sci-libs/adolc: move large patches to devspace

Signed-off-by: Sam James <sam@gentoo.org>

7 files changed, 16 insertions, 611 deletions

diff --git a/sci-libs/adolc/Manifest b/sci-libs/adolc/Manifest
index d392825b3a04..2fa163cefb08 100644
--- a/sci-libs/adolc/Manifest
+++ b/sci-libs/adolc/Manifest
@@ -1 +1,2 @@
+DIST adolc-2.7.2-patches.tar.bz2 6227 BLAKE2B 6ed9ca3c3128233308b6f4a57d839ac668a031a4d48e612b79929541b496dff67e463197c3c5233bda459fba17422827df6c81fba986ea7fe2affbee2cb8cbf0 SHA512 b468753efbde773c5c7d7f0211abee049193d9b64405ae57a4a902a93a4c06e4f205f531aeee9f30d7dddef19243e1a76b77a8e8727d8e36ee3867f5990e2fbb
 DIST adolc-2.7.2.tar.gz 2447479 BLAKE2B 0f871ce1dcb50bb14684e45e265cf45807f514dd3ca0dbaaedede2c7117d34cc5a34b0096a34c8ec37023e50aec7fd4be6561819d6297771e7f7fcaa7ba0e507 SHA512 b896650077367fd7388a6c5a40e5d8bb3f19af9e3bc5b067fd1d9a769809b77ccdfb5ef11ef481ab791c0f040401aaed0053cba55d4c2a3383c0d056122280f6
diff --git a/sci-libs/adolc/adolc-2.7.2.ebuild b/sci-libs/adolc/adolc-2.7.2.ebuild
index 0f101d7e1fbb..db20fd6e78a1 100644
--- a/sci-libs/adolc/adolc-2.7.2.ebuild
+++ b/sci-libs/adolc/adolc-2.7.2.ebuild
@@ -13,6 +13,7 @@ if [[ ${PV} == *9999 ]]; then
 	EGIT_REPO_URI="https://github.com/coin-or/ADOL-C"
 else
 	SRC_URI="https://github.com/coin-or/ADOL-C/archive/releases/${PV}.tar.gz -> ${P}.tar.gz"
+	SRC_URI+=" https://dev.gentoo.org/~sam/distfiles/${CATEGORY}/${PN}/${PN}-2.7.2-patches.tar.bz2"
 	KEYWORDS="~alpha amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv x86 ~amd64-linux ~x86-linux"
 	S="${WORKDIR}/ADOL-C-releases-${PV}"
 fi
@@ -28,10 +29,10 @@ RDEPEND="
 DEPEND="${RDEPEND}"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-2.5.0-no-colpack.patch
-	"${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch
-	"${FILESDIR}"/${PN}-2.6.2-dash.patch
-	"${FILESDIR}"/${P}-swig-python-configure.patch
+	"${WORKDIR}"/${PN}-2.5.0-no-colpack.patch
+	"${WORKDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch
+	"${WORKDIR}"/${PN}-2.6.2-dash.patch
+	"${WORKDIR}"/${P}-swig-python-configure.patch
 )
 
 src_prepare() {
diff --git a/sci-libs/adolc/adolc-9999.ebuild b/sci-libs/adolc/adolc-9999.ebuild
index eeaa03bdcee1..cbdfaa7bdb8d 100644
--- a/sci-libs/adolc/adolc-9999.ebuild
+++ b/sci-libs/adolc/adolc-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -11,6 +11,7 @@ HOMEPAGE="https://projects.coin-or.org/ADOL-C/"
 if [[ ${PV} == *9999 ]]; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/coin-or/ADOL-C"
+	SRC_URI="https://dev.gentoo.org/~sam/distfiles/${CATEGORY}/${PN}/${PN}-2.7.2-patches.tar.bz2"
 else
 	SRC_URI="https://github.com/coin-or/ADOL-C/archive/releases/${PV}.tar.gz -> ${P}.tar.gz"
 	KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
@@ -28,11 +29,16 @@ RDEPEND="
 DEPEND="${RDEPEND}"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-2.5.0-no-colpack.patch
-	"${FILESDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch
-	"${FILESDIR}"/${PN}-2.6.2-dash.patch
+	"${WORKDIR}"/${PN}-2.5.0-no-colpack.patch
+	"${WORKDIR}"/${PN}-2.5.0-pkgconfig-no-ldflags.patch
+	"${WORKDIR}"/${PN}-2.6.2-dash.patch
 )
 
+src_unpack() {
+	git-r3_src_unpack
+	default
+}
+
 src_prepare() {
 	default
 	eautoreconf
diff --git a/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch b/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch
deleted file mode 100644
