Pyiron atomistic split #1283

niklassiemer · 2021-01-08T11:04:15Z

Initializing the transition to pyiron_atomistic by renaming the pyiron directory to pyiron_atomistic.

docs/conf.py

jan-janssen · 2021-01-08T15:19:06Z

The error message is not very intuitive:

======================================================================
1891
ERROR: test_run (interactive.test_scipyminimizer.TestSxExtOptInteractive)
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----------------------------------------------------------------------
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Traceback (most recent call last):
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  File "/home/runner/work/pyiron/pyiron/tests/interactive/test_scipyminimizer.py", line 32, in test_run
1895
    minim.run()
1896
  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyiron_base/generic/util.py", line 213, in decorated
1897
    return function(*args, **kwargs)
1898
  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyiron_base/job/generic.py", line 669, in run
1899
    self._run_if_new(debug=debug)
1900
  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyiron_base/job/generic.py", line 1336, in _run_if_new
1901
    self.validate_ready_to_run()
1902
  File "/home/runner/work/pyiron/pyiron/pyiron_atomistic/atomistics/job/interactivewrapper.py", line 89, in validate_ready_to_run
1903
    self.ref_job.validate_ready_to_run()
1904
AttributeError: 'NoneType' object has no attribute 'validate_ready_to_run'
1905

1906
======================================================================
1907
ERROR: test_run_pressure (interactive.test_scipyminimizer.TestSxExtOptInteractive)
1908
----------------------------------------------------------------------
1909
Traceback (most recent call last):
1910
  File "/home/runner/work/pyiron/pyiron/tests/interactive/test_scipyminimizer.py", line 47, in test_run_pressure
1911
    minim.run()
1912
  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyiron_base/generic/util.py", line 213, in decorated
1913
    return function(*args, **kwargs)
1914
  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyiron_base/job/generic.py", line 669, in run
1915
    self._run_if_new(debug=debug)
1916
  File "/usr/share/miniconda/envs/test/lib/python3.8/site-packages/pyiron_base/job/generic.py", line 1336, in _run_if_new
1917
    self.validate_ready_to_run()
1918
  File "/home/runner/work/pyiron/pyiron/pyiron_atomistic/atomistics/job/interactivewrapper.py", line 89, in validate_ready_to_run
1919
    self.ref_job.validate_ready_to_run()
1920
AttributeError: 'NoneType' object has no attribute 'validate_ready_to_run'
1921

1922
----------------------------------------------------------------------

niklassiemer · 2021-01-08T15:33:40Z

Actually, I think we have a problem due to
https://github.com/pyiron/pyiron_base/blob/9fce7ef80c9e58a2a4e109ced403c3c371d7c292/pyiron_base/job/generic.py#L1050
where we reference pyiron_atomistic in base! I will raise an issue in pyiron_base.

# Conflicts: # pyiron_atomistic/atomistics/job/interactivewrapper.py # pyiron_atomistic/atomistics/job/sqs.py # pyiron_atomistic/gaussian/gaussian.py # pyiron_atomistic/gpaw/gpaw.py # pyiron_atomistic/lammps/base.py # pyiron_atomistic/vasp/potential.py

…istic_split

coveralls · 2021-01-09T07:56:07Z

Pull Request Test Coverage Report for Build 473788709

179 of 200 (89.5%) changed or added relevant lines in 64 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 64.607%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistic/init.py	48	49	97.96%
pyiron_atomistic/atomistics/master/convergence_volume.py	0	1	0.0%
pyiron_atomistic/atomistics/master/sqsmaster.py	0	1	0.0%
pyiron_atomistic/atomistics/nma/nma.py	0	1	0.0%
pyiron_atomistic/atomistics/structure/atoms.py	7	8	87.5%
pyiron_atomistic/dft/master/convergence_encut_parallel.py	0	1	0.0%
pyiron_atomistic/dft/master/convergence_encut_serial.py	0	1	0.0%
pyiron_atomistic/dft/master/convergence_kpoint_parallel.py	0	1	0.0%
pyiron_atomistic/dft/master/murnaghan_dft.py	0	1	0.0%
pyiron_atomistic/lammps/interactive.py	4	5	80.0%

Totals
Change from base Build 473726633:	0.0%
Covered Lines:	10529
Relevant Lines:	16297

💛 - Coveralls

jan-janssen · 2021-01-09T09:26:03Z

As the unit tests seem to be working now we should discuss the next steps:

We should add a backwards compatibility interface at least for the project class, the atoms class and the functions commonly used to convert ASE structures and pymatgen structures to pyiron structures and back.
Once the backwards compatibility interface is added we should merge these changes.
After the merge we can create the separate pyiron_atomistic repository.

jan-janssen · 2021-01-09T09:41:55Z

The test installation notebook fails:

Traceback (most recent call last):
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  File "/usr/share/miniconda/envs/test/bin/papermill", line 10, in <module>
356
    sys.exit(papermill())
357
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 829, in __call__
358
    return self.main(*args, **kwargs)
359
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 782, in main
360
    rv = self.invoke(ctx)
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  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
362
    return ctx.invoke(self.callback, **ctx.params)
363
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 610, in invoke
364
    return callback(*args, **kwargs)
365
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/decorators.py", line 21, in new_func
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    return f(get_current_context(), *args, **kwargs)
367
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/cli.py", line 240, in papermill
368
    execute_notebook(
369
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/execute.py", line 118, in execute_notebook
370
    raise_for_execution_errors(nb, output_path)
371
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
372
    raise error
373
papermill.exceptions.PapermillExecutionError: 
374
---------------------------------------------------------------------------
375
Exception encountered at "In [3]":
376
---------------------------------------------------------------------------
377
ModuleNotFoundError                       Traceback (most recent call last)
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<ipython-input-3-cf39f0701255> in <module>
379
----> 1 import pyiron
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      2 pyiron.__file__  # location where pyiron is installed
381

