Re: [PR PATCH] [Updated] [WIP] New package: sagemath-9.5.beta7

[tornaria <tornaria@users.noreply.github.com>]

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There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages sagemath
https://github.com/void-linux/void-packages/pull/34030

[WIP] New package: sagemath-9.5.beta7
This is WIP, so I can get feedback.

Right now there is some issue with relocation, since `/builddir/sage-9.5.beta5` leaks all over the place. In particular starting sage complains this directory is missing... but it seems to work.

I'm unsure if the package name should be `sage` or `sagemath`.

A patch file from https://github.com/void-linux/void-packages/pull/34030.patch is attached

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From e483ed0e729742ec8eb83eb81d0f7007ad95708e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 22 Nov 2021 19:24:50 -0300
Subject: [PATCH 1/9] sympow: do not mess with fpu control word

It turns out doing that on musl results in wrong output for doubles.
Moreover any cpu with sse2 should not be using fp registers anyway.

For i686 without sse, the configure will figure out that floats are
80 bits and add -ffloat-store to CFLAGS to force them to be 64 bits.

A simple way to test it is to run

    $ sympow -curve '[0,0,0,0,1]' -analrank
    ...
    Analytic Rank is 0 : L-value 7.01091e-01

When broken this prints "7.01092e-01" instead.

The actual value computed to 128 bits with pari is:

    $ echo 'elllseries(ellinit([0,0,0,0,1]),1)' | gp -q
    0.70109105266272713058750953952514706773

so the glibc output is the correct one.

What is broken is not computing but printing, as fmt_fp in musl uses
long double, which means messing with fpu control word breaks it.
This is important since sagemath parses sympow output.

This affects sagemath doctests as in

    $ sage -t src/sage/lfunctions/sympow.py
    ...
    (3 failures)

After this commit, the doctest in question passes.
---
 .../patches/dont-change-fpu-control-word.patch   | 16 ++++++++++++++++
 srcpkgs/sympow/template                          |  2 +-
 2 files changed, 17 insertions(+), 1 deletion(-)
 create mode 100644 srcpkgs/sympow/patches/dont-change-fpu-control-word.patch

diff --git a/srcpkgs/sympow/patches/dont-change-fpu-control-word.patch b/srcpkgs/sympow/patches/dont-change-fpu-control-word.patch
new file mode 100644
index 000000000000..2a1155111268
--- /dev/null
+++ b/srcpkgs/sympow/patches/dont-change-fpu-control-word.patch
@@ -0,0 +1,16 @@
+--- a/Configure	2021-11-22 22:20:42.512565997 -0300
++++ b/Configure	2021-11-22 23:10:09.986457874 -0300
+@@ -154,9 +154,10 @@
+ done
+ 
+ # Select the most appropriate FPU control scheme
+-for FLAG in '-DISOC99_FENV' '-DFPUCONTROLH' '-Dx86'; do
+-    try_add_CFLAG $FLAG && break
+-done
++## disable messing with fpu control word -- not worth it
++# for FLAG in '-DISOC99_FENV' '-DFPUCONTROLH' '-Dx86'; do
++#     try_add_CFLAG $FLAG && break
++# done
+ 
+ # Some flags to try as last resort.  These hurt performance, so only add
+ # them if needed.
diff --git a/srcpkgs/sympow/template b/srcpkgs/sympow/template
index d484cf847f57..48e2399b72e3 100644
--- a/srcpkgs/sympow/template
+++ b/srcpkgs/sympow/template
@@ -1,7 +1,7 @@
 # Template file for 'sympow'
 pkgname=sympow
 version=2.023.6
-revision=2
+revision=3
 wrksrc=${pkgname}-v${version}
 build_style=configure
 make_build_target=all

From 6b25dfcb8e39077d1283daa31e621c1ac8227454 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 11 Nov 2021 09:39:20 -0300
Subject: [PATCH 2/9] hooks: option to skip 03-rewrite-python-shebang

---
 common/hooks/pre-pkg/03-rewrite-python-shebang.sh | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/common/hooks/pre-pkg/03-rewrite-python-shebang.sh b/common/hooks/pre-pkg/03-rewrite-python-shebang.sh
index 07162ad2c69b..c0f2198e44cf 100644
--- a/common/hooks/pre-pkg/03-rewrite-python-shebang.sh
+++ b/common/hooks/pre-pkg/03-rewrite-python-shebang.sh
@@ -4,6 +4,10 @@
 hook() {
 	local pyver= shebang= off=
 
+	if [ -n "$_no_python_shebang" ]; then
+		return 0
+	fi
+
 	if [ -d ${PKGDESTDIR}/usr/lib/python* ]; then
 		pyver="$(find ${PKGDESTDIR}/usr/lib/python* -prune -type d | grep -o '[[:digit:]]\.[[:digit:]]\+$')"
 	fi

From 0962da75c6bb03ae4757480178a1949f3457c41b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 11 Nov 2021 10:36:03 -0300
Subject: [PATCH 3/9] New package: sage-9.5.beta5

---
 srcpkgs/sage/template | 74 +++++++++++++++++++++++++++++++++++++++++++
 srcpkgs/sage/update   |  3 ++
 2 files changed, 77 insertions(+)
 create mode 100644 srcpkgs/sage/template
 create mode 100644 srcpkgs/sage/update

