From cf7c8750b56173caeb7f8497ad53298704fd7e99 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 19:42:47 -0500
Subject: [PATCH 01/42] Push parts of travis into separate shell scripts

---
 .travis.yml           | 75 ++-----------------------------------------
 doc/travis_notes.txt  | 22 ++-----------
 tools/travis_build.sh | 59 ++++++++++++++++++++++++++++++++++
 tools/travis_setup.sh | 12 +++++++
 4 files changed, 76 insertions(+), 92 deletions(-)
 create mode 100644 tools/travis_build.sh
 create mode 100644 tools/travis_setup.sh

diff --git a/.travis.yml b/.travis.yml
index a59390c2..122189e6 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,19 +22,7 @@ before_install:
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
-    - travis_retry pip install wheel flake8 coveralls nose
-    - travis_retry pip uninstall -y numpy
-
-    # on Python 2.7, use the system versions of numpy, scipy, and matplotlib
-    # and the minimum version of cython and networkx
-    -   if [[  $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
-            travis_retry sudo apt-get install python-scipy python-matplotlib;
-            pip install https://github.com/cython/cython/archive/0.19.2.tar.gz;
-            pip install https://github.com/networkx/networkx/archive/networkx-1.8.tar.gz;
-        fi
-
-    - travis_retry pip install -r requirements.txt $WHEELHOUSE;
-    - python check_bento_build.py
+    - tools/travis_setup.sh
 
 install:
     - tools/header.py "Dependency versions"
@@ -43,64 +31,7 @@ install:
     - python setup.py build_ext --inplace
 
 script:
-    - tools/header.py "Run all tests with minimum dependencies"
-    - nosetests --exe -v skimage
-
-    - tools/header.py "Pep8 and Flake tests"
-    - flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
-
-    - tools/header.py "Install optional dependencies"
-
-    # Install Qt and then update the Matplotlib settings
-    -   if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
-            sudo apt-get install -q python-qt4;
-            export SCI_QT_API=PyQt4;
-
-        else
-            sudo apt-get install -q libqt4-dev;
-             travis_retry pip install PySide $WHEELHOUSE;
-             python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install;
-             export SCI_QT_API=Pyside;
-        fi
-
-    # Matplotlib settings - must be after we install Pyside
-    - export MPL_DIR=$HOME/.config/matplotlib
-    - mkdir -p $MPL_DIR
-    - touch $MPL_DIR/matplotlibrc
-    - "echo 'backend : Agg' > $MPL_DIR/matplotlibrc"
-    - "echo 'backend.qt4 : '$SCI_QT_API >> $MPL_DIR/matplotlibrc"
-
-    # - imread does NOT support py3.2
-    -   if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
-            sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools;
-            travis_retry pip install imread;
-        fi
-
-    # TODO: update when SimpleITK become available on py34 or hopefully pip
-    -   if [[  $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
-            travis_retry easy_install SimpleITK;
-         fi
-
-    - travis_retry sudo apt-get install libfreeimage3
-    - travis_retry pip install astropy
-
-    -   if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
-            travis_retry pip install pyamg;
-        fi
-
-    - tools/header.py "Run doc examples"
-    - export PYTHONPATH=$(pwd):$PYTHONPATH
-    - for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-    - for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-
-    - tools/header.py "Run tests with all dependencies"
-    # run tests again with optional dependencies to get more coverage
-    # measure coverage on py3.3
-    -   if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
-            nosetests --exe -v --with-doctest --with-cov --cover-package skimage;
-        else
-            nosetests --exe -v --with-doctest skimage;
-        fi
+    - tools/travis_build.sh
 
 after_success:
-    - coveralls;
+    - coveralls
diff --git a/doc/travis_notes.txt b/doc/travis_notes.txt
index 09d04889..c5d5c99c 100644
--- a/doc/travis_notes.txt
+++ b/doc/travis_notes.txt
@@ -3,26 +3,8 @@
   http://lint.travis-ci.org/ is recommended elsewhere but does not give helpful
   error reports.
 - Make sure all of your "-" lines start on the same column
-- Make sure all of your "if" lines are aligned with the "else" and "fi" lines
-- Recommend using tab stops (but not tab chars) everywhere for alignment
-- "If" blocks must be on one travis statement and have semicolons at the
-  end of each line:
-
-```
-    -   if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then
-            echo "2.7";
-        else
-            echo "Not 2.7";
-        end
-```
-
-- "If" blocks cannot contain comments
-- All travis commands are run with `eval` and quotes are taken as literal
-  characters unless you wrap the whole line in quotes:
-`echo "hello : world"` is interpreted as `echo \"hello : world\"`
-`"echo 'hello : world'"` is interpreted as `echo 'hello : world'`
-`"echo 'hello : '$(MYVAR)'world'"` is interpreted as
-  `echo 'hello : $(MYVAR)world'`
+- Use shell scripts for `before_install` and `script` or any part that
+  has conditional statements
 - Use `travis_retry` before a command to have it try several times before
 failing (useful for installing from third party sources)
 - Feel free to cancel a build rather than waiting for it to go to completion
diff --git a/tools/travis_build.sh b/tools/travis_build.sh
new file mode 100644
index 00000000..79b8f9b5
--- /dev/null
+++ b/tools/travis_build.sh
@@ -0,0 +1,59 @@
+./header.py "Run all tests with minimum dependencies"
+nosetests --exe -v skimage
+
+./header.py "Pep8 and Flake tests"
+flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
+
+./header.py "Install optional dependencies"
+
+# Install Qt and then update the Matplotlib settings
+if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+    sudo apt-get install -q python-qt4
+    export SCI_QT_API=PyQt4
+
+else
+    sudo apt-get install -q libqt4-dev
+     travis_retry pip install PySide $WHEELHOUSE
+     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
+     export SCI_QT_API=PySide
+fi
+
+# Matplotlib settings - must be after we install Pyside
+export MPL_DIR=$HOME/.config/matplotlib
+mkdir -p $MPL_DIR
+touch $MPL_DIR/matplotlibrc
+echo 'backend : Agg' > $MPL_DIR/matplotlibrc
+echo 'backend.qt4 : '$SCI_QT_API >> $MPL_DIR/matplotlibrc
+
+# imread does NOT support py3.2
+if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
+    sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
+    travis_retry pip install imread
+fi
+
+# TODO: update when SimpleITK become available on py34 or hopefully pip
+if [[  $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
+    travis_retry easy_install SimpleITK
+fi
+
+travis_retry sudo apt-get install libfreeimage3
+travis_retry pip install astropy
+
+if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
+    travis_retry pip install pyamg
+fi
+
+./header.py "Run doc examples"
+export PYTHONPATH=$(pwd):$PYTHONPATH
+for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
+for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
+
+./header.py "Run tests with all dependencies"
+# run tests again with optional dependencies to get more coverage
+# measure coverage on py3.3
+if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
+    nosetests --exe -v --with-doctest --with-cov --cover-package skimage
+else
+    nosetests --exe -v --with-doctest skimage
+fi
+
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
new file mode 100644
index 00000000..c6d8c566
--- /dev/null
+++ b/tools/travis_setup.sh
@@ -0,0 +1,12 @@
+travis_retry pip install wheel flake8 coveralls nose
+
+# on Python 2.7, use the system versions of numpy, scipy, and matplotlib
+# and the minimum version of cython and networkx
+if [[  $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+    travis_retry sudo apt-get install python-scipy python-matplotlib
+    pip install https://github.com/cython/cython/archive/0.19.2.tar.gz
+    pip install https://github.com/networkx/networkx/archive/networkx-1.8.tar.gz
+fi
+
+travis_retry pip install  -r requirements.txt $WHEELHOUSE
+python check_bento_build.py

