fix opt crash when taking multiple consecutive sum.

.gitignore

@@ -10,6 +10,7 @@
 *.log
 *.nav
 *.out
+*.pdf
 *.snm
 *.toc
 *.vrb

.mailmap

@@ -7,11 +7,8 @@
 # #
 # # This file is up-to-date if the command git log --format="%aN <%aE>" | sort -u
 # # gives no duplicates.
-Jörg Bornschein <jb@capsec.org> Joerg Bornschein <bornschein@fias.uni-frankfurt.de>
-Eric Hunsberger <hunse@ctn> hunse <hunse@ctn>
-Jan Schlüter <github@jan-schlueter.de> f0k <github@jan-schlueter.de>
+
 Rami Al-Rfou' <rmyeid@gmail.com> Rami Al-Rfou <rmyeid@gmail.com>
-Arnaud Bergeron <abergeron@gmail.com> <abergeron@gmail.com>
 <abergeron@gmail.com> <anakha@kami.(none)>
 David Warde-Farley <wardefar@iro.umontreal.ca> David Warde-Farley <dwf@cs.toronto.edu>
 David Warde-Farley <wardefar@iro.umontreal.ca> David Warde Farley <dwf@cs.toronto.edu>
@@ -20,19 +17,14 @@ Douglas Eck <douglas.eck@gmail.com> eckdoug@waits.local <eckdoug@waits.local>
 Dumitru Erhan <dumitru.erhan@gmail.com> dumitru@deepnets.mtv.corp.google.com <dumitru@deepnets.mtv.corp.google.com>
 Dumitru Erhan <dumitru.erhan@gmail.com> erhandum@bikat.iro.umontreal.ca <erhandum@bikat.iro.umontreal.ca>
 Francois Savard <devnull@localhost> fsavard <devnull@localhost>
-Steven Pigeon <pigeon@iro.umontreal.ca> steven-pigeon <pigeon@iro.umontreal.ca>
+
 #     5	Firstname Lastname <firstname.lastname@example.net>
 #     4	Laboratoire d'Informatique des Systemes Adaptatifs <lisa@iro.umontreal.ca>
 #     6	Li Yao <yaoli@iro>
 #     1	olivier@ordinateur-de-olivier.local <olivier@ordinateur-de-olivier.local>
 #     2	onze <onzeonline@gmail.com>
 #    25	projects@lgcm <projects@lgcm>
 #     1	tutorial/debug_faq.txt <devnull@localhost>
-Bogdan Budescu <bbudescu@gmail.com> bbudescu <bbudescu@gmail.com>
-Sebastian Berg <sebastian@sipsolutions.net> seberg <sebastian@sipsolutions.net>
-Huy Nguyen <huy@huyng.com> huyng <huy@huyng.com>
-Wei Li <kuantkid@gmail.com> kuantkid <kuantkid@gmail.com>
-Ethan Buchman <ebuchman@uoguelph.ca> ebuchman <ebuchman@uoguelph.ca>
 Frederic Bastien <nouiz@nouiz.org> Frederic Bastien <bastienf@briaree1.rqchp.qc.ca>
 Frederic Bastien <nouiz@nouiz.org> Frederic Bastien <bastienf@iro.umontreal.ca>
 Frederic Bastien <nouiz@nouiz.org> Frédéric Bastien <nouiz@nouiz.org>
@@ -63,7 +55,6 @@ James Bergstra <james.bergstra@gmail.com> james@mackie <james@mackie>
 James Bergstra <james.bergstra@gmail.com> james@x40.unstable <james@x40.unstable>
 James Bergstra <james.bergstra@gmail.com> test_rng_mrg.py <devnull@localhost>
 John Salvatier <jsalvatier@gmail.com> jsalvatier <jsalvatier@gmail.com>
-John Salvatier <jsalvatier@gmail.com> john salvatier <jsalvatier@gmail.com>
 Joseph Turian <turian@iro.umontreal.ca> Joseph Turian <turian@gmail.com>
 Joseph Turian <turian@iro.umontreal.ca> turian@grenat.iro.umontreal.ca <turian@grenat.iro.umontreal.ca>
 Joseph Turian <turian@iro.umontreal.ca> turian@lgcm <turian@lgcm>
@@ -92,4 +83,3 @@ Sander Dieleman <sanderdieleman@gmail.com> benanne <sanderdieleman@gmail.com>
 Xavier Glorot <glorotxa@iro.umontreal.ca> glorotxa <glorotxa@iro.umontreal.ca>
 Xavier Glorot <glorotxa@iro.umontreal.ca> glorotxa@timide.iro.umontreal.ca <glorotxa@timide.iro.umontreal.ca>
 Yoshua Bengio <bengioy@iro.umontreal.ca> bengioy@bengio-mac.local <bengioy@bengio-mac.local>
-Sina Honari <honaris@iro.umontreal.ca> SinaHonari <sina2222@gmail.com>

