Fix scipy-1.7.2 build failure on Cygwin

[slel]

Sage 9.5.beta9 + #33043 fails to build scipy-1.7.2
on Cygwin.

Initial report:

• sage-release, 2021-12

Issues/PRs:

• .github/workflows/ci.yml: Add cygwin boostorg/math#727 - add Cygwin CI (superseded by 729)
• Cygwin, FreeBSD: Do not define BOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS boostorg/math#728 - boost_math_tools_config.patch (superseded by 729)
• Cygwin, FreeBSD and Long Doubles boostorg/math#729 - combined PR (merged)
• BUG: SciPy 1.7.x build failure on Cygwin scipy/scipy#15296 - SciPy 1.7.x build failure on Cygwin
• boost/math/tools/config.hpp: Cherry pick boostorg/math #729 scipy/boost-headers-only#5

CC: @dimpase @mkoeppe @slel

Component: porting: Cygwin

Keywords: scipy

Author: Matthias Koeppe

Branch: 9070a03

Reviewer: Samuel Lelièvre

Issue created by migration from https://trac.sagemath.org/ticket/33080

[dimpase]

comment:1

logs please

[mkoeppe]

comment:3

I see this build failure now also in https://github.com/mkoeppe/sage/runs/4635610425?check_suite_focus=true (tested with the update to 1.7.3 in #33049)

[mkoeppe]

comment:4

  scipy/stats/_boost/src/beta_ufunc.cxx:3903:46:   required from here
  /opt/sage-4525b51c9c556e7d1bf7a4d90ee129c6b7f1d9a7/var/tmp/sage/build/scipy-1.7.3/src/scipy/_lib/boost/boost/math/tools/promotion.hpp:148:37: error: static assertion failed: Sorry, but this platform does not have sufficient long double support for the special functions to be reliably implemented.
    148 |          BOOST_STATIC_ASSERT_MSG((0 == ::boost::is_same<type, long double>::value), "Sorry, but this platform does not have sufficient long double support for the special functions to be reliably implemented.");
error: Command "g++ -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -DOPENSSL_NO_SSL3=1 -fdebug-prefix-map=/pub/devel/python/python38/python38-3.8.12-1.x86_64/build=/usr/src/debug/python38-3.8.12-1 -fdebug-prefix-map=/pub/devel/python/python38/python38-3.8.12-1.x86_64/src/Python-3.8.12=/usr/src/debug/python38-3.8.12-1 -ggdb -O2 -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fstack-protector-strong --param=ssp-buffer-size=4 -DOPENSSL_NO_SSL3=1 -fdebug-prefix-map=/pub/devel/python/python38/python38-3.8.12-1.x86_64/build=/usr/src/debug/python38-3.8.12-1 -fdebug-prefix-map=/pub/devel/python/python38/python38-3.8.12-1.x86_64/src/Python-3.8.12=/usr/src/debug/python38-3.8.12-1 -D_GNU_SOURCE -DBOOST_MATH_DOMAIN_ERROR_POLICY=ignore_error -DBOOST_MATH_EVALUATION_ERROR_POLICY=user_error -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=false -Iscipy/stats/_boost/include/ -Iscipy/stats/_boost/src/ -I/opt/sage-4525b51c9c556e7d1bf7a4d90ee129c6b7f1d9a7/lib/python3.8/site-packages/numpy/core/include -I/opt/sage-4525b51c9c556e7d1bf7a4d90ee129c6b7f1d9a7/var/tmp/sage/build/scipy-1.7.3/src/scipy/_lib/boost -I/opt/sage-4525b51c9c556e7d1bf7a4d90ee129c6b7f1d9a7/lib/python3.8/site-packages/numpy/core/include -Ibuild/src.cygwin-3.3.3-x86_64-3.8/numpy/distutils/include -I/opt/sage-4525b51c9c556e7d1bf7a4d90ee129c6b7f1d9a7/include -I/usr/include/python3.8 -c scipy/stats/_boost/src/beta_ufunc.cxx -o build/temp.cygwin-3.3.3-x86_64-3.8/scipy/stats/_boost/src/beta_ufunc.o -MMD -MF build/temp.cygwin-3.3.3-x86_64-3.8/scipy/stats/_boost/src/beta_ufunc.o.d -std=c++14 -msse -msse2 -msse3" failed with exit status 1

[mkoeppe]

comment:5

Use of (vendored) boost was introduced in scipy 1.7.0

[mkoeppe]

comment:6

This is with gcc-g++ 11.2.0-1

[mkoeppe]

comment:7

This is coming in through https://github.com/scipy/boost-headers-only/blob/ca02b3b71579fe4913e3e4d1153c34868ec95769/boost/math/tools/config.hpp#L31

[mkoeppe]

comment:8

Also affects FreeBSD apparently, and the porters just patch it out: https://cgit.freebsd.org/ports/tree/science/py-scipy/files/patch-scipy___lib_boost_boost_math_tools_config.hpp

[mkoeppe]

comment:9

Upstream boost: https://github.com/boostorg/math/blob/develop/include/boost/math/tools/config.hpp

[mkoeppe]

comment:10

Neither of these projects has a Cygwin CI (and obviously no FreeBSD CI):

• https://github.com/boostorg/math/blob/develop/.github/workflows/ci.yml
• https://github.com/scipy/scipy/tree/master/.github/workflows

[mkoeppe]

Branch: u/mkoeppe/fix_scipy_1_7_2_build_failure_on_cygwin

[sagetrac-git]

Commit: 1eccca3

[sagetrac-git]

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

1eccca3

build/pkgs/scipy/patches/boost_math_tools_config.patch: Fixup

[mkoeppe]

Author: Matthias Koeppe

[mkoeppe]

Reviewer: https://github.com/mkoeppe/sage/actions/runs/1624899707

[sagetrac-git]

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

9070a03

build/pkgs/scipy/patches/boost_math_tools_config.patch: Fixup

[sagetrac-git]

Changed commit from 1eccca3 to 9070a03

[mkoeppe]

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/1624899707 to https://github.com/mkoeppe/sage/actions/runs/1625005817

[mkoeppe]

comment:18

I don't seem to be getting Windows runners on GH Actions at the moment, so manual testing of this branch on Cygwin would be helpful

[mkoeppe]

comment:19

This branch fixes the issue, as can be seen in the successful run https://github.com/mkoeppe/sage/runs/4646463107?check_suite_focus=true

[slel]

comment:23

This lets the scipy-1.7.2 spkg build for me.

Thanks for the fix and for sending pull requests
to Boost and opening an issue for SciPy.

Should the the patch or the commit messages
mention the inspiration is from FreeBSD?

Or is the discussion here enough?

One way or the other, you can set to
positive review on my behalf.

[slel]

Changed reviewer from https://github.com/mkoeppe/sage/actions/runs/1625005817 to Samuel Lelièvre

[mkoeppe]

Changed reviewer from Samuel Lelièvre to Samuel Lelièvre

[mkoeppe]

comment:24

Thanks for testing!

[mkoeppe]

comment:25

Replying to @slel:

Should the the patch or the commit messages
mention the inspiration is from FreeBSD?

Or is the discussion here enough?

I think it's fine as is.

[vbraun]

Changed branch from u/mkoeppe/fix_scipy_1_7_2_build_failure_on_cygwin to 9070a03

[mkoeppe]

Changed commit from 9070a03 to none