From 4233e9fb3afde7acf9a7b28c98c30f69e923774f Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 19:45:30 -0500
Subject: [PATCH 02/42] Remove variable exports

---
 tools/travis_build.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/travis_build.sh b/tools/travis_build.sh
index 79b8f9b5..f45875ae 100644
--- a/tools/travis_build.sh
+++ b/tools/travis_build.sh
@@ -9,17 +9,17 @@ flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
 # Install Qt and then update the Matplotlib settings
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
     sudo apt-get install -q python-qt4
-    export SCI_QT_API=PyQt4
+    SCI_QT_API=PyQt4
 
 else
     sudo apt-get install -q libqt4-dev
      travis_retry pip install PySide $WHEELHOUSE
      python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
-     export SCI_QT_API=PySide
+     SCI_QT_API=PySide
 fi
 
 # Matplotlib settings - must be after we install Pyside
-export MPL_DIR=$HOME/.config/matplotlib
+MPL_DIR=$HOME/.config/matplotlib
 mkdir -p $MPL_DIR
 touch $MPL_DIR/matplotlibrc
 echo 'backend : Agg' > $MPL_DIR/matplotlibrc
@@ -44,7 +44,7 @@ if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
 fi
 
 ./header.py "Run doc examples"
-export PYTHONPATH=$(pwd):$PYTHONPATH
+PYTHONPATH=$(pwd):$PYTHONPATH
 for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
 for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
 

From b1f7bd813312df45f1c8ef2280aaa3d58e3042e0 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 19:48:50 -0500
Subject: [PATCH 03/42] Add shebang lines

---
 tools/travis_build.sh | 1 +
 tools/travis_setup.sh | 1 +
 2 files changed, 2 insertions(+)

diff --git a/tools/travis_build.sh b/tools/travis_build.sh
index f45875ae..7ed37c56 100644
--- a/tools/travis_build.sh
+++ b/tools/travis_build.sh
@@ -1,3 +1,4 @@
+#!/usr/bin/sh
 ./header.py "Run all tests with minimum dependencies"
 nosetests --exe -v skimage
 
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index c6d8c566..ad740a69 100644
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -1,3 +1,4 @@
+#!/usr/bin/sh
 travis_retry pip install wheel flake8 coveralls nose
 
 # on Python 2.7, use the system versions of numpy, scipy, and matplotlib

From 0bad613568bab7f39cc60fc3593dca976c6c1b76 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 19:51:00 -0500
Subject: [PATCH 04/42] Add explicit sh executable

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 122189e6..fbefad0b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,7 +22,7 @@ before_install:
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
-    - tools/travis_setup.sh
+    - sh tools/travis_setup.sh
 
 install:
     - tools/header.py "Dependency versions"
@@ -31,7 +31,7 @@ install:
     - python setup.py build_ext --inplace
 
 script:
-    - tools/travis_build.sh
+    - sh tools/travis_build.sh
 
 after_success:
     - coveralls

From 87d3a07b71003f37ab31a22b9cc51e991e3999a9 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 20:01:43 -0500
Subject: [PATCH 05/42] Reorganize files

---
 .travis.yml                  | 25 +++++++++++++--
 tools/travis_build.sh        | 60 ------------------------------------
 tools/travis_get_optional.sh | 39 +++++++++++++++++++++++
 tools/travis_setup.sh        |  6 ++--
 4 files changed, 65 insertions(+), 65 deletions(-)
 delete mode 100644 tools/travis_build.sh
 create mode 100644 tools/travis_get_optional.sh

diff --git a/.travis.yml b/.travis.yml
index fbefad0b..4a4288fd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,7 +22,7 @@ before_install:
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
-    - sh tools/travis_setup.sh
+    - travis_retry sh tools/travis_setup.sh
 
 install:
     - tools/header.py "Dependency versions"
@@ -31,7 +31,28 @@ install:
     - python setup.py build_ext --inplace
 
 script:
-    - sh tools/travis_build.sh
+    - tools/header.py "Run all tests with minimum dependencies"
+    - nosetests --exe -v skimage
+
+    - tools/header.py "Pep8 and Flake tests"
+    - flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
+
+    - travis_retry sh tools/travis_get_optional.sh
+
+    - tools/header.py "Run doc examples"
+    - export PYTHONPATH=$(pwd):$PYTHONPATH
+    - for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
+    - for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
+
+    - tools/header.py "Run tests with all dependencies"
+    # run tests again with optional dependencies to get more coverage
+    # measure coverage on py3.3
+    -   if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
+            nosetests --exe -v --with-doctest --with-cov --cover-package skimage;
+        else
+            nosetests --exe -v --with-doctest skimage;
+        fi
+
 
