, adding python311 as current version.

dhomeier · 2023-02-15T01:22:47Z

@dmacks concerning #920 (comment), which would obviously be superseded by this, the builds are using identical flags and order whether set up with pkg-config, pkgconf or ppkg-config. But regarding the circular dependency through meson and glib2, I have tested the scipy-py310 build with meson 1.0.0 and ppkg-config, and am seeing

found pkg-config '/opt/x64/bin/ppkg-config' but it is Strawberry Perl and thus broken. Ignoring...
Found Pkg-config: NO

just as noted in #918 (comment).
Scipy eventually seems to find its libraries some other way, but I am not sure if the build is complete (it is failing a number of tests).
I have not attempted to build any glib2 > 2.59, but it does not appear ppkg-config will resolve the circular deps issue.

dmacks · 2023-02-17T19:38:38Z

Test-building as we speak. Tools/Scripts/pathfix.py is a script that can fix all the #! lines. And it's written in python, so it's a nice ~~chicken~~snake-and-egg non-solution here:)

Debian's got some useful-looking patches for py311 (I looked only at that one because it's a totally new package). Especially test-no-random-order.diff would be a big help for us as packagers to see what changes during re-re-rebuild cycles (applicable on older pyXX as well).

dmacks · 2023-02-18T06:00:37Z

python39 throws warnings configure: WARNING: unrecognized options: --with-pkgconfig

python39 and python310 (all I've tested so far) fail a self-test on 10.13:

======================================================================
ERROR: test_name_resolution (test.test_pkgutil.PkgutilTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/build.build/python310-3.10.10-1/Python-3.10.10/Lib/test/test_pkgutil.py", line 263, in test_name_resolution
    mod = importlib.import_module(uw)
  File "/sw/build.build/python310-3.10.10-1/Python-3.10.10/Lib/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1004, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'é'

which looks like python/cpython/issues/85326. Is it passing for you? Are you on a APFS disk rather than my HFS+? If so, then just need to have that test get skipped.

Update: For this test, 311 also fails, 38 is clean.

dmacks · 2023-02-18T06:43:23Z

python38 looks good. In fact, the current (3.8.13-2) failed .deb validation:

Error: Compiled python module points to fink install dir.
	Offending file: /sw/lib/python3.8/__pycache__/_bootlocale.cpython-38.opt-2.pyc

which is resolved in this update.

There are a bunch of #!/usr/bin/env python3 (and a few #!/usr/bin/env python) still in lib/ but I don't know if any are actually user-facing vs just demos and tests.

nieder · 2023-02-18T14:10:23Z

Data point: 3.8-3.10 pass on 10.14.6. 3.11 hung on test_socket. When I disabled that test, 3.11 passed everything else

dmacks · 2023-02-18T16:53:49Z

I see some SyntaxError messages while byte-compiling.

For python311:

+ perl -pi -e 's,/sw/build.build/python311-3.11.2-1/Python-3.11.2,/sw/lib/python3.11/config-3.11-darwin,;s/-lintl //' _sysconfigdata__darwin_darwin.py
+ DYLD_LIBRARY_PATH=/sw/build.build/root-python311-3.11.2-1/sw/lib
+ /sw/build.build/root-python311-3.11.2-1/sw/bin/python3.11 -m compileall -f -o 0 -o 1 -o 2 _sysconfigdata__darwin_darwin.py Tools
[...]
Compiling 'Tools/c-analyzer/c_parser/parser/_delim.py'...
***   File "Tools/c-analyzer/c_parser/parser/_delim.py", line 37
    ''')
       ^
SyntaxError: f-string: empty expression not allowed

For python310, the same one as python311, and also:

+ DYLD_LIBRARY_PATH=/sw/build.build/root-python310-3.10.10-1/sw/lib
+ /sw/build.build/root-python310-3.10.10-1/sw/bin/python3.10 -m compileall -o 0 -o 1 -o 2 Tools
[...]
Compiling 'Tools/test2to3/maintest.py'...
***   File "Tools/test2to3/maintest.py", line 8
    except ImportError, e:
           ^^^^^^^^^^^^^^
SyntaxError: multiple exception types must be parenthesized
[...]
Compiling 'Tools/test2to3/test/test_foo.py'...
***   File "Tools/test2to3/test/test_foo.py", line 7
    print 'In test_foo, using Python %s...' % (sys.version_info,)
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?
[...]
Compiling 'Tools/test2to3/test2to3/hello.py'...
***   File "Tools/test2to3/test2to3/hello.py", line 3
    print "Hello, world"
    ^^^^^^^^^^^^^^^^^^^^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(...)?

