Fix sqsgenerator version bump #569

dgehringer · 2022-03-21T10:16:36Z

Fixes SQSJob to work with both versions v0.0.5 and v0.1.

left HDF format and input parameters untouched -> backwards compatibilty
deprecation warning whe importing v0.0.5
CI notebook sqs.ipynb runs with both versions ( v0.0.5 and v0.1)
improved input validation -> warnings if composition is changes
new features of v0.1 are not included -> backwards compatibilty

Fixes #564

💡 added in code-documentation

coveralls · 2022-03-21T10:26:50Z

Pull Request Test Coverage Report for Build 2017139991

19 of 76 (25.0%) changed or added relevant lines in 1 file are covered.
1 unchanged line in 1 file lost coverage.
Overall coverage decreased (-0.2%) to 70.325%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/atomistics/job/sqs.py	19	76	25.0%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/atomistics/job/sqs.py	1	39.53%

Totals
Change from base Build 2003890928:	-0.2%
Covered Lines:	11875
Relevant Lines:	16886

💛 - Coveralls

jan-janssen · 2022-03-21T14:41:39Z

The coverage fails to push the test statistics - but I guess that is a general issue with forks

jan-janssen · 2022-03-21T14:49:41Z

The backwards compatibility to 0.0.5 seems to be broken:

File ~/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/atomistics/job/sqs.py:354, in SQSJob.run_static(self)
[340](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:340)
    353 def run_static(self):
[341](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:341)
--> 354     self._lst_of_struct, decmp, iterations, cycle_time = get_sqs_structures(
[342](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:342)
    355         structure=self.structure,
[343](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:343)
    356         mole_fractions={k: v for k, v in self.input.mole_fractions.items()},
[344](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:344)
    357         weights=self.input.weights,
[345](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:345)
    358         objective=self.input.objective,
[346](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:346)
    359         iterations=self.input.iterations,
[347](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:347)
    360         output_structures=self.input.n_output_structures,
[348](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:348)
    361         num_threads=self.server.cores,
[349](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:349)
    362     )
[350](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:350)
    363     for i, structure in enumerate(self._lst_of_struct):
[351](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:351)
    364         with self.project_hdf5.open("output/structures/structure_" + str(i)) as h5:
[352](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:352)

[353](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:353)
File ~/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/atomistics/job/sqs.py:138, in get_sqs_structures(structure, mole_fractions, weights, objective, iterations, output_structures, num_threads)
[354](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:354)
    136 # preprocess mole-fractions, to print warnings is necessary
[355](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:355)
    137 num_atoms = len(structure)
[356](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:356)
--> 138 composition = mole_fractions_to_composition(mole_fractions, num_atoms)
[357](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:357)
    139 mole_fractions = map_dict(lambda n: n/num_atoms, composition)
[358](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:358)
    141 iterator = ParallelSqsIterator(
[359](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:359)
    142     structure, mole_fractions, weights, num_threads=num_threads
[360](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:360)
    143 )
[361](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:361)

[362](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:362)
File ~/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/atomistics/job/sqs.py:105, in mole_fractions_to_composition(mole_fractions, num_atoms)
[363](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:363)
     99     warnings.warn(
[364](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:364)
    100         'It is not possible to distribute the species properly. Therefore one "{}" atom was removed. '
[365](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:365)
    101         'This changes the input mole-fraction specification. '
[366](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:366)
    102         '"{}" -> "{}"'.format(removed_species, mole_fractions, map_dict(lambda n: n/num_atoms, composition)))
[367](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:367)
    103 else:
[368](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:368)
    104     # something else is wrong with the mole-fractions input
[369](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:369)
--> 105     raise ValueError('Cannot interpret mole-fraction dict {}'.format(mole_fractions))
[370](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:370)
    107 return composition
[371](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:371)

[372](https://github.com/pyiron/pyiron_atomistics/runs/5625294004?check_suite_focus=true#step:6:372)
ValueError: Cannot interpret mole-fraction dict {'Ni': 0.8, 'Cr': 0.2}

jan-janssen · 2022-03-21T14:56:59Z

Also with the latest version the same error message appears. Can this be related to the input parameters being a DataContainer rather than a python dictionary? Maybe @pmrv can help.

dgehringer · 2022-03-21T15:44:22Z

The backwards compatibility to 0.0.5 seems to be broken:

That should be fixed. It was caused by a wrong condition

jan-janssen

Looks good to me

dgehringer added 10 commits March 17, 2022 16:31

fix imports for sqsgenerator v0.1

5a6ce0b

implement utility function for chem. form.

ac9df5d

move existing function to deprecated branch

cc728d4

convert-mole-fractions to atom occupation

c5f9f9f

🐛 fix DEPRECATED_SQS_API state bug

557279d

♻️ spaces around kwargs

e21d461

utility function for backward compat. with v0.0.05

e484461

backward compat. with v0.0.05 of get_sqs_structures

7f18faf

add preprocessing for mole-fractions v0.0.5

86c6c1f

✏️ spelling issues

d11fba5

💡 added in code-documentation

dgehringer requested review from jan-janssen and niklassiemer March 21, 2022 10:16

dgehringer changed the title ~~Fix sqsgenerator version bump #564~~ Fix sqsgenerator version bump Mar 21, 2022

jan-janssen added the format_black reformat the code using the black standard label Mar 21, 2022

Update environment-notebooks.yml

5de97dc

jan-janssen added format_black reformat the code using the black standard and removed format_black reformat the code using the black standard labels Mar 21, 2022

black formatting

2c963b2

🐛 fix wrong condition when checking mole-fractions

c6aedac

jan-janssen approved these changes Mar 21, 2022

View reviewed changes

niklassiemer merged commit 5085314 into pyiron:master Apr 11, 2022

jan-janssen mentioned this pull request Apr 11, 2022

Bump pyiron-atomistics from 0.2.40 to 0.2.42 pyiron/pyiron#1408

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Fix sqsgenerator version bump #569

Fix sqsgenerator version bump #569

dgehringer commented Mar 21, 2022

coveralls commented Mar 21, 2022 •

edited

jan-janssen commented Mar 21, 2022

jan-janssen commented Mar 21, 2022

jan-janssen commented Mar 21, 2022

dgehringer commented Mar 21, 2022

jan-janssen left a comment

Fix sqsgenerator version bump #569

Fix sqsgenerator version bump #569

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dgehringer commented Mar 21, 2022

coveralls commented Mar 21, 2022 • edited

Pull Request Test Coverage Report for Build 2017139991

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jan-janssen commented Mar 21, 2022

jan-janssen commented Mar 21, 2022

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coveralls commented Mar 21, 2022 •

edited