 after_success:
     - coveralls
diff --git a/tools/travis_build.sh b/tools/travis_build.sh
deleted file mode 100644
index 7ed37c56..00000000
--- a/tools/travis_build.sh
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/usr/bin/sh
-./header.py "Run all tests with minimum dependencies"
-nosetests --exe -v skimage
-
-./header.py "Pep8 and Flake tests"
-flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
-
-./header.py "Install optional dependencies"
-
-# Install Qt and then update the Matplotlib settings
-if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
-    sudo apt-get install -q python-qt4
-    SCI_QT_API=PyQt4
-
-else
-    sudo apt-get install -q libqt4-dev
-     travis_retry pip install PySide $WHEELHOUSE
-     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
-     SCI_QT_API=PySide
-fi
-
-# Matplotlib settings - must be after we install Pyside
-MPL_DIR=$HOME/.config/matplotlib
-mkdir -p $MPL_DIR
-touch $MPL_DIR/matplotlibrc
-echo 'backend : Agg' > $MPL_DIR/matplotlibrc
-echo 'backend.qt4 : '$SCI_QT_API >> $MPL_DIR/matplotlibrc
-
-# imread does NOT support py3.2
-if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
-    sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
-    travis_retry pip install imread
-fi
-
-# TODO: update when SimpleITK become available on py34 or hopefully pip
-if [[  $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
-    travis_retry easy_install SimpleITK
-fi
-
-travis_retry sudo apt-get install libfreeimage3
-travis_retry pip install astropy
-
-if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
-    travis_retry pip install pyamg
-fi
-
-./header.py "Run doc examples"
-PYTHONPATH=$(pwd):$PYTHONPATH
-for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-
-./header.py "Run tests with all dependencies"
-# run tests again with optional dependencies to get more coverage
-# measure coverage on py3.3
-if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
-    nosetests --exe -v --with-doctest --with-cov --cover-package skimage
-else
-    nosetests --exe -v --with-doctest skimage
-fi
-
diff --git a/tools/travis_get_optional.sh b/tools/travis_get_optional.sh
new file mode 100644
index 00000000..b43a44dc
--- /dev/null
+++ b/tools/travis_get_optional.sh
@@ -0,0 +1,39 @@
+#!/usr/bin/sh
+./header.py "Install optional dependencies"
+
+# Install Qt and then update the Matplotlib settings
+if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+    sudo apt-get install -q python-qt4
+    SCI_QT_API=PyQt4
+
+else
+    sudo apt-get install -q libqt4-dev
+    pip install PySide $WHEELHOUSE
+    python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
+    SCI_QT_API=PySide
+fi
+
+# Matplotlib settings - must be after we install Pyside
+MPL_DIR=$HOME/.config/matplotlib
+mkdir -p $MPL_DIR
+touch $MPL_DIR/matplotlibrc
+echo 'backend : Agg' > $MPL_DIR/matplotlibrc
+echo 'backend.qt4 : '$SCI_QT_API >> $MPL_DIR/matplotlibrc
+
+# imread does NOT support py3.2
+if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
+    sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
+    pip install imread
+fi
+
+# TODO: update when SimpleITK become available on py34 or hopefully pip
+if [[  $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
+    easy_install SimpleITK
+fi
+
+sudo apt-get install libfreeimage3
+pip install astropy
+
+if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
+    pip install pyamg
+fi
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index ad740a69..af14be4d 100644
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -1,13 +1,13 @@
 #!/usr/bin/sh
-travis_retry pip install wheel flake8 coveralls nose
+pip install wheel flake8 coveralls nose
 
 # on Python 2.7, use the system versions of numpy, scipy, and matplotlib
 # and the minimum version of cython and networkx
 if [[  $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
-    travis_retry sudo apt-get install python-scipy python-matplotlib
+    sudo apt-get install python-scipy python-matplotlib
     pip install https://github.com/cython/cython/archive/0.19.2.tar.gz
     pip install https://github.com/networkx/networkx/archive/networkx-1.8.tar.gz
 fi
 
-travis_retry pip install  -r requirements.txt $WHEELHOUSE
+pip install  -r requirements.txt $WHEELHOUSE
 python check_bento_build.py

From 7cb084b9c4916ff7428efec79bad9acc8625df50 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 20:12:22 -0500
Subject: [PATCH 06/42] Use an explicit matrix

---
 .travis.yml | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 4a4288fd..c6bf6f56 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,21 +7,24 @@
 
 language: python
 
-python:
-    - 2.6
-    - "2.7_with_system_site_packages"
-    - 3.2
-    - 3.3
-    - 3.4
+env: TEST_ARGS=""
 
-env:
-    WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+matrix:
+  include:
+    - python: "2.6"
+    - python: "2.7_with_system_site_packages"
+    - python: "3.2"
+    - python: "3.3"
+      env: TEST_ARGS="--with-cov --cover-package"
+    - python: "3.4"
 
 before_install:
     - export DISPLAY=:99.0
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
+    - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+
     - travis_retry sh tools/travis_setup.sh
 
 install:
@@ -46,13 +49,7 @@ script:
 
     - tools/header.py "Run tests with all dependencies"
     # run tests again with optional dependencies to get more coverage
-    # measure coverage on py3.3
-    -   if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
-            nosetests --exe -v --with-doctest --with-cov --cover-package skimage;
-        else
-            nosetests --exe -v --with-doctest skimage;
-        fi
-
+    - nosetests --exe -v --with-doctest $TEST_ARGS
 
 after_success:
     - coveralls

From d415486a211eb470366a41edc57bf0442ef6b9ac Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 20:26:21 -0500
Subject: [PATCH 07/42] Try removing the explicit env

---
 .travis.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index c6bf6f56..58206877 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,8 +7,6 @@
 
 language: python
 
-env: TEST_ARGS=""
-
 matrix:
   include:
     - python: "2.6"

From 81d54983382bed9107d805f200186c45aaa09b6e Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 20:34:25 -0500
Subject: [PATCH 08/42] Put the TEST_ARGS in travis_setup.sh

---
 .travis.yml           | 15 +++++++--------
 tools/travis_setup.sh |  6 ++++++
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 58206877..47983033 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,14 +7,12 @@
 
 language: python
 
-matrix:
-  include:
-    - python: "2.6"
-    - python: "2.7_with_system_site_packages"
-    - python: "3.2"
-    - python: "3.3"
-      env: TEST_ARGS="--with-cov --cover-package"
-    - python: "3.4"
+python:
+- 2.6
+- "2.7_with_system_site_packages"
+- 3.2
+- 3.3
+- 3.4
 
 before_install:
     - export DISPLAY=:99.0
@@ -47,6 +45,7 @@ script:
 
