Use git ls-files to collect files for code quality tests (#5751)

* Use `git ls-files` in code quality tests

This way we can test all checked-in files more easily.

* Fix code quality issues

* Make tests/test_code_quality_py work under Python 3

* Fix code quality issues in classifiers.txt

.github/CONTRIBUTING.md

@@ -1,67 +1,67 @@
 # How to contribute
 
-We welcome users' contributions! However, we do have some requests for how contributions 
+We welcome users' contributions! However, we do have some requests for how contributions
 should be made. Please read these guidelines in order to avoid surprises down the road.
 
 ## Choosing something to work on
 
-The issue tracker has a list of items that you can start working on, classified by the labels: 
+The issue tracker has a list of items that you can start working on, classified by the labels:
 
 * [`type:feature`](https://github.com/bokeh/bokeh/labels/type:%20feature)
 * [`type:task`](https://github.com/bokeh/bokeh/labels/type:%20task)
 * [`type:bug`](https://github.com/bokeh/bokeh/labels/type:%20bug)
 
-In order to avoid duplication of effort, it's always a good idea to comment on an issue 
+In order to avoid duplication of effort, it's always a good idea to comment on an issue
 and let everybody know that you intend to work on it.
 
 ## Opening a new issue
 
-1. Avoid duplicate reports. Search [GitHub](https://github.com/bokeh/bokeh/issues) and 
-   the [mailing list](https://groups.google.com/a/continuum.io/forum/#!forum/bokeh) for 
+1. Avoid duplicate reports. Search [GitHub](https://github.com/bokeh/bokeh/issues) and
+   the [mailing list](https://groups.google.com/a/continuum.io/forum/#!forum/bokeh) for
    similar or identical issues. Keyword searches for your error messages are usually effective.
 2. The issue may already be resolved. If possible, try to reproduce the issue using most recent
-   [development build](http://bokeh.pydata.org/docs/installation.html#developer-builds) of bokeh, 
-   or even better, by building and installed from the `master` branch. 
-3. Try to include a *minimal*, self-contained, reproducible test case or example. The more code 
-   or data we have to have to reproduce the issue, the less likely we will be able to. 
+   [development build](http://bokeh.pydata.org/docs/installation.html#developer-builds) of bokeh,
+   or even better, by building and installed from the `master` branch.
+3. Try to include a *minimal*, self-contained, reproducible test case or example. The more code
+   or data we have to have to reproduce the issue, the less likely we will be able to.
 4. Include relevant system information. At minimum, you should provide output of:
 
       `python -c "import bokeh; print(bokeh.__version__)"`
 
 5. Include relevant browser information (if the issue is browser-related). Just saying that you
-   use Chrome is generally not sufficient. We may ask you for additional information to 
+   use Chrome is generally not sufficient. We may ask you for additional information to
    reproduce and fix the issue.
-6. Include relevant JavaScript console and/or `bokeh serve` logs. 
-7. If the problem is user interface related, it is *always* good to include a screenshot. 
+6. Include relevant JavaScript console and/or `bokeh serve` logs.
+7. If the problem is user interface related, it is *always* good to include a screenshot.
 8. State the expected behavior.
 
 ## Creating a pull request (PR)
 
-1. Make sure that there is a corresponding issue for your change first. If there isn't yet, 
+1. Make sure that there is a corresponding issue for your change first. If there isn't yet,
    create one.
 2. Create a fork of the Bokeh repository on GitHub (this is only done before *first*) contribution).
 3. Create a branch off the `master` branch with a meaningful name. Preferably include issue number
-   and a few keywords, so that we will have a rough idea what the branch refers to, without looking 
+   and a few keywords, so that we will have a rough idea what the branch refers to, without looking
    up the issue. As an example: `786_property_names`.
 4. Commit your changes and push them to GitHub.
-5. Create a pull request against the origin's `master` branch. The PR must have a meaningful title 
+5. Create a pull request against the origin's `master` branch. The PR must have a meaningful title
    and a message explaining what was achieved, what remains to be done, maybe an example, etc.
-6. We don't accept code contributions without tests. If there are valid reasons for not including a 
+6. We don't accept code contributions without tests. If there are valid reasons for not including a
    test, please discuss this in the issue.
 7. We will review your PR as time permits. Reviewers may comment on your contributions, ask
    you questions regarding the implementation or request changes. If changes are requested, don't
    start a new PR, (push new commits to the existing one). Do *NOT* rebase, amend, or cherry-pick
-   published commits. Any of those actions will make us start the review from scratch. If you need 
+   published commits. Any of those actions will make us start the review from scratch. If you need
    updates from `master`, just merge it into your branch.
 
 ## DOs and DON'Ts
 
 * **DO** follow our coding style.
-* **DO** include new tests when adding new features. 
-* **DO** include regression tests when fixing bugs. 
+* **DO** include new tests when adding new features.
+* **DO** include regression tests when fixing bugs.
 * **DO** keep the discussions focused. When a new or related topic comes up it's often better to
   create new issue than to side track the discussion.
 * **DON'T** surprise us with big pull requests. Instead, file an issue and start a discussion so we
   can agree on a direction before you invest a large amount of time.
-* **DON'T** commit code that you didn't write. If you find BSD license compatible code that you 
+* **DON'T** commit code that you didn't write. If you find BSD license compatible code that you
   think would be useful to add to this project, file an issue and start a discussion first.