index 779890c8cf2b..000000000000
--- a/sci-libs/adolc/files/adolc-2.5.0-no-colpack.patch
+++ /dev/null
@@ -1,57 +0,0 @@
- autoconf/colpack.m4 | 23 +++++++++++++----------
- 1 file changed, 13 insertions(+), 10 deletions(-)
-
-diff --git a/autoconf/colpack.m4 b/autoconf/colpack.m4
-index 9792786..bd4ba5e 100644
---- a/autoconf/colpack.m4
-+++ b/autoconf/colpack.m4
-@@ -8,20 +8,20 @@ AC_ARG_WITH(colpack,
- AS_HELP_STRING([--with-colpack=DIR],[path to the colpack library and headers [default=system libraries]])],
- [
- colpack=$withval
--COLPACK_CFLAGS="-I$colpack/include"
--if test x${_lib} != xlib ; then
--   D[[0]]="$colpack/${_lib}"
--   D[[1]]="$colpack/lib"
--else
--   D[[0]]="$colpack/${_lib}"
--fi
- ],
- [
- COLPACK_CFLAGS=""
- COLPACK_LIBS="-lColPack"
- D[[0]]=""
- ])
--
-+if test x$colpack != xno; then
-+COLPACK_CFLAGS="-I$colpack/include"
-+if test x${_lib} != xlib ; then
-+   D[[0]]="$colpack/${_lib}"
-+   D[[1]]="$colpack/lib"
-+else
-+   D[[0]]="$colpack/${_lib}"
-+fi
- AC_LANG_PUSH([C++])
- save_CXXFLAGS="$CXXFLAGS"
- save_CPPFLAGS="$CPPFLAGS"
-@@ -33,8 +33,8 @@ have_colpackheaders=no
- CPPFLAGS="$save_CPPFLAGS"
- CXXFLAGS="$save_CXXFLAGS"
- ])
--for ((i=0; i < ${#D[@]} ; i++)); do
--COLPACK_LIBDIR="${D[[$i]]}"
-+for i in ${D[@]}; do
-+COLPACK_LIBDIR="${i}"
- if test -n "$COLPACK_LIBDIR" ; then
- COLPACK_LIBS="-L$COLPACK_LIBDIR -lColPack -Wl,-rpath,$COLPACK_LIBDIR"
- fi
-@@ -56,6 +56,9 @@ else
- fi
- done
- AC_LANG_POP([C++])
-+else
-+    have_colpack=no
-+fi
- 
- AM_CONDITIONAL(HAVE_LIBCOLPACK,[test x$have_colpack = xyes])
- if test x$have_colpack = xyes; then 
diff --git a/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch b/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch
deleted file mode 100644
index 258f835ca9e8..000000000000
--- a/sci-libs/adolc/files/adolc-2.5.0-pkgconfig-no-ldflags.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- a/adolclib.pc.in	2014-05-21 09:09:10.060824555 -0700
-+++ b/adolclib.pc.in	2014-05-21 09:09:10.060824555 -0700
-@@ -7,5 +7,5 @@
- Version: @PACKAGE_VERSION@
- Description: Algorithmic Differentiation Library for C/C++
- Requires: 
--Libs: -L${libdir} -l@adolclib@ -Wl,-rpath,${libdir} @LDFLAGS@ @LIBS@
-+Libs: -L${libdir} -l@adolclib@ @LIBS@
- Cflags: -I${includedir}
diff --git a/sci-libs/adolc/files/adolc-2.6.2-dash.patch b/sci-libs/adolc/files/adolc-2.6.2-dash.patch
deleted file mode 100644
index b8d4fe5ad64d..000000000000
--- a/sci-libs/adolc/files/adolc-2.6.2-dash.patch
+++ /dev/null
@@ -1,146 +0,0 @@
---- a/configure.ac	2016-08-31 12:49:35.000000000 +0000
-+++ b/configure.ac	2017-03-04 00:58:02.354372332 +0000
-@@ -29,12 +29,12 @@
- 
- adolclib=adolc
- 
--if test "x$CFLAGS" == x ; then
-+if test "x$CFLAGS" = x ; then
-     ac_shell_cflags="not_set"
- else
-     ac_shell_cflags="$CFLAGS"
- fi
--if test "x$CXXFLAGS" == x ; then
-+if test "x$CXXFLAGS" = x ; then
-     ac_shell_cxxflags="not_set"
- else
-     ac_shell_cxxflags="$CXXFLAGS"
-@@ -231,12 +231,12 @@
-    AC_MSG_RESULT(no)
-    ])
- 
--if test x$adolc_harddebug == xyes ; then
-+if test x$adolc_harddebug = xyes ; then
- adolc_debug=yes
- AC_DEFINE(ADOLC_HARDDEBUG,1,[ADOL-C hard debug mode])
- fi
- 
--if test x$adolc_debug == xyes ; then
-+if test x$adolc_debug = xyes ; then
- AC_DEFINE(ADOLC_DEBUG,1,[ADOL-C debug mode])
- fi
- 
-@@ -254,7 +254,7 @@