     - tools/header.py "Run tests with all dependencies"
     # run tests again with optional dependencies to get more coverage
+    # we get TEST_ARGS from travis_setup.sh
     - nosetests --exe -v --with-doctest $TEST_ARGS
 
 after_success:
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index af14be4d..5595f769 100644
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -11,3 +11,9 @@ fi
 
 pip install  -r requirements.txt $WHEELHOUSE
 python check_bento_build.py
+
+if [[  $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
+    export TEST_ARGS="--with-cov --cover-package skimage"
+else
+    export TEST_ARGS=""
+fi

From 184b9fece3aad4726faef7d7b406d5b611311d7b Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 21:06:01 -0500
Subject: [PATCH 09/42] Specify Qt API

---
 tools/travis_get_optional.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/travis_get_optional.sh b/tools/travis_get_optional.sh
index b43a44dc..45007915 100644
--- a/tools/travis_get_optional.sh
+++ b/tools/travis_get_optional.sh
@@ -5,12 +5,14 @@
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
     sudo apt-get install -q python-qt4
     SCI_QT_API=PyQt4
+    export QT_API=pyqt
 
 else
     sudo apt-get install -q libqt4-dev
     pip install PySide $WHEELHOUSE
     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
     SCI_QT_API=PySide
+    export QT_API=PySide
 fi
 
 # Matplotlib settings - must be after we install Pyside

From adfe6b3c3e9d223c8d2ac5a046e68388ef5f077d Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 21:17:04 -0500
Subject: [PATCH 10/42] Rename variable to MPL_QT_API

---
 tools/travis_get_optional.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/travis_get_optional.sh b/tools/travis_get_optional.sh
index 45007915..ccc297c9 100644
--- a/tools/travis_get_optional.sh
+++ b/tools/travis_get_optional.sh
@@ -4,14 +4,14 @@
 # Install Qt and then update the Matplotlib settings
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
     sudo apt-get install -q python-qt4
-    SCI_QT_API=PyQt4
+    MPL_QT_API=PyQt4
     export QT_API=pyqt
 
 else
     sudo apt-get install -q libqt4-dev
     pip install PySide $WHEELHOUSE
     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
-    SCI_QT_API=PySide
+    MPL_QT_API=PySide
     export QT_API=PySide
 fi
 
@@ -20,7 +20,7 @@ MPL_DIR=$HOME/.config/matplotlib
 mkdir -p $MPL_DIR
 touch $MPL_DIR/matplotlibrc
 echo 'backend : Agg' > $MPL_DIR/matplotlibrc
-echo 'backend.qt4 : '$SCI_QT_API >> $MPL_DIR/matplotlibrc
+echo 'backend.qt4 : '$MPL_QT_API >> $MPL_DIR/matplotlibrc
 
 # imread does NOT support py3.2
 if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then

From 5f719d19ebe22be504d858faf4ac83c13a9a4043 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 22:04:42 -0500
Subject: [PATCH 11/42] Put the whole script in an sh file

---
 .travis.yml                  | 20 ++-----------------
 tools/travis_get_optional.sh | 38 ++++++++++++++++++++++++++++++++++--
 tools/travis_setup.sh        | 10 +++-------
 3 files changed, 41 insertions(+), 27 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 47983033..a2fe2e84 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -21,7 +21,7 @@ before_install:
 
     - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
 
-    - travis_retry sh tools/travis_setup.sh
+    - ./tools/travis_setup.sh
 
 install:
     - tools/header.py "Dependency versions"
@@ -30,23 +30,7 @@ install:
     - python setup.py build_ext --inplace
 
 script:
-    - tools/header.py "Run all tests with minimum dependencies"
-    - nosetests --exe -v skimage
-
-    - tools/header.py "Pep8 and Flake tests"
-    - flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
-
-    - travis_retry sh tools/travis_get_optional.sh
-
-    - tools/header.py "Run doc examples"
-    - export PYTHONPATH=$(pwd):$PYTHONPATH
-    - for f in doc/examples/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-    - for f in doc/examples/applications/*.py; do python "$f"; if [ $? -ne 0 ]; then exit 1; fi done
-
-    - tools/header.py "Run tests with all dependencies"
-    # run tests again with optional dependencies to get more coverage
-    # we get TEST_ARGS from travis_setup.sh
-    - nosetests --exe -v --with-doctest $TEST_ARGS
+    - ./tools/travis_test.sh
 
 after_success:
     - coveralls
diff --git a/tools/travis_get_optional.sh b/tools/travis_get_optional.sh
index ccc297c9..1a3a9a59 100644
--- a/tools/travis_get_optional.sh
+++ b/tools/travis_get_optional.sh
@@ -1,5 +1,13 @@
-#!/usr/bin/sh
-./header.py "Install optional dependencies"
+#!/bin/sh
+set -ex
+
+tools/header.py "Run all tests with minimum dependencies"
+nosetests --exe -v skimage
+
+tools/header.py "Pep8 and Flake tests"
+flake8 --exit-zero --exclude=test_*,six.py skimage doc/examples viewer_examples
+
+tools/header.py "Install optional dependencies"
 
 # Install Qt and then update the Matplotlib settings
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
@@ -39,3 +47,29 @@ pip install astropy
 if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
     pip install pyamg
 fi
+
+tools/header.py "Run doc examples"
+PYTHONPATH=$(pwd):$PYTHONPATH
+for f in doc/examples/*.py;
+do python "$f";
+    if [ $? -ne 0 ]; then
+        exit 1;
+    fi
+done
+
+for f in doc/examples/applications/*.py;
+do python "$f";
+    if [ $? -ne 0 ]; then
+        exit 1;
+    fi
+done
+
+tools/header.py "Run tests with all dependencies"
+# run tests again with optional dependencies to get more coverage
+if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
+    export TEST_ARGS="--with-cov --cover-package skimage"
+else
+    export TEST_ARGS=""
+fi
+nosetests --exe -v --with-doctest $TEST_ARGS
+
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index 5595f769..9ef667e7 100644
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -1,4 +1,6 @@
-#!/usr/bin/sh
+#!/bin/sh
+set -ex
+
 pip install wheel flake8 coveralls nose
 