For python39, the same maintest.py and hello.py as python310, but test_foo.py is instead:

Compiling 'Tools/test2to3/test/test_foo.py'...
***   File "Tools/test2to3/test/test_foo.py", line 7
    print 'In test_foo, using Python %s...' % (sys.version_info,)
          ^
SyntaxError: invalid syntax

test2to3 is removed altogether as of 311ish (python/cpython/pull/26981) so we can ignore those (or maybe we should even nuke it?)

dmacks · 2023-02-18T17:11:39Z

Debian has an interesting packaging approach, where they move the tkinter component (and a few others) to a separately-built package (https://packages.debian.org/source/sid/python3-stdlib-extensions). That gets a heavy dependency (tcltk) out of the main pythonXX package, which can both help resolve some dep-cycles. And it also makes the python-interp package lighter, which is important if we are increasing our reliance on it as a build-tool for other packages.

That shouldn't hold up things here, but it could be helpful in the future, and the jump to a new pythonXX is a cleaner time to start doing it than simply a new version or revision once we already have a given XX. I'll send it to Issues once this PR closes, but it relates to existing Debian patches, something already mentioned here.

dhomeier · 2023-02-18T17:52:54Z

test2to3 is removed altogether as of 311ish (python/cpython/pull/26981) so we can ignore those (or maybe we should even nuke it?)

Yes, those are obviously not meant to be called directly without running them to 2to3 first, so for clarity that directory should perhaps be exempt from the compileall.

There are a bunch of #!/usr/bin/env python3 (and a few #!/usr/bin/env python) still in lib/ but I don't know if any are actually user-facing vs just demos and tests.

And even a #! /usr/local/bin/python |-D! I think their primary purpose is providing system library functions, but as they generally have __main__ entry points, in principle they could be called directly. No idea if that makes sense for any of them, but perhaps better to fix them like the ones in Tools/scripts.

nieder · 2023-02-18T21:55:32Z

On 12.6

3.8 fails this:

test_mkfifo_dir_fd (test.test_posix.PosixTester) ... Fatal Python error: Segmentation fault

Current thread 0x0000000110c74600 (most recent call first):
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/test_posix.py", line 1260 in test_mkfifo_dir_fd
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/case.py", line 633 in _callTestMethod
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/case.py", line 676 in run
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/case.py", line 736 in __call__
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/suite.py", line 122 in run
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/suite.py", line 84 in __call__
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/suite.py", line 122 in run
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/suite.py", line 84 in __call__
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/unittest/runner.py", line 176 in run
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/support/__init__.py", line 2030 in _run_suite
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/support/__init__.py", line 2152 in run_unittest
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/test_posix.py", line 1892 in test_main
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/runtest.py", line 234 in _runtest_inner2
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/runtest.py", line 270 in _runtest_inner
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/runtest.py", line 153 in _runtest
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/runtest.py", line 193 in runtest
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/main.py", line 318 in rerun_failed_tests
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/main.py", line 694 in _main
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/main.py", line 637 in main
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/libregrtest/main.py", line 715 in main
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/__main__.py", line 2 in <module>
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/runpy.py", line 87 in _run_code
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/runpy.py", line 194 in _run_module_as_main
make: *** [Makefile:1142: test] Segmentation fault: 11

3.9, 3.10, 3.11 pass tests but have SyntaxErrors like @dmacks (didn't pay attention if they're also present on 10.14.6)

dmacks · 2023-02-18T23:42:00Z

The syntax error in _delim.py in 3.10 and 3.11 is python/cpython/issues/102033

dmacks · 2023-02-18T23:53:50Z

On 12.6

* 3.8 fails this:

test_mkfifo_dir_fd (test.test_posix.PosixTester) ... Fatal Python error: Segmentation fault

Current thread 0x0000000110c74600 (most recent call first):
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/test_posix.py", line 1260 in test_mkfifo_dir_fd

Is this python/cpython/issues/97897 (whicih would specifcally affect OS X 12.x when using OS X 13.x SDK?) that seems like upstream fixes with 6d0a0191a4e5477bd843e62c24d7f3bcad4fd5fc ?

nieder · 2023-02-19T15:30:31Z

On 12.6
* 3.8 fails this:
test_mkfifo_dir_fd (test.test_posix.PosixTester) ... Fatal Python error: Segmentation fault

Current thread 0x0000000110c74600 (most recent call first):
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/test_posix.py", line 1260 in test_mkfifo_dir_fd
Is this python/cpython/issues/97897 (whicih would specifcally affect OS X 12.x when using OS X 13.x SDK?) that seems like upstream fixes with 6d0a0191a4e5477bd843e62c24d7f3bcad4fd5fc ?