diff --git a/srcpkgs/sage/template b/srcpkgs/sage/template
new file mode 100644
index 000000000000..2ef437238cb5
--- /dev/null
+++ b/srcpkgs/sage/template
@@ -0,0 +1,74 @@
+# Template file for 'sage'
+pkgname=sage
+version=9.5.beta5
+revision=1
+build_style=configure
+configure_args=--prefix=/usr/lib/sage-${version}
+make_check_target=ptest
+short_desc="Open source mathematics software"
+maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
+license="GPL-3.0-or-later"
+homepage="http://sagemath.org/"
+distfiles="http://mirrors.mit.edu/sage/src/sage-$version.tar.gz"
+checksum=3b78ee848450d6881902bf68f4f3af17e1647e72c51e5fcdcb412c938ecbce57
+
+case ${version} in
+	# url for devel is different
+	*.beta*|*.rc*)
+		distfiles=${distfiles/sage\/src/sage\/devel}
+		;;
+esac
+
+# first we try to build native; we'll worry about cross later
+# besides, some dependencies are nocross
+nocross=yes
+
+# for now, to make install faster
+nostrip=yes
+
+# don't rewrite python shebang as sage uses its own python (for now)
+_no_python_shebang=yes
+
+do_install() {
+	vcopy /usr/lib/sage-${version} usr/lib/
+	vmkdir usr/bin
+	ln -s /usr/lib/sage-${version}/bin/sage ${DESTDIR}/usr/bin/
+}
+
+### copied from sage-deps, to keep in sync
+
+# hard dependencies
+makedepends+=" gcc make m4 perl binutils git tar libgomp-devel"
+
+# recommended dependencies
+makedepends+=" gcc-fortran openssl-devel"
+
+# bootstrap dependencies
+makedepends+=" automake gettext gettext-devel"
+
+# other host dependencies
+makedepends+=" cmake curl git ninja pandoc patch pkg-config python3 tox"
+
+# already in void
+makedepends+="
+ CoinMP-devel R arb-devel boost-devel bzip2-devel ecl eclib-devel
+ ecm-devel flintlib-devel freetype-devel gc-devel gd-devel giac-devel
+ glpk-devel gmp-devel gmpxx-devel gp2c graphviz gsl-devel isl-devel
+ libatomic_ops-devel libcurl-devel libffi-devel libmpc-devel
+ libpng-devel libxml2-devel mpfr-devel ncurses-devel openblas-devel
+ pari-devel pari-elldata-small pari-galdata pari-galpol-small
+ pari-seadata pcre-devel perl-File-Slurp perl-JSON perl-Term-ReadKey
+ perl-Term-ReadLine-Gnu perl-XML-LibXML perl-XML-LibXSLT
+ perl-XML-Writer ppl-devel python3-devel readline-devel sqlite-devel
+ zeromq-devel zlib-devel
+ FlintQS SuiteSparse-devel cddlib-devel fflas-ffpack fplll-devel gf2x-devel
+ givaro-devel igraph-devel iml-devel lcalc-devel linbox-devel
+ m4ri-devel m4rie-devel mpfi-devel ntl-devel perl-SVG rankwidth-devel
+ singular sympow zn_poly symmetrica-devel planarity-devel qhull libqhull-devel
+"
+
+# TODO: standard
+# brial cliquer gfan libbraiding libhomfly lrcalc nauty palp tachyon
+
+# TODO: optional
+# 4ti2 coxeter3 libnauty libsemigroups lrslib perl_mongodb
diff --git a/srcpkgs/sage/update b/srcpkgs/sage/update
new file mode 100644
index 000000000000..f797813dcde6
--- /dev/null
+++ b/srcpkgs/sage/update
@@ -0,0 +1,3 @@
+# for now, check both stable and devel releases
+site="http://mirrors.mit.edu/sage/src/
+http://mirrors.mit.edu/sage/devel/"

From 7cfead0840766a381c15e94e194645dbeb8df255 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 13 Nov 2021 00:08:27 -0300
Subject: [PATCH 4/9] sagemath: update to sage-9.5.beta6

Also:
 - rename pkg from sage to sagemath
 - now it will build sage in-place at /usr/lib/sage-$version
 - the resulting pkg contains a lot of useless stuff that comes with the
   distribution; we'll have to clean up. E.g. SAGE_ROOT/upstream is
   definitely unnecessary (1.2G); possibly SAGE_ROOT/pkgs or at least
   SAGE_ROOT/pkgs/sagemath-standard/build (2.6G).
---
 srcpkgs/{sage => sagemath}/template | 46 +++++++++++++++++++++--------
 srcpkgs/{sage => sagemath}/update   |  1 +
 2 files changed, 35 insertions(+), 12 deletions(-)
 rename srcpkgs/{sage => sagemath}/template (67%)
 rename srcpkgs/{sage => sagemath}/update (90%)

diff --git a/srcpkgs/sage/template b/srcpkgs/sagemath/template
similarity index 67%
rename from srcpkgs/sage/template
rename to srcpkgs/sagemath/template
index 2ef437238cb5..fa5189ad259e 100644
--- a/srcpkgs/sage/template
+++ b/srcpkgs/sagemath/template
@@ -1,41 +1,63 @@
-# Template file for 'sage'
-pkgname=sage
-version=9.5.beta5
+# Template file for 'sagemath'
+pkgname=sagemath
+version=9.5.beta6
 revision=1
+wrksrc=sage-$version
 build_style=configure
-configure_args=--prefix=/usr/lib/sage-${version}
+configure_args="--enable-build-as-root"
 make_check_target=ptest
+# for now skip building docs
+make_build_target=build
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-3.0-or-later"
 homepage="http://sagemath.org/"
 distfiles="http://mirrors.mit.edu/sage/src/sage-$version.tar.gz"
-checksum=3b78ee848450d6881902bf68f4f3af17e1647e72c51e5fcdcb412c938ecbce57
+checksum=7bae8cbb4db73147bd698261497102524bfadeb71ca66b1c68e96827bd5a8975
+
+# path where sage will be installed
+_SAGE_ROOT=/usr/lib/sage-${version}
 
 case ${version} in
 	# url for devel is different
-	*.beta*|*.rc*)
-		distfiles=${distfiles/sage\/src/sage\/devel}
-		;;
+	*.beta*|*.rc*) distfiles=${distfiles/sage\/src/sage\/devel} ;;
 esac
 
-# first we try to build native; we'll worry about cross later
-# besides, some dependencies are nocross
+# for now, skip check in ci, since we still have a few tests failing
+make_check=ci-skip
+
+# for now, just build native; we'll worry about cross later
+# besides, some dependencies are nocross (e.g. ntl)
 nocross=yes
 
 # for now, to make install faster
 nostrip=yes
 
+# don't shlib_provide anything
+noshlibprovides=yes
+
 # don't rewrite python shebang as sage uses its own python (for now)
 _no_python_shebang=yes
 
+post_extract() {
+	# sage wants to be built in place so let $wrksrc be a symlink
+	mv -T $wrksrc $_SAGE_ROOT
+	ln -sfT $_SAGE_ROOT $wrksrc
+}
+
+do_clean() {
+	# undo post_extract()
+	rm $wrksrc
+	mv $_SAGE_ROOT $wrksrc
+}
+
 do_install() {
 	vcopy /usr/lib/sage-${version} usr/lib/
 	vmkdir usr/bin
-	ln -s /usr/lib/sage-${version}/bin/sage ${DESTDIR}/usr/bin/
+	ln -s $_SAGE_ROOT/sage ${DESTDIR}/usr/bin/
 }
 
-### copied from sage-deps, to keep in sync
+### copied from sage-deps, to be kept in sync
 