-   AC_MSG_RESULT(yes)
-   ])
- 
--if test x$adolc_stdczero == xyes; then
-+if test x$adolc_stdczero = xyes; then
- AC_DEFINE(ADOLC_ADOUBLE_STDCZERO,1,[ADOL-C adouble zeroing mode])
- fi
- 
-@@ -271,7 +271,7 @@
-   AC_MSG_RESULT(no)
-   ])
- 
--if test x$adolc_late_init == xyes; then
-+if test x$adolc_late_init = xyes; then
- AC_DEFINE(ADOLC_ADOUBLE_LATEINIT,1,[ADOL-C adouble late initialization mode])
- fi
- 
-@@ -288,7 +288,7 @@
-   AC_MSG_RESULT(no)
-   ])
- 
--if test x$adolc_tserrno == xyes ; then
-+if test x$adolc_tserrno = xyes ; then
- AC_DEFINE(ADOLC_THREADSAVE_ERRNO,1,[ADOL-C thread save errno mode])
- fi
- 
-@@ -376,8 +376,8 @@
-             [AS_HELP_STRING([--with-cflags=FLAGS],
-                             [use CFLAGS=FLAGS (default: -O2)])],
-             [ac_adolc_cflags="$withval"
--             if test x${adolc_debug} == xyes ||
--                test x${adolc_harddebug} == xyes ; then
-+             if test "x${adolc_debug}" = xyes ||
-+                test "x${adolc_harddebug}" = xyes ; then
-                 ac_adolc_cflags="$ac_adolc_cflags -g -O0"
-              fi
-              ac_adolc_cflags="$ac_adolc_cflags $ac_adolc_openmpflag"
-@@ -385,8 +385,8 @@
-              AC_MSG_RESULT($ac_adolc_cflags)],
-             [if test "$ac_shell_cflags" = "not_set"; then
-                 ac_adolc_cflags="-O2"
--                if test x${adolc_debug} == xyes ||
--                   test x${adolc_harddebug} == xyes ; then
-+                if test "x${adolc_debug}" = xyes ||
-+                   test "x${adolc_harddebug}" = xyes ; then
-                    ac_adolc_cflags="-g -O0 -Wall -ansi"
-                 fi
-              else
-@@ -402,8 +402,8 @@
-             [AS_HELP_STRING([--with-cxxflags=FLAGS],
-                             [use CXXFLAGS=FLAGS (default: -O2)])],
-             [ac_adolc_cxxflags="$withval"
--             if test x${adolc_debug} == xyes ||
--                test x${adolc_harddebug} == xyes ; then
-+             if test x${adolc_debug} = xyes ||
-+                test x${adolc_harddebug} = xyes ; then
-                 ac_adolc_cxxflags="$ac_adolc_cxxflags -g -O0"
-              fi
-              ac_adolc_cxxflags="$ac_adolc_cxxflags $ac_adolc_openmpflag"
-@@ -411,8 +411,8 @@
-              AC_MSG_RESULT($ac_adolc_cxxflags)],
-             [if test "$ac_shell_cxxflags" = "not_set"; then
-                 ac_adolc_cxxflags="-O2"
--                if test x${adolc_debug} == xyes ||
--                   test x${adolc_harddebug} == xyes ; then
-+                if test x${adolc_debug} = xyes ||
-+                   test x${adolc_harddebug} = xyes ; then
-                    ac_adolc_cxxflags="-g -O0 -Wall"
-                 fi
-              else
-@@ -445,7 +445,7 @@
-   ])
- AC_MSG_RESULT($tapedoc_values)
- 
--if test x$tapedoc_values == xyes; then
-+if test x$tapedoc_values = xyes; then
- AC_DEFINE(ADOLC_TAPE_DOC_VALUES,1,[ADOL-C tape_doc routine computes values])
- fi
- 
-@@ -614,7 +614,7 @@
-         break
-     fi
- done
--if test "x${pdir}" == "x/" ; then
-+if test "x${pdir}" = "x/" ; then
-     writable=false
- fi
- if ! ${writable} ; then
-@@ -626,15 +626,6 @@
-     warn=true
- fi
- 
--case ${prefix} in 
--   ${HOME}|${HOME}/*)
--if $warn ; then
--    for (( i=5; i>0; i-- )); do
--        echo -ne "\rPlease read the above messages carefully, continuing in ${i} seconds"
