Merge update

.github/ISSUE_TEMPLATE.md

@@ -16,6 +16,8 @@
 
 * Spyder Version:
 * Python Version:
+* Qt Version:
+* PyQt Version:
 * Operating system:
 
 

CHANGELOG.md

@@ -1,5 +1,77 @@
 # History of changes
 
+## Version 3.1.3 (2017-02-20)
+
+### Bugs fixed
+
+**Issues**
+
+* [Issue 4139](https://github.com/spyder-ide/spyder/issues/4139) - Nan value in dataframe editor crash Spyder
+* [Issue 4128](https://github.com/spyder-ide/spyder/issues/4128) - Add the version of PyQt in the report of the issue
+* [Issue 4127](https://github.com/spyder-ide/spyder/issues/4127) - UnboundLocalError: local variable 'img_path' referenced before assignment
+* [Issue 4122](https://github.com/spyder-ide/spyder/issues/4122) - Spyder closes after completing Run settings dialog for a first run.
+* [Issue 4096](https://github.com/spyder-ide/spyder/issues/4096) - More issues with autoindentation
+* [Issue 4088](https://github.com/spyder-ide/spyder/issues/4088) - Crash when saving an image in the IPython console
+* [Issue 4086](https://github.com/spyder-ide/spyder/issues/4086) - Error when launching a new Editor window from the options in the menu.
+* [Issue 4085](https://github.com/spyder-ide/spyder/issues/4085) - Crash in "New window" when opening new file.
+* [Issue 4076](https://github.com/spyder-ide/spyder/issues/4076) - Add tests to verify that importing .mat files is working
+* [Issue 4074](https://github.com/spyder-ide/spyder/issues/4074) - Identation broken after statements with closing parenthesis followed by more code
+* [Issue 4072](https://github.com/spyder-ide/spyder/issues/4072) - Case sensitive replace does not respect case
+* [Issue 4066](https://github.com/spyder-ide/spyder/issues/4066) - Spyder core dumps if an opened variable in variable explorer gets deleted
+* [Issue 4063](https://github.com/spyder-ide/spyder/issues/4063) - Spyder crashes when killing the current process to start a new one
+* [Issue 4053](https://github.com/spyder-ide/spyder/issues/4053) - Spyder 3.1.2 cannot connect to kernel as 3.0.2
+* [Issue 4052](https://github.com/spyder-ide/spyder/issues/4052) - Maximising current pane fails and hangs Spyder 3.1.x
+* [Issue 4050](https://github.com/spyder-ide/spyder/issues/4050) - Wrong binary in Python 3 wheels
+* [Issue 4041](https://github.com/spyder-ide/spyder/issues/4041) - Create a way to add tests for the whole app
+* [Issue 4037](https://github.com/spyder-ide/spyder/issues/4037) - Tabs as indentation - characters being removed in editor
+* [Issue 4030](https://github.com/spyder-ide/spyder/issues/4030) - Inconsistent icon for "Find symbols in file..."
+* [Issue 4005](https://github.com/spyder-ide/spyder/issues/4005) - Find in Files not working after 3.1.0 update
+* [Issue 3992](https://github.com/spyder-ide/spyder/issues/3992) - Remove unnecessary newlines in run cell
+* [Issue 3972](https://github.com/spyder-ide/spyder/issues/3972) - Remove file path from Editor's plugin title
+* [Issue 3970](https://github.com/spyder-ide/spyder/issues/3970) - Error when editing markdown
+* [Issue 3917](https://github.com/spyder-ide/spyder/issues/3917) - Failed to import data in Variable Explorer on Windows
+* [Issue 3476](https://github.com/spyder-ide/spyder/issues/3476) - New breakpoints can't be created in the IPython console
+
+In this release 25 issues were closed
+
+**Pull requests**
+