.travis.yml

@@ -3,49 +3,42 @@
 
 language: python
 python:
-  - "2.6"
+  - "2.5"
 #  - "2.7"
 #  - "3.2"
-
 # command to install dependencies
 before_install:
-  - sudo apt-get install -q libatlas3gf-base libatlas-dev liblapack-dev gfortran
-# Install miniconda to avoid compiling scipy
-  - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
-  - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda/bin:$PATH
-  - conda update --yes conda
-
+  - sudo apt-get install -qq libatlas3gf-base libatlas-dev liblapack-dev gfortran
+#  - sudo apt-get install -qq libopenblas-dev
 install:
-# We support scipy 0.7.2, but it is not available on conda.
-# So we test with 0.11. Our internal buildbot have 0.7.2.
-  - conda create --yes -q -n py26 python=2.6 numpy=1.6 scipy=0.11 nose=1.1 pip
-  - source activate py26
-  - pip install pydot
-  - pip install . --no-deps --use-mirrors
-
+# If we don't install numpy before SciPy 0.10.1, the SciPy installations fails.
+  - "pip install -q numpy==1.5 --use-mirrors"
+# We support scipy 0.7.2, but it is not available on pypi anymore.
+# So we test with 0.8. Our internal buildbot have 0.7.2.
+# We install it later only for the PART that need it.
+#  - "pip install -q scipy==0.8 --use-mirrors"
+  - "pip install . --no-deps --use-mirrors"
 # command to run tests
 env:
-  - PART="theano/scan_module/"
-  - PART="theano/sandbox theano/sparse theano/scalar/ theano/tensor/nnet/"
-  - PART="theano/tensor/tests/test_basic.py theano/tensor/signal/ theano/compile/ theano/gof/ theano/misc/ theano/tests/ theano/compat"
+  - PART="theano/tensor/nnet/ theano/tensor/signal/ theano/compile/ theano/gof/ theano/misc/ theano/tests/ theano/compat theano/scan_module/"
+# This part is select such that all scipy code is there.
+# We install scipy only for this part to make the test time faster.
+  - PART="theano/sandbox theano/sparse theano/scalar/"
+  - PART="theano/tensor/tests/test_basic.py"
   - PART="-e test_basic.py theano/tensor/tests"
-
 script:
-  - export THEANO_FLAGS=blas.ldflags="-lblas -lgfortran",warn.ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise
+  - "if [ `expr \"$PART\" : '.*sparse'` -gt \"0\" ]; then pip install scipy==0.8 --use-mirrors; fi"
+  - export THEANO_FLAGS=warn.ignore_bug_before=all,on_opt_error=raise,on_shape_error=raise
   - python --version
   - uname -a
   - free -m
   - df -h
   - ulimit -a
-  - echo "$PART"
-  - theano-nose -v $PART
-  - theano-cache list
+  - echo $PART
+  - theano-nose $PART
+
 
 #after_script:
 after_failure:
   - cat /home/travis/.pip/pip.log
 #after_success:
-
-cache: apt

MANIFEST.in

@@ -1,10 +1,7 @@
 global-include *.txt
-global-include *.c
 global-include *.cu
 global-include *.cuh
-global-include *.h
 global-include *.sh
-global-include *.pkl
 recursive-include docs
 include bin/theano-cache
 include bin/theano-nose