Various interactive function fixes #258

olgabot · 2015-02-04T01:22:06Z

Interactive classifier saving: interactive_classifier savefile doesn't work #218
Interactive PCA saving
Is it mergable?
Did it pass the tests?
If it introduces new functionality in scripts/ is it tested?
Check for code coverage. To run code coverage on only the file you changed,
for example flotilla/compute/splicing.py, use this command:
py.test --cov flotilla/compute/splicing.py --cov-report term-missing flotilla/test/compute/test_splicing.py
which will show you which lines aren't covered by the tests.
Do the new functions have descriptive
numpydoc
style docstrings?
If it adds a new plot, is it documented in the gallery?
Is it well formatted? Look at make pep8 and make lint output
Is it documented in the doc/releases/?
Was a spellchecker run on the source code and documentation after changes were made?

Shorten test suite time

…uring _filename_from_resource but can't use non-staticmethod methods on an uninstantiated class

…otting features to be documented as ipython notebooks and added to the tutorial

Add requirement for non-plotting examples to be documented as ipython notebooks

Supplemental data

* origin/master: (77 commits) Add finished supplementaldata ipynb Add option and test for user-specified flotilla directory fix pep8 Get supplemental resource name, not name of supplemental fix resource --> supplemental in reading all supplemental data actually iterate over the items of name_to_df Clarify where example plots should go, add requirement for new non-plotting features to be documented as ipython notebooks and added to the tutorial initial addition of ipynb for supplementaldata move _is_absolute_path to not a method of Study because it's needed during _filename_from_resource but can't use non-staticmethod methods on an uninstantiated class Add test for embarking on a datapackage with supplemental data Add supplemental data to reading/loading of the datapackage Add newline to sys.stdout message pep8 fixes add release notes Add release notes lint fixes pep8 fixes (hopefully will fix failing tests) initial tests of supplemental seem to work remove "_fixed", "_no_na" fixtures initial commit of supplemental data ...

coveralls · 2015-03-17T03:35:29Z

Coverage decreased (-0.05%) to 52.58% when pulling ab69a62 on interactive_fixes into fc88ff0 on master.

jasongrout · 2015-03-26T15:24:39Z

Sorry, I didn't see your note until just now. With IPython, we test interactive things with a casperjs-based test suite that tests the whole chain (sets up a notebook server, runs javascript, and then tests the results of the user actions in the browser). It's messy, but it works and gives us end-to-end tests.

olgabot · 2015-03-26T21:09:43Z

Jason, thanks for the response! I know you're busy. I'll have to take a
look at that casperjs system to see how this can be integrated. Do you have
a favorite example in the test suite?

On Thu, Mar 26, 2015 at 8:24 AM Jason Grout [email protected]
wrote:

Sorry, I didn't see your note until just now. With IPython, we test
interactive things with a casperjs-based test suite that tests the whole
chain (sets up a notebook server, runs javascript, and then tests the
results of the user actions in the browser). It's messy, but it works and
gives us end-to-end tests.

—
Reply to this email directly or view it on GitHub
#258 (comment).

jasongrout · 2015-03-26T22:17:17Z

No, I don't have any favorite examples in the ipython js test suite. They're all complicated and not very intuitive :). But you can look here for some examples: https://github.com/ipython/ipython/tree/master/IPython/html/tests/widgets

mlovci and others added 30 commits January 10, 2015 16:44

fixed feature_renamer for strings

bc93b87

changed to s3 destination for metadata

39695d4

add numpydoc docstrings to PR checklist

80c9386

http: --> https: for raw githubuser content

963c4ec

Change http to https for raw githubuser content

01bfb1a

fix shalek2013 datapackage url title

4038270

Merge branch 'master' of github.com:YeoLab/flotilla

cf5d99d

remove references to local server

48b6b05

add example of how to run test coverage on only the file you changed

6c35f57

Add release notes about modalities

0a748e6

Add counts of modalities, and a test for them

ab6c712

Update modality estimator to bayesian version

984fb19

start making modalitiy bar plotter

0c8e364

Properly intialized modality estimator

a8afc3f

remove stacked bar plot

ef26a44

Remove bootstrapped kws, add docstrings

91558fc

Add plot_modalities_bars plot

583d476

improve docstrings

da0656b

Calculate modalities on all the data when groupby is None

740364d

modalities_counts --> modality_counts

14439fd

add test for modality assignments

4b558cf

remove ambiguous modality

2555e1a

draw modalities grouped barplot legend outside of plot

7b02821

Add Study-level modality assignments and modality

2272414

calculate counts from memoized assignments

211a9ca

Add plot for percentages

e177cf5

add whitegrid style for percentage plots

1ef4965

add legend for percentage bar plots

e0c0264

rewrite modality_counts test to be like the code

b94a55c

change test min_samples params so they're larger

79f8d9f

olgabot added 23 commits March 12, 2015 15:59

initial tests of supplemental seem to work

4b86fc1

pep8 fixes (hopefully will fix failing tests)

3e589dd

lint fixes

5681048

Add release notes

ce93758

Merge pull request #267 from YeoLab/shorten_test_suite_time

5dd63d3

Shorten test suite time

fix supplemental/spikein merge conflict

ce91f11

add release notes

f3e1436

pep8 fixes

3ca34ee

Add newline to sys.stdout message

24c1fff

Add supplemental data to reading/loading of the datapackage

d28eaaf

Add test for embarking on a datapackage with supplemental data

9040761

move _is_absolute_path to not a method of Study because it's needed d…

6e12d23

…uring _filename_from_resource but can't use non-staticmethod methods on an uninstantiated class

initial addition of ipynb for supplementaldata

4e00dfc

Clarify where example plots should go, add requirement for new non-pl…

663ce48

…otting features to be documented as ipython notebooks and added to the tutorial

actually iterate over the items of name_to_df

7bc0818

fix resource --> supplemental in reading all supplemental data

054ba2e

Get supplemental resource name, not name of supplemental

986571a

fix pep8

b2aeaea

Add option and test for user-specified flotilla directory

bb92407

Add finished supplementaldata ipynb

8c7705e

Merge pull request #276 from YeoLab/pr_checklist_examples

8a5c59b

Add requirement for non-plotting examples to be documented as ipython notebooks

Merge pull request #272 from YeoLab/supplemental_data

fc88ff0

Supplemental data

olgabot added 2 commits July 6, 2015 15:47

pep8 fixes

6798ce4

pep8 fixes

3ac20d2

olgabot force-pushed the master branch from 8f79ec6 to 0a903c2 Compare July 7, 2015 15:45

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Various interactive function fixes #258

Various interactive function fixes #258

olgabot commented Feb 4, 2015

coveralls commented Mar 17, 2015

jasongrout commented Mar 26, 2015

olgabot commented Mar 26, 2015

jasongrout commented Mar 26, 2015

Various interactive function fixes #258

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Various interactive function fixes #258

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olgabot commented Feb 4, 2015

coveralls commented Mar 17, 2015

jasongrout commented Mar 26, 2015

olgabot commented Mar 26, 2015

jasongrout commented Mar 26, 2015