fedora: Add python3-devel system packages, standardize build/pkgs/python3/distros/*.txt, fix cysignals build on fedora

[mkoeppe]

Currently, on fedora-31-standard we do not find a system package that passes the python3 spkg-configure test (https://github.com/mkoeppe/sage/runs/563300830).

In this ticket, we add the needed system packages to build/pkgs/python3/distros/fedora.txt.

Also, for uniformity, we move some system packages from build/pkgs/cygwin.txt to build/pkgs/python3/distros/cygwin.txt so that they are only available in a standard build but not a minimal build.

We also add the system package information for python3 for some more distributions in preparation for supporting them.

Using system python3 on fedora leads to a compilation error with cysignals, which we work around.

Upstream: Reported upstream. No feedback yet.

CC: @dimpase @kiwifb

Component: porting

Author: Matthias Koeppe

Branch/Commit: 385e7db

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/29473

[mkoeppe]

comment:1

Tests at https://github.com/mkoeppe/sage/actions/runs/73584944

[mkoeppe]

comment:2

This correctly rejects old python3s for fedora < 29 and too new python3 for fedora-32-standard.

It accepts python3.7 on fedora-29-standard (https://github.com/mkoeppe/sage/runs/570853071)
but then runs into trouble compiling cysignals:

    gcc -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -fPIC -DCYTHON_CLINE_IN_TRACEBACK=0 -U_FORTIFY_SOURCE -Isrc/cysignals -Isrc -I/sage/local/include -I/usr/include/python3.7m -c build/src/cysignals/signals.c -o build/temp.linux-x86_64-3.7/build/src/cysignals/signals.o -pthread
    In file included from build/src/cysignals/signals.c:1552:
    build/src/cysignals/implementation.c:27:2: error: #error "cysignals must be compiled without _FORTIFY_SOURCE"
     #error "cysignals must be compiled without _FORTIFY_SOURCE"
      ^~~~~
    error: command 'gcc' failed with exit status 1
    Running setup.py install for cysignals: finished with status 'error'

Same on fedora-30-standard, fedora-31-standard.

[mkoeppe]

Branch: u/mkoeppe/fedora__add_python3_devel_system_packages__standardize_build_pkgs_python3_distros___txt

[mkoeppe]

New commits:

689a728

fedora: Add python3-devel system packages, standardize build/pkgs/python3/distros/*.txt

[mkoeppe]

Commit: 689a728

[sagetrac-git]

Changed commit from 689a728 to 385e7db

[sagetrac-git]

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

385e7db

build/pkgs/cysignals/spkg-install.in: Override -Wp,-D_FORTIFY_SOURCE from fedora python3

[mkoeppe]

comment:7

Tests at https://github.com/mkoeppe/sage/actions/runs/73955490

[mkoeppe]

comment:9

What's happening here is that cysignals tries to make sure that _FORTIFY_SOURCE is undefined by using Extension(undef_macros=...) (https://github.com/sagemath/cysignals/blob/master/setup.py#L46). distutils.ccompiler.CCompiler.gen_preprocess_options generates the compiler flag -U_FORTIFY_SOURCE from that.

However, Fedora uses -Wp,-D_FORTIFY_SOURCE=2, which is passed directly to the C preprocessor and overrides the -U flag.
We override that by passing -Wp,-U_FORTIFY_SOURCE via CPPFLAGS in the spkg-install script.

[mkoeppe]

comment:10

This should probably be reported upstream, but to which?

[mkoeppe]

Upstream: Reported upstream. No feedback yet.

[mkoeppe]

comment:11

Reported at sagemath/cysignals#120

[mkoeppe]

comment:12

This can be observed to work correctly for fedora-29-standard (https://github.com/mkoeppe/sage/runs/572856776), fedora-30-standard (https://github.com/mkoeppe/sage/runs/572856797), fedora-31-standard (https://github.com/mkoeppe/sage/runs/572856814).

Ready for review

[mkoeppe]

comment:13

Needs review... let's get this into the next beta please

[dimpase]

Reviewer: Dima Pasechnik

[dimpase]

comment:14

lgtm. Regarding upstream, not sure if cysignals has a maintainer now, or Jeroen abandoned it.

[mkoeppe]

comment:15

Thanks!

[vbraun]

Changed branch from u/mkoeppe/fedora__add_python3_devel_system_packages__standardize_build_pkgs_python3_distros___txt to 385e7db