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Fix failing splicing compute tests and get rid of various code smells #316

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0280594
make explained variance ratio graph shorter
olgabot Mar 13, 2015
8491d41
change wspace and hspace to 0
olgabot Mar 13, 2015
be2aec9
make yticklabels of heatmap smaller
olgabot Mar 13, 2015
520abf2
increase wspace, hspace, actually get yticklabels
olgabot Mar 13, 2015
09d9b5a
Add another column to gridspec, remove ax_empty
olgabot Mar 13, 2015
67aef3d
revert back to when figure was "good enough"
olgabot Mar 13, 2015
85f0f3e
shrink yticklabels of PC heatmap down to 12 (from 13)
olgabot Mar 13, 2015
5b4e875
shrink yticklabels down to 11 pt font
olgabot Mar 13, 2015
f995cfc
add colorbar label
olgabot Mar 13, 2015
366705d
Despine only the scatter and line plots, not the the heatmap
olgabot Mar 13, 2015
9398bc0
Add release notes
olgabot Mar 13, 2015
ce93758
Add release notes
olgabot Mar 13, 2015
5dd63d3
Merge pull request #267 from YeoLab/shorten_test_suite_time
olgabot Mar 13, 2015
66e8c4a
fix merge conflict
olgabot Mar 14, 2015
ce91f11
fix supplemental/spikein merge conflict
olgabot Mar 14, 2015
f3e1436
add release notes
olgabot Mar 16, 2015
3ca34ee
pep8 fixes
olgabot Mar 16, 2015
24c1fff
Add newline to sys.stdout message
olgabot Mar 16, 2015
d28eaaf
Add supplemental data to reading/loading of the datapackage
olgabot Mar 16, 2015
9040761
Add test for embarking on a datapackage with supplemental data
olgabot Mar 16, 2015
6e12d23
move _is_absolute_path to not a method of Study because it's needed d…
olgabot Mar 16, 2015
4e00dfc
initial addition of ipynb for supplementaldata
olgabot Mar 16, 2015
663ce48
Clarify where example plots should go, add requirement for new non-pl…
olgabot Mar 16, 2015
7bc0818
actually iterate over the items of name_to_df
olgabot Mar 16, 2015
054ba2e
fix resource --> supplemental in reading all supplemental data
olgabot Mar 16, 2015
986571a
Get supplemental resource name, not name of supplemental
olgabot Mar 16, 2015
b2aeaea
fix pep8
olgabot Mar 16, 2015
bb92407
Add option and test for user-specified flotilla directory
olgabot Mar 16, 2015
8c7705e
Add finished supplementaldata ipynb
olgabot Mar 16, 2015
8206a59
fix modality priors
olgabot Mar 16, 2015
f87e50b
Add docstrings and set minimum samples to be 10
olgabot Mar 16, 2015
75b54dc
Fix tests for modality assignments
olgabot Mar 16, 2015
164d2c5
fix pep8
olgabot Mar 16, 2015
e3ac7b5
merged up to master
olgabot Mar 16, 2015
4352e28
removed _fixed from test_splicingdata
olgabot Mar 16, 2015
8a5c59b
Merge pull request #276 from YeoLab/pr_checklist_examples
olgabot Mar 16, 2015
cdeb225
actually save the minimum number of samples
olgabot Mar 16, 2015
300a57e
Add release notes
olgabot Mar 16, 2015
b05ffc6
Add release notes about documenting
olgabot Mar 16, 2015
fc88ff0
Merge pull request #272 from YeoLab/supplemental_data
olgabot Mar 17, 2015
0c2f544
Fix pep8, add docstring
olgabot Mar 17, 2015
7e77203
Add docstring for plot
olgabot Mar 17, 2015
ab45aaa
pep8+docstrings
olgabot Mar 17, 2015
9464f90
add release notes
olgabot Mar 17, 2015
4afb11f
Add supplementaldata to tutorial
olgabot Mar 17, 2015
bfa166d
Merge pull request #278 from YeoLab/supplemental_data
olgabot Mar 17, 2015
a17486c
Move installing packages for documentation to only happen if this bra…
olgabot Mar 17, 2015
36453f1
Merge pull request #277 from YeoLab/study_save_min_samples
olgabot Mar 17, 2015
61ea979
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot Mar 17, 2015
a788b66
fix pep8 errors created by removal of "_fixed"
olgabot Mar 17, 2015
6780653
add ipython notebook
olgabot Mar 18, 2015
63c398f
add modalities ipython notebook to tutorial.rst
olgabot Mar 18, 2015
d58b977
Add release notes
olgabot Mar 18, 2015
4552526
Merge branch 'master' into modality_priors
olgabot Mar 18, 2015
8fafe2a
Merge branch 'modality_priors'
olgabot Mar 18, 2015
ac92137
fix merge conflict in tutorial.rst and v0.2.6.rst
olgabot Mar 18, 2015
19208b3
remove mention of "scripts/" directory in PR checklist
olgabot Mar 18, 2015
4db36ee
add citation for PR checklist
olgabot Mar 18, 2015
17d153c
place the PCA legend in the "best" place
olgabot Mar 18, 2015
2f9e6e9
Add release notes about PCA legend
olgabot Mar 18, 2015
87293eb
Auto-expand plot_gene violins to the number of phenotypes
olgabot Apr 8, 2015
42cbcb8
Change default plotting markers from a circle to a variety of symbols
olgabot Apr 8, 2015
c653e55
Add "data_type" to error message of no feature id found
olgabot Apr 8, 2015
905cb68
Fix gridspec_kws --> gridspec_kw typo
olgabot Apr 8, 2015
c827e26
add tests for plot_gene, plot_event!