CHANGELOG

@@ -11,7 +11,7 @@
     - #3931 [component: docs] Update datetimetickformatter docstring with actual default formats from the js side
     - #4602 [API: charts] No x-axis labels on bar graphs with a single bar
     - #4680 [component: bokehjs] [widgets] Datatable header height not large enough to fit header text - in jupyter notebook
-    - #4861 [component: bokehjs] Hovertool showing canvas coordinates not data coordinates 
+    - #4861 [component: bokehjs] Hovertool showing canvas coordinates not data coordinates
     - #5305 [component: docs] [component: examples] [component: server] Embed/animated fails with "did not find model"
     - #5306 [component: examples] [py2] Embed/embed_multiple fails with unicode error on py2
     - #5315 [component: examples] [component: server] [regression] Extension implementation load path problems in apps
@@ -27,13 +27,13 @@
     - #5377 [component: docs] Correct comment in dimension example plot
     - #5382 [component: bokehjs] Help tool icon doesn't have transparent background
     - #5389 Creating a line plot with `x_axis_type='log'` fails when `x_max < 1`
-    - #5392 [component: bokehjs] [regression] Tools cause hard crash on safari after import/export pr 
+    - #5392 [component: bokehjs] [regression] Tools cause hard crash on safari after import/export pr
     - #5398 Datatable css conflict with bootstrap css
     - #5404 Functickformatter.from_py_func() example valueerror
     - #5413 [component: bokehjs] Can't use categorical axis with figure using rects
     - #5453 [py2] Tabe completion on bokeh.palettes doesn't work in python 2
     - #5467 [component: docs] Docstring not reflecting correct function signature
-    - #5479 [layout] Merged toolbar is not created properly when row/column layouts added to gridplot 
+    - #5479 [layout] Merged toolbar is not created properly when row/column layouts added to gridplot
     - #5490 Some named palettes raise valueerror
     - #5522 [component: docs] Bokeh doc website not rendered correctly in ie 11 on win 7
     - #5524 [component: server] [regression] --num-procs broken
@@ -64,7 +64,7 @@
     - #5199 [API: models] Add support bokehjs writable and bokeh readonly properties
     - #5317 Add a colorblind and d3 palettes
     - #5329 Ability to remove tools from plot generated by mpl.to_bokeh
-    - #5417 [component: bokehjs] [widgets] Extend textinput with `placeholder` 
+    - #5417 [component: bokehjs] [widgets] Extend textinput with `placeholder`
     - #5435 [component: bokehjs] [enh] add js callback for streaming data
     - #5446 [API: plotting] [component: docs] Improve glyph method function signatures
     - #5471 [component: bokehjs] [enh] add custom classes to elements
@@ -93,7 +93,7 @@
     - #5362 [component: build] Remove old bokeh-server
     - #5372 [component: server] Remove develop mode stub
     - #5375 [component: tests] [notebook] Notebook image diff tests broken due to "missing kernel"
-    - #5376 Change palette references for the brewer qualitative palettes to be slices 
+    - #5376 Change palette references for the brewer qualitative palettes to be slices
     - #5384 [component: docs] Small docs fixes
     - #5395 [component: build] Please consider adding classifiers to setup.py
     - #5400 [component: examples] Add imdb usage notice to movies app
@@ -2677,7 +2677,7 @@
     - #395 Added script for load and install the extension.
     - #396 Added a little notebook to explain some ways to use the bokeh extension.
     - #397 Added script to generate changelog.
-	  - #399 let figure() accept keyword arguments for next plot
+    - #399 let figure() accept keyword arguments for next plot
     - #411 Add point hit testing to other circle-like glyphs
   * bugfixes:
     - #377 np not imported, zeros_like is

LICENSE.txt

@@ -12,17 +12,17 @@ this list of conditions and the following disclaimer in the documentation
 and/or other materials provided with the distribution.
 
 Neither the name of Continuum Analytics nor the names of any contributors
-may be used to endorse or promote products derived from this software 
+may be used to endorse or promote products derived from this software
 without specific prior written permission.
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
-ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
-LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
-CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
 THE POSSIBILITY OF SUCH DAMAGE.

bokeh/core/compat/mplexporter/latest_commit.txt

@@ -3,4 +3,3 @@ Author: Jake Vanderplas <vanderplas@astro.washington.edu>
 Date:   Sat Apr 19 08:18:20 2014 -0700
 
     BUG: correctly handle color='none'
-

bokeh/sampledata/percent-bachelors-degrees-women-usa.csv

@@ -40,4 +40,4 @@ Year,Agriculture,Architecture,Art and Performance,Biology,Business,Communication
 2008,47.570834,42.71173041,60.7,59.30576517,48.88802678,62.4,17.8,79.19632674,16.5,67.59402834,70.2,85.2,43.3,40.7,77.2,81.7,49.4
 2009,48.66722357,43.34892051,61,58.48958333,48.84047414,62.8,18.1,79.5329087,16.8,67.96979204,69.3,85.1,43.3,40.7,77.1,82,49.4
 2010,48.73004227,42.06672091,61.3,59.01025521,48.75798769,62.5,17.6,79.61862451,17.2,67.92810557,69,85,43.1,40.2,77,81.7,49.3
-2011,50.03718193,42.7734375,61.2,58.7423969,48.18041792,62.2,18.2,79.43281184,17.5,68.42673015,69.5,84.8,43.1,40.1,76.7,81.9,49.2
+2011,50.03718193,42.7734375,61.2,58.7423969,48.18041792,62.2,18.2,79.43281184,17.5,68.42673015,69.5,84.8,43.1,40.1,76.7,81.9,49.2