382
ModuleNotFoundError: No module named 'pyiron'

jan-janssen · 2021-01-09T09:44:10Z

As well as the structure notebook:

Traceback (most recent call last):
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  File "/usr/share/miniconda/envs/test/bin/papermill", line 10, in <module>
318
    sys.exit(papermill())
319
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 829, in __call__
320
    return self.main(*args, **kwargs)
321
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 782, in main
322
    rv = self.invoke(ctx)
323
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
324
    return ctx.invoke(self.callback, **ctx.params)
325
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 610, in invoke
326
    return callback(*args, **kwargs)
327
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/decorators.py", line 21, in new_func
328
    return f(get_current_context(), *args, **kwargs)
329
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/cli.py", line 240, in papermill
330
    execute_notebook(
331
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/execute.py", line 118, in execute_notebook
332
    raise_for_execution_errors(nb, output_path)
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  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
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    raise error
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papermill.exceptions.PapermillExecutionError: 
336
---------------------------------------------------------------------------
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Exception encountered at "In [8]":
338
---------------------------------------------------------------------------
339
ModuleNotFoundError                       Traceback (most recent call last)
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<ipython-input-8-2a50d2c1ecbf> in <module>
341
----> 1 from pyiron import create_ase_bulk, create_surface
342

343
ModuleNotFoundError: No module named 'pyiron'

Annd the gamma surface notebook:

Traceback (most recent call last):
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  File "/usr/share/miniconda/envs/test/bin/papermill", line 10, in <module>
186
    sys.exit(papermill())
187
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 829, in __call__
188
    return self.main(*args, **kwargs)
189
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 782, in main
190
    rv = self.invoke(ctx)
191
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 1066, in invoke
192
    return ctx.invoke(self.callback, **ctx.params)
193
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/core.py", line 610, in invoke
194
    return callback(*args, **kwargs)
195
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/click/decorators.py", line 21, in new_func
196
    return f(get_current_context(), *args, **kwargs)
197
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/cli.py", line 240, in papermill
198
    execute_notebook(
199
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/execute.py", line 118, in execute_notebook
200
    raise_for_execution_errors(nb, output_path)
201
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/papermill/execute.py", line 230, in raise_for_execution_errors
202
    raise error
203
papermill.exceptions.PapermillExecutionError: 
204
---------------------------------------------------------------------------
205
Exception encountered at "In [3]":
206
---------------------------------------------------------------------------
207
ModuleNotFoundError                       Traceback (most recent call last)
208
<ipython-input-3-9a3ec904e189> in <module>
209
----> 1 from pyiron.atomistics.master.parallel import AtomisticParallelMaster
210
      2 from pyiron_base.master.parallel import JobGenerator
211

212
ModuleNotFoundError: No module named 'pyiron'

jan-janssen · 2021-01-09T10:00:32Z

I try to fix the notebooks in pyiron/pyiron_atomistics#2

jan-janssen · 2021-01-09T14:31:43Z

The conda package is now available https://anaconda.org/conda-forge/pyiron_atomistics/

niklassiemer added 6 commits January 8, 2021 11:31

Rename pyiron to pyiron_atomistic

1b82e0c

Revert rename in the environment.yml

821d50c

Revert rename in setup.py

b832c9d

Merge branch 'master' into pyiron_atomistic_split

f4420ef

Rename versionfile_source in setup.cfg

4dcf35f

Update notebooks

53671a7

jan-janssen reviewed Jan 8, 2021

View reviewed changes

docs/conf.py Outdated Show resolved Hide resolved

niklassiemer and others added 3 commits January 8, 2021 16:44

Revert rename of readthedocs config file.

509f532

Merge remote-tracking branch 'origin/prevent_mirror' into pyiron_atom…

f5f2eab

…istic_split

jan-janssen and others added 3 commits January 9, 2021 09:00

Merge remote-tracking branch 'origin/master' into pyiron_atomistic_split

806dc12

Fix coverage

558671d

Update setup.py

1e7dd25

jan-janssen mentioned this pull request Jan 9, 2021

Atomistic vs. Atomistics pyiron/pyiron_atomistics#4

Closed

jan-janssen closed this Jan 10, 2021

jan-janssen deleted the pyiron_atomistic_split branch March 18, 2021 10:04

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Pyiron atomistic split #1283

Pyiron atomistic split #1283

niklassiemer commented Jan 8, 2021

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coveralls commented Jan 9, 2021 •

edited

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jan-janssen commented Jan 9, 2021

Pyiron atomistic split #1283

Pyiron atomistic split #1283

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niklassiemer commented Jan 8, 2021

jan-janssen commented Jan 8, 2021

niklassiemer commented Jan 8, 2021

coveralls commented Jan 9, 2021 • edited

Pull Request Test Coverage Report for Build 473788709

💛 - Coveralls

jan-janssen commented Jan 9, 2021

jan-janssen commented Jan 9, 2021

jan-janssen commented Jan 9, 2021

jan-janssen commented Jan 9, 2021

jan-janssen commented Jan 9, 2021

coveralls commented Jan 9, 2021 •

edited