Update species data location #282
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Add requirement for non-plotting examples to be documented as ipython notebooks
Supplemental data
Add supplementaldata to tutorial
…nch is going to be part of documentation
Study save min samples
* 'master' of github.com:YeoLab/flotilla: (81 commits) Add supplementaldata to tutorial Add release notes about documenting Add release notes actually save the minimum number of samples 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 ...
* master: 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 initial tests of supplemental seem to work initial commit of supplemental data
* modality_priors: Add release notes add modalities ipython notebook to tutorial.rst add ipython notebook fix pep8 errors created by removal of "_fixed" Move installing packages for documentation to only happen if this branch is going to be part of documentation removed _fixed from test_splicingdata fix pep8 Fix tests for modality assignments Add docstrings and set minimum samples to be 10 fix modality priors change min samples to default to 10 instead of 0.5 forgot parens around bimodal model parameters change min_samples to 10 shift bimodal and middle distributions to start with parameters more ddifferent than 1, and make bimodal an exponential prior
…at allows you to only read in hte first nrows of a file
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Update the species data location to https://s3-us-west-2.amazonaws.com/flotilla (which I have access to edit), and fix up the reading of these files to set the first column as the index, and updated the hg19 data to include cell cycle, and more useful things.
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.pywhich will show you which lines aren't covered by the tests.
numpydoc
style docstrings?
examples/, and is that notebook added todoc/tutorial.rst?If it adds a new plot, is it documented in the gallery, as a.pyfilein
examples/?make pep8andmake lintoutputchanges were made?