olgabot Apr 8, 2015
98eca91
fix test for metadata plotting markers
olgabot Apr 8, 2015
25d5cab
force phenotype_groupby to always be a series
olgabot Apr 8, 2015
5e8b7f1
Auto-adjust violin size in plot_pca
olgabot Apr 8, 2015
c71f086
Test plot_pca with violins
olgabot Apr 8, 2015
9030cca
Add release notes
olgabot Apr 8, 2015
b178977
Merge pull request #285 from YeoLab/variable_width_violin_plots
olgabot Apr 8, 2015
13067fa
make sure boolean columns are used as sample/feature subsets
olgabot Apr 8, 2015
510051b
Actually test if things were plotted to the axes
olgabot Apr 10, 2015
6afcc34
Add a feature renamer if there wasn't one
olgabot Apr 10, 2015
2b406df
pep8 fixes
olgabot Apr 10, 2015
9e46069
Add release notes
olgabot Apr 10, 2015
9efbcbd
fix merge conflict (more things in release ntoes
olgabot Apr 10, 2015
f5bbf28
Merge branch 'decomposition_heatmap_pcs'
olgabot Apr 10, 2015
a47f61f
pep8 fixes
olgabot Apr 10, 2015
6078455
Add release notes about fixing boolean subset columns for metadata
olgabot Apr 10, 2015
6ab59c1
Merge pull request #251 from waffle-iron/master
olgabot Apr 10, 2015
55247a8
Add jsonschema to doc install requirements
olgabot Apr 10, 2015
0c9a657
temporarily change master branch for testing
olgabot Apr 10, 2015
dfec06b
Merge pull request #290 from YeoLab/boolean_feature_subsets
olgabot Apr 10, 2015
c634d25
install ipython and jsonschema using conda
olgabot Apr 10, 2015
d7f1f6b
don't run test suite for now
olgabot Apr 10, 2015
c8abd2d
say yes to install
olgabot Apr 10, 2015
7102bc6
change max depth
olgabot Apr 10, 2015
6899dc7
remove plot_modalities_reduced for now
olgabot Apr 10, 2015
4e86ce6
Make sure REPO_URL_GITHUB is defined
olgabot Apr 10, 2015
9122823
trying whatever I can for things to get included in the tutorial
olgabot Apr 10, 2015
41f48e6
trying to include things in the tutorial
olgabot Apr 10, 2015
17ff007
comment out plotting functions for now
olgabot Apr 10, 2015
5e915a9
use brainspan instead of shalek2013 data as examples
olgabot Apr 10, 2015
cd7aed1
add release notes
olgabot Apr 10, 2015
0d02b72
Merge pull request #296 from YeoLab/doc_ipynb_fixes
olgabot Apr 10, 2015
213e9a7
remove dev from version number
olgabot Apr 10, 2015
21f12a6
Add date to 0.2.6
olgabot Apr 10, 2015
2afd1f9
Version bump to 0.2.7dev
olgabot Apr 10, 2015
53a8744
change MASTER to real master
olgabot Apr 10, 2015
8c5c82f
change MASTER to tutorial for now
olgabot Apr 20, 2015
11d3e18
remove sudo from the pip install because it seems to be using a diffe…
olgabot Apr 20, 2015
73cdc38
use flotilla._shalek2013 as example instead of the string
olgabot Apr 20, 2015
2a96b51
move building the docs into the testing script (if the docs don't bui…
olgabot Apr 20, 2015
9f8afaf
Use only ipython2 to make documentaion
olgabot Apr 20, 2015
08304ae
add documentation tools from seaborn
olgabot Apr 20, 2015
85f7e47
use seaborn style code for making ipython notebooks of documentation …
olgabot Apr 20, 2015
74aa466
use blog version of shalek2013
olgabot Apr 20, 2015
7aeef8a
Add release notes about documentation
olgabot Apr 20, 2015
916d961
Update makefile for making ipython notebook documentation
olgabot Apr 20, 2015
e10c2fa
add folder that's autodownloaded for the shalek and satija data
olgabot Apr 20, 2015
55de4ec
add a separate conda requirements file
olgabot Apr 20, 2015
7f972b3
moved programs from .travis.yml to conda_requriements.txt
olgabot Apr 20, 2015
4158a5b
cleaned up conda install command
olgabot Apr 20, 2015
32bcd9f
fix usage of conda install with a file
olgabot Apr 20, 2015
e8b0ed4
add separate conda_requirements installation document for building docs