--        sleep 1
--    done
--    echo -e "\rPlease read the above messages carefully                                 "
--fi
- echo \
- "
- *****************************************************************************
-@@ -660,8 +651,6 @@
- 
- *****************************************************************************
- "
--;;
--esac
- if test "x$enable_static" != "xno" ; then
- echo \
- " Linking a user program with a static ADOL-C library will always result
diff --git a/sci-libs/adolc/files/adolc-2.7.2-swig-python-configure.patch b/sci-libs/adolc/files/adolc-2.7.2-swig-python-configure.patch
deleted file mode 100644
index c434f6556836..000000000000
--- a/sci-libs/adolc/files/adolc-2.7.2-swig-python-configure.patch
+++ /dev/null
@@ -1,391 +0,0 @@
-https://bugs.gentoo.org/730750
-https://github.com/coin-or/ADOL-C/commit/8b53408d08f41ddaba2dea5655d332b13fc4c78b.patch
-https://github.com/coin-or/ADOL-C/commit/06b3b665fc0253ee17f0208bd06cdc130e103741.patch
-https://github.com/coin-or/ADOL-C/commit/25a69c486829ddaa19c115afc05cb7cf3b4e2410.patch
-https://github.com/coin-or/ADOL-C/commit/e41d32ba6dab09a3e58b22f1f042e49cd5ee917f.patch
-https://github.com/coin-or/ADOL-C/commit/0787a350cc181192cfd203b0f75941bcbd9c3e3a.patch
-https://github.com/coin-or/ADOL-C/commit/0b3dd1747f90f68b17dc5f1bd3a5d898e3bc77fb.patch
-----
-From e41d32ba6dab09a3e58b22f1f042e49cd5ee917f Mon Sep 17 00:00:00 2001
-From: Andrea Walther <walthand@math55020.mathematik.hu-berlin.de>
-Date: Tue, 22 Sep 2020 10:47:27 +0200
-Subject: [PATCH] fix prefix and provide --enable-python
-
----
- configure.ac | 19 ++++++++++++++++++-
- 1 file changed, 18 insertions(+), 1 deletion(-)
-
-diff --git a/configure.ac b/configure.ac
-index 6c2c88f9..b6aaeaa7 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -71,6 +71,17 @@ if test x"${adolc_medipack_support}" = xyes ; then
- AC_DEFINE(ADOLC_MEDIPACK_SUPPORT,1,[defined if MeDiPack support is to be compiled in])
- fi
- 
-+
-+AC_MSG_CHECKING(whether to build ADOL-C with python/swig support)
-+AC_ARG_ENABLE(python,
-+              [AS_HELP_STRING([--enable-python],[build ADOL-C with python/swig support [default=disabled]])],
-+	      [adolc_python_support=$enableval],[adolc_python_support=no])
-+AC_MSG_RESULT($adolc_python_support)
-+AM_CONDITIONAL(BUILD_ADOLC_python_SUPPORT,[test x${adolc_python_support} = xyes])
-+if test x"${adolc_python_support}" = xyes ; then
-+AC_DEFINE(ADOLC_python_SUPPORT,1,[defined if python/swig support is to be compiled in])
-+fi
-+
- LT_PREREQ([2.2.6])
- # checks for programs
- AC_PROG_CXX
-@@ -651,6 +662,10 @@ if test x$sparse = xyes && test x$have_colpack = xno; then
-   Only sparsity patterns can be computed\033@<:@0m"
-     warn=true
- fi
-+echo \
-+"  Build with python:		      ${adolc_python_support}"
-+
-+if test x$adolc_python_support = xyes ; then
- if test x$sparse = xyes && test x$python_found = xyes && test x$SWIG != xno; then
-    echo \
- "  Build with python swig module:      yes"
-@@ -660,7 +675,7 @@ else
-    if test x$sparse = xno && test x$python_found = xyes && test x$SWIG != xno; then
-      echo \
- "(due to sparse drivers disabled)"
--  elif test x$sparse = xyes && ( $test x$python_found = xno || test x$SWIG = xno ); then
-+  elif test x$sparse = xyes && ( test x$python_found = xno || test x$SWIG = xno ); then
