Remove python 2 Support in MDPOW #178

ALescoulie · 2021-08-03T06:11:17Z

Removing Python 2 Compatibility

Since we now have a release supporting 2.7 and 3.x we can safely remove support for python 2 for future version. To begin that process I removed some of the ugly patching in the tests, and switched everything to future imports.

Still to do

Remove six dependency from code

codecov · 2021-08-03T06:15:03Z

Codecov Report

Merging #178 (2d50f75) into develop (9c5b966) will decrease coverage by 0.19%.
The diff coverage is 75.00%.

@@             Coverage Diff             @@
##           develop     #178      +/-   ##
===========================================
- Coverage    73.14%   72.94%   -0.20%     
===========================================
  Files            9        9              
  Lines         1400     1386      -14     
  Branches       189      188       -1     
===========================================
- Hits          1024     1011      -13     
+ Misses         295      294       -1     
  Partials        81       81

Impacted Files	Coverage Δ
mdpow/__init__.py	`100.00% <ø> (ø)`
mdpow/config.py	`71.75% <0.00%> (-0.43%)`	⬇️
mdpow/filelock.py	`89.74% <ø> (-0.26%)`	⬇️
mdpow/forcefields.py	`85.36% <0.00%> (-0.18%)`	⬇️
mdpow/log.py	`88.88% <ø> (-0.59%)`	⬇️
mdpow/equil.py	`80.45% <100.00%> (-0.08%)`	⬇️
mdpow/fep.py	`68.51% <100.00%> (-0.05%)`	⬇️
mdpow/restart.py	`73.10% <100.00%> (-0.45%)`	⬇️
mdpow/run.py	`62.14% <100.00%> (-0.22%)`	⬇️

Continue to review full report at Codecov.

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orbeckst

Leave the from . import MODULE — that's the correct way to import a module inside a package. See other comments inline.

I'll try to get PR #182 and #176 merged (for 0.7.1) as soon as possible so that this can come afterwards and I don't have to do backports of fixes. You'll then also have an updated CHANGES to add your CHANGES in a 0.8.0 section.

mdpow/__init__.py

mdpow/equil.py

mdpow/fep.py

mdpow/restart.py

mdpow/tests/test_analysis_alchemlyb.py

orbeckst · 2021-08-04T07:08:41Z

mdpow/tests/test_analysis_alchemlyb.py

-                # patch paths
-        elif sys.version_info.major == 2:
-            G = pickle.load(gsolv.open())
+        with open(gsolv, 'rb') as f:


same comment as above

mdpow/tests/test_emin.py

orbeckst · 2021-08-04T07:09:10Z

mdpow/tests/test_equilibration_script.py

-from . import tempdir as td
+import mdpow.tests.tempdir as td


orbeckst · 2021-08-04T07:11:05Z

mdpow/tests/test_fep_script.py

-from . import tempdir as td
+import mdpow.tests.tempdir as td


orbeckst · 2021-08-05T18:50:41Z

As soon as PR #186 is merged and 0.7.1 is released #181 , this PR is the next thing to complete so that everthing else can start with a leaner code base.

ALescoulie · 2021-08-05T22:29:26Z

@orbeckst I replaced the imports as instructed, one issue is noticed is with exception syntax in the scripts, should I fix that here or make another pull request?

orbeckst · 2021-08-05T23:47:11Z

If you can make the scripts Py 3 then do that to, please.

I found it very useful to run them as described in the examples/README (in PR #186 ). We really need tests for the scripts ... #172

ALescoulie · 2021-08-06T03:05:47Z

@orbeckst and @VOD555 How do these changes look. I still need to merge it with upstream develop.

orbeckst

Somehow the merge/rebase reverted many changes that are in develop. Please check and rebase cleanly against develop.

orbeckst · 2021-08-09T23:17:48Z

mdpow/equil.py

+from . import config as config
+from . import forcefields as forcefields


"as" not needed

orbeckst · 2021-08-09T23:18:15Z

doc/sphinx/source/conf.py

-html_logo = "_static/mdpow-logo.png"
+#html_logo = None


reverted commits on develop! undo

orbeckst · 2021-08-09T23:18:22Z

doc/sphinx/source/conf.py

-html_favicon = "_static/mdpow.ico"
+#html_favicon = None


reverted commits on develop! undo

orbeckst · 2021-08-09T23:21:20Z

doc/sphinx/source/conf.py

-                       'https://gromacswrapper.readthedocs.io/en/latest': None,
+                       'https://gromacswrapper.readthedocs.org/en/latest/': None,


reverted commits on develop (I think, check develop) undo?

orbeckst · 2021-08-09T23:21:28Z

doc/sphinx/source/index.txt

-Nevertheless, you should *always* check the topology and runinput
+Nevertheless, you should _always_ check the topology and runinput


reverted commits on develop! undo

orbeckst · 2021-08-09T23:21:33Z

doc/sphinx/source/index.txt

@@ -141,6 +141,7 @@ For current issues and open feature requests please look through the
   fep
   utilities
   forcefields
+   tables


reverted commits on develop! undo

orbeckst · 2021-08-09T23:21:53Z

doc/sphinx/source/scripts.txt

   compound and one solvent. All parameters except the solvent are specified in
   the *RUNFILE*.

