[gentoo-commits] proj/sci:master commit in: sci-mathematics/Macaulay2/, sci-mathematics/Macaulay2/files/

[Andrew Ammerlaan]

commit:     1331916dfa9c5dfa3956973cdf12ad37c4c19634
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 06:30:24 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 06:30:24 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1331916d

sci-mathematics/Macaulay: remove pack, py2 only

build system explicitly looks for py2

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-mathematics/Macaulay2/Macaulay2-9999.ebuild    | 178 ---------------------
 .../Macaulay2/files/70Macaulay2-gentoo.el          |  11 --
 sci-mathematics/Macaulay2/files/9999-lapack.patch  |  50 ------
 .../files/9999-paths-of-external-programs.patch    |  73 ---------
 .../Macaulay2/files/paths-of-dependencies.patch    |  48 ------
 sci-mathematics/Macaulay2/metadata.xml             |  15 --
 6 files changed, 375 deletions(-)

diff --git a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild
deleted file mode 100644
index 5b4e608c7..000000000
--- a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild
+++ /dev/null
@@ -1,178 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools elisp-common flag-o-matic git-r3 python-single-r1 toolchain-funcs
-
-FACTORY="factory-4.0.0+m4"
-FACTORY_GFTABLES="factory.4.0.1-gftables"
-
-DESCRIPTION="Research tool for commutative algebra and algebraic geometry"
-HOMEPAGE="https://faculty.math.illinois.edu/Macaulay2"
-BASE_URI="https://faculty.math.illinois.edu/Macaulay2/Downloads/OtherSourceCode/"
-SRC_URI="
-	${BASE_URI}/${FACTORY}.tar.gz
-	${BASE_URI}/${FACTORY_GFTABLES}.tar.gz
-	${BASE_URI}/gtest-1.7.0.tar.gz"
-EGIT_REPO_URI="git://github.com/Macaulay2/M2.git"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS=""
-IUSE="debug emacs +optimization"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-	sys-process/time
-	virtual/pkgconfig
-	app-arch/unzip
-	app-text/dos2unix"
-# Unzip and dos2unix just for normaliz
-
-RDEPEND="${PYTHON_DEPS}
-	sys-libs/gdbm
-	dev-libs/ntl
-	sci-mathematics/pari[gmp]
-	>=sys-libs/readline-6.1
-	dev-libs/libxml2:2
-	sci-mathematics/flint[gc(-)]
-	sci-mathematics/frobby
-	sci-mathematics/4ti2
-	sci-mathematics/nauty
-	>=sci-mathematics/normaliz-2.8
-	sci-mathematics/gfan
-	sci-libs/mpir[cxx]
-	dev-libs/mpfr
-	sci-libs/cdd+
-	sci-libs/cddlib
-	sci-libs/lrslib[gmp]
-	virtual/blas
-	virtual/lapack
-	dev-util/ctags
-	sys-libs/ncurses
-	>=dev-libs/boehm-gc-7.2_alpha6[threads]
-	dev-libs/libatomic_ops
-	emacs? ( app-editors/emacs )"
-
-SITEFILE=70Macaulay2-gentoo.el
-
-S="${WORKDIR}/${PN}-${PV}/"
-
-RESTRICT="mirror"
-
-src_unpack (){
-	# unpack "Normaliz2.8.zip"
-	git-r3_src_unpack
-	# Undo one level of directory until git allows to checkout
-	# subdirectories
-	mv "${S}"/M2/* "${S}" || die
-	# Need to get rid of this now because install wants this location later
-	rm -r "${S}/M2" || die
-}
-
-pkg_setup () {
-	tc-export CC CPP CXX PKG_CONFIG
-	append-cppflags "-I/usr/include/frobby"
-	# gtest needs python:2
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	# Put updated Normaliz.m2 in place
-	# cp "${WORKDIR}/Normaliz2.8/Macaulay2/Normaliz.m2" \
-	# 	"${S}/Macaulay2/packages" || die
-	# dos2unix "${S}/Macaulay2/packages/Normaliz.m2" || die
-
-	# Patching .m2 files to look for external programs in
-	# /usr/bin
-	eapply "${FILESDIR}"/${PV}-paths-of-external-programs.patch
