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Metadata marker#297

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olgabot wants to merge 2034 commits intomasterfrom
metadata_marker
Open

Metadata marker#297
olgabot wants to merge 2034 commits intomasterfrom
metadata_marker

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@olgabot olgabot commented Apr 10, 2015

fix saving markers from metadata

  • Is it mergable?
  • Did it pass the tests?
  • If it introduces new functionality in 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 feature, is it documented as an IPython Notebook in
    examples/, and is that notebook added to doc/tutorial.rst?
  • If it adds a new plot, is it documented in the gallery, as a .py file
    in examples/?
  • 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?

olgabot and others added 30 commits January 13, 2015 17:37
@olgabot
turn on grid for ax_bayesfactor
20dbf41
@olgabot
Add plot example for plot_event_modality_estimation
ab0ba3d
@olgabot
Add comment about readme badge in doc/releases/v0.2.5.txt
833fb39
@olgabot
make font size smaller, add renamed to fig text
8524082
@olgabot
change example for plot_event_modality_estimation
2ded4a8
@olgabot
add uniform at _logsumexp step
ba019c8
@olgabot
Merge pull request #237 from YeoLab/readme_fixes
b4d8535 
README fixes
@olgabot
fix test_logsumexp test
7207532
@olgabot
Add flag to py.test to show top 20 tests with the longest durations
5cd6aff
@olgabot
add numpydoc style docstrings to contributing.md
61c8166
@olgabot
Merge branch 'bayesian_modalities'
7c6f714 
* bayesian_modalities: (78 commits)
  Add flag to py.test to show top 20 tests with the longest durations
  fix test_logsumexp test
  add uniform at _logsumexp step
  change example for plot_event_modality_estimation
  make font size smaller, add renamed to fig text
  Add plot example for plot_event_modality_estimation
  turn on grid for ax_bayesfactor
  add phantom text for xlabel
  add xlabel to loglik for padding, change xticks of violin, smaller font for figtext
  add event ID using figtext which won't resize the axes
  Add renamed event id to event estimation plot
  move xlabel to loglik, fix formatting
  dropna for seaborn violinplot
  fix logsumexps
  fix reference to modality_colors
  add modality_colors to argument
  add plot_modalities_lavalamps to gallery
  fix call to modality_visualizer.event_estimation
  add plot_event_modality_estimation to show logliks and bayes factors for a modality
  Add feature_ids to plot_modalities_lavalamps, and docstring
  ...
@olgabot
Merge branch 'master' of github.com:YeoLab/flotilla
ec0ad72 
* 'master' of github.com:YeoLab/flotilla:
  Add comment about readme badge in doc/releases/v0.2.5.txt
  Fix build badge for Travis-CI
  added feature standardization to cluster plot by default
  added feature standardization to cluster plot by default
  remove references to local server
  changed to s3 destination for metadata
  fixed feature_renamer for strings
@olgabot
Initial commit for cosine transform pca
bc19063
@olgabot
Move cosine transform code out of SplicingData.reduce() and into Spli…
0e4368f 
…cingData._subset_and_standardize so it's accessible to all functions which require standardized data
@olgabot
Removed SplicingData.reduce since now SplicingData._subset_and_standa…
f39983d 
…rdize does a cosine transform
@olgabot
Add test for SplicingData._subset_and_standardize
e89cb91
@olgabot
fix reduce bug
971b313
@gitter-badger
Added Gitter badge
643f77c
@olgabot
Add example of pac splicing
46fcdc8
don't cache feature_renamer series
e17613d
@olgabot
update plot_two_features and plot_two_samples tests to always use fea…
631a7c0 
…tures/samples with at least 10 observations
@olgabot
properly access features with enough observations
6c8d81c
@olgabot
properly except get_ipython()
a4b8bb6
@olgabot
Remove matplotlib inline call (user needs to do this themselves, and …
265ee7e 
…it messes up "make lint")
@olgabot
update make lint call to not exclude everything
28ad908
@olgabot
Add release note about removing matplotlib inline
214c691
@olgabot
Add cosine transform about splicing pca to release notes
40cebad
@olgabot
Add docstring for SplicingData._subset_and_standardize
c1646f6
@olgabot
Fix up BaseData._subset_and_standardize docstring, with a concise one…
f7ef4c0 
…-line summary, then a longer summary beneath. And change language of boolean from "whether or not" to "If True, .."
@olgabot
remove whitespace for pep8
a5fc37c
olgabot added 24 commits March 18, 2015 11:58
@olgabot
remove mention of "scripts/" directory in PR checklist
19208b3
@olgabot
add citation for PR checklist
4db36ee
@olgabot
place the PCA legend in the "best" place
17d153c
@olgabot
Add release notes about PCA legend
2f9e6e9
@olgabot
Auto-expand plot_gene violins to the number of phenotypes
87293eb
@olgabot
Change default plotting markers from a circle to a variety of symbols
42cbcb8
@olgabot
Add "data_type" to error message of no feature id found
c653e55
@olgabot
Fix gridspec_kws --> gridspec_kw typo
905cb68
@olgabot
add tests for plot_gene, plot_event!
c827e26
@olgabot
fix test for metadata plotting markers
98eca91
@olgabot
force phenotype_groupby to always be a series
25d5cab
@olgabot
Auto-adjust violin size in plot_pca
5e8b7f1
@olgabot
Test plot_pca with violins
c71f086
@olgabot
Add release notes
9030cca
@olgabot
Merge pull request #285 from YeoLab/variable_width_violin_plots
b178977 
Flexible plotting with many samples
@olgabot
Actually test if things were plotted to the axes
510051b
@olgabot
Add a feature renamer if there wasn't one
6afcc34
@olgabot
pep8 fixes
2b406df
@olgabot
Add release notes
9e46069
@olgabot
fix merge conflict (more things in release ntoes
9efbcbd
@olgabot
Merge branch 'decomposition_heatmap_pcs'
f5bbf28 
* decomposition_heatmap_pcs: (31 commits)
  Add release notes
  pep8 fixes
  Add a feature renamer if there wasn't one
  Actually test if things were plotted to the axes
  add release notes
  pep8+docstrings
  Add docstring for plot
  Fix pep8, add docstring
  Add release notes
  Despine only the scatter and line plots, not the the heatmap
  add colorbar label
  shrink yticklabels down to 11 pt font
  shrink yticklabels of PC heatmap down to 12 (from 13)
  revert back to when figure was "good enough"
  Add another column to gridspec, remove ax_empty
  increase wspace, hspace, actually get yticklabels
  make yticklabels of heatmap smaller
  change wspace and hspace to 0
  make explained variance ratio graph shorter
  fix ax pcs colorbar
  ...
@olgabot
add new markers to MetaData._phenotype_to_marker which is actually st…
9333972 
…ored
@olgabot
add all other phenotypes to in unique phenotypes besides the ones in …
7e1d5a6 
…phenotype_order
@olgabot
remove marker making code from MetaData.__init__
533f9f6
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coveralls commented Apr 10, 2015

Coverage Status

Coverage decreased (-0.0%) to 53.73% when pulling 947ed16 on metadata_marker into dfec06b on master.

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coveralls commented Apr 10, 2015

Coverage Status

Coverage decreased (-0.0%) to 53.73% when pulling 947ed16 on metadata_marker into dfec06b on master.

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