olgabot Apr 20, 2015
8fe35c6
auto-say es to ipython-notebook 2
olgabot Apr 20, 2015
46ad877
add ipython to regular conda requirements
olgabot Apr 20, 2015
fd18091
remove ipython notebook from pre-install
olgabot Apr 20, 2015
cce2450
make nb_to_doc and nbstripoutput executable
olgabot Apr 20, 2015
b7ee55a
fix conversion of ipython notebooks to rst files
olgabot Apr 20, 2015
331734b
change MASTER branch to real master
olgabot Apr 20, 2015
3e0045f
Turn tests back on :)
olgabot Apr 20, 2015
285160e
Merge pull request #301 from YeoLab/tutorial
olgabot Apr 20, 2015
bfd3d6c
remove "dev" from version
olgabot Apr 20, 2015
a1adb01
Add dates to release notes
olgabot Apr 20, 2015
0930ba7
make sure to reinstall flotilla in documentation
olgabot Apr 20, 2015
6e7dab2
add note to release ntoes
olgabot Apr 20, 2015
9e39240
add combat license
olgabot Jan 31, 2015
99b00c6
add combat.py
olgabot Jan 31, 2015
2653d69
initial commit for adding combat functionality
olgabot Feb 3, 2015
c415723
Add metadata_ignore_subset_cols
olgabot May 8, 2015
59049d7
Set the first column as the index for importing feature data
olgabot May 8, 2015
7eab2f5
make a dict of the colors directly rather than through a defaultdict
olgabot May 8, 2015
9d60d78
use L2 norm for vector sizes
olgabot May 8, 2015
fb8a2fb
Use flake8 instead of pyflakes so can exclude "external" directory
olgabot May 8, 2015
53a4f58
don't install pyflakes or pep8 in travis anymore since now using flake8
olgabot May 8, 2015
50ceddc
Add flake8 to requirements
olgabot May 8, 2015
33b7625
Take out reference to pep8 and add a welcome statement to contributin…
olgabot May 8, 2015
49af2e4
remove pep8 command
olgabot May 8, 2015
6851662
Merge pull request #253 from YeoLab/combat_batch_effects
olgabot May 8, 2015
4acc5e0
only do "make lint" on python2
olgabot May 19, 2015
e7831d0
change splicing na threshold max to 0.5 and not 1
olgabot May 19, 2015
d3553fa
Merge branch 'py3k_test_fixes'
olgabot May 19, 2015
6c4b001
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot May 19, 2015
4e4adc9
remove pep8 since using flake8 now
olgabot May 19, 2015
a3f3583
Add auto-deployment to PyPI on tagged branches
olgabot May 20, 2015
bfb04cb
Merge branch 'travis_pypi'
olgabot May 20, 2015
1a9b428
Merge branch 'master' of github.com:YeoLab/flotilla
olgabot May 20, 2015
7818f76
version bump to 0.2.8dev
olgabot May 21, 2015
c67b25b
Update combat code to work with multiple covariates in the batches
olgabot May 22, 2015
7fca3f6
Merge pull request #306 from YeoLab/update_combat
olgabot May 22, 2015
b873e0c
Simplify README.rst for PyPI
olgabot May 22, 2015
337852c
un-indent lists so they don't appear as quotes
olgabot May 22, 2015
3fa098b
trailing unindented list
olgabot May 22, 2015
e3fb5f8
By default, rasterize the lavalamp plot
olgabot May 22, 2015
8c57616
raster is the wrong keyword, use rasterized
olgabot May 22, 2015
21f9108
Fix tidy_splicing_with_expression to deal with when splicing events m…
olgabot May 23, 2015
f6c0c99
use coverage instead of pytest-cov to calculate coverage (something i…
olgabot May 23, 2015
85b7ece
Add release notes
olgabot May 23, 2015
d72f492
Remove rasterizing release notes, add release notes for this correct …
olgabot May 23, 2015
3b815c8
lint fixes and remove commented code
olgabot May 23, 2015
80c23fa
Remove commented code
olgabot May 23, 2015
00aef52
Fix over-indentation for lint
olgabot May 23, 2015
9ba8822
pep8 in study objects
olgabot May 28, 2015
9143306
Merge pull request #309 from YeoLab/splicing_multiple_expression_ids
olgabot May 28, 2015
3028b71
Update combat code to work with multiple covariates in the batches