-      echo \
- "(due to python/swig missing)"
-   else
-@@ -668,6 +683,8 @@ else
- "(due to sparse drivers disabled and python/swig missing)"
-   fi
- fi
-+fi
-+
- echo
- 
- echo \
-From 8b53408d08f41ddaba2dea5655d332b13fc4c78b Mon Sep 17 00:00:00 2001
-From: Kshitij Kulshreshtha <kkhere.geo@gmail.com>
-Date: Tue, 31 Mar 2020 22:42:23 +0200
-Subject: [PATCH] Fix out-of-tree build for swig
-
----
- ADOL-C/swig/Makefile.am    |  4 +--
- ADOL-C/swig/setup.py       | 65 +++++++++++++++++++++++++++-----------
- ADOL-C/swig/swigprocess.py | 34 +++++++++++---------
- Makefile.am                |  3 +-
- configure.ac               |  6 ++++
- 5 files changed, 75 insertions(+), 37 deletions(-)
-
-diff --git a/ADOL-C/swig/Makefile.am b/ADOL-C/swig/Makefile.am
-index 04a52cd0..b1d5569b 100644
---- a/ADOL-C/swig/Makefile.am
-+++ b/ADOL-C/swig/Makefile.am
-@@ -12,7 +12,7 @@
- 
- ACLOCAL_AMFLAGS = -I autoconf
- 
--EXTRA_DIST = swigprocess.py adolc-r.i adolc-python.i adubswigfuncs.h adolc_all_in.hpp matrixmemory.hpp pyedfclasses.hpp
-+EXTRA_DIST = swigprocess.py adolc-r.i adolc-python.i adubswigfuncs.hpp adolc_all_in.hpp matrixmemory.hpp pyedfclasses.hpp
- 
- clean-local:
- 	-rm -rf python R *.cpp *.cxx *.o *.h include
-@@ -20,6 +20,6 @@ clean-local:
- if PYTHONFOUND
- if SPARSE
- install:
--	CXX=${CXX} ${PYTHON} setup.py install --prefix=${prefix} --only-swig
-+	CXX=${CXX} ${PYTHON} ${srcdir}/setup.py build --only-swig --lib-prefix=${prefix} @python_srcbase@ install --prefix=${prefix}
- endif
- endif
-diff --git a/ADOL-C/swig/setup.py b/ADOL-C/swig/setup.py
-index 7a9a25c4..5bd98c3a 100644
---- a/ADOL-C/swig/setup.py
-+++ b/ADOL-C/swig/setup.py
-@@ -11,6 +11,10 @@
- ##############################################################################
- 
- from __future__ import print_function
-+import sys, os
-+
-+sys.path = [ os.path.dirname(os.path.abspath(__file__)) ] + sys.path
-+
- from swigprocess import prepare_flat_header
- from numpy.distutils import misc_util as np_dist
- from distutils.core import setup, Extension
-@@ -18,7 +22,6 @@
- from distutils.command.build_ext import build_ext
- from distutils.command.build import build
- from distutils.command.install import install
--import os
- import subprocess
- 
- def compile_dynlib(prefix,colpackdir,boostdir):
-@@ -88,14 +91,34 @@ def finalize_options(self):
-         prefix = self.lib_prefix
-         print('prefix = ', prefix)
-         self.include_dirs.append(os.path.join(prefix,'include'))
--        self.library_dirs.append(os.path.join(prefix,'lib64'))
--        self.rpath.append(os.path.join(prefix,'lib64'))
--        prepare_flat_header()
-+        import ctypes as c
-+        plen = c.sizeof(c.c_void_p(0))
-+        if plen == 8:
-+            self.library_dirs.append(os.path.join(prefix,'lib64'))
-+            self.rpath.append(os.path.join(prefix,'lib64'))
-+        else:
-+            self.library_dirs.append(os.path.join(prefix,'lib'))
-+            self.rpath.append(os.path.join(prefix,'lib'))
-+        buildobj = self.get_finalized_command('build')
-+        self.src = buildobj.src
-+        prepare_flat_header(self.src)
-+        self.swig_opts = ['-c++', '-I' + self.src]
-+        self.finalized = 1
- 
-+    def build_extension(self, ext):
-+        if self.src != '.':
-+            import shutil
