Merge branch 'develop' into t/17489/remove_redundant_factorial___from…

…_rings_arith_py

* develop: (192 commits)
  Updated Sage version to 6.5.beta3
  Make sure the m4 sub folder is included by default when we call autoconf.
  Fixed bug with incomplete initial conditions
  trac #17508: Reviewer's remarks 2
  trac #17475 correct bad wikipedia role
  trac #17508: Reviewer's remarks
  Upgrade Maxima to 5.35.1
  17441: Removed redundant check
  Minor improvements regarding number field embeddings.
  Trac 7401: rearrange/extend doctests
  Trac 7401: some typographic fixes in doctest
  trac #17508: Reformat the 'docstring' section of the developer's manual
  When determining embeddings, leave coefficients rational.
  Only consider real embeddings if old embedding is into real lazy field.
  ignore return_vertex_weights option
  Change UFD check to call is_field.
  Add is_unique_factorization_domain for integer_mod and polynomial rings
  trac #15514: Added check for graphs with loops
  Fixed tests in calculus module
  trac: #15514 Added option for total domination number
  ...

COPYING.txt

@@ -88,6 +88,7 @@ pari                        GPLv2+
 patch                       GPLv2+
 pexpect                     Python License
 pillow                      Apache License 2.0
+pip                         MIT License
 pkgconf                     ISC License (equivalent to Simplified BSD)
 pkgconfig                   MIT License
 polybori                    GPLv2+

VERSION.txt

@@ -1 +1 @@
-Sage version 6.5.beta2, released 2014-12-04
+Sage version 6.5.beta3, released 2014-12-18

build/deps

@@ -79,6 +79,7 @@ all-sage: \
      $(INST)/$(PARI) \
      $(INST)/$(PEXPECT) \
      $(INST)/$(PILLOW) \
+     $(INST)/$(PIP) \
      $(INST)/$(PKGCONF) \
      $(INST)/$(PKGCONFIG) \
      $(INST)/$(POLYBORI) \
@@ -243,6 +244,9 @@ $(INST)/$(PARI_GALDATA):
 $(INST)/$(PARI_SEADATA_SMALL):
 	+$(PIPE) "$(SAGE_SPKG) $(PARI_SEADATA_SMALL) 2>&1" "tee -a $(SAGE_LOGS)/$(PARI_SEADATA_SMALL).log"
 
+$(INST)/$(PIP): $(INST)/$(PYTHON) $(INST)/$(SETUPTOOLS)
+	+$(PIPE) "$(SAGE_SPKG) $(PIP) 2>&1" "tee -a $(SAGE_LOGS)/$(PIP).log"
+
 $(INST)/$(POLYBORI): $(INST)/$(PYTHON) $(INST)/$(IPYTHON) \
          $(INST)/$(SCONS) $(INST)/$(BOOST_CROPPED) \
          $(INST)/$(M4RI) $(INST)/$(GD)

build/install

@@ -328,6 +328,7 @@ PARI_SEADATA_SMALL=`newest_version pari_seadata_small`
 PATCH=`newest_version patch`
 PEXPECT=`newest_version pexpect`
 PILLOW=`newest_version pillow`
+PIP=`newest_version pip`
 PKGCONF=`newest_version pkgconf`
 PKGCONFIG=`newest_version pkgconfig`
 POLYBORI=`newest_version polybori`

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=0f967b9ca98cae14812330184bc194d856061516
-md5=c0e386d4c47d2c67b0539a887b854374
-cksum=2809241126
+sha1=7df2518840c5f58481a970d8b1de534ca54fe928
+md5=9e2fdde9e4a7f182e4487bcb973ee044
+cksum=1438863796