-
-	# Shortcircuit lapack tests
-	eapply "${FILESDIR}"/${PV}-lapack.patch
-
-	eapply_user
-
-	# Factory is a statically linked library which (in this flavor) are not used by any
-	# other program. We build it internally and don't install it.
-	cp "${DISTDIR}/${FACTORY}.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	cp "${DISTDIR}/${FACTORY_GFTABLES}.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-	# Macaulay2 developers want that gtest is built internally because
-	# the documentation says it may fail if build with options not the
-	# same as the tested program.
-	cp "${DISTDIR}/gtest-1.7.0.tar.gz" "${S}/BUILD/tarfiles/" \
-		|| die "copy failed"
-
-	eautoreconf
-}
-
-src_configure (){
-	# Recommended in bug #268064 Possibly unecessary
-	# but should not hurt anybody.
-	if ! use emacs; then
-		tags="ctags"
-	fi
-
-	# configure instead of econf to enable install with --prefix
-	./configure LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" \
-		--prefix="${D}/usr" \
-		--disable-encap \
-		--disable-strip \
-		--with-issue=Gentoo \
-		$(use_enable optimization optimize) \
-		$(use_enable debug) \
-		--enable-build-libraries="factory" \
-		--with-unbuilt-programs="4ti2 gfan normaliz nauty cddplus lrslib" \
-		|| die "failed to configure Macaulay"
-}
-
-src_compile() {
-	# Parallel build not supported yet
-	# emake -j1
-	# For trunk builds we may wish to ignore example errors
-	emake IgnoreExampleErrors=true -j1
-
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs" || die
-		elisp-compile *.el
-	fi
-}
-
-src_test() {
-	# No parallel tests yet & Need to increase the time
-	# limit for long running tests in Schubert2 to pass
-	emake TLIMIT=550 -j1 check
-}
-
-src_install () {
-	# Parallel install not supported yet
-	# NumericalAlgebraicGeometry fails (during install too?)
-	emake IgnoreExampleErrors=true -j1 install
-
-	# Remove emacs files and install them in the
-	# correct place if use emacs
-	rm -rf "${ED}"/usr/share/emacs/site-lisp || die
-	if use emacs; then
-		cd "${S}/Macaulay2/emacs" || die
-		elisp-install ${PN} *.elc *.el
-		elisp-site-file-install "${FILESDIR}/${SITEFILE}"
-	fi
-}
-
-pkg_postinst() {
-	if use emacs; then
-		elisp-site-regen
-		elog "If you want to set a hot key for Macaulay2 in Emacs add a line similar to"
-		elog "(global-set-key [ f12 ] 'M2)"
-		elog "in order to set it to F12 (or choose a different one)."
-	fi
-}
-
-pkg_postrm() {
-	use emacs && elisp-site-regen
-}

diff --git a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el b/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
deleted file mode 100644
index ac86e2132..000000000
--- a/sci-mathematics/Macaulay2/files/70Macaulay2-gentoo.el
+++ /dev/null
@@ -1,11 +0,0 @@
-;; sci-mathematics/Macaulay2 init file
-
-(add-to-list 'load-path "/usr/share/emacs/site-lisp/Macaulay2")
-
-(defvar M2-exe "/usr/bin/M2" "*The default Macaulay2 executable name.")
-(autoload 'M2 "M2.el" "Run Macaulay 2 in a buffer." t)
-(autoload 'Macaulay2 "M2" "Run Macaulay 2 in a buffer, non-interactive." t)
-(autoload 'M2-mode "M2" "Macaulay 2 editing mode" t)
-(autoload 'm2-mode "M2" "Macaulay 2 editing mode, name in lower case" t)
-(autoload 'm2-comint-mode "M2" "Macaulay 2 command interpreter mode, name in lower case" t)
-(setq auto-mode-alist (append auto-mode-alist '(("\\.m2$" . M2-mode))))
\ No newline at end of file