 # hard dependencies
 makedepends+=" gcc make m4 perl binutils git tar libgomp-devel"
diff --git a/srcpkgs/sage/update b/srcpkgs/sagemath/update
similarity index 90%
rename from srcpkgs/sage/update
rename to srcpkgs/sagemath/update
index f797813dcde6..c33aba4e6df2 100644
--- a/srcpkgs/sage/update
+++ b/srcpkgs/sagemath/update
@@ -1,3 +1,4 @@
+pkgname=sage
 # for now, check both stable and devel releases
 site="http://mirrors.mit.edu/sage/src/
 http://mirrors.mit.edu/sage/devel/"

From 63c3e5960b171bdea8a63c08251f904307128c06 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 13 Nov 2021 07:40:55 -0300
Subject: [PATCH 5/9] sagemath: revbump for changes

 - include patch fixing build of pyzmq on musl
 - add gengetopts and texinfo to makedepends
 - first attempt at cleanup: remove upstream sources and build artifacts
---
 srcpkgs/sagemath/patches/fix-pyzmq-musl.patch | 15 +++++++++++++++
 srcpkgs/sagemath/template                     |  9 +++++++--
 2 files changed, 22 insertions(+), 2 deletions(-)
 create mode 100644 srcpkgs/sagemath/patches/fix-pyzmq-musl.patch

diff --git a/srcpkgs/sagemath/patches/fix-pyzmq-musl.patch b/srcpkgs/sagemath/patches/fix-pyzmq-musl.patch
new file mode 100644
index 000000000000..9190830d835e
--- /dev/null
+++ b/srcpkgs/sagemath/patches/fix-pyzmq-musl.patch
@@ -0,0 +1,15 @@
+diff --git a/build/pkgs/pyzmq/spkg-install.in b/build/pkgs/pyzmq/spkg-install.in
+index 0ce404ee5a..b7260c6d27 100644
+--- a/build/pkgs/pyzmq/spkg-install.in
++++ b/build/pkgs/pyzmq/spkg-install.in
+@@ -1,6 +1,9 @@
+ # Since we use environment vars we have to generate setup.cfg
+ 
+-echo "[build_ext]" > src/setup.cfg
++echo "[global]" > src/setup.cfg
++echo "skip_check_zmq = True" >> src/setup.cfg
++
++echo "[build_ext]" >> src/setup.cfg
+ 
+ # (I tried putting quotes around $SAGE_LOCAL to allow for spaces in
+ # the path---which is never used but is a good habit to support---but
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index fa5189ad259e..56166cd44272 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
 version=9.5.beta6
-revision=1
+revision=2
 wrksrc=sage-$version
 build_style=configure
 configure_args="--enable-build-as-root"
@@ -52,7 +52,11 @@ do_clean() {
 }
 
 do_install() {
-	vcopy /usr/lib/sage-${version} usr/lib/
+	vcopy $_SAGE_ROOT usr/lib/
+	# cleanup: upstream sources and build artifacts
+	rm -rf ${DESTDIR}/$_SAGE_ROOT/upstream
+	rm -rf ${DESTDIR}/$_SAGE_ROOT/pkgs/*/build
+	# symlink main binary
 	vmkdir usr/bin
 	ln -s $_SAGE_ROOT/sage ${DESTDIR}/usr/bin/
 }
@@ -87,6 +91,7 @@ makedepends+="
  givaro-devel igraph-devel iml-devel lcalc-devel linbox-devel
  m4ri-devel m4rie-devel mpfi-devel ntl-devel perl-SVG rankwidth-devel
  singular sympow zn_poly symmetrica-devel planarity-devel qhull libqhull-devel
+ gengetopt texinfo
 "
 
 # TODO: standard

From 6d80881d35949067e13d1b1c8f77525ead03cd00 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 14 Nov 2021 18:23:29 -0300
Subject: [PATCH 6/9] sagemath: revbump to 9.5.beta6_3 for changes

 - add depends needed for runtime and for testing
 - add python_version=3
 - disable skipping 03-rewrite-python-shebang as it seems to be harmless
   after adding python_version=3
 - fix cleaning up of $wrksrc and $_SAGE_ROOT
 - use sage-${version}_${revision} for the binary symlink; this way it
   won't override whatever sage is installed in the system so I can test
   on a live system.
---
 srcpkgs/sagemath/template | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 56166cd44272..cfe97e039974 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,19 +1,24 @@
 # Template file for 'sagemath'
 pkgname=sagemath
 version=9.5.beta6
-revision=2
+revision=3
 wrksrc=sage-$version
 build_style=configure
 configure_args="--enable-build-as-root"
 make_check_target=ptest
 # for now skip building docs
 make_build_target=build
+depends="giac git FlintQS zn_poly sympow
+ pari-elldata-small pari-galdata pari-galpol-small pari-seadata-small
+ flintlib-devel gsl-devel ntl-devel eclib-devel pari-devel mpfr-devel
+ m4ri-devel gd-devel libpng-devel fflas-ffpack pkg-config gcc-fortran"
 short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-3.0-or-later"
 homepage="http://sagemath.org/"
 distfiles="http://mirrors.mit.edu/sage/src/sage-$version.tar.gz"
 checksum=7bae8cbb4db73147bd698261497102524bfadeb71ca66b1c68e96827bd5a8975
+python_version=3
 
 # path where sage will be installed
 _SAGE_ROOT=/usr/lib/sage-${version}
@@ -37,7 +42,8 @@ nostrip=yes
 noshlibprovides=yes
 
 # don't rewrite python shebang as sage uses its own python (for now)
-_no_python_shebang=yes
+# after python_version=3, this seems harmless... strange...
+#_no_python_shebang=yes
 
 post_extract() {
 	# sage wants to be built in place so let $wrksrc be a symlink
@@ -46,9 +52,12 @@ post_extract() {
 }
 
 do_clean() {
-	# undo post_extract()
-	rm $wrksrc
-	mv $_SAGE_ROOT $wrksrc
+	rm -rf $wrksrc $_SAGE_ROOT
+}
+
+post_build() {
+	# install pytest for more tests
+	./sage -i pytest
 }
 
 do_install() {
@@ -58,7 +67,9 @@ do_install() {
 	rm -rf ${DESTDIR}/$_SAGE_ROOT/pkgs/*/build
 	# symlink main binary
 	vmkdir usr/bin
-	ln -s $_SAGE_ROOT/sage ${DESTDIR}/usr/bin/
+	# for now use sage-${version}_${revision} so it doesn't override
+	# other sage installed in the system
+	ln -sfT $_SAGE_ROOT/sage ${DESTDIR}/usr/bin/sage-${version}_${revision}
 }
 
 ### copied from sage-deps, to be kept in sync

From 442e3dfd448344ce1843b68417367a975f2bfc94 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sat, 20 Nov 2021 19:01:21 -0300
Subject: [PATCH 7/9] sagemath: update to 9.5.beta7.