Yes, that looks like the bug. Unfortunately, it hasn't been ported back to the 3.8 branch, and the patch doesn't apply cleanly (a lot of the #define HAVE_* logic doesn't exist in the 3.8 branch).

dmacks · 2023-02-19T17:30:51Z

On 12.6
* 3.8 fails this:
test_mkfifo_dir_fd (test.test_posix.PosixTester) ... Fatal Python error: Segmentation fault

Current thread 0x0000000110c74600 (most recent call first):
  File "/opt/sw/build.build/python38-3.8.16-1/Python-3.8.16/Lib/test/test_posix.py", line 1260 in test_mkfifo_dir_fd
Is this python/cpython/issues/97897 (whicih would specifcally affect OS X 12.x when using OS X 13.x SDK?) that seems like upstream fixes with 6d0a0191a4e5477bd843e62c24d7f3bcad4fd5fc ?
Yes, that looks like the bug. Unfortunately, it hasn't been ported back to the 3.8 branch, and the patch doesn't apply cleanly (a lot of the #define HAVE_* logic doesn't exist in the 3.8 branch).

On my 10.13:

checking for mkfifoat... no
checking for mknod... yes
checking for mknodat... no

It sounds like the problem is autoconf is detecting (for you) something that exists but doesn't actually work, whereas for me it isn't even detected and so the source does something else.

Adding ac_cv_func_mkfifoat=no ac_cv_func_mknodat=no to ConfigureParams, that becomes

checking for mkfifoat... (cached) no
checking for mknod... yes
checking for mknodat... (cached) no

nieder · 2023-02-20T11:53:08Z

I tried to hack the upstream mkfifoat patch to work on the 3.8 branch. The test still fails.
On 12.6 (13.1 SDK), this is the configure output for 3.8 (and 3.9):

checking for mkfifoat... yes
checking for mknod... yes
checking for mknodat... yes

Adding ac_cv_func_mkfifoat=no ac_cv_func_mknodat=no to %c makes all tests pass for python38 on 12.6.
All the code around this mentions macOS 13, so it does look like something is being detected on macOS 12 when it shouldn't.

For CompileScript:

# https://github.com/python/cpython/issues/97897
if [ `uname -r | cut -f1 -d.` -eq 12 ]; then
	MKFIFOAT_CONFIG_PARAMS="ac_cv_func_mkfifoat=no ac_cv_func_mknodat=no
fi
	./configure %c $MKFIFOAT_CONFIG_PARAMS $DIST_CONFIG_PARAMS

$DIST_CONFIG_PARAMS exists, but is not defined anywhere. Would be interesting to see if macOS 11 has this issue to modify the conditional.

dmacks · 2023-02-20T14:58:08Z

That wouldn't be the first time I've seen XCode SDK at some point start defaulting to "next higher version" According to the bug-report, there's confusion when it builds for what appears to be available but then tries to run with (obviously) the current version. The advance here is that at least there was a compile-time warning about it, albeit one that didn't seem as dire as it actually is.

dmacks · 2023-02-20T15:03:09Z

DIST_CONFIG_PARAMS is used in some pythonXX builds, and I guess sits there inertly for when what it implemented was no longer needed. See ecbc060

dmacks · 2023-02-22T10:09:49Z

The minimal fix for the _delim.py syntax-error in python310 and python311 is sobolevn/cpython@a930d37 (thanks upstream!)

dmacks · 2023-02-24T22:41:25Z

This PR is dragging out a bit, so I'm forking the python311 portion to #1002, where we can work on splitting off tk before this new lang-version package lands in public repo. Please do not merge the py11 packages of this PR.

nieder · 2023-02-27T02:27:37Z

3.8 needs just ac_cv_func_mkfifoat=no ac_cv_func_mknodat=no on macOS 12.
3.9 seems fine as is everywhere.
3.10 would need sobolevn/cpython@a930d37.

I can cherry pick the individual commits from here, add the changes described. @dhomeier: thoughts?

Co-authored by: Daniel Macks <[email protected]>

Co-authored by: Hanspeter Niederstrasser <[email protected]>

Co-authored by: Daniel Macks <[email protected]>

dhomeier · 2023-02-27T03:02:31Z

Thanks all for looking into the failures! I have tested all on 12.6; pushing the corresponding 3.11 fixes here as well so they may be later applied to #1002.

nieder · 2023-02-27T12:28:08Z

10.9-libcxx/stable/main/finkinfo/languages/python38.info

@@ -37,7 +37,7 @@ BuildDepends: <<
 	readline8,
 	sqlite3-dev (>= 3.30.1-1),
 	openssl300-dev (>= 3.0.1-1),
-	pkgconfig (>= 0.9.0-1),
+	pkgconf,


ppkg-config? And fix $PKG_CONFIG down below to match?