+* [PR 4175](https://github.com/spyder-ide/spyder/pull/4175) - PR: Set new breakpoints in the IPython console while on a debugging session
+* [PR 4171](https://github.com/spyder-ide/spyder/pull/4171) - PR: Re-run flaky tests several times
+* [PR 4165](https://github.com/spyder-ide/spyder/pull/4165) - PR: Loading spydata files now uncompress them inside a temp folder
+* [PR 4152](https://github.com/spyder-ide/spyder/pull/4152) - PR: Skip matlab import test if SciPy is not installed.
+* [PR 4151](https://github.com/spyder-ide/spyder/pull/4151) - PR: Make tests more reliable
+* [PR 4148](https://github.com/spyder-ide/spyder/pull/4148) - PR: Use an older Miniconda version for Python 3
+* [PR 4144](https://github.com/spyder-ide/spyder/pull/4144) - PR: Some fixes for Find in files
+* [PR 4142](https://github.com/spyder-ide/spyder/pull/4142) - PR: Gracefully handle ValueError in DataFrameModel
+* [PR 4140](https://github.com/spyder-ide/spyder/pull/4140) - PR: Disable some tests on Windows because they are timing out recurrently
+* [PR 4133](https://github.com/spyder-ide/spyder/pull/4133) - PR: Add an initialization value to img_path
+* [PR 4130](https://github.com/spyder-ide/spyder/pull/4130) - PR: Correctly stop pytest's on failure
+* [PR 4129](https://github.com/spyder-ide/spyder/pull/4129) - PR: Add Qt and PyQt version in the report of the issue
+* [PR 4125](https://github.com/spyder-ide/spyder/pull/4125) - PR: Make loading IPython kernels by using their ids to work again
+* [PR 4113](https://github.com/spyder-ide/spyder/pull/4113) - PR: Add a validation for the PyQt version used to show a message in the Python console
+* [PR 4110](https://github.com/spyder-ide/spyder/pull/4110) - PR: Add more tests for the main window
+* [PR 4109](https://github.com/spyder-ide/spyder/pull/4109) - PR: Fix maximize button
+* [PR 4106](https://github.com/spyder-ide/spyder/pull/4106) - PR: Prevent some crashes and errors when editing objects in the Variable Explorer
+* [PR 4105](https://github.com/spyder-ide/spyder/pull/4105) - PR: Fix hard crash when trying to open files in a new editor window
+* [PR 4104](https://github.com/spyder-ide/spyder/pull/4104) - PR: Pin Jedi to 0.9.0
+* [PR 4102](https://github.com/spyder-ide/spyder/pull/4102) - PR: Added Matlab files import tests
+* [PR 4097](https://github.com/spyder-ide/spyder/pull/4097) - PR: Add a validation for editorstack existence
+* [PR 4082](https://github.com/spyder-ide/spyder/pull/4082) - PR: More autoindentation fixes
+* [PR 4079](https://github.com/spyder-ide/spyder/pull/4079) - PR: Add a flag to use case sensitive search/replace
+* [PR 4069](https://github.com/spyder-ide/spyder/pull/4069) - PR: Fix executable name in Python 3 wheels
+* [PR 4043](https://github.com/spyder-ide/spyder/pull/4043) - PR: Use the "at" symbol to represent the symbol finder everywhere
+* [PR 4042](https://github.com/spyder-ide/spyder/pull/4042) - PR: Unindent with tabs was deleting some text.
+* [PR 4034](https://github.com/spyder-ide/spyder/pull/4034) - PR: Fix error when using TextSH (default highligher)
+* [PR 4006](https://github.com/spyder-ide/spyder/pull/4006) - PR: Remove unnecessary new lines when running cells
+* [PR 3975](https://github.com/spyder-ide/spyder/pull/3975) - PR: Remove file path from the Editor's plugin title.
+
+In this release 29 pull requests were merged
+
+
+----
+
+
 ## Version 3.1.2 (2017-01-24)
 