 # on Python 2.7, use the system versions of numpy, scipy, and matplotlib
@@ -11,9 +13,3 @@ fi
 
 pip install  -r requirements.txt $WHEELHOUSE
 python check_bento_build.py
-
-if [[  $TRAVIS_PYTHON_VERSION == 3.3 ]]; then
-    export TEST_ARGS="--with-cov --cover-package skimage"
-else
-    export TEST_ARGS=""
-fi

From b68643afc262b4ed463805029ea6b570237f88bb Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 23:00:26 -0500
Subject: [PATCH 12/42] Make shell scripts executable

---
 tools/travis_get_optional.sh | 0
 tools/travis_setup.sh        | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 tools/travis_get_optional.sh
 mode change 100644 => 100755 tools/travis_setup.sh

diff --git a/tools/travis_get_optional.sh b/tools/travis_get_optional.sh
old mode 100644
new mode 100755
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
old mode 100644
new mode 100755

From f39775add6794f04628887ff4ee5a1c967ef3104 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Thu, 9 Oct 2014 23:01:04 -0500
Subject: [PATCH 13/42] Remove the travis numpy

---
 tools/travis_setup.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index 9ef667e7..6ab65da3 100755
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -2,6 +2,7 @@
 set -ex
 
 pip install wheel flake8 coveralls nose
+pip uninstall -y numpy
 
 # on Python 2.7, use the system versions of numpy, scipy, and matplotlib
 # and the minimum version of cython and networkx

From b594f0afa07f924ea7ebfb37d28849faf94e3154 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:00:17 -0500
Subject: [PATCH 14/42] Rename the script

---
 tools/{travis_get_optional.sh => travis_test.sh} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tools/{travis_get_optional.sh => travis_test.sh} (100%)

diff --git a/tools/travis_get_optional.sh b/tools/travis_test.sh
similarity index 100%
rename from tools/travis_get_optional.sh
rename to tools/travis_test.sh

From ba1193b15ba218c5c01e7738b6b4a8218e810b0c Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:17:39 -0500
Subject: [PATCH 15/42] Switch shell to bash

---
 tools/travis_setup.sh | 2 +-
 tools/travis_test.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index 6ab65da3..4678dafa 100755
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/usr/bin/bash
 set -ex
 
 pip install wheel flake8 coveralls nose
diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 1a3a9a59..a309a32d 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/usr/bin/bash
 set -ex
 
 tools/header.py "Run all tests with minimum dependencies"

From 5511639938578b5ffb8e4517755b8d9a6ea040a5 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:25:48 -0500
Subject: [PATCH 16/42] Use more generic shebang

---
 tools/travis_setup.sh | 2 +-
 tools/travis_test.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index 4678dafa..c71e3d7a 100755
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/bash
+#!/usr/bin/env bash
 set -ex
 
 pip install wheel flake8 coveralls nose
diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index a309a32d..c0cab37a 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/bash
+#!#!/usr/bin/env bash
 set -ex
 
 tools/header.py "Run all tests with minimum dependencies"

From 10cc476f7f4516ba67d385d1796e65db56e3307d Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:33:35 -0500
Subject: [PATCH 17/42] Try to get system matplotlib to pass requirments.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 435803b9..98f3b77f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 cython>=0.19.2
-matplotlib>=1.1.1
+matplotlib>=1.1.0
 numpy>=1.6.1
 scipy>=0.9
 six>=1.3

From 29e51a0604e3da65afdadbed161a720ae7aafd68 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:36:54 -0500
Subject: [PATCH 18/42] Fix shebang line

---
 tools/travis_test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index c0cab37a..acbc1241 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -1,4 +1,4 @@
-#!#!/usr/bin/env bash
+#!/usr/bin/env bash
 set -ex
 
 tools/header.py "Run all tests with minimum dependencies"

From fdfb24269422948c2b2fdc80379e6375a293b45f Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:50:02 -0500
Subject: [PATCH 19/42] Update the notes

---
 doc/travis_notes.txt | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/doc/travis_notes.txt b/doc/travis_notes.txt
index c5d5c99c..37f5d4a1 100644
--- a/doc/travis_notes.txt
+++ b/doc/travis_notes.txt
@@ -3,10 +3,19 @@
   http://lint.travis-ci.org/ is recommended elsewhere but does not give helpful
   error reports.
 - Make sure all of your "-" lines start on the same column
-- Use shell scripts for `before_install` and `script` or any part that
+- Use bash scripts for `before_install` and `script` or any part that
   has conditional statements
+   - Make sure they are "executable" (chmod +x)
+   - Use the following header:
+
+   ```
+     #!/usr/bin/env bash
+     set -ex
+   ```
+
 - Use `travis_retry` before a command to have it try several times before
-failing (useful for installing from third party sources)
+failing (useful for installing from third party sources).  Note that this
+command is not available within a bash script.
 - Feel free to cancel a build rather than waiting for it to go to completion
   if you have made a change to that branch.
 - A VM with 64bit Ubuntu 12.04 is a huge help for debugging.

From 6e326add184840234f64b7a472449e5da78136d2 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:51:03 -0500
Subject: [PATCH 20/42] The python path should include the parent directory now

---
 tools/travis_test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index acbc1241..f79cbc2b 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -49,7 +49,7 @@ if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
 fi
 
 tools/header.py "Run doc examples"
-PYTHONPATH=$(pwd):$PYTHONPATH
+PYTHONPATH="..":$PYTHONPATH
 for f in doc/examples/*.py;
 do python "$f";
     if [ $? -ne 0 ]; then

From 73e639e3b614ad2b784d507ac708246dde02a974 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 05:53:04 -0500
Subject: [PATCH 21/42] Fix formatting of 'for' loops

---
 tools/travis_test.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index f79cbc2b..5f062542 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -50,15 +50,15 @@ fi
 
 tools/header.py "Run doc examples"
 PYTHONPATH="..":$PYTHONPATH
-for f in doc/examples/*.py;
-do python "$f";
+for f in doc/examples/*.py; do
+    python "$f";
     if [ $? -ne 0 ]; then
         exit 1;
     fi
 done
 
-for f in doc/examples/applications/*.py;
-do python "$f";
+for f in doc/examples/applications/*.py; do
+    python "$f";
     if [ $? -ne 0 ]; then
         exit 1;
     fi

From e146c3eea5ea9449a1601a7d36eba20e9c60b86e Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:11:26 -0500
Subject: [PATCH 22/42] Clean up formatting and a comment

---
 tools/travis_setup.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index c71e3d7a..67b0a046 100755
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -6,11 +6,11 @@ pip uninstall -y numpy
 