-+            sources = ext.sources
-+            newSrc = []
-+            for s in iter(sources):
-+                shutil.copy(self.src + '/' + s, '.')
-+            ext.include_dirs.append(self.src)
-+        super(build_swigadolc,self).build_extension(ext)
- 
- class buildthis(build,object):
-     command_name = 'build'
-     user_options = build.user_options + [
-+        ('src=', None, 'path of the source directory of swig module'),
-         ('lib-prefix=', None, 'prefix to install adolc library'),
-         ('colpack-dir=', None, 'directory in which colpack is installed'),
-         ('boost-dir=', None, 'directory in which boost is installed'),
-@@ -111,11 +134,26 @@ def lib_doesnot_exist(self):
- 
-     def initialize_options(self):
-         super(buildthis,self).initialize_options()
-+        self.src = None
-         self.lib_prefix = None
-         self.colpack_dir = None
-         self.boost_dir = None
-         self.only_swig = None
- 
-+    def finalize_options(self):
-+        super(buildthis,self).finalize_options()
-+        if self.src is None:
-+            self.src = '.'
-+        if self.lib_prefix is None:
-+            self.lib_prefix = os.path.join(os.environ['HOME'],'adolc_base')
-+        if self.colpack_dir is None:
-+            self.colpack_dir = os.path.join(os.environ['HOME'],'adolc_base')
-+        if self.boost_dir is None:
-+            self.boost_dir = '/usr'
-+        if self.only_swig is None:
-+            self.only_swig = False
-+        self.finalized = 1
-+
-     #sub_commands = [ ('build_lib', lib_doesnot_exist),
-     #                 ('build_ext', None) ]
-     sub_commands = [ ('build_lib', None),
-@@ -137,22 +175,13 @@ def initialize_options(self):
-         super(installthis,self).initialize_options()
- 
-     def finalize_options(self):
-+        self.set_undefined_options('build',
-+                                   ('lib_prefix','lib_prefix'),
-+                                   ('colpack_dir', 'colpack_dir'),
-+                                   ('boost_dir', 'boost_dir'),
-+                                   ('only_swig', 'only_swig'))
-         super(installthis,self).finalize_options()
--        if self.lib_prefix is None:
--            self.lib_prefix = os.path.join(os.environ['HOME'],'adolc_base')
--        if self.colpack_dir is None:
--            self.colpack_dir = os.path.join(os.environ['HOME'],'adolc_base')
--        if self.boost_dir is None:
--            self.boost_dir = '/usr'
--        if self.only_swig is None:
--            self.only_swig = False
-         self.finalized = 1
--        buildobj = self.distribution.get_command_obj('build')
--        buildobj.set_undefined_options('install',
--                                       ('lib_prefix','lib_prefix'),
--                                       ('colpack_dir', 'colpack_dir'),
--                                       ('boost_dir', 'boost_dir'),
--                                       ('only_swig', 'only_swig'))
-         
- incdirs = np_dist.get_numpy_include_dirs()
- #python_ldflags = subprocess.check_output(['python-config','--ldflags'],universal_newlines=True)
-diff --git a/ADOL-C/swig/swigprocess.py b/ADOL-C/swig/swigprocess.py
-index bd5fe03d..f9de5551 100644
---- a/ADOL-C/swig/swigprocess.py
-+++ b/ADOL-C/swig/swigprocess.py
-@@ -10,6 +10,7 @@