Have not tested this, but python310 did not report any errors of the kind in #996 (comment), so it's probably safe to switch as well.

TheSin- · 2023-02-27T13:19:18Z

pkg-config is fixed now, the issue was glib2 which I fixed a while back.

dhomeier · 2023-02-27T14:29:04Z

So no more circular deps??

nieder · 2024-03-01T13:14:42Z

Getting a test failure in test_xml_etree, even bumping to latest 3.10.13:

FAIL: test_simple_xml (test.test_xml_etree.XMLPullParserTest) (chunk_size=5)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/build.build/python310-3.10.13-1/Python-3.10.13/Lib/test/test_xml_etree.py", line 1414, in test_simple_xml
    self.assert_event_tags(parser, [
  File "/sw/build.build/python310-3.10.13-1/Python-3.10.13/Lib/test/test_xml_etree.py", line 1396, in assert_event_tags
    self.assertEqual([(action, elem.tag) for action, elem in events],
AssertionError: Lists differ: [('end', 'element')] != [('end', 'element'), ('end', 'empty-element')]

Second list contains 1 additional elements.
First extra element 1:
('end', 'empty-element')

- [('end', 'element')]
+ [('end', 'element'), ('end', 'empty-element')]

Wonder if it's related to a libxml2 change (haven't looked yet).

dmacks · 2024-03-01T13:20:55Z

Getting a test failure in test_xml_etree, even bumping to latest 3.10.13:

FAIL: test_simple_xml (test.test_xml_etree.XMLPullParserTest) (chunk_size=5)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/sw/build.build/python310-3.10.13-1/Python-3.10.13/Lib/test/test_xml_etree.py", line 1414, in test_simple_xml
    self.assert_event_tags(parser, [
  File "/sw/build.build/python310-3.10.13-1/Python-3.10.13/Lib/test/test_xml_etree.py", line 1396, in assert_event_tags
    self.assertEqual([(action, elem.tag) for action, elem in events],
AssertionError: Lists differ: [('end', 'element')] != [('end', 'element'), ('end', 'empty-element')]

Second list contains 1 additional elements.
First extra element 1:
('end', 'empty-element')

- [('end', 'element')]
+ [('end', 'element'), ('end', 'empty-element')]

Wonder if it's related to a libxml2 change (haven't looked yet).

Or new expat (per https://www.linuxfromscratch.org/blfs/view/svn/general/python3.html)

dmacks · 2024-03-02T06:30:33Z

Python-upstream confirms there are test-failures due to the just-released expat-2.6.0 and has fixes. python/cpython#115133

nieder · 2024-03-02T11:02:24Z

What's left here (apart from expat fixes which are available 3.8-3.12 from upstream and python3.11 getting its own PR for Tk-icide) ? Some of pythons here use pkgconf (3.8, 3.9, 3.11) and others use ppkg-config (3.10). I never followed the discussion as to which was less dep heavy or what, but #923 suggests that others are moving towards pkgconf.

dmacks · 2024-03-04T14:35:14Z

Offloaded a separate tracking ticket for the expat issue (which also ponders what versions of pythonXX we should continue to support at all).

dhomeier added 4 commits February 15, 2023 00:38

python310 update to 3.10.10 and openssl300 build

8e1a010

New package python311 3.11.2

62d3fd1

python39 update to 3.9.15 and openssl300 build

23e24f5

python38 update to 3.8.16 and openssl300 build

39f3b48

dhomeier added new package Packages that do not yet exist in Fink. new upstream Package has an updated upstream version labels Feb 14, 2023

This was referenced Feb 15, 2023

Python 3.9.13 + 3.10.5 updates with build against openssl300 #920

Closed

Add pkgconf package as a replacement for pkgconfig #923

Open

dmacks mentioned this pull request Feb 24, 2023

New package python311 3.11.2 #1002

Draft

dhomeier added 2 commits February 27, 2023 03:48

Fix compileall failures in python310 (omitting test2to3)

1a9b9f2

Co-authored by: Daniel Macks <[email protected]>

Fix compileall failures in python39 (omitting test2to3)

8e3181a

dhomeier added 2 commits February 27, 2023 03:54

Avoid compileall failures and mkfifo_dir_fd segfault in python38

8cc9e48

Co-authored by: Hanspeter Niederstrasser <[email protected]>

DNM: Fix compileall failures in python311 (omitting test2to3)

9c2c9ea

Co-authored by: Daniel Macks <[email protected]>

nieder reviewed Feb 27, 2023

View reviewed changes

dmacks mentioned this pull request Mar 4, 2024

expat-2.6.0 breaks pythonXX build #1129

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Python updates with openssl300 #996

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Python updates with openssl300 #996

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