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Add python3 compatibility #299

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wants to merge 2,138 commits into from
Closed

Add python3 compatibility #299

wants to merge 2,138 commits into from

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jessicalettes
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  • 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
Add go term domains and name to growing defaultdict, and return None …
1073d16 
…if no GO categories were enriched
@olgabot
make sure to create defaultdict properly
cd2e250
@olgabot
df.empty is attribute, not method
457c65e
@olgabot
also say error for why species data wasn't loaded
861cfd8
@olgabot
better error message
e72dba6
@olgabot
access 0th value because 0th item by series may not be valid
554c59d
@olgabot
make sure provided domains are converted to frozenset, and fix logic …
ff28167 
…for checking domain of GO term
@olgabot
also check that features of interest overlap with GO term
b6300e4
@olgabot
Make GeneOntologyData accessible from base flotilla
2143049
@olgabot
Sort dataframe by p value
8c71cbf
@olgabot
Add tests for gene ontology data
d8d4ea4
@olgabot
fix tests after refactoring
5cc8be4
@olgabot
add example gene ontology data
2eabe5a
@olgabot
Fix tests and add more for a total of 98% coverage!
d50b551
@olgabot
remove go.py (replaced with the data model)
502375a
@olgabot
Fix lint errors because pyflakes got majorly strict
66d8b81
@olgabot
remove plot_study_sample_legend because it's unused
7a68a43
@olgabot
fix pep8
0e6f05e
@olgabot
fix bug addded while linting
99187a1
@olgabot
speeding up test suite time
b3d81df
@olgabot
add more tests for Study
5393026
@olgabot
fix up plot_two_feature tests
2b104cb
@olgabot
Add GO to release notes
fb27eb8
@olgabot
Merge pull request YeoLab#266 from YeoLab/gene_ontology
ebc00d7 
Gene ontology
@olgabot
update date on release notes
bea9ca7
@olgabot
Merge branch 'master' of github.com:YeoLab/flotilla
726c128 
* 'master' of github.com:YeoLab/flotilla: (31 commits)
  Add GO to release notes
  fix bug addded while linting
  fix pep8
  remove plot_study_sample_legend because it's unused
  Fix lint errors because pyflakes got majorly strict
  remove go.py (replaced with the data model)
  Fix tests and add more for  a total of 98% coverage!
  add example gene ontology data
  Add tests for gene ontology data
  Sort dataframe by p value
  Make GeneOntologyData accessible from base flotilla
  also check that features of interest overlap with GO term
  make sure provided domains are converted to frozenset, and fix logic for checking domain of GO term
  access 0th value because 0th item by series may not be valid
  better error message
  also say error for why species data wasn't loaded
  df.empty is attribute, not method
  make sure to create defaultdict properly
  Add go term domains and name to growing defaultdict, and return None if no GO categories were enriched
  stdout --> warnings
  ...
@olgabot
update version 0.2.5dev --> 0.2.5 for release
33a0f46
@olgabot
version bump to 0.2.6dev
a3b9289
@olgabot
save the GO data with the package
4dd890f
@olgabot
start rewriting test for saving
40bec13
@jessicalettes
changed colors from an atribute to a property
a4ba0b2
@jessicalettes
added (
ac8489b
@jessicalettes
changed iteritems to items for python3
7bddb37
@jessicalettes
fixed print statements for python3
882dbb0
@jessicalettes
imported urllib2 as urllib
03ef19f
@jessicalettes
fixed 1D error by creating modality_names variable
5c8d5ba
@jessicalettes
changed .next to .__next__ for python 3
e7ac8a9
@jessicalettes
change iteritems to items
0fea949
@jessicalettes
made a not_subsets variable to prevent dictionary size changed during…
6fc61f2 
… iteration
@jessicalettes
changed iteritems to items
7a72d95
@jessicalettes
cast all_phenotypes to list, next to __next__, iteritems to items
33c768d
@jessicalettes
next to __next__
4b96169
@jessicalettes
cast map and zip objects to list
a9c0a8a
@jessicalettes
cast zip object to list type
f203005
@jessicalettes
changed iteritems to items
497ccb4
@jessicalettes
changed xrange to range
787ad0c
@jessicalettes
cast map to list
c24d5c8
@jessicalettes
cast zip to list and change next to --next--
08cb0a5
@jessicalettes
fixed list
83b6b03
@jessicalettes
use python 3
b69c30d
@jessicalettes
fixed next to work for python 2 and 3
752ea6a
@jessicalettes
changed iteritems to items for python3
465dfbb
@jessicalettes
changed iteritems to items, changed uppercase to ascii_uppercase and …
5066840 
…changed wb to wt for gzip
@jessicalettes
changed iteritems to items for python3
e1f17f4
@jessicalettes
fixed next() for python3
03036e1
@jessicalettes
converted map to a list
6b1c30a
@jessicalettes
fix pep8 errors
e29a4e4
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3 participants
@jessicalettes @olgabot @mlovci