Upgrade pybind11 to 2.6.0 to fix "critical incompatibility with Python 3.9.0"

[mkoeppe]

(from #30184)

From https://pybind11.readthedocs.io/en/latest/

Warning

Combining older versions of pybind11 (< 2.6.0) with the brand-new Python 3.9.0 will trigger undefined behavior that typically manifests as crashes during interpreter shutdown (but could also destroy your data. You have been warned.)

We recommend that you wait for Python 3.9.1 slated for release in December, which will include a fix that resolves this problem. In the meantime, please update to the latest version of pybind11 (2.6.0 or newer), which includes a temporary workaround specifically when Python 3.9.0 is detected at runtime.

https://pypi.org/project/pybind11/#history

pybind11 is a dependency of scipy.

CC: @dimpase @slel @vbraun

Component: packages: standard

Author: Matthias Koeppe

Branch/Commit: 5b7784d

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/30803

[mkoeppe]

comment:1

2.6.0 is not released yet, but there is 2.6.0rc3, released 2020-10-16

[mkoeppe]

Branch: u/mkoeppe/upgrade_pybind11

[mkoeppe]

Commit: 6444d52

[mkoeppe]

New commits:

6444d52

build/pkgs/pybind11: Update to 2.6.0rc3

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

Reviewer: https://github.com/mkoeppe/sage/actions/runs/318265052

[dimpase]

comment:9

They have released 2.6.0: https://pypi.org/project/pybind11/2.6.0/

[sagetrac-git]

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

5b7784d

build/pkgs/pybind11: Update to 2.6.0

[sagetrac-git]

Changed commit from 6444d52 to 5b7784d

[mkoeppe]

comment:12

Needs review

[dimpase]

comment:13

it's not related to this ticket but I see

2020-10-21T20:11:50.1507150Z Got:
2020-10-21T20:11:50.1507600Z     ld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer macOS version (10.15) than being linked (10.9)
2020-10-21T20:11:50.1508320Z     ld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer macOS version (10.15) than being linked (10.9)
2020-10-21T20:11:50.1509050Z     ld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer macOS version (10.15) than being linked (10.9)

in https://github.com/mkoeppe/sage/runs/1282662700?check_suite_focus=true

[dimpase]

comment:14

LGTM, also this: https://github.com/mkoeppe/sage/actions/runs/318265052

[dimpase]

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/318265052 to Dima Pasechnik

[vbraun]

Changed branch from u/mkoeppe/upgrade_pybind11 to 5b7784d