---
 srcpkgs/sagemath/template | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index cfe97e039974..3f9a3e9e077f 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -1,7 +1,7 @@
 # Template file for 'sagemath'
 pkgname=sagemath
-version=9.5.beta6
-revision=3
+version=9.5.beta7
+revision=1
 wrksrc=sage-$version
 build_style=configure
 configure_args="--enable-build-as-root"
@@ -17,7 +17,7 @@ maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-3.0-or-later"
 homepage="http://sagemath.org/"
 distfiles="http://mirrors.mit.edu/sage/src/sage-$version.tar.gz"
-checksum=7bae8cbb4db73147bd698261497102524bfadeb71ca66b1c68e96827bd5a8975
+checksum=b81e1fe22d1b990bf1230260241ead016470da1f2f7b260f562d50f74c2904c7
 python_version=3
 
 # path where sage will be installed

From f165af50129b01e61b67c57659aa2af0d21e897b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 22 Nov 2021 10:23:03 -0300
Subject: [PATCH 8/9] sagemath: add more dependencies

Also:
 - add patches so more doctests pass
 - add do_check() to skip building docs
 - use https for distfiles
---
 ...08fd9d56d022ed28592f93f07ec8dce530ef.patch |  49 ++++++
 ...b99e0270f80cf03b80418372f45274f46051.patch | 163 ++++++++++++++++++
 ...a86908daf60b25e66e6a189c51ada7e0a732.patch |  25 +++
 .../patches/skip-optional-dochtml.patch       |  13 ++
 srcpkgs/sagemath/template                     |  15 +-
 5 files changed, 260 insertions(+), 5 deletions(-)
 create mode 100644 srcpkgs/sagemath/patches/17e308fd9d56d022ed28592f93f07ec8dce530ef.patch
 create mode 100644 srcpkgs/sagemath/patches/2ee7b99e0270f80cf03b80418372f45274f46051.patch
 create mode 100644 srcpkgs/sagemath/patches/f5f7a86908daf60b25e66e6a189c51ada7e0a732.patch
 create mode 100644 srcpkgs/sagemath/patches/skip-optional-dochtml.patch