- ## 
- ##############################################################################
- 
-+from __future__ import print_function
- import re
- import os.path
- import sys
-@@ -191,22 +192,25 @@ def finalClean(headfile,outfiles):
-     for f in glob.glob('*.o'):
-         os.remove(f)
- 
--def prepare_flat_header():
--    sys.path = [ os.getcwd() ] + sys.path
--    p = os.getcwd() + '/../include/adolc'
--    for (dp, dn, fn) in os.walk(p):
--        ndp = re.sub(r'\.\./',r'',dp)
--        for f in iter(fn):
--            lines = readFile(dp + "/" + f)
--            lines = comment_all_includes(lines)
--            lines = uncomment_local_includes(lines)
--            try:
--                os.makedirs(ndp)
--            except:
--                pass
--            writeOutput(lines, ndp + "/" + f)
-+def prepare_flat_header(src_base='.'):
-+    pl = [ os.getcwd() + '/../include/adolc' ]
-+    print('src_base = ', src_base)
-+    if src_base != '.':
-+        pl = [ src_base + '/../include/adolc' ] + pl
-+    for p in iter(pl):
-+        for (dp, dn, fn) in os.walk(p):
-+            ndp = re.sub(r'^.*\.\./',r'',dp)
-+            for f in iter(fn):
-+                lines = readFile(dp + "/" + f)
-+                lines = comment_all_includes(lines)
-+                lines = uncomment_local_includes(lines)
-+                try:
-+                    os.makedirs(ndp)
-+                except:
-+                    pass
-+                writeOutput(lines, ndp + "/" + f)
-     
--    invoke_cpp('adolc_all_in.hpp', 'adolc_all_pre.hpp')
-+    invoke_cpp(src_base + '/' + 'adolc_all_in.hpp', 'adolc_all_pre.hpp')
-     lines = readFile('adolc_all_pre.hpp')
-     lines = reinstate_nonlocal_include(lines)
-     writeOutput(lines,'adolc_all.hpp')
-diff --git a/Makefile.am b/Makefile.am
-index fb66e9f3..123ac905 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -24,13 +24,12 @@ EXTRA_DIST           = TODO BUGS LICENSE update_versions.sh \
-                        ADOL-C/doc/tapebasic.pdf ADOL-C/doc/tapebasic.eps \
-                        ADOL-C/doc/tap_point.pdf ADOL-C/doc/tap_point.eps \
-                        MSVisualStudio/v14/adolc.sln MSVisualStudio/v14/adolc.vcxproj \
--                       MSVisualStudio/v14/ColPack_Readme_VC++.txt \
-                        MSVisualStudio/v14/ColPack.vcxproj \
-                        MSVisualStudio/v14/sparse/config.h.in MSVisualStudio/v14/nosparse/config.h.in \
-                        MSVisualStudio/v14/x64/sparse/config.h.in MSVisualStudio/v14/x64/nosparse/config.h.in \
-                        MSVisualStudio/v14/sparse/config.h MSVisualStudio/v14/nosparse/config.h \
-                        MSVisualStudio/v14/x64/sparse/config.h MSVisualStudio/v14/x64/nosparse/config.h \
--                       MSVisualStudio/v14/Readme_VC++.txt \
-+                       MSVisualStudio/v14/README_VC++.md \
-                        MSVisualStudio/v14/installer.sh \
-                        adolc.spec.in adolc.spec \
-                        update_versions.sh
-diff --git a/configure.ac b/configure.ac
-index ddb08de1..6c2c88f9 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -501,6 +501,12 @@ fi
- AM_PATH_PYTHON([2.7],[python_found=yes],[python_found=no])
- AC_PATH_PROG(SWIG, swig, [no])
- AM_CONDITIONAL(PYTHONFOUND, [test x$python_found = xyes && test x$SWIG != xno])
