Re: [PR PATCH] [Updated] [WIP] New package: sagemath-9.5.beta5

[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.beta5
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 34773deb2ca2fdbea3d61f5cf93e9aec8ac79beb 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 1/6] 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 9bda4cb647d64026e2e82f99ef8a1a251c96c628 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 2/6] 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 21a5106c8b7b48ca751cd71503dc9b0e31f9cc38 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 3/6] 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 38f69160565dc1334195cc3b549e0e99f128056f 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 4/6] 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 4dc5be66df29ef22f8d1a02fc42a974e442686c4 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 5/6] 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 65e8719b8e0e6ee7dc25073e158b843eef7f94e4 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 6/6] 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