diff --git a/srcpkgs/sagemath/patches/17e308fd9d56d022ed28592f93f07ec8dce530ef.patch b/srcpkgs/sagemath/patches/17e308fd9d56d022ed28592f93f07ec8dce530ef.patch
new file mode 100644
index 000000000000..e295bb91af5b
--- /dev/null
+++ b/srcpkgs/sagemath/patches/17e308fd9d56d022ed28592f93f07ec8dce530ef.patch
@@ -0,0 +1,49 @@
+From 17e308fd9d56d022ed28592f93f07ec8dce530ef Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 15 Nov 2021 23:37:15 -0500
+Subject: Trac #32880: use GAP instead of Singular to test
+ _get_shared_lib_path().
+
+We still have a doctest for _get_shared_lib_path() that tries to find
+the path to libSingular; however, we no longer actually need it to
+find libSingular because the path to libSingular is contained in
+LIBSINGULAR_PATH.
+
+Since _get_shared_lib_path() is a bit fragile, this commit replaces
+that test case with one for libgap, which is still always installed
+via SPKG and for which we still need _get_shared_lib_path() to be able
+to find the path.
+---
+ src/sage/env.py | 12 ++----------
+ 1 file changed, 2 insertions(+), 10 deletions(-)
+
+diff --git a/src/sage/env.py b/src/sage/env.py
+index 40ace13..3bd4826 100644
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -267,20 +267,12 @@ def _get_shared_lib_path(*libnames: str) -> Optional[str]:
+ 
+     EXAMPLES::
+ 
+-        sage: import sys
+-        sage: from fnmatch import fnmatch
+         sage: from sage.env import _get_shared_lib_path
+-        sage: lib_filename = _get_shared_lib_path("Singular", "singular-Singular")
+-        sage: if sys.platform == 'cygwin':
+-        ....:     pattern = "*/cygSingular-*.dll"
+-        ....: elif sys.platform == 'darwin':
+-        ....:     pattern = "*/libSingular-*.dylib"
+-        ....: else:
+-        ....:     pattern = "*/lib*Singular-*.so"
+-        sage: fnmatch(str(lib_filename), pattern)
++        sage: "gap" in _get_shared_lib_path("gap")
+         True
+         sage: _get_shared_lib_path("an_absurd_lib") is None
+         True
++
+     """
+ 
+     for libname in libnames:
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/2ee7b99e0270f80cf03b80418372f45274f46051.patch b/srcpkgs/sagemath/patches/2ee7b99e0270f80cf03b80418372f45274f46051.patch
new file mode 100644
index 000000000000..32e641edb3aa
--- /dev/null
+++ b/srcpkgs/sagemath/patches/2ee7b99e0270f80cf03b80418372f45274f46051.patch
@@ -0,0 +1,163 @@
+From 2ee7b99e0270f80cf03b80418372f45274f46051 Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Samuel=20Leli=C3=A8vre?= <samuel.lelievre@gmail.com>
+Date: Sat, 20 Nov 2021 13:34:16 +0100
+Subject: 32905: abs tol for some CBF and RBF doctests
+
+---
+ src/sage/functions/gamma.py    |  2 +-
+ src/sage/rings/complex_arb.pyx |  6 +++---
+ src/sage/rings/real_arb.pyx    | 24 ++++++++++++------------
+ src/sage/symbolic/function.pyx |  2 +-
+ 4 files changed, 17 insertions(+), 17 deletions(-)
+
+diff --git a/src/sage/functions/gamma.py b/src/sage/functions/gamma.py
+index 3a4deef..307deb1 100644
+--- a/src/sage/functions/gamma.py
++++ b/src/sage/functions/gamma.py
+@@ -1049,7 +1049,7 @@ class Function_beta(GinacFunction):
+         r"""
+         TESTS::
+ 
+-            sage: RBF(beta(sin(3),sqrt(RBF(2).add_error(1e-8)/3)))
++            sage: RBF(beta(sin(3),sqrt(RBF(2).add_error(1e-8)/3)))  # abs tol 6e-7
+             [7.407662 +/- 6.17e-7]
+         """
+         return [x, y]
+diff --git a/src/sage/rings/complex_arb.pyx b/src/sage/rings/complex_arb.pyx
+index ce9b1b1..7e10ec9 100644
+--- a/src/sage/rings/complex_arb.pyx
++++ b/src/sage/rings/complex_arb.pyx
+@@ -4189,7 +4189,7 @@ cdef class ComplexBall(RingElement):
+ 
+         TESTS:
+ 
+-            sage: CBF(Ei(I))
++            sage: CBF(Ei(I))  # abs tol 1e-16
+             [0.337403922900968 +/- 3.76e-16] + [2.51687939716208 +/- 2.01e-15]*I
+         """
+         cdef ComplexBall result = self._new()
+@@ -4239,7 +4239,7 @@ cdef class ComplexBall(RingElement):
+ 
+         TESTS:
+ 
+-            sage: CBF(Ci(I))
++            sage: CBF(Ci(I))  # abs tol 1e-17
+             [0.837866940980208 +/- 4.72e-16] + [1.570796326794897 +/- 5.54e-16]*I
+         """
+         cdef ComplexBall result = self._new()
+@@ -4291,7 +4291,7 @@ cdef class ComplexBall(RingElement):
+ 
+         TESTS:
+ 
+-            sage: CBF(Chi(I))
++            sage: CBF(Chi(I))  # abs tol 1e-16
+             [0.337403922900968 +/- 3.25e-16] + [1.570796326794897 +/- 5.54e-16]*I
+         """
+         cdef ComplexBall result = self._new()
+diff --git a/src/sage/rings/real_arb.pyx b/src/sage/rings/real_arb.pyx
+index 80a840e..49caa63 100644
+--- a/src/sage/rings/real_arb.pyx
++++ b/src/sage/rings/real_arb.pyx
+@@ -3489,12 +3489,12 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1).Ei()
++            sage: RBF(1).Ei()  # abs tol 5e-16
+             [1.89511781635594 +/- 4.94e-15]
+ 
+         TESTS::
+ 
+-            sage: RBF(Ei(1))
++            sage: RBF(Ei(1))  # abs tol 5e-16
+             [1.89511781635594 +/- 4.94e-15]
+         """
+         cdef RealBall res = self._new()
+@@ -3531,12 +3531,12 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1).Ci()
++            sage: RBF(1).Ci()  # abs tol 1e-16
+             [0.337403922900968 +/- 3.25e-16]
+ 
+         TESTS::
+ 
+-            sage: RBF(Ci(1))
++            sage: RBF(Ci(1))  # abs tol 1e-16
+             [0.337403922900968 +/- 3.25e-16]
+         """
+         cdef RealBall res = self._new()
+@@ -3575,12 +3575,12 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(1).Chi()
++            sage: RBF(1).Chi()  # abs tol 1e-17
+             [0.837866940980208 +/- 4.72e-16]
+ 
+         TESTS::
+ 
+-            sage: RBF(Chi(1))
++            sage: RBF(Chi(1))  # abs tol 1e-17
+             [0.837866940980208 +/- 4.72e-16]
+         """
+         cdef RealBall res = self._new()
+@@ -3597,7 +3597,7 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(3).li()
++            sage: RBF(3).li()  # abs tol 1e-15
+             [2.16358859466719 +/- 4.72e-15]
+ 
+         TESTS::
+@@ -3621,7 +3621,7 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(3).Li()
++            sage: RBF(3).Li()  # abs tol 1e-15
+             [1.11842481454970 +/- 7.61e-15]
+         """
+         cdef RealBall res = self._new()
+@@ -3648,9 +3648,9 @@ cdef class RealBall(RingElement):
+ 
+         EXAMPLES::
+ 
+-            sage: RBF(sin(3)).beta(RBF(2/3).sqrt())
++            sage: RBF(sin(3)).beta(RBF(2/3).sqrt())  # abs tol 1e-13
+             [7.407661629415 +/- 1.07e-13]
+-            sage: RealBallField(100)(7/2).beta(1)
++            sage: RealBallField(100)(7/2).beta(1)  # abs tol 1e-30
+             [0.28571428571428571428571428571 +/- 5.23e-30]
+             sage: RealBallField(100)(7/2).beta(1, 1/2)
+             [0.025253813613805268728601584361 +/- 2.53e-31]
+@@ -3685,9 +3685,9 @@ cdef class RealBall(RingElement):
+ 
+             sage: RBF(1/2).gamma()
+             [1.772453850905516 +/- ...e-16]
+-            sage: RBF(gamma(3/2, RBF(2).sqrt()))
++            sage: RBF(gamma(3/2, RBF(2).sqrt()))  # abs tol 2e-17
+             [0.37118875695353 +/- 3.00e-15]
+-            sage: RBF(3/2).gamma_inc(RBF(2).sqrt())
++            sage: RBF(3/2).gamma_inc(RBF(2).sqrt())  # abs tol 2e-17
+             [0.37118875695353 +/- 3.00e-15]
+ 
+         .. SEEALSO::
+diff --git a/src/sage/symbolic/function.pyx b/src/sage/symbolic/function.pyx
+index 89cdce5..480a601 100644
+--- a/src/sage/symbolic/function.pyx
++++ b/src/sage/symbolic/function.pyx
+@@ -626,7 +626,7 @@ cdef class Function(SageObject):
+             sage: b = RBF(3/2, 1e-10)
+             sage: airy_ai(b)
+             airy_ai([1.500000000 +/- 1.01e-10])
+-            sage: gamma(b, 1)
++            sage: gamma(b, 1)  # abs tol 4.5e-9
+             [0.50728223 +/- 4.67e-9]
+             sage: hurwitz_zeta(b, b)
+             hurwitz_zeta([1.500000000 +/- 1.01e-10], [1.500000000 +/- 1.01e-10])
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/f5f7a86908daf60b25e66e6a189c51ada7e0a732.patch b/srcpkgs/sagemath/patches/f5f7a86908daf60b25e66e6a189c51ada7e0a732.patch
new file mode 100644
index 000000000000..ec0467757ee7
--- /dev/null
+++ b/srcpkgs/sagemath/patches/f5f7a86908daf60b25e66e6a189c51ada7e0a732.patch
@@ -0,0 +1,25 @@
+From f5f7a86908daf60b25e66e6a189c51ada7e0a732 Mon Sep 17 00:00:00 2001
+From: Antonio Rojas <arojas@archlinux.org>
+Date: Sat, 30 Oct 2021 10:21:52 +0200
+Subject: Fix test failure caused by new warning
+
+---
+ src/sage/lfunctions/pari.py | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/sage/lfunctions/pari.py b/src/sage/lfunctions/pari.py
+index 0aaf91c..33d5266 100644
+--- a/src/sage/lfunctions/pari.py
++++ b/src/sage/lfunctions/pari.py
+@@ -316,7 +316,7 @@ def lfun_number_field(K):
+         sage: L(3)
+         1.15202784126080
+         sage: L(0)
+-        0.000000000000000
++        ...0.000000000000000
+     """
+     return pari.lfuncreate(K)
+ 
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/skip-optional-dochtml.patch b/srcpkgs/sagemath/patches/skip-optional-dochtml.patch
new file mode 100644
index 000000000000..e49b18a52fbc
--- /dev/null
+++ b/srcpkgs/sagemath/patches/skip-optional-dochtml.patch
@@ -0,0 +1,13 @@
+diff --git a/src/bin/sage-runtests b/src/bin/sage-runtests
+index 288c889bd1..b9a4d3038a 100755
+--- a/src/bin/sage-runtests
++++ b/src/bin/sage-runtests
+@@ -15,7 +15,7 @@ os.environ['SAGE_STARTUP_FILE'] = os.path.join(DOT_SAGE, 'init-doctests.sage')
+ 
+ def _get_optional_defaults():
+     """Return the default value for the --optional flag."""
+-    optional = ['sage', 'dochtml', 'optional']
++    optional = ['sage', 'optional']
+ 
+     # This should be good-enough to determine if we are in a sage source
+     # repository working tree
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index 3f9a3e9e077f..d4130be12a7a 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -16,7 +16,7 @@ short_desc="Open source mathematics software"
 maintainer="Gonzalo Tornaría <tornaria@cmat.edu.uy>"
 license="GPL-3.0-or-later"
 homepage="http://sagemath.org/"
-distfiles="http://mirrors.mit.edu/sage/src/sage-$version.tar.gz"
+distfiles="https://mirrors.mit.edu/sage/src/sage-$version.tar.gz"
 checksum=b81e1fe22d1b990bf1230260241ead016470da1f2f7b260f562d50f74c2904c7
 python_version=3
 