-   Arguments:
-
-   .. option:: RUNFILE
-
-      The runfile :file:`runinput.yml` with all configuration parameters.
-
-
   Options:


everything: reverted commits on develop! undo

orbeckst · 2021-08-12T23:24:49Z

@ALescoulie please ping me when you have addressed the comments and want me to review again.

ALescoulie · 2021-08-13T01:58:56Z

@orbeckst I think I addressed the current issues. Sorry about the chaos that is scripts.txt, for some reason a bunch of spaces are being shown as deleted despite me just copying the original. For some reason one of the test_p_transfer tests is failing, but a few threads say it's an error with pandas 1.3.0.

edit: I forgot to update my own conda env, works on GitHub actions.

orbeckst · 2021-08-17T00:08:13Z

I removed 2.7 status check requirements from develop.

Will finish review tonight (and then hopefully merge).

mdpow/fep.py

orbeckst

I have to apply the fixes where some commits reverted code on develop. Will check again and then merge.

orbeckst · 2021-08-17T00:17:52Z

mdpow/fep.py

-   :members:
-   :inherited-members:
-


Suggested change

:members:

:inherited-members:

:members:

:inherited-members:

mdpow/forcefields.py

orbeckst · 2021-08-17T00:24:21Z

mdpow/forcefields.py

-#: Solvents available in GROMACS; the keys of the dictionary
-#: are the forcefields.


Suggested change

#: Solvents available in GROMACS; the keys of the dictionary

#: are the forcefields.

#: Solvents available in GROMACS; the keys of the dictionary

#: are the forcefields.

mdpow/forcefields.py

mdpow/tests/test_analysis_alchemlyb.py

mdpow/tests/test_emin.py

scripts/mdpow-cfg2yaml.py

scripts/mdpow-equilibrium

orbeckst

more reversals

mdpow/fep.py

orbeckst

more reverts

mdpow/fep.py

mdpow/forcefields.py

fix Becksteinlab#177

- removed Python 2 from setup.py metadata - updated CHANGES

remove python 2 * fix Becksteinlab#177 * update setup.py and CHANGES Co-authored-by: ALescoulie <[email protected]> Co-authored-by: Oliver Beckstein <[email protected]>

ALescoulie and others added 6 commits August 2, 2021 22:40

Remove __future__ imports

f6fc6d1

Remove __future__ imports from tests

57cc89d

Replace relative imports in module

fb0e0b0

Replace relative imports in tests

1d3b911

Remove python 2 from tests

f734283

Add files via upload

61d0db7

orbeckst requested changes Aug 4, 2021

View reviewed changes

orbeckst added this to the 0.8.0 milestone Aug 4, 2021

orbeckst linked an issue Aug 4, 2021 that may be closed by this pull request

Remove Python 2 Support #177

Closed

ALescoulie added 7 commits August 5, 2021 15:05

merge changes from upstream

44ccd86

Merge remote-tracking branch 'origin/remove_python2' into remove_python2

2193360

Update tests imports

f568ae5

Update __init__.py imports

d20e971

Update equil.py imports

007e34a

Update fep.py imports

4d48e44

Update run.py imports

e32f57c

ALescoulie added 2 commits August 5, 2021 15:34

Replace _pickle with pickle

a3a5504

Adding six import to fep.py

8831064

updating exception syntax in scripts

640535f

Merge branch 'develop' into remove_python2

f5c1c35

orbeckst requested changes Aug 9, 2021

View reviewed changes

ALescoulie added 3 commits August 12, 2021 16:42

revert merge

c2dee60

revert merge

43f512a

Fix test_fep_script.py import

ccef815

orbeckst assigned ALescoulie Aug 17, 2021

orbeckst reviewed Aug 17, 2021

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remove python 2

d8091ea

fix Becksteinlab#177

orbeckst force-pushed the remove_python2 branch 2 times, most recently from 77a576f to 82590b9 Compare August 17, 2021 09:49

update setup.py and CHANGES

2d50f75

- removed Python 2 from setup.py metadata - updated CHANGES

orbeckst force-pushed the remove_python2 branch from 82590b9 to 2d50f75 Compare August 17, 2021 09:50

orbeckst approved these changes Aug 17, 2021

View reviewed changes

orbeckst merged commit fcff52a into Becksteinlab:develop Aug 17, 2021

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Remove python 2 Support in MDPOW #178

Remove python 2 Support in MDPOW #178

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		from . import config as config
		from . import forcefields as forcefields

		'https://gromacswrapper.readthedocs.io/en/latest': None,
		'https://gromacswrapper.readthedocs.org/en/latest/': None,

		Nevertheless, you should always check the topology and runinput
		Nevertheless, you should _always_ check the topology and runinput

		#: Solvents available in GROMACS; the keys of the dictionary
		#: are the forcefields.

		html_logo = "_static/mdpow-logo.png"
		#html_logo = None

		html_favicon = "_static/mdpow.ico"
		#html_favicon = None

Remove python 2 Support in MDPOW #178

Remove python 2 Support in MDPOW #178

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ALescoulie commented Aug 3, 2021 • edited Loading

Removing Python 2 Compatibility

Still to do

codecov bot commented Aug 3, 2021 • edited Loading

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orbeckst commented Aug 12, 2021

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ALescoulie commented Aug 3, 2021 •

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