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-60
+61

build/pkgs/fricas/SPKG.txt

@@ -0,0 +1,20 @@
+= fricas =
+
+== Description ==
+
+This package install the software fricas.
+
+== License ==
+
+Modified BSD license.
+
+== Upstream Contact ==
+
+http://fricas.sourceforge.net/
+
+== Dependencies ==
+
+Put a bulleted list of dependencies here:
+
+* ecl
+

build/pkgs/fricas/checksums.ini

@@ -0,0 +1,4 @@
+tarball=fricas-VERSION.tar.bz2
+sha1=689b3e474579655b76686a56a1928ef411cb179b
+md5=ba4f3927d93f49b0d866e5e80fc5bf18
+cksum=2927195574

build/pkgs/fricas/package-version.txt

@@ -0,0 +1 @@
+1.2.4

build/pkgs/fricas/spkg-install

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+cd src
+
+./configure --prefix="$SAGE_LOCAL" \
+            --libdir="$SAGE_LOCAL/lib" \
+            --with-lisp=ecl
+
+if [ $? -ne 0 ]; then
+    echo >&2 "Error configuring fricas."
+    exit 1
+fi
+
+$MAKE
+if [ $? -ne 0 ]; then
+    echo >&2 "Error building fricas."
+    exit 1
+fi
+
+$MAKE -j1 install
+if [ $? -ne 0 ]; then
+    echo >&2 "Error installing fricas."
+    exit 1
+fi

build/pkgs/iml/SPKG.txt

@@ -22,13 +22,14 @@ Website: http://www.cs.uwaterloo.ca/~astorjoh/iml.html
  * Arne Storjohann astorjoh@uwaterloo.ca
 
 == Dependencies ==
- * GMP/MPIR
+ * GMP
  * ATLAS
 
 == Special Update/Build Instructions ==
 
- * Various files should be made executable. Run spkg-src after
-   extracting the sources to src/ to fix this.
+ * As of version 1.0.4, you need to repackage the upstream tarball
+   using the spkg-src script because there was a bugfix version of 1.0.4
+   reposted upstream without version number bump.
 
 === Patches ===
 

build/pkgs/iml/checksums.ini

@@ -1,4 +1,4 @@
 tarball=iml-VERSION.tar.bz2
-sha1=713a19f1076ddde07a7c3a45493440b745bd266b
-md5=b5958c8d6ba89fff96ee82af6854cf7d
-cksum=3114321274
+sha1=72355b1f4c4df8cd3ecf5fcbcbd72c9ad9afdba7
+md5=362f1a6a1d2df0c5f0ab41e5d2c87ac7
+cksum=507867168

build/pkgs/iml/package-version.txt

@@ -1 +1 @@
-1.0.4
+1.0.4p1

build/pkgs/iml/spkg-install

@@ -31,15 +31,12 @@ if [ "$SAGE64" = "yes" ]; then
     CFLAGS="-m64 $CFLAGS"
 fi
 
-EXTRA_BLAS=""
 if [ $UNAME = "Darwin" ]; then
-    # copy cblas headers from gsl
-    cp ../patches/gsl_cblas.h cblas.h
-    EXTRA_BLAS="--with-cblas=-lcblas"
+    IML_CONFIGURE="--with-cblas=-lcblas $IML_CONFIGURE"
 fi
 
 ./configure --prefix="$SAGE_LOCAL" --libdir="$SAGE_LOCAL/lib" \
-    --enable-shared --with-default="$SAGE_LOCAL" "$EXTRA_BLAS" 
+    --enable-shared --with-default="$SAGE_LOCAL" "$IML_CONFIGURE" 
 if [ $? -ne 0 ]; then
     echo >&2 "Error configuring IML."
     exit 1

build/pkgs/iml/spkg-src

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+
+VERSION="1.0.4"
+PATCHLEVEL="p1"
+
+if [ $# -ne 0 ]; then
+    UPSTREAM_SOURCE_DIRECTORY=$1
+    echo "Using tarballs from $UPSTREAM_SOURCE_DIRECTORY instead of downloading"
+fi
+
+SPKG_ROOT=`pwd`
+
+set -e
+shopt -s extglob
+
+# Download sources
+URL="http://www.cs.uwaterloo.ca/~astorjoh/"
+if [ -z "$UPSTREAM_SOURCE_DIRECTORY" ]; then
+    tar xjf <( curl -L "$URL/iml-$VERSION.tar.bz2" )
+else
+    tar xjf "$UPSTREAM_SOURCE_DIRECTORY/iml-$VERSION.tar.bz2"
+fi
+
+mv "iml-$VERSION" "iml-$VERSION$PATCHLEVEL"
+tar cjf "iml-$VERSION$PATCHLEVEL.tar.bz2" "iml-$VERSION$PATCHLEVEL"

build/pkgs/ipython/package-version.txt

@@ -1 +1 @@
-2.3.0
+2.3.0.p0