#11886: fix scipy so it builds on OS X Lion
-------------------------------------------+--------------------------------
Reporter: jhpalmieri | Owner: tbd
Type: defect | Status: needs_work
Priority: major | Milestone: sage-4.7.2
Component: packages | Keywords: scipy spkg
upgrade update lion darwin 11
Work_issues: | Upstream: Fixed upstream,
but not in a stable release.
Reviewer: Mike Hansen, Leif Leonhardy | Author: John Palmieri
Merged: | Dependencies:
-------------------------------------------+--------------------------------
Changes (by leif):
* status: positive_review => needs_work
* reviewer: Mike Hansen => Mike Hansen, Leif Leonhardy
* upstream: N/A => Fixed upstream, but not in a stable release.
Comment:
Minor thing (another copy-paste accident):
The changelog entries should have `===` (instead of `==`):
{{{
#!diff
diff --git a/SPKG.txt b/SPKG.txt
--- a/SPKG.txt
+++ b/SPKG.txt
@@ -26,20 +26,24 @@
* Python, which in Sage has numerous dependencies
* Numpy
* Fortran
+ * GNU patch
== Special Update/Build Instructions ==
- * None
+ * Make sure the patches still apply.
+ The ones added in the scipy-0.9.p0 spkg (#11886) were all taken from
+ (unstable) upstream, so can presumably be removed once we upgrade to
+ a new stable version.
== Changelog ==
-== scipy-0.9.p0 (John Palmieri, 30 Sept 2011) ==
+=== scipy-0.9.p0 (John Palmieri, 30 Sept 2011) ===
* #11886: get scipy to build on OS X 10.7 Lion, using the patches from
https://github.com/scipy/scipy/commit/effa6f68f8ada57b79864852b609ff06d2527306
-== scipy-0.9 (F. Bissey; 16 March 2011) ===
+=== scipy-0.9 (F. Bissey; 16 March 2011) ===
* updated the source to 0.9.0. No patches needed.
-== scipy-0.8 (S. Reiterer, F. Bissey, D. Kirkby, J. H. Palmieri; 14
October 2010) ===
+=== scipy-0.8 (S. Reiterer, F. Bissey, D. Kirkby, J. H. Palmieri; 14
October 2010) ===
* #9808 Upgrade to scipy 0.8.
* Deleted outdated patches
* spkg install changed by F. Bissey, because g95 makes trouble on OS X.
}}}
(The merger script is btw. likely to reject the spkg otherwise.)
[[BR]]
`spkg-install` isn't executable.
GNU patch should be added to the dependencies. (See diff above).
{{{
#!sh
if [ $? -ne 0 ]; then
echo "Error patching setup.py"
exit 1
fi
}}}
should get removed, since no patch gets applied to `setup.py`.
There are a few typos in the comments, and `spkg-install` lacks the usual
sanity check.
{{{
#!diff
diff --git a/spkg-install b/spkg-install
--- a/spkg-install
+++ b/spkg-install
@@ -1,10 +1,18 @@
#!/usr/bin/env bash
-# These flags confuse numpy's distutils. In particular,
+
+if [ -z "$SAGE_LOCAL" ]; then
+ echo >&2 "Error: SAGE_LOCAL undefined - exiting..."
+ echo >&2 "Maybe run 'sage -sh'?"
+ exit 1
+fi
+
+# These flags confuse numpy's distutils. In particular,
# if they are set empty bad things happen.
+unset CFLAGS CXXFLAGS SHAREDFLAGS
+echo "Note: CFLAGS, CXXFLAGS and SHAREDFLAGS are taken from distutils,"
+echo " so their current settings are ignored."
-unset CFLAGS CXXFLAGS SHAREDFLAGS
-
-if [ `uname` = "Darwin" ]; then
+if [ "$UNAME" = "Darwin" ]; then
unset ATLAS
unset BLAS
unset LAPACK
@@ -23,43 +31,38 @@
export F90="$SAGE_LOCAL/bin/sage_fortran"
export F95="$SAGE_LOCAL/bin/sage_fortran"
-
-# This avoid problems on some systems -- until we officially
-# support umfpack (which we will likely do, since cvxopt
-# I think includes it).
-# http://projects.scipy.org/pipermail/scipy-user/2006-July/008661.html
-# (Currently swig gets invoked by scipy when building the umfpack
interace,
+# This avoids problems on some systems -- until we officially
+# support umfpack (which we will likely do, since cvxopt I think includes
it):
+UMFPACK="None"; export UMFPACK
+# See http://projects.scipy.org/pipermail/scipy-
user/2006-July/008661.html
+# (Currently SWIG gets invoked by scipy when building the umfpack
interface,
# which is bad.)
-UMFPACK="None"; export UMFPACK
+
+# Remove previous installation (if any):
rm -rf "$SAGE_LOCAL"/lib/python/site-packages/scipy
cd src/
+# Apply patches (if any):
for patch in ../patches/*.patch; do
patch -p1 <"$patch"
if [ $? -ne 0 ]; then
- echo >&2 "Error applying '$patch'"
+ echo >&2 "Error applying '$patch'."
exit 1
fi
done
+# Build:
+python setup.py build
if [ $? -ne 0 ]; then
- echo "Error patching setup.py"
- exit 1
-fi
-
-# Build
-python setup.py build
-if [ $? -ne 0 ]; then
- echo "Error building scipy."
+ echo >&2 "Error building scipy."
exit 1
fi
-# Intall
-python setup.py install
+# Install:
+python setup.py install
if [ $? -ne 0 ]; then
- echo "Error installing scipy."
+ echo >&2 "Error installing scipy."
exit 1
fi
-
}}}
(Take whatever you like, or I could upload an updated spkg.)
I'm not sure whether we should only remove an old installation upon a
successful build, after `python setup.py build`, but before running
`python setup.py install`.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/11886#comment:5>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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