 # on Python 2.7, use the system versions of numpy, scipy, and matplotlib
 # and the minimum version of cython and networkx
-if [[  $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
+if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
     sudo apt-get install python-scipy python-matplotlib
     pip install https://github.com/cython/cython/archive/0.19.2.tar.gz
     pip install https://github.com/networkx/networkx/archive/networkx-1.8.tar.gz
 fi
 
-pip install  -r requirements.txt $WHEELHOUSE
+pip install -r requirements.txt $WHEELHOUSE
 python check_bento_build.py

From d3172b33501bb6cbf8b8afad6c831991ac866d72 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:12:38 -0500
Subject: [PATCH 23/42] Keep consistent with calling convention

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index a2fe2e84..028796fa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -21,7 +21,7 @@ before_install:
 
     - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
 
-    - ./tools/travis_setup.sh
+    - tools/travis_setup.sh
 
 install:
     - tools/header.py "Dependency versions"
@@ -30,7 +30,7 @@ install:
     - python setup.py build_ext --inplace
 
 script:
-    - ./tools/travis_test.sh
+    - tools/travis_test.sh
 
 after_success:
     - coveralls

From 5dbf433eef0aed66f087076637e4f399e686c0f5 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:13:26 -0500
Subject: [PATCH 24/42] Put the WHEELHOUSE as a global variable

---
 .travis.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 028796fa..75f259a0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,6 +7,9 @@
 
 language: python
 
+env:
+    WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+
 python:
 - 2.6
 - "2.7_with_system_site_packages"
@@ -19,8 +22,6 @@ before_install:
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
-    - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
-
     - tools/travis_setup.sh
 
 install:

From 16f2393958a86603e62fa8a91b0748a473a46aed Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:14:27 -0500
Subject: [PATCH 25/42] Put the other env variables up top as well

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 75f259a0..6c67cc17 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,6 +9,8 @@ language: python
 
 env:
     WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+    PYTHONWARNINGS="all"
+    DISPLAY=:99.0
 
 python:
 - 2.6
@@ -18,7 +20,6 @@ python:
 - 3.4
 
 before_install:
-    - export DISPLAY=:99.0
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
 
@@ -27,7 +28,6 @@ before_install:
 install:
     - tools/header.py "Dependency versions"
     - tools/build_versions.py
-    - export PYTHONWARNINGS=all
     - python setup.py build_ext --inplace
 
 script:

From 2d4604a3cf71edb394293d04ed591bc2db81f0c5 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:16:49 -0500
Subject: [PATCH 26/42] Move dependency output to setup script

---
 .travis.yml           | 3 ---
 tools/travis_setup.sh | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 6c67cc17..f1ad920e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,12 +22,9 @@ python:
 before_install:
     - sh -e /etc/init.d/xvfb start
     - sudo apt-get update
-
     - tools/travis_setup.sh
 
 install:
-    - tools/header.py "Dependency versions"
-    - tools/build_versions.py
     - python setup.py build_ext --inplace
 
 script:
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index 67b0a046..a542a0ec 100755
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -14,3 +14,6 @@ fi
 
 pip install -r requirements.txt $WHEELHOUSE
 python check_bento_build.py
+
+tools/header.py "Dependency versions"
+tools/build_versions.py

From ef215de3a93e1bddf9ff9e56f46d753f51158bbf Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:29:42 -0500
Subject: [PATCH 27/42] Install skimage so we do not have to fool with
 PYTHONPATH

---
 .travis.yml          | 1 +
 tools/travis_test.sh | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index f1ad920e..c774db01 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -26,6 +26,7 @@ before_install:
 
 install:
     - python setup.py build_ext --inplace
+    - python setup.py install
 
 script:
     - tools/travis_test.sh
diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 5f062542..98275418 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -49,7 +49,6 @@ if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
 fi
 
 tools/header.py "Run doc examples"
-PYTHONPATH="..":$PYTHONPATH
 for f in doc/examples/*.py; do
     python "$f";
     if [ $? -ne 0 ]; then

From 9c7cee33ab94215fa6aee0333909990236b545a6 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:30:57 -0500
Subject: [PATCH 28/42] Use a straight install

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index c774db01..9a63850b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -25,7 +25,6 @@ before_install:
     - tools/travis_setup.sh
 
 install:
-    - python setup.py build_ext --inplace
     - python setup.py install
 
 script:

From c52a42975d6e69006473e67b6739c0b6962c6fd0 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:33:52 -0500
Subject: [PATCH 29/42] Move env variable to before_install

---
 .travis.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 9a63850b..5659d255 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,11 +7,6 @@
 
 language: python
 
-env:
-    WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
-    PYTHONWARNINGS="all"
-    DISPLAY=:99.0
-
 python:
 - 2.6
 - "2.7_with_system_site_packages"
@@ -21,7 +16,10 @@ python:
 
 before_install:
     - sh -e /etc/init.d/xvfb start
+    - export DISPLAY=:99.0
     - sudo apt-get update
+    - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+    - export PYTHONWARNINGS="all"
     - tools/travis_setup.sh
 
 install:

From 3a0f0ccb86fd9358303d25c3a9585dd4ddd210ba Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:34:35 -0500
Subject: [PATCH 30/42] Add whitespace

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 5659d255..ae1d9425 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -18,6 +18,7 @@ before_install:
     - sh -e /etc/init.d/xvfb start
     - export DISPLAY=:99.0
     - sudo apt-get update
+
     - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
     - export PYTHONWARNINGS="all"
     - tools/travis_setup.sh

From 0e3c8382f34a25eb9b6fb1b44122ade35b502c89 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 06:37:35 -0500
Subject: [PATCH 31/42] Remove whitespace

---
 tools/travis_test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 98275418..71e3ef03 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -31,13 +31,13 @@ echo 'backend : Agg' > $MPL_DIR/matplotlibrc
 echo 'backend.qt4 : '$MPL_QT_API >> $MPL_DIR/matplotlibrc
 
 # imread does NOT support py3.2
-if [[  $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
+if [[ $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
     sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
     pip install imread
 fi
 
 # TODO: update when SimpleITK become available on py34 or hopefully pip
-if [[  $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
+if [[ $TRAVIS_PYTHON_VERSION != 3.4 ]]; then
     easy_install SimpleITK
 fi
 

From 095160f1c63327d25cd0f5c98c56f79b869f66cf Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 07:12:38 -0500
Subject: [PATCH 32/42] Reinstate the separate build step

---
 .travis.yml          | 1 +
 tools/travis_test.sh | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index ae1d9425..ac551dc5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -24,6 +24,7 @@ before_install:
     - tools/travis_setup.sh
 
 install:
+    - python setup.py build_ext --inplace
     - python setup.py install
 
 script:
diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 71e3ef03..8af29582 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -20,7 +20,7 @@ else
     pip install PySide $WHEELHOUSE
     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
     MPL_QT_API=PySide
-    export QT_API=PySide
+    export QT_API=pyside
 fi
 
 # Matplotlib settings - must be after we install Pyside

From 53892e215366d39228a793a621289c242e5c167e Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 09:01:18 -0500
Subject: [PATCH 33/42] Move the rest of the code to the scripts.