@@ -47,6 +47,7 @@ noshlibprovides=yes
 
 post_extract() {
 	# sage wants to be built in place so let $wrksrc be a symlink
+	rm -rf $_SAGE_ROOT
 	mv -T $wrksrc $_SAGE_ROOT
 	ln -sfT $_SAGE_ROOT $wrksrc
 }
@@ -72,6 +73,11 @@ do_install() {
 	ln -sfT $_SAGE_ROOT/sage ${DESTDIR}/usr/bin/sage-${version}_${revision}
 }
 
+do_check() {
+	# since make check will build the docs, run test like this instead
+	./sage -tp ${XBPS_MAKEJOBS} --all
+}
+
 ### copied from sage-deps, to be kept in sync
 
 # hard dependencies
@@ -103,10 +109,9 @@ makedepends+="
  m4ri-devel m4rie-devel mpfi-devel ntl-devel perl-SVG rankwidth-devel
  singular sympow zn_poly symmetrica-devel planarity-devel qhull libqhull-devel
  gengetopt texinfo
+ brial-devel cliquer-devel gfan libbraiding-devel libhomfly-devel
+ lrcalc-devel nauty-devel palp tachyon
 "
 
-# TODO: standard
-# brial cliquer gfan libbraiding libhomfly lrcalc nauty palp tachyon
-
 # TODO: optional
-# 4ti2 coxeter3 libnauty libsemigroups lrslib perl_mongodb
+# 4ti2 coxeter3 libsemigroups lrslib pdf2svg perl_mongodb polymake

From b971fa9d0ce6f514e5a7749d9f14ae843ae57fbe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Mon, 22 Nov 2021 15:16:23 -0300
Subject: [PATCH 9/9] sagemath: more changes

 - do not install pytest, which is still broken (pending trac 31924)
 - add patch from sagemath trac 32892
 - replace the patch to fix the build of pyzmq on musl by a different
   one from sagemath trac 32828 which is what will be merged upstream
 - patch to fix doctest failure on musl (src/sage/misc/gperftools.py)
 - rebase on latest sympow rev to fix doctest failure on musl
   (src/sage/lfunctions/sympow.py)
 - enable check on CI to see what happens...
---
 ...hat-fixes-ctypes.util.find_library-c.patch |  64 +++++++++
 ...754ad30c6a1bd1fdbd6d62011055bf13b24a.patch |  27 ++++
 srcpkgs/sagemath/patches/fix-pyzmq-musl.patch |  15 --
 .../patches/trac-32828-fix-pyzmq.patch        | 134 ++++++++++++++++++
 srcpkgs/sagemath/template                     |  15 +-
 5 files changed, 235 insertions(+), 20 deletions(-)
 create mode 100644 srcpkgs/sagemath/patches/0001-Add-a-patch-that-fixes-ctypes.util.find_library-c.patch
 create mode 100644 srcpkgs/sagemath/patches/89b8754ad30c6a1bd1fdbd6d62011055bf13b24a.patch
 delete mode 100644 srcpkgs/sagemath/patches/fix-pyzmq-musl.patch
 create mode 100644 srcpkgs/sagemath/patches/trac-32828-fix-pyzmq.patch