olgabot May 22, 2015
effec4a
Simplify README.rst for PyPI
olgabot May 22, 2015
97eb519
un-indent lists so they don't appear as quotes
olgabot May 22, 2015
d949afb
trailing unindented list
olgabot May 22, 2015
01f9e8d
Fix tidy_splicing_with_expression to deal with when splicing events m…
olgabot May 23, 2015
13a9301
use coverage instead of pytest-cov to calculate coverage (something i…
olgabot May 23, 2015
59b076a
Add release notes
olgabot May 23, 2015
42097f3
Remove rasterizing release notes, add release notes for this correct …
olgabot May 23, 2015
e868717
lint fixes and remove commented code
olgabot May 23, 2015
3c8b362
Remove commented code
olgabot May 23, 2015
f98a103
Fix over-indentation for lint
olgabot May 23, 2015
ad47f36
pep8 in study objects
olgabot May 28, 2015
9f77583
Add release notes, fix naming and make sure releases are described in…
olgabot May 28, 2015
b19728e
Merge pull request #308 from YeoLab/raster_lavalamp
olgabot May 28, 2015
b3d02c4
Stepwise modality estimation
olgabot May 29, 2015
b2e69a8
Add tests for stepwise modality estimation
olgabot May 29, 2015
71990dd
Add stepwise modality estimation for a single event
olgabot May 29, 2015
aed3874
uniform --> ambiguous
olgabot May 29, 2015
7ef2cf8
Close plots after plotting tests
olgabot May 29, 2015
e4434fe
whitespace for pep8
olgabot May 30, 2015
dc990b9
add release notes
olgabot May 30, 2015
888c5f1
Merge pull request #310 from YeoLab/stepwise_modalities
olgabot May 30, 2015
5448dea
update all NMF and modality calculations to require 20 samples, fix b…
olgabot Jun 9, 2015
304959a
change number of samples to 50 for splicing testing
olgabot Jun 9, 2015
75f749e
use n=20 as default instead of n=0.5
olgabot Jun 9, 2015
5c7cea3
fix tests for splicing modalities and NMF space
olgabot Jun 9, 2015
7761406
update all NMF and modality calculations to require 20 samples, fix b…
olgabot Jun 9, 2015
0a0e9ac
change number of samples to 50 for splicing testing
olgabot Jun 9, 2015
6946175
use n=20 as default instead of n=0.5
olgabot Jun 9, 2015
65703c4
fix tests for splicing modalities and NMF space
olgabot Jun 9, 2015
5bed758
if there are zero non-NA values in a dataset, make sure all its log b…
olgabot Jun 10, 2015
0f57cf9
Merge remote-tracking branch 'origin/splicing_min20' into splicing_min20
olgabot Jun 10, 2015
e742b7c
don't estimate modalities on data iwth no counts
olgabot Jun 10, 2015
ccedfb6
Add violinplots from temposeq ipython
olgabot Jul 1, 2015
c2100a6
Require seaborn 0.6 for violinplot and stripplot
olgabot Jul 1, 2015
4c752f6
fix logic
olgabot Jul 1, 2015
3fd682c
Add docstrings
olgabot Jul 1, 2015
c3b6c68
Add splicing-specific parameters for violinplots in plot_feature
olgabot Jul 1, 2015
a0f57a4
propagate changes to BaseData._violinplot
olgabot Jul 1, 2015
3eaf890
fix bugs in calculating modalites
olgabot Jul 6, 2015
2c9ead1
modality_assignments is always a series, so do not specify columns or…
olgabot Jul 6, 2015
ab75dfc
remove all events with na
olgabot Jul 6, 2015
0a17b89
remove "big nmf" computations - do it by user specified hand
olgabot Jul 6, 2015
5097d23
move all NMF related things out of BaseData and into SplicingData only
olgabot Jul 6, 2015
92362d8
add docstring and reformat nmf_space_transitions
olgabot Jul 6, 2015
58e6459
remove nmf space from plot_feature
olgabot Jul 6, 2015
994a294
remove plot_big_nmf_space test
olgabot Jul 6, 2015
bffa703
Return an NA series if all splicing events are NA
olgabot Jul 6, 2015
d681563
remove plot_modalities_lavalamps
olgabot Jul 6, 2015
747a536
remove nmf space from splicingdata feature plotting
olgabot Jul 6, 2015
312e7c5
remove spikein data