diff --git a/sci-mathematics/Macaulay2/files/9999-lapack.patch b/sci-mathematics/Macaulay2/files/9999-lapack.patch
deleted file mode 100644
index e9a434eeb..000000000
--- a/sci-mathematics/Macaulay2/files/9999-lapack.patch
+++ /dev/null
@@ -1,50 +0,0 @@
---- configure.ac	2012-10-24 09:29:55.240498786 -0700
-+++ configure.ac.2	2012-10-30 15:07:27.172846300 -0700
-@@ -1285,46 +1285,7 @@
- done
- test $BUILD_factory = yes && BUILTLIBS="$SINGULARLIBS $BUILTLIBS"
- 
--# we need to do the fortran library testing last, in case AC_SEARCH_LIBS adds
--# one of them to $LIBS, making it impossible to check for the presence of C or
--# C++ libraries.  (I'm not sure why putting -llapack on the gcc command line
--# needlessly causes the library to be linked against.)
--FORTRANUSED=no
--if test "$LAPACK" = yes
--then AC_MSG_CHECKING([whether the vecLib framework is available])
--     SAVELIBS=$LIBS LIBS="-framework vecLib $LIBS"
--     AC_LANG(C)
--     AC_LINK_IFELSE(
--	 [AC_LANG_PROGRAM(,[sgemv_();dgetrf_();])],
--	 [
--	     AC_MSG_RESULT(yes)
--	     ],
--	 [
--	     AC_MSG_RESULT(no)
--	     LIBS=$SAVELIBS
--	     FORTRANUSED=yes
--	     if test $BUILD_lapack = no
--	     then AC_LANG(Fortran)
--	     	  if test "$FC" = ""
--		  then AC_MSG_ERROR(no fortran compiler found)
--		  else AC_MSG_NOTICE(using fortran compiler $FC)
--		  fi
--		  AC_SEARCH_LIBS(sgemv,blas f77blas,,BUILD_lapack=yes)
--		  AC_SEARCH_LIBS(dgetrf,lapack,,BUILD_lapack=yes)
--	     fi
--	 ])
--fi
--test $BUILD_lapack = yes && BUILTLIBS="-llapack -lblas $BUILTLIBS"
--
--if test $BUILD_lapack = yes
--then # test whether the fortran compiler can handle lapack, which, starting with
--     # version 3.2, requires fortran 90, not fortran 77
--    AC_LANG(Fortran)
--    AC_MSG_CHECKING([whether the fortran compiler is modern enough for lapack])
--    AC_COMPILE_IFELSE([instrinsic maxloc],
--	AC_MSG_ERROR(the fortran compiler ($FC) does not support the Fortran 90 language required for compiling lapack),
--	AC_MSG_RESULT(yes))
--fi
-+BUILTLIBS="$(${PKG_CONFIG} --libs lapack) $BUILTLIBS"
- 
- if test $BUILD_memtailor = yes
- then BUILTLIBS="-lmemtailor $BUILTLIBS"

