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Update to py37 #256

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Update to py37 #256

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@RobertArbon RobertArbon commented Nov 28, 2020 •
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  • Implement feature / fix bug
  • Add tests
  • Update changelog

Currently Osprey doesn't build with Python 3.7 or higher. This is due to a number of problems which this PR fixes.

  1. No more sklearn.externals.joblib. system joblib is imported now. Datasetsloader default is system joblib.
  2. MSMBuilder not compatible with py37. MSMBuilder tests are now optional. Changed build recipe to exclude MSMBuilder.
  3. Pandas ix is now fully deprecated. Using .loc instead.
  4. numpy skipif decorator not found. changed import statement to find it.

Also changed some other things:

  1. Made tests of optional packages (GPy, MSMBuilder, Hyperopt) dependent on the try/except pattern rather than the module in sys.modules pattern.
  2. Included basic PyEMMA test.
  3. a test that was using MSMBuilder now uses sklearn instead.
  4. yaml.load requires Loader variable. Not essential but fixed anyway.
  5. check_scoring import deprecated in next sklearn version. changed import statement to be future comptible. Not essential.

unknown and others added 28 commits October 6, 2018 12:40
Merge branch 'Refactor' into Development
0ae6093
Merge branch 'Refactor' into Development
07c0be1 
Refactor has passed all tests.  Still to fold hyperopt_tpe into new structure and to re-jig input files
Merge remote-tracking branch 'RobertArbon/Development' into Development
daf0f91
Merge branch 'Refactor' into Development
fc357b2
travis typos again (trying to get build on development)
0a4dc6c
ci on master and development
2019042
Merge branch 'Refactor' into Development
8f68b09
another travis ci type development --> Development
c1dd18d
Merge branch 'Refactor' into Development
b8463e9
Merge branch 'Refactor' into Development
8b7e996
travil yaml deploy python version is 3.6
1de1113
Merge remote-tracking branch 'origin/master' into Development
d96ebc3 
Updating the latest few commits from master branch.
This makes my Development up to date with the master branch which includes my
refactor.
updated miniconda repo
e006a46
typo in repo url
d2a86d4
added 3.7 and 3.8 to py matrix
206de1d
using system joblib instead of sklearn. numpy decorators updated. Dro…
dac6204 
…pback to old methods still in place
updated yaml.load call to include safeloader
6b6f37b
replaced ix with loc in dataframe subsetting
b4ae4c8
increased samples in regression test as it wasn't passing
7a2b603
updated build receipe to stop msmbuilder
d12d1a9
added test for pyemma estimator
ff3b944
msmbuilder tests skipped properly
fafe4b8
updated sklearn import
4842b8a
test cli skeleton uses sklearn not msmbuilder
1eed06b
skipping msmbuilder cli_worker_and_dump tests if msmbuilder not insta…
f440f9d 
…lled
tests now test for optional imports, and msmbuilder now optional
bfc322f
build receip doesn't inlcude msmbuilder in test
9bf9f95
updated changelog
a564309
@RobertArbon RobertArbon marked this pull request as ready for review November 29, 2020 12:23
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