diff --git a/srcpkgs/sagemath/patches/0001-Add-a-patch-that-fixes-ctypes.util.find_library-c.patch b/srcpkgs/sagemath/patches/0001-Add-a-patch-that-fixes-ctypes.util.find_library-c.patch
new file mode 100644
index 000000000000..4f89c2bd8fbc
--- /dev/null
+++ b/srcpkgs/sagemath/patches/0001-Add-a-patch-that-fixes-ctypes.util.find_library-c.patch
@@ -0,0 +1,64 @@
+From dc1a0e8168a9ffb4fbf07dd03c0846b4933a6dbe Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
+Date: Mon, 22 Nov 2021 23:57:37 -0300
+Subject: [PATCH] Add a patch that fixes ctypes.util.find_library('c')
+
+The issue causes a failure doctesting src/sage/misc/gperftools.py
+---
+ .../python3/patches/musl-find_library.patch   | 44 +++++++++++++++++++
+ 1 file changed, 44 insertions(+)
+ create mode 100644 build/pkgs/python3/patches/musl-find_library.patch
+
+diff --git a/build/pkgs/python3/patches/musl-find_library.patch b/build/pkgs/python3/patches/musl-find_library.patch
+new file mode 100644
+index 0000000000..82f436b407
+--- /dev/null
++++ b/build/pkgs/python3/patches/musl-find_library.patch
+@@ -0,0 +1,44 @@
++--- a/Lib/ctypes/util.py
+++++ b/Lib/ctypes/util.py
++@@ -204,6 +204,41 @@
++         def find_library(name, is64 = False):
++             return _get_soname(_findLib_crle(name, is64) or _findLib_gcc(name))
++ 
+++    elif True:
+++
+++        # Patched for Alpine Linux / musl - search manually system paths
+++        def _is_elf(filepath):
+++            try:
+++                with open(filepath, 'rb') as fh:
+++                    return fh.read(4) == b'\x7fELF'
+++            except:
+++                return False
+++
+++        def find_library(name):
+++            from glob import glob
+++            # absolute name?
+++            if os.path.isabs(name):
+++                return name
+++            # special case for libm, libcrypt and libpthread and musl
+++            if name in ['m', 'crypt', 'pthread']:
+++                name = 'c'
+++            elif name in ['libm.so', 'libcrypt.so', 'libpthread.so']:
+++                name = 'libc.so'
+++            # search in standard locations (musl order)
+++            paths = ['/lib', '/usr/local/lib', '/usr/lib']
+++            if 'LD_LIBRARY_PATH' in os.environ:
+++                paths = os.environ['LD_LIBRARY_PATH'].split(':') + paths
+++            for d in paths:
+++                f = os.path.join(d, name)
+++                if _is_elf(f):
+++                    return os.path.basename(f)
+++
+++                prefix = os.path.join(d, 'lib'+name)
+++                for suffix in ['.so', '.so.*']:
+++                    for f in glob('{0}{1}'.format(prefix, suffix)):
+++                        if _is_elf(f):
+++                            return os.path.basename(f)
+++
++     else:
++ 
++         def _findSoname_ldconfig(name):
+-- 
+2.34.0
+
diff --git a/srcpkgs/sagemath/patches/89b8754ad30c6a1bd1fdbd6d62011055bf13b24a.patch b/srcpkgs/sagemath/patches/89b8754ad30c6a1bd1fdbd6d62011055bf13b24a.patch
new file mode 100644
index 000000000000..ea05b2b6a524
--- /dev/null
+++ b/srcpkgs/sagemath/patches/89b8754ad30c6a1bd1fdbd6d62011055bf13b24a.patch
@@ -0,0 +1,27 @@
+From 89b8754ad30c6a1bd1fdbd6d62011055bf13b24a Mon Sep 17 00:00:00 2001
+From: Tobias Diez <code@tobiasdiez.com>
+Date: Wed, 17 Nov 2021 22:24:32 +0100
+Subject: Fix exit code for pytest in case of no matched files
+
+---
+ src/bin/sage-runtests | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/src/bin/sage-runtests b/src/bin/sage-runtests
+index 882456d..8b362ca 100755
+--- a/src/bin/sage-runtests
++++ b/src/bin/sage-runtests
+@@ -157,6 +157,10 @@ if __name__ == "__main__":
+         if args.verbose:
+             pytest_options.append("-v")
+         exit_code_pytest = pytest.main(pytest_options + args.filenames)
++        if exit_code_pytest == 5:
++            # Exit code 5 means there were no test files, pass in this case
++            exit_code_pytest = 0
++
+     except ModuleNotFoundError:
+         print("Pytest is not installed, skip checking tests that rely on it.")
+ 
+-- 
+cgit v1.0-1-gd88e
+
diff --git a/srcpkgs/sagemath/patches/fix-pyzmq-musl.patch b/srcpkgs/sagemath/patches/fix-pyzmq-musl.patch
deleted file mode 100644
index 9190830d835e..000000000000
--- a/srcpkgs/sagemath/patches/fix-pyzmq-musl.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/build/pkgs/pyzmq/spkg-install.in b/build/pkgs/pyzmq/spkg-install.in
-index 0ce404ee5a..b7260c6d27 100644
---- a/build/pkgs/pyzmq/spkg-install.in
-+++ b/build/pkgs/pyzmq/spkg-install.in
-@@ -1,6 +1,9 @@
- # Since we use environment vars we have to generate setup.cfg
- 
--echo "[build_ext]" > src/setup.cfg
-+echo "[global]" > src/setup.cfg
-+echo "skip_check_zmq = True" >> src/setup.cfg
-+
-+echo "[build_ext]" >> src/setup.cfg
- 
- # (I tried putting quotes around $SAGE_LOCAL to allow for spaces in
- # the path---which is never used but is a good habit to support---but
diff --git a/srcpkgs/sagemath/patches/trac-32828-fix-pyzmq.patch b/srcpkgs/sagemath/patches/trac-32828-fix-pyzmq.patch
new file mode 100644
index 000000000000..426932c95c9b
--- /dev/null
+++ b/srcpkgs/sagemath/patches/trac-32828-fix-pyzmq.patch
@@ -0,0 +1,134 @@
+diff --git a/build/pkgs/pyzmq/checksums.ini b/build/pkgs/pyzmq/checksums.ini
+index 3824fd2ce9..20509db618 100644
+--- a/build/pkgs/pyzmq/checksums.ini
++++ b/build/pkgs/pyzmq/checksums.ini
+@@ -1,5 +1,5 @@
+ tarball=pyzmq-VERSION.tar.gz
+-sha1=50abf6482a6395f15dce0b2774021e12c9f4faad
+-md5=f261acf884460e93d30f7113c8e9242e