---
 .travis.yml           | 6 ------
 tools/travis_setup.sh | 5 +++++
 tools/travis_test.sh  | 4 ++++
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ac551dc5..2b6451ca 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,12 +15,6 @@ python:
 - 3.4
 
 before_install:
-    - sh -e /etc/init.d/xvfb start
-    - export DISPLAY=:99.0
-    - sudo apt-get update
-
-    - export WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
-    - export PYTHONWARNINGS="all"
     - tools/travis_setup.sh
 
 install:
diff --git a/tools/travis_setup.sh b/tools/travis_setup.sh
index a542a0ec..f7602aef 100755
--- a/tools/travis_setup.sh
+++ b/tools/travis_setup.sh
@@ -1,6 +1,11 @@
 #!/usr/bin/env bash
 set -ex
 
+sh -e /etc/init.d/xvfb start
+sudo apt-get update
+
+WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+
 pip install wheel flake8 coveralls nose
 pip uninstall -y numpy
 
diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 8af29582..62cfe948 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -1,6 +1,10 @@
 #!/usr/bin/env bash
 set -ex
 
+export DISPLAY=:99.0
+export PYTHONWARNINGS="all"
+WHEELHOUSE="--no-index --find-links=http://wheels.scikit-image.org/"
+
 tools/header.py "Run all tests with minimum dependencies"
 nosetests --exe -v skimage
 

From b37913d63c7853539c1f19c130df78598203a0df Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 11:28:33 -0500
Subject: [PATCH 34/42] Use a null backend during the doc examples

---
 tools/travis_test.sh | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 62cfe948..25245ee2 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -27,13 +27,6 @@ else
     export QT_API=pyside
 fi
 
-# Matplotlib settings - must be after we install Pyside
-MPL_DIR=$HOME/.config/matplotlib
-mkdir -p $MPL_DIR
-touch $MPL_DIR/matplotlibrc
-echo 'backend : Agg' > $MPL_DIR/matplotlibrc
-echo 'backend.qt4 : '$MPL_QT_API >> $MPL_DIR/matplotlibrc
-
 # imread does NOT support py3.2
 if [[ $TRAVIS_PYTHON_VERSION != 3.2 ]]; then
     sudo apt-get install -q libtiff4-dev libwebp-dev libpng12-dev xcftools
@@ -52,6 +45,13 @@ if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
     pip install pyamg
 fi
 
+# Matplotlib settings - do not show figures during doc examples
+MPL_DIR=$HOME/.config/matplotlib
+mkdir -p $MPL_DIR
+touch $MPL_DIR/matplotlibrc
+echo 'backend : Template' > $MPL_DIR/matplotlibrc
+
+
 tools/header.py "Run doc examples"
 for f in doc/examples/*.py; do
     python "$f";
@@ -67,6 +67,11 @@ for f in doc/examples/applications/*.py; do
     fi
 done
 
+# Now configure Matplotlib to use Qt4
+echo 'backend: Agg' > $MPL_DIR/matplotlibrc
+echo 'backend.qt4 : '$MPL_QT_API >> $MPL_DIR/matplotlibrc
+
+
 tools/header.py "Run tests with all dependencies"
 # run tests again with optional dependencies to get more coverage
 if [[ $TRAVIS_PYTHON_VERSION == 3.3 ]]; then

From f5b30bf86750115922eaa9744053ce0b4cff0488 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 20:15:33 -0500
Subject: [PATCH 35/42] Formatting

---
 tools/travis_test.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 25245ee2..6ed95049 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -54,16 +54,16 @@ echo 'backend : Template' > $MPL_DIR/matplotlibrc
 
 tools/header.py "Run doc examples"
 for f in doc/examples/*.py; do
-    python "$f";
+    python "$f"
     if [ $? -ne 0 ]; then
-        exit 1;
+        exit 1
     fi
 done
 
 for f in doc/examples/applications/*.py; do
-    python "$f";
+    python "$f"
     if [ $? -ne 0 ]; then
-        exit 1;
+        exit 1
     fi
 done
 

From 283e759b378ec4cf8eca388e1fbfc93b380b4501 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Fri, 10 Oct 2014 22:07:04 -0500
Subject: [PATCH 36/42] Matplotlibrc was in a different location in mpl 1.1.1

---
 tools/travis_test.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index 6ed95049..c3e14423 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -17,6 +17,7 @@ tools/header.py "Install optional dependencies"
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
     sudo apt-get install -q python-qt4
     MPL_QT_API=PyQt4
+    MPL_DIR=$HOME/.matplotlibrc
     export QT_API=pyqt
 
 else
@@ -24,6 +25,7 @@ else
     pip install PySide $WHEELHOUSE
     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
     MPL_QT_API=PySide
+    MPL_DIR=$HOME/.config/matplotlibrc
     export QT_API=pyside
 fi
 
@@ -46,7 +48,6 @@ if [[ $TRAVIS_PYTHON_VERSION == 2.* ]]; then
 fi
 
 # Matplotlib settings - do not show figures during doc examples
-MPL_DIR=$HOME/.config/matplotlib
 mkdir -p $MPL_DIR
 touch $MPL_DIR/matplotlibrc
 echo 'backend : Template' > $MPL_DIR/matplotlibrc

From 3b63e19412f9aa1e4b20cd0285bb810561cd356e Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 11 Oct 2014 04:37:00 -0500
Subject: [PATCH 37/42] Fix MPL_DIR location