diff --git a/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch b/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch
deleted file mode 100644
index 4c090deec..000000000
--- a/sci-mathematics/Macaulay2/files/9999-paths-of-external-programs.patch
+++ /dev/null
@@ -1,73 +0,0 @@
-diff -U 3 -dHrN M2source/Macaulay2/packages/FourTiTwo.m2 M2source.patch/Macaulay2/packages/FourTiTwo.m2
---- M2source/Macaulay2/packages/FourTiTwo.m2	2011-09-22 14:36:51.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/FourTiTwo.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -47,7 +47,7 @@
- 
- path'4ti2 = (options FourTiTwo).Configuration#"path"
- -- NOTE: the absolute path should be put into the .init file for 4ti2 inside the .Macaulay2 directory.
--if path'4ti2 == "" then path'4ti2 = prefixDirectory | currentLayout#"programs"
-+if path'4ti2 == "" then path'4ti2 = "/usr/bin/"
- 
- getFilename = () -> (
-      filename := temporaryFileName();
-diff -U 3 -dHrN M2source/Macaulay2/packages/gfanInterface.m2 M2source.patch/Macaulay2/packages/gfanInterface.m2
---- M2source/Macaulay2/packages/gfanInterface.m2	2011-05-14 12:00:59.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/gfanInterface.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -25,7 +25,7 @@
-      }
- 
- gfan'path = gfanInterface#Options#Configuration#"path"
--if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs"
-+if gfan'path == "" then gfan'path = "/usr/bin/"
- if instance(gfan'path, String) then gfan'path = {gfan'path}
- if not instance(gfan'path,List) then error "expected configuration option gfan'path to be a list of strings or a string"
- gfan'path = join(
-diff -U 3 -dHrN M2source/Macaulay2/packages/NautyGraphs.m2 M2source.patch/Macaulay2/packages/NautyGraphs.m2
---- M2source/Macaulay2/packages/NautyGraphs.m2	2011-08-26 11:05:30.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/NautyGraphs.m2	2011-09-24 21:25:53.000000000 +0100
-@@ -32,7 +32,7 @@
- -- Check the ~/.Macaulay2/init-NautyGraphs.m2 file for the absolute path.
- -- If it's not there, then use the M2-Programs directory.
- nauty'path = (options NautyGraphs).Configuration#"path";
--if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
-+if nauty'path == "" then nauty'path = "/usr/bin/";
- 
- -------------------
- -- Exports
-diff -U 3 -dHrN M2source/Macaulay2/packages/Nauty.m2 M2source.patch/Macaulay2/packages/Nauty.m2
---- M2source/Macaulay2/packages/Nauty.m2	2011-08-26 11:05:30.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/Nauty.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -48,7 +48,8 @@
- -- Check the ~/.Macaulay2/init-Nauty.m2 file for the absolute path.
- -- If it's not there, then use the M2-Programs directory.
- nauty'path = (options Nauty).Configuration#"path";
--if nauty'path == "" then nauty'path = prefixDirectory | currentLayout#"programs";
-+if nauty'path == "" then nauty'path = "/usr/bin/";
-+
- 
- -------------------
- -- Exports
-diff -U 3 -dHrN M2source/Macaulay2/packages/Normaliz.m2 M2source.patch/Macaulay2/packages/Normaliz.m2
---- M2source/Macaulay2/packages/Normaliz.m2	2011-05-25 16:47:50.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/Normaliz.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -166,7 +166,7 @@
-         nmzExec="normaliz";
-     );
- --    return nmzExec;
--    return prefixDirectory | currentLayout#"programs" | nmzExec;
-+    return "/usr/bin/" | nmzExec;
- );
- 
- 
-diff -U 3 -dHrN M2source/Macaulay2/packages/StatePolytope.m2 M2source.patch/Macaulay2/packages/StatePolytope.m2
---- M2source/Macaulay2/packages/StatePolytope.m2	2010-09-10 16:47:20.000000000 +0100
-+++ M2source.patch/Macaulay2/packages/StatePolytope.m2	2011-09-24 21:24:12.000000000 +0100
-@@ -31,7 +31,7 @@
- 
- 
- gfanCommand = (options StatePolytope)#Configuration#"gfan command"
--if gfanCommand === "gfan" then gfanCommand = prefixDirectory | currentLayout#"programs" | gfanCommand
-+if gfanCommand === "gfan" then gfanCommand = "/usr/bin/" | gfanCommand
- gfanCommand = "!" | gfanCommand
- 
- --The next two functions print out the ring and the ideal in the format required by gfan