 ### Bugs fixed
@@ -858,7 +930,7 @@ In this release 50 pull requests were merged
 ----
 
 
-## Version 3.0beta1/beta2 (2016-12-11)
+## Version 3.0beta1/beta2 (2015-12-11)
 
 ### Bugfixes
 

README.md

@@ -143,7 +143,7 @@ a Python version greater than 2.7 (Python 3.2 is not supported anymore).
 * **Python** 2.7 or 3.3+
 * **PyQt5** 5.2+ or **PyQt4** 4.6+: PyQt5 is recommended.
 * **qtconsole** 4.2.0+: Enhanced Python interpreter.
-* **Rope** and **Jedi**: Editor code completion, calltips
+* **Rope** and **Jedi** 0.9.0: Editor code completion, calltips
   and go-to-definition.
 * **Pyflakes**: Real-time code analysis.
 * **Sphinx**: Rich text mode for the Help pane.

RELEASE.md

@@ -4,7 +4,7 @@ To release a new version of Spyder you need to follow these steps:
 
 * Update CHANGELOG.md
 
-* Update Announcements.txt
+* Update Announcements.md
 
 * Update version in `__init__.py` (set release version, remove 'dev0')
 

circle.yml

@@ -11,10 +11,14 @@ machine:
     CONDA_DEPENDENCIES_FLAGS: "--quiet"
     CONDA_DEPENDENCIES: >
       rope jedi pyflakes sphinx pygments pylint pep8 psutil nbconvert qtawesome pickleshare
-      qtpy pyzmq chardet mock nomkl pandas pytest pytest-cov numpydoc
-    PIP_DEPENDENCIES: "coveralls pytest-qt"
+      qtpy pyzmq chardet mock nomkl pandas pytest pytest-cov numpydoc scipy
+    PIP_DEPENDENCIES: "coveralls pytest-qt flaky"
 
 dependencies:
+  pre:
+    # We need to run a window manager to avoid focus problems when running our tests.
+    # See https://github.com/TestFX/TestFX/issues/158#issuecomment-62421691
+    - sudo apt-get install matchbox-window-manager
   override:
     # First convert PY_VERSIONS to an array and then select the python version based on the CIRCLE_NODE_INDEX
     - export PY_VERSIONS=($PY_VERSIONS) &&
@@ -26,6 +30,9 @@ dependencies:
       source activate test &&
       conda install -q ciocheck -c spyder-ide --no-update-deps &&
       python setup.py install > /dev/null;
+    - DISPLAY=:99 /usr/bin/matchbox-window-manager:
+        background: true
+    - sleep 5
 
 test:
   override:

continuous_integration/appveyor/install.ps1

@@ -8,9 +8,9 @@ $MINICONDA_URL = "http://repo.continuum.io/miniconda/"
 function DownloadMiniconda ($python_version, $platform_suffix) {
     $webclient = New-Object System.Net.WebClient
     if ($python_version -match "3.5") {
-        $filename = "Miniconda3-latest-Windows-" + $platform_suffix + ".exe"
+        $filename = "Miniconda3-4.2.12-Windows-" + $platform_suffix + ".exe"
     } else {
-        $filename = "Miniconda-latest-Windows-" + $platform_suffix + ".exe"
+        $filename = "Miniconda2-latest-Windows-" + $platform_suffix + ".exe"
     }
     $url = $MINICONDA_URL + $filename
 
@@ -90,7 +90,7 @@ function InstallPipPackages ($python_home, $spec) {
 function main () {
     InstallMiniconda $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
     InstallCondaPackages $env:PYTHON "conda=4.2.* conda-build=2.0.0 pytest pytest-cov mock"
-    InstallPipPackages $env:PYTHON "pytest-qt"
+    InstallPipPackages $env:PYTHON "pytest-qt flaky"
 }
 
 

continuous_integration/appveyor/run_test.bat

@@ -2,7 +2,7 @@
 set TEST_CI_APP=True
 
 :: Set extra packages
-set EXTRA_PACKAGES=pandas sympy pillow
+set EXTRA_PACKAGES=pandas sympy pillow scipy
 
 :: Move to a tmp dir before doing the installation
 mkdir C:\projects\tmp
@@ -17,12 +17,6 @@ conda install -q -y --use-local spyder-dev
 :: Install extra packages
 conda install -q -y %EXTRA_PACKAGES%
 
-:: Test that the app starts correctly
-echo ------- Testing the app ---------
-echo.
-echo %time%
-:: skipping spyder || exit 1
-echo Success!
-echo %time%
-echo.
-echo ---------------------------------
+:: NOTE: We don't run Spyder here because it times out
+:: most of the time. However, the whole window is now
+:: run as part of our pytest's.

continuous_integration/conda-recipes/spyder/meta.yaml

@@ -23,7 +23,7 @@ requirements:
     - rope 0.9.*  # [py34 or py35]
     - rope  # [py27]
     - pyflakes
-    - jedi
+    - jedi 0.9.*
     - qtconsole
     - nbconvert
     - pygments

continuous_integration/travis/build_test.sh

@@ -9,7 +9,7 @@ cd $FULL_SPYDER_CLONE
 if [ $TRAVIS_PULL_REQUEST != "false" ] ; then
     git checkout travis_pr_$TRAVIS_PULL_REQUEST
 else
-    git checkout master
+    git checkout $TRAVIS_BRANCH
 fi
 