-+if test ${abs_top_srcdir} != ${abs_top_builddir} ; then
-+   python_srcbase='--src=${abs_srcdir}'
-+else
-+   python_srcbase=''
-+fi
-+AC_SUBST(python_srcbase)
- ###########################################################################
- #                      COIN_PATCH_LIBTOOL_CYGWIN                          #
- ###########################################################################
-
-From 25a69c486829ddaa19c115afc05cb7cf3b4e2410 Mon Sep 17 00:00:00 2001
-From: Kshitij Kulshreshtha <kkhere.geo@gmail.com>
-Date: Wed, 1 Apr 2020 02:36:12 +0200
-Subject: [PATCH] another small fix for swig, this time for in-tree check
-
----
- ADOL-C/swig/setup.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/ADOL-C/swig/setup.py b/ADOL-C/swig/setup.py
-index e6023679..4ec9a7cc 100644
---- a/ADOL-C/swig/setup.py
-+++ b/ADOL-C/swig/setup.py
-@@ -105,7 +105,7 @@ def finalize_options(self):
-         self.finalized = 1
- 
-     def build_extension(self, ext):
--        if self.src != '.':
-+        if os.path.abspath(os.path.realpath(self.src)) != os.path.abspath('.'):
-             import shutil
-             sources = ext.sources
-             newSrc = []
-From 0787a350cc181192cfd203b0f75941bcbd9c3e3a Mon Sep 17 00:00:00 2001
-From: Andrea Walther <walthand@math55020.mathematik.hu-berlin.de>
-Date: Tue, 22 Sep 2020 11:58:09 +0200
-Subject: [PATCH] small change in configure.ac for swig module
-
----
- configure.ac | 6 ++++++
- 1 file changed, 6 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index b6aaeaa7..58380e55 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -509,6 +509,7 @@ if test x$tapedoc_values == xyes; then
- AC_DEFINE(ADOLC_TAPE_DOC_VALUES,1,[ADOL-C tape_doc routine computes values])
- fi
- 
-+if test x$adolc_python_support == xyes; then
- AM_PATH_PYTHON([2.7],[python_found=yes],[python_found=no])
- AC_PATH_PROG(SWIG, swig, [no])
- AM_CONDITIONAL(PYTHONFOUND, [test x$python_found = xyes && test x$SWIG != xno])
-@@ -517,7 +518,12 @@ if test ${abs_top_srcdir} != ${abs_top_builddir} ; then
- else
-    python_srcbase=''
- fi
-+else
-+   AM_CONDITIONAL(PYTHONFOUND, [test x$adolc_python_support])
-+   python_srcbase=''
-+fi
- AC_SUBST(python_srcbase)
-+end
- ###########################################################################
- #                      COIN_PATCH_LIBTOOL_CYGWIN                          #
- ###########################################################################
-From 0b3dd1747f90f68b17dc5f1bd3a5d898e3bc77fb Mon Sep 17 00:00:00 2001
-From: Andrea Walther <walthand@math55020.mathematik.hu-berlin.de>
-Date: Wed, 23 Sep 2020 08:54:54 +0200
-Subject: [PATCH] small fixes in configure.ac
-
----
- configure.ac | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 58380e55..88671274 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -519,11 +519,11 @@ else
-    python_srcbase=''
- fi
- else
--   AM_CONDITIONAL(PYTHONFOUND, [test x$adolc_python_support])
-+   AM_CONDITIONAL(PYTHONFOUND, [test x$adolc_python_support = xyes])
-    python_srcbase=''
- fi
- AC_SUBST(python_srcbase)
--end
-+
- ###########################################################################
- #                      COIN_PATCH_LIBTOOL_CYGWIN                          #
- ###########################################################################