---
 tools/travis_test.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/travis_test.sh b/tools/travis_test.sh
index c3e14423..df3a484d 100755
--- a/tools/travis_test.sh
+++ b/tools/travis_test.sh
@@ -17,7 +17,7 @@ tools/header.py "Install optional dependencies"
 if [[ $TRAVIS_PYTHON_VERSION == 2.7* ]]; then
     sudo apt-get install -q python-qt4
     MPL_QT_API=PyQt4
-    MPL_DIR=$HOME/.matplotlibrc
+    MPL_DIR=$HOME/.matplotlib
     export QT_API=pyqt
 
 else
@@ -25,7 +25,7 @@ else
     pip install PySide $WHEELHOUSE
     python ~/virtualenv/python${TRAVIS_PYTHON_VERSION}/bin/pyside_postinstall.py -install
     MPL_QT_API=PySide
-    MPL_DIR=$HOME/.config/matplotlibrc
+    MPL_DIR=$HOME/.config/matplotlib
     export QT_API=pyside
 fi
 

From 0c35d132032d23cc9b4b2a18119eb9fda1179aa9 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 11 Oct 2014 05:12:04 -0500
Subject: [PATCH 38/42] Add a try/catch for RectangleTool.disconnect_events

---
 skimage/viewer/canvastools/recttool.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/skimage/viewer/canvastools/recttool.py b/skimage/viewer/canvastools/recttool.py
index 5d658533..25b6df88 100644
--- a/skimage/viewer/canvastools/recttool.py
+++ b/skimage/viewer/canvastools/recttool.py
@@ -50,7 +50,10 @@ class RectangleTool(CanvasToolBase, RectangleSelector):
             props['edgecolor'] = props['facecolor']
         RectangleSelector.__init__(self, self.ax, lambda *args: None,
                                    rectprops=props)
-        self.disconnect_events()  # events are handled by the viewer
+        try:
+            self.disconnect_events()  # events are handled by the viewer
+        except AttributeError:
+            pass  # older versions of MPL do not have this method
         # Alias rectangle attribute, which is initialized in RectangleSelector.
         self._rect = self.to_draw
         self._rect.set_animated(True)

From 532e46017240701d481ae85a4285778ec232bb39 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 11 Oct 2014 07:21:32 -0500
Subject: [PATCH 39/42] Disconnect the events manually

---
 skimage/viewer/canvastools/recttool.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/skimage/viewer/canvastools/recttool.py b/skimage/viewer/canvastools/recttool.py
index 25b6df88..fcd10aca 100644
--- a/skimage/viewer/canvastools/recttool.py
+++ b/skimage/viewer/canvastools/recttool.py
@@ -50,10 +50,10 @@ class RectangleTool(CanvasToolBase, RectangleSelector):
             props['edgecolor'] = props['facecolor']
         RectangleSelector.__init__(self, self.ax, lambda *args: None,
                                    rectprops=props)
-        try:
-            self.disconnect_events()  # events are handled by the viewer
-        except AttributeError:
-            pass  # older versions of MPL do not have this method
+        # Events are handled by the viewer
+        for c in self.cids:
+            self.canvas.mpl_disconnect(c)
+
         # Alias rectangle attribute, which is initialized in RectangleSelector.
         self._rect = self.to_draw
         self._rect.set_animated(True)

From 72292f73c0a77a4489b9889f86b8e32d4270cb30 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 11 Oct 2014 09:15:10 -0500
Subject: [PATCH 40/42] Use a manual hack to remove the canvas events for old
 MPL

---
 skimage/viewer/canvastools/recttool.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/skimage/viewer/canvastools/recttool.py b/skimage/viewer/canvastools/recttool.py
index fcd10aca..ce81c38d 100644
--- a/skimage/viewer/canvastools/recttool.py
+++ b/skimage/viewer/canvastools/recttool.py
@@ -51,8 +51,11 @@ class RectangleTool(CanvasToolBase, RectangleSelector):
         RectangleSelector.__init__(self, self.ax, lambda *args: None,
                                    rectprops=props)
         # Events are handled by the viewer
-        for c in self.cids:
-            self.canvas.mpl_disconnect(c)
+        try:
+            self.disconnect_events()
+        except AttributeError:
+            # disconnect the events manually (hack for older mpl verions)
+            [self.canvas.mpl_disconnect(i) for i in range(5)]
 
         # Alias rectangle attribute, which is initialized in RectangleSelector.
         self._rect = self.to_draw

From 725c376d78d7d8e6a7c49e1352ada7864f1c5c92 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 11 Oct 2014 14:34:55 -0500
Subject: [PATCH 41/42] Make sure we disconnect all the signals

---
 skimage/viewer/canvastools/recttool.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/viewer/canvastools/recttool.py b/skimage/viewer/canvastools/recttool.py
index ce81c38d..41e9ab1e 100644
--- a/skimage/viewer/canvastools/recttool.py
+++ b/skimage/viewer/canvastools/recttool.py
@@ -55,7 +55,7 @@ class RectangleTool(CanvasToolBase, RectangleSelector):
             self.disconnect_events()
         except AttributeError:
             # disconnect the events manually (hack for older mpl verions)
-            [self.canvas.mpl_disconnect(i) for i in range(5)]
+            [self.canvas.mpl_disconnect(i) for i in range(10)]
 
         # Alias rectangle attribute, which is initialized in RectangleSelector.
         self._rect = self.to_draw

From 0fabb0c3ab45fd805a6d623979b0cb8b96e75d02 Mon Sep 17 00:00:00 2001
From: Steven Silvester <steven.silvester@ieee.org>
Date: Sat, 11 Oct 2014 18:28:36 -0500
Subject: [PATCH 42/42] Fix comment typo

---
 skimage/viewer/canvastools/recttool.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skimage/viewer/canvastools/recttool.py b/skimage/viewer/canvastools/recttool.py
index 41e9ab1e..8932e180 100644
--- a/skimage/viewer/canvastools/recttool.py
+++ b/skimage/viewer/canvastools/recttool.py
@@ -54,7 +54,7 @@ class RectangleTool(CanvasToolBase, RectangleSelector):
         try:
             self.disconnect_events()
         except AttributeError:
-            # disconnect the events manually (hack for older mpl verions)
+            # disconnect the events manually (hack for older mpl versions)
             [self.canvas.mpl_disconnect(i) for i in range(10)]
 
         # Alias rectangle attribute, which is initialized in RectangleSelector.