olgabot Jul 6, 2015
69ab2ed
remove SpikeInData, move study.py out of DataModel
olgabot Jul 6, 2015
3e29a27
remove all mentions of spikein data
olgabot Jul 6, 2015
b276ff1
remove spikein data from datapackage
olgabot Jul 6, 2015
1539123
force phenotype groupby series to always have a name
olgabot Jul 6, 2015
8574748
auto-assign order if None
olgabot Jul 6, 2015
5013f87
remove commented out code, fix Study import
olgabot Jul 6, 2015
0fbca9b
fix typo and add whitespace
olgabot Jul 6, 2015
eef1e6d
Filter what to set for axis attributes
olgabot Jul 6, 2015
bce3f97
Specify norm_features=False for SplicingData.plot_clutstermap
olgabot Jul 6, 2015
386dd6c
change argument order for super
olgabot Jul 6, 2015
dc23ded
Add newline after finished with populating gene ontology database
olgabot Jul 6, 2015
3ea6fda
Add docstring for plot_clustermap
olgabot Jul 6, 2015
29e5ff0
Fix weird scoping in lambda
olgabot Jul 6, 2015
6772a88
add docstring for plot_correlations
olgabot Jul 6, 2015
bbfcd78
also rename mask's columns
olgabot Jul 6, 2015
bbe06ea
also rename mask's index and columns
olgabot Jul 6, 2015
0a0bcda
pep8
olgabot Jul 6, 2015
01364f7
force groupby to be a series if it isn't
olgabot Jul 6, 2015
534cf51
don't use keywords for mapping stats
olgabot Jul 6, 2015
ba8b8dd
use string split to see if there's any whitespace rather than checkin…
olgabot Jul 6, 2015
672208a
get explicit names of events to continue estimating modalities for, r…
olgabot Jul 6, 2015
18c8afa
remove nmf space from plot_event and plot_gene
olgabot Jul 6, 2015
889ce5f
If multiple features matching that name, then make multiple violinplo…
olgabot Jul 6, 2015
dead704
Add col_wrap for violinplots
olgabot Jul 6, 2015
0deffdb
add col_wrap for plot_event and plot_gene
olgabot Jul 6, 2015
c592cee
unify function calls for plot_feature
olgabot Jul 6, 2015
ffcf8eb
don't provide fig or axesgrid to plot_feature
olgabot Jul 6, 2015
937c888
Remove all big_nmf_* stuff
olgabot Jul 6, 2015
ba4fb9b
remove test_plot_big_nmf_space_transitions
olgabot Jul 6, 2015
ab21952
move test_study out of test/data_model
olgabot Jul 6, 2015
3687039
comment out checking for number of plotted items
olgabot Jul 6, 2015
8e8b070
lint fixes
olgabot Jul 6, 2015
6efdbf9
bump version to 0.3.0, add release notes
olgabot Jul 7, 2015
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5 changes: 4 additions & 1 deletion CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -106,7 +106,10 @@ before the pull request is merged.
- [ ] Do the new functions have descriptive
[numpydoc](https://github.com/numpy/numpy/blob/master/doc/HOWTO_DOCUMENT.rst.txt)
style docstrings?
- [ ] If it adds a new plot, is it documented in the gallery?
- [ ] 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
5 changes: 4 additions & 1 deletion doc/releases/v0.2.6.txt
Original file line number Diff line number Diff line change
@@ -6,6 +6,9 @@ This is a patch release, with non-breaking changes from 0.2.5.
New features
~~~~~~~~~~~~

- Add a :py:class:`.data_model.SupplementalData` data type, which allows the
user to store any ``pandas.DataFrame`` on the :py:class:`.data_model.Study`
object as `study.supplemental`. This is essentially user-driven caching.

Plotting functions
~~~~~~~~~~~~~~~~~~
@@ -28,4 +31,4 @@ Miscellaneous

- Streamlined test suite to test fewer things at a time, which shortened the
test suite from ~20 minutes to ~3 minutes, about 85% time savings.
- Improved accuracy (fewer false positives) in splicing modality estimation
- Improved accuracy (fewer false positives) in splicing modality estimation
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