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Python update #170

Merged
merged 66 commits into from
Jul 30, 2021
Merged

Python update #170

merged 66 commits into from
Jul 30, 2021

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ALescoulie
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New draft of MDPOW upgrade to python 3 with changes suggested by @orbeckst with recent commits from @VOD555. Made some changes compared to previous pull request, in particular removing extraneous style updates to improve reviewing process and separating and labeling commits.

  1. Updated tests to avoid reading errors when opening pickle file. Also replaced outdated yield tests.
  2. Updated ci workflow to test python 3.8.
  3. Replaced outdated import statements. in particular substituting cPickle for six.load.cPiclke.
  4. Replaced outdated merge_dicts function in config.py with recursive method that works in python 2 and Added deepcopy method in fep.py with method that works in python 3.

Repeat of #166

ALescoulie and others added 30 commits July 22, 2021 17:51
@ALescoulie
Update tests for python 3 compatibility
471572a
@ALescoulie
Update ci workflow for python 3.8
46fa863
@ALescoulie
Update merge_dicts in config.py
3514416
@ALescoulie
Update equil.py imports and exceptions
9dc7685
@ALescoulie
Update fep.py imports __deepcopy__ and exceptions
946204f
@ALescoulie
Fix filelock.py
64734d6
@ALescoulie
Update restart.py imports
246b8f1
@ALescoulie
Update run.py imports and exceptions
02482bc
@ALescoulie
Update tests to current
3c8b27f
@ALescoulie
Update project information
c836208
@ALescoulie
Update workflow to current
1cd3811
@ALescoulie
Update scripts and fix outdated script exception syntax
c6b8c9d
@ALescoulie
Update tests for python compatibility
3ed5c74
@ALescoulie
Undoing path changes in tests
6779c73
@ALescoulie
Updating log for python 2 compatibility
a9dc7fd
@ALescoulie
Add argparse to mdpow-pow, correcting github account on AUTHORS
05e4977
@ALescoulie
Adding comment to test_analysis.py
fc90717
@ALescoulie
Replacing izip import with six.moves.zip
1e023df
@orbeckst
Merge branch 'develop' into python_update
704a54e
@ALescoulie
Adding __future__ imports to to tests
3ca7624
@ALescoulie
Merge remote-tracking branch 'origin/python_update' into python_update
1794890
@ALescoulie
Simplifying merge_dicts
6238f10
@ALescoulie
Simplifications for config.py
4594b4e
@ALescoulie
Simplifications for equil.py
51b37b0
@ALescoulie
Simplifify __deepcopy__ in fep.py
4cd8192
@ALescoulie
Raise assert_almost_equal threshold and add xfail
19ee8cf
@orbeckst
Merge branch 'develop' into python_update
413e714
@orbeckst
fixed docs: version variable
f94469a
@orbeckst
Merge branch 'develop' into python_update
0f35f98
@ALescoulie
Update docs
5418760
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codecov bot commented Jul 30, 2021 •
edited
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Codecov Report

Merging #170 (0edb862) into develop (d279f50) will increase coverage by 0.54%.
The diff coverage is 63.49%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #170      +/-   ##
===========================================
+ Coverage    68.43%   68.98%   +0.54%     
===========================================
  Files            9        9              
  Lines         1375     1396      +21     
  Branches       166      190      +24     
===========================================
+ Hits           941      963      +22     
  Misses         363      363              
+ Partials        71       70       -1
Impacted Files Coverage Δ
mdpow/forcefields.py 85.54% <ø> (ø)
mdpow/run.py 62.35% <25.00%> (ø)
mdpow/fep.py 59.37% <53.57%> (+0.56%) ⬆️
mdpow/equil.py 80.53% <62.50%> (+0.22%) ⬆️
mdpow/restart.py 66.66% <66.66%> (+2.44%) ⬆️
mdpow/config.py 72.18% <84.21%> (+1.08%) ⬆️
mdpow/filelock.py 90.00% <100.00%> (ø)
... and 1 more

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@orbeckst orbeckst self-requested a review July 30, 2021 01:20
orbeckst
orbeckst approved these changes Jul 30, 2021
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Excellent work! Thank you for bringing MDPOW to the present, @ALescoulie .

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I'll just wait for the CI before squash-merging.

The mdpow scripts should now work under Python 3, too, but because we don't have tests that's still something to be seen.

@orbeckst orbeckst added this to the 0.7 milestone Jul 30, 2021
@orbeckst orbeckst linked an issue Jul 30, 2021 that may be closed by this pull request
support Python 3 #84
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@orbeckst orbeckst merged commit 4d2498b into Becksteinlab:develop Jul 30, 2021
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It is done, hooray!

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Congratulations @ALescoulie !

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support Python 3
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@ALescoulie @orbeckst