diff --git a/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch b/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch
deleted file mode 100644
index f8117a5fa..000000000
--- a/sci-mathematics/Macaulay2/files/paths-of-dependencies.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-diff -rupN 1.3.1/Macaulay2/packages/FourTiTwo.m2 1.3.1-pathspatched/Macaulay2/packages/FourTiTwo.m2
---- 1.3.1/Macaulay2/packages/FourTiTwo.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/FourTiTwo.m2	2009-11-16 11:41:01.000000000 +0100
-@@ -47,7 +47,7 @@ export {
- 
- path'4ti2 = (options FourTiTwo).Configuration#"path"
- -- NOTE: the absolute path should be put into the .init file for 4ti2 inside the .Macaulay2 directory.
--if path'4ti2 == "" then path'4ti2 = prefixDirectory | currentLayout#"programs"
-+if path'4ti2 == "" then path'4ti2 = "/usr/bin/"
- 
- getFilename = () -> (
-      filename := temporaryFileName();
-diff -rupN 1.3.1/Macaulay2/packages/gfanInterface.m2 1.3.1-pathspatched/Macaulay2/packages/gfanInterface.m2
---- 1.3.1/Macaulay2/packages/gfanInterface.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/gfanInterface.m2	2009-11-16 11:41:17.000000000 +0100
-@@ -26,7 +26,7 @@ export {
-      }
- 
- gfan'path = gfanInterface#Options#Configuration#"path"
--if gfan'path == "" then gfan'path = prefixDirectory | currentLayout#"programs"
-+if gfan'path == "" then gfan'path = "/usr/bin/"
- 
- fig2dev'path = gfanInterface#Options#Configuration#"fig2devpath"
- 
-diff -rupN 1.3.1/Macaulay2/packages/Normaliz.m2 1.3.1-pathspatched/Macaulay2/packages/Normaliz.m2
---- 1.3.1/Macaulay2/packages/Normaliz.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/Normaliz.m2	2009-11-16 11:42:01.000000000 +0100
-@@ -30,7 +30,7 @@ export{setNmzExecPath, getNmzExecPath,
- 
- 
- -- initialising some values
--nmzExecPath=prefixDirectory|currentLayout#"programs";
-+nmzExecPath="/usr/bin/";
- nmzDataPath="";
- nmzFilename="";
- nmzUserCalled=true;  -- wether the user calls a method
-diff -rupN 1.3.1/Macaulay2/packages/StatePolytope.m2 1.3.1-pathspatched/Macaulay2/packages/StatePolytope.m2
---- 1.3.1/Macaulay2/packages/StatePolytope.m2	2009-11-12 18:40:50.000000000 +0100
-+++ 1.3.1-pathspatched/Macaulay2/packages/StatePolytope.m2	2009-11-16 11:41:13.000000000 +0100
-@@ -31,7 +31,7 @@ export { 
- 
- 
- gfanCommand = (options StatePolytope)#Configuration#"gfan command"
--if gfanCommand === "gfan" then gfanCommand = prefixDirectory | currentLayout#"programs" | gfanCommand
-+if gfanCommand === "gfan" then gfanCommand = "/usr/bin/" | gfanCommand
- gfanCommand = "!" | gfanCommand
- 
- --The next two functions print out the ring and the ideal in the format required by gfan

diff --git a/sci-mathematics/Macaulay2/metadata.xml b/sci-mathematics/Macaulay2/metadata.xml
deleted file mode 100644
index 703c18dee..000000000
--- a/sci-mathematics/Macaulay2/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tom111@×××.de</email>
-		<name>Thomas Kahle</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-mathematics@g.o</email>
-		<name>Gentoo Mathematics Project</name>
-	</maintainer>
-	<use>
-		<flag name="optimization">Disable to build with -O0 for debugging.</flag>
-	</use>
-</pkgmetadata>