 # -- Build package

continuous_integration/travis/install.sh

@@ -38,7 +38,7 @@ install_conda()
     if [ "$PY_VERSION" = "2.7" ]; then
         wget "http://repo.continuum.io/miniconda/Miniconda-$MINICONDA_VERSION-$MINICONDA_OS.sh" -O miniconda.sh;
     else
-        wget "http://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VERSION-$MINICONDA_OS.sh" -O miniconda.sh;
+        wget "http://repo.continuum.io/miniconda/Miniconda3-4.2.12-$MINICONDA_OS.sh" -O miniconda.sh;
     fi
 
     bash miniconda.sh -b -p "$HOME/miniconda";

continuous_integration/travis/modules_test.sh

@@ -11,7 +11,7 @@ cd $FULL_SPYDER_CLONE
 if [ $TRAVIS_PULL_REQUEST != "false" ] ; then
     git checkout travis_pr_$TRAVIS_PULL_REQUEST
 else
-    git checkout master
+    git checkout $TRAVIS_BRANCH
 fi
 
 # Depth 1

continuous_integration/travis/run_test.sh

@@ -10,7 +10,7 @@ export TEST_CI_APP=True
 # We install them here and not in travis_install.sh to see if
 # Spyder is correctly pulling its deps (some of them are shared
 # with mpl)
-export EXTRA_PACKAGES="nomkl pandas sympy pillow"
+export EXTRA_PACKAGES="nomkl pandas sympy pillow scipy"
 
 # Install our builds of Spyder
 if [ "$USE_CONDA" = true ] ; then
@@ -30,7 +30,11 @@ fi
 
 
 # Testing that the app starts and runs
-spyder
+if [[ "$USE_CONDA" = false && "$TRAVIS_PYTHON_VERSION" != "2.7" ]] ; then
+    spyder3
+else
+    spyder
+fi
 if [ $? -ne 0 ]; then
     exit 1
 fi

doc/installation.rst

@@ -161,7 +161,7 @@ The requirements to run Spyder are:
   enhanced Python interpreter.
 
 * `Rope <http://rope.sourceforge.net/>`_ >=0.9.4 and
-  `Jedi <http://jedi.jedidjah.ch/en/latest/>` 0.8.1 -- for code completion,
+  `Jedi <http://jedi.jedidjah.ch/en/latest/>` 0.9.0 -- for code completion,
   go-to-definition and calltips on the Editor.
 
 * `Pyflakes <http://pypi.python.org/pypi/pyflakes>`_  -- for real-time

runtests.py

@@ -9,20 +9,30 @@
 """
 
 # Standard library imports
-import sys
+import os
 
 # Third party imports
 import qtpy  # to ensure that Qt4 uses API v2
 import pytest
 
 
+# To activate/deactivate certain things for pytest's only
+os.environ['SPYDER_PYTEST'] = 'True'
+
+
 def main():
     """
     Run pytest tests.
     """
     errno = pytest.main(['-x', 'spyder',  '-v', '-rw', '--durations=10',
                          '--cov=spyder', '--cov-report=term-missing'])
-    sys.exit(errno)
+
+    # sys.exit doesn't work here because some things could be running
+    # in the background (e.g. closing the main window) when this point
+    # is reached. And if that's the case, sys.exit does't stop the
+    # script (as you would expected).
+    if errno != 0:
+        raise SystemExit(errno)
 
 if __name__ == '__main__':
     main()

setup.py

@@ -271,7 +271,7 @@ def run(self):
 
 install_requires = [
     'rope_py3k' if PY3 else 'rope>=0.9.4',
-    'jedi',
+    'jedi==0.9.0',
     'pyflakes',
     'pygments>=2.0',
     'qtconsole>=4.2.0',
@@ -293,7 +293,8 @@ def run(self):
 
     setup_args['entry_points'] = {
         'gui_scripts': [
-            'spyder = spyder.app.start:main'
+            '{} = spyder.app.start:main'.format(
+                'spyder3' if PY3 else 'spyder')
         ]
     }
 

spyder/__init__.py

@@ -27,7 +27,7 @@
 OTHER DEALINGS IN THE SOFTWARE.
 """
 
-version_info = (3, 2, 0, "dev0")
+version_info = (3, 1, 4, "dev0")
 
 __version__ = '.'.join(map(str, version_info))
 __license__ = __doc__