+-cksum=1661206741
++sha1=d8bb8cb345c0bfd9e67a95ac796bf4b10354dde6
++md5=ecf13c72fbea05ba5ddc771295409d48
++cksum=1680251717
+ upstream_url=https://pypi.io/packages/source/p/pyzmq/pyzmq-VERSION.tar.gz
+diff --git a/build/pkgs/pyzmq/package-version.txt b/build/pkgs/pyzmq/package-version.txt
+index 0398faf11c..8326e27f9b 100644
+--- a/build/pkgs/pyzmq/package-version.txt
++++ b/build/pkgs/pyzmq/package-version.txt
+@@ -1 +1 @@
+-22.2.1
++22.3.0
+diff --git a/build/pkgs/pyzmq/spkg-install.in b/build/pkgs/pyzmq/spkg-install.in
+index 0ce404ee5a..069d87767f 100644
+--- a/build/pkgs/pyzmq/spkg-install.in
++++ b/build/pkgs/pyzmq/spkg-install.in
+@@ -1,17 +1,11 @@
+-# Since we use environment vars we have to generate setup.cfg
+-
+-echo "[build_ext]" > src/setup.cfg
+-
+-# (I tried putting quotes around $SAGE_LOCAL to allow for spaces in
+-# the path---which is never used but is a good habit to support---but
+-# that simply does not work. Sorry.)
+-
+-echo "library_dirs = $SAGE_LOCAL/lib/" >> src/setup.cfg
+-echo "include_dirs = $SAGE_LOCAL/include/" >> src/setup.cfg
+-
+-echo "[configure]" >> src/setup.cfg
+-
+ cd src
+ 
++# Generate setup.cfg
++cat > setup.cfg <<EOF
++[global]
++zmq_prefix = $SAGE_LOCAL
++no_libzmq_extension = True
++EOF
++
+ # Configure and install
+ sdh_pip_install .
+diff --git a/build/pkgs/setuptools/checksums.ini b/build/pkgs/setuptools/checksums.ini
+index 6a280871e7..d9290d04ff 100644
+--- a/build/pkgs/setuptools/checksums.ini
++++ b/build/pkgs/setuptools/checksums.ini
+@@ -1,5 +1,5 @@
+ tarball=setuptools-VERSION.tar.gz
+-sha1=5d97de0e774b2269c85685a4aa8fd5956bcfd2bb
+-md5=ff20ab7e0d51c5ad0a9438c50e598c06
+-cksum=3564252314
++sha1=cd4e5d1f7c47f86354fc89d040d869cde244da3b
++md5=79b36f59270a6f2e45d6a9a0c6dc68c1
++cksum=430889097
+ upstream_url=https://pypi.io/packages/source/s/setuptools/setuptools-VERSION.tar.gz
+diff --git a/build/pkgs/setuptools/package-version.txt b/build/pkgs/setuptools/package-version.txt
+index e6ea636051..aec1257e4c 100644
+--- a/build/pkgs/setuptools/package-version.txt
++++ b/build/pkgs/setuptools/package-version.txt
+@@ -1 +1 @@
+-58.2.0
++59.2.0
+diff --git a/build/pkgs/zeromq/checksums.ini b/build/pkgs/zeromq/checksums.ini
+index ea8c36bce5..dc802612dd 100644
+--- a/build/pkgs/zeromq/checksums.ini
++++ b/build/pkgs/zeromq/checksums.ini
+@@ -1,4 +1,5 @@
+ tarball=zeromq-VERSION.tar.gz
+-sha1=1132f839d703486c4ee1cf22f056585dfbb329c2
+-md5=a1c95b34384257e986842f4d006957b8
+-cksum=136261411
++sha1=47277a64749049123d1401600e8cfbab10a3ae28
++md5=c897d4005a3f0b8276b00b7921412379
++cksum=1500782345
++upstream_url=https://github.com/zeromq/libzmq/releases/download/vVERSION/zeromq-VERSION.tar.gz
+diff --git a/build/pkgs/zeromq/package-version.txt b/build/pkgs/zeromq/package-version.txt
+index df0228dfae..eda862a98c 100644
+--- a/build/pkgs/zeromq/package-version.txt
++++ b/build/pkgs/zeromq/package-version.txt
+@@ -1 +1 @@
+-4.2.5
++4.3.4
+diff --git a/build/pkgs/zeromq/patches/getrandom.patch b/build/pkgs/zeromq/patches/getrandom.patch
+deleted file mode 100644
+index e665114e1c..0000000000
+--- a/build/pkgs/zeromq/patches/getrandom.patch
++++ /dev/null
+@@ -1,39 +0,0 @@
+-Patch taken from upstream git repo
+-and after running aclocal && autoconf
+-and removing changes to autotools input files
+-
+-commit 4ff814f204ee38177a392526cf12c8c0019b480f
+-Author: Luca Boccassi <luca.boccassi@gmail.com>
+-Date:   Wed May 9 10:41:20 2018 +0100
+-
+-    Problem: getrandom test does not check if it's working
+-
+-    Solution: check return value in autoconf and CMake. On some platforms
+-    the function is available but not implemented (eg: GNU/Hurd).
+-
+-diff -ru zeromq-4.2.5//builds/cmake/Modules/ZMQSourceRunChecks.cmake b/builds/cmake/Modules/ZMQSourceRunChecks.cmake
+---- zeromq-4.2.5//builds/cmake/Modules/ZMQSourceRunChecks.cmake	2018-03-23 20:33:36.000000000 +0100
+-+++ b/builds/cmake/Modules/ZMQSourceRunChecks.cmake	2018-07-24 12:39:23.340035053 +0200
+-@@ -287,7 +287,8 @@
+- int main (int argc, char *argv [])
+- {
+-     char buf[4];
+--    getrandom(buf, 4, 0);
+-+    int rc = getrandom(buf, 4, 0);
+-+    return rc == -1 ? 1 : 0;
+- }
+- "
+-     ZMQ_HAVE_GETRANDOM)
+-diff -ru zeromq-4.2.5//configure b/configure
+---- zeromq-4.2.5//configure	2018-03-23 20:34:18.000000000 +0100
+-+++ b/configure	2018-07-24 12:39:49.018035120 +0200
+-@@ -23315,7 +23315,8 @@
+- int main (int argc, char *argv [])
+- {
+-     char buf[4];
+--    getrandom(buf, 4, 0);
+-+    int rc = getrandom(buf, 4, 0);
+-+    return rc == -1 ? 1 : 0;
+- }
+- 
+- _ACEOF
diff --git a/srcpkgs/sagemath/template b/srcpkgs/sagemath/template
index d4130be12a7a..622ee06d85b8 100644
--- a/srcpkgs/sagemath/template
+++ b/srcpkgs/sagemath/template
@@ -29,7 +29,7 @@ case ${version} in
 esac
 
 # for now, skip check in ci, since we still have a few tests failing
-make_check=ci-skip
+#make_check=ci-skip
 
 # for now, just build native; we'll worry about cross later
 # besides, some dependencies are nocross (e.g. ntl)
@@ -56,10 +56,15 @@ do_clean() {
 	rm -rf $wrksrc $_SAGE_ROOT
 }
 
-post_build() {
-	# install pytest for more tests
-	./sage -i pytest
-}
+# DISABLED pytest since it brings more harm than good
+# it seems currently all it does is to look for files matching
+# *_test.py and run pytest on those, but I don't think these are meant
+# to be run on pytest (and one even gives a failure...)
+#
+# post_build() {
+# 	# install pytest for more tests
+# 	./sage -i pytest
+# }
 
 do_install() {
 	vcopy $_SAGE_ROOT usr/lib/