Fix brian optional spkg for new workflow

[kcrisman]

See #14962. We have to either fix the newest version checking in brian or (better) get rid of it completely.

This would be an ideal time to upgrade brian to a new version and use the patch file instead of the py file for the one fix that is in it.

Updated spkg:

• http://sage.math.washington.edu/home/vbraun/spkg/brian-1.4.1.p0.spkg

CC: @sagetrac-uri @vbraun

Component: packages: optional

Author: Karl-Dieter Crisman

Reviewer: Volker Braun

Issue created by migration from https://trac.sagemath.org/ticket/15261

[kcrisman]

comment:1

Here's my current diff. I won't have time to upgrade and test today, but hopefully tomorrow. Note that

$ diff -Naur src/brian/units.py patches/units.py

actually returns a lot of whitespace changes so this is better from that standpoint as well.

diff --git a/SPKG.txt b/SPKG.txt
--- a/SPKG.txt
+++ b/SPKG.txt
@@ -31,9 +31,11 @@
 
 == Changelog ==
 
+=== brian-1.2.1.p1 (Karl-Dieter Crisman, 7 October 2013) ===
+ * Change spkg-install for transition to git
+
 === brian-1.2.1.p0 (Oriol Castejon, 3rd August 2010) ===
  * Version for Sage of the Python package Brian released.
-
  * Minor change added to avoid problems with Brian units and Sage Integers and 
    RealNumbers.
 
diff --git a/spkg-install b/spkg-install
--- a/spkg-install
+++ b/spkg-install
@@ -6,42 +6,16 @@
    exit 1
 fi
 
-############################## Check dependencies ##############################
-NUMPY=`cd $SAGE_ROOT/spkg/standard/; ./newest_version numpy`
-if [ $? -ne 0 ]; then
-    echo "Failed to find numpy.  Please install the numpy spkg."
-    exit 1
-fi
+cd src
 
-SCIPY=`cd $SAGE_ROOT/spkg/standard/; ./newest_version scipy`
-if [ $? -ne 0 ]; then
-    echo "Failed to find scipy.  Please install the scipy spkg."
-    exit 1
-fi
-
-MATPLOTLIB=`cd $SAGE_ROOT/spkg/standard/; ./newest_version matplotlib`
-if [ $? -ne 0 ]; then
-    echo "Failed to find matplotlib.  Please install the matplotlib spkg."
-    exit 1
-fi
-
-SYMPY=`cd $SAGE_ROOT/spkg/standard/; ./newest_version sympy`
-if [ $? -ne 0 ]; then
-    echo "Failed to find sympy.  Please install the sympy spkg."
-    exit 1
-fi
-################################################################################
-
-
-################################ Apply patches #################################
-cp patches/units.py src/brian/units.py
-if [ $? -ne 0 ]; then
-    echo "Error copying patch."
-    exit 1
-fi
-################################################################################
-
-cd src
+# Apply patch so that Sage reals and integers do not conflict
+for patch in ../patches/*.patch; do
+   patch -p1 <"$patch"
+   if [ $? -ne 0 ]; then
+       echo "Error applying '$patch'."
+       exit 1
+   fi
+done
 
 python setup.py build
 if [ $? -ne 0 ]; then

I may have to change the p1 to something else or change the patch file slightly.

[kcrisman]

comment:2

I do get

sage: import brian
.../sage-5.11.rc0/local/lib/python2.7/site-packages/brian/utils/sparse_patch/__init__.py:34: UserWarning: Couldn't find matching sparse matrix patch for scipy version 0.12.0, but in most cases this shouldn't be a problem.
  warnings.warn("Couldn't find matching sparse matrix patch for scipy version %s, but in most cases this shouldn't be a problem." % scipy.__version__)

Presumably an upgrade would fix this - e.g. 1.4.1, which seems to be most recent.

[kcrisman]

Description changed:

--- 
+++ 
@@ -1,3 +1,7 @@
 See #14962.  We have to either fix the newest version checking in brian or (better) get rid of it completely.
 
 This would be an ideal time to upgrade brian to a new version and use the patch file instead of the py file for the one fix that is in it.
+
+I have two different spkgs to try.
+* http://sage.math.washington.edu/home/kcrisman/brian-1.2.1.p1.spkg
+* http://sage.math.washington.edu/home/kcrisman/brian-1.4.1.p0.spkg

[kcrisman]

comment:3

I have two different ones to try. I think I got the patches right for the upgrade. Oriol, can you check that this still works for your clash issue with Sage-defined types?

[kcrisman]

Author: Karl-Dieter Crisman

[vbraun]

Reviewer: Volker Braun

[vbraun]

Description changed:

--- 
+++ 
@@ -2,6 +2,5 @@
 
 This would be an ideal time to upgrade brian to a new version and use the patch file instead of the py file for the one fix that is in it.
 
-I have two different spkgs to try.
-* http://sage.math.washington.edu/home/kcrisman/brian-1.2.1.p1.spkg
-* http://sage.math.washington.edu/home/kcrisman/brian-1.4.1.p0.spkg
+Updated spkg:
+* http://sage.math.washington.edu/home/vbraun/spkg/brian-1.4.1.p0.spkg

[vbraun]

comment:5

Looks good to me. I've repacked it with gnu tar instead of bsd tar, no other changes.