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Bump pyiron-base from 0.5.29 to 0.5.30 #893

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merged 3 commits into from
Dec 15, 2022

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@dependabot dependabot bot commented on behalf of github Dec 5, 2022

Bumps pyiron-base from 0.5.29 to 0.5.30.

Release notes

Sourced from pyiron-base's releases.

pyiron_base-0.5.30

What's Changed

Full Changelog: pyiron/pyiron_base@pyiron_base-0.5.29...pyiron_base-0.5.30

Commits
  • a6e52c7 Merge pull request #932 from pyiron/copy_refactor
  • 773bfea Merge pull request #888 from pyiron/copy_name
  • bbc855b remove duplicated line?
  • 04342a8 Pull if statement from _copy_database_entry
  • 960d92d Remove test that checks that the bug fixed here exists
  • f3184ed Merge pull request #928 from pyiron/rewrite_child_names
  • 67a9ed5 Move getitem() to GenericMaster (#927)
  • d8c6380 Rewrite the child_name() property
  • 265e385 Merge pull request #926 from pyiron/interactive_close_fix
  • cfee623 interactive close fix
  • Additional commits viewable in compare view

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@dependabot dependabot bot added the dependencies Pull requests that update a dependency file label Dec 5, 2022
@jan-janssen
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@dependabot recreate

@dependabot dependabot bot force-pushed the dependabot/pip/pyiron-base-0.5.30 branch from 7f78713 to a04e65d Compare December 5, 2022 18:32
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coveralls commented Dec 5, 2022

Pull Request Test Coverage Report for Build 3623425201

  • 0 of 0 changed or added relevant lines in 0 files are covered.
  • 1 unchanged line in 1 file lost coverage.
  • Overall coverage decreased (-0.006%) to 68.656%

Files with Coverage Reduction New Missed Lines %
pyiron_atomistics/interactive/scipy_minimizer.py 1 86.94%
Totals Coverage Status
Change from base Build 3622625190: -0.006%
Covered Lines: 12113
Relevant Lines: 17643

💛 - Coveralls

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---------------------------------------------------------------------------
[205](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:206)
Exception encountered at "In [9]":
[206](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:207)
---------------------------------------------------------------------------
[207](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:208)
AttributeError                            Traceback (most recent call last)
[208](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:209)
Cell In[9], line 1
[209](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:210)
----> 1 job_lst_master.run()
[210](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:211)

[211](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:212)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/utils/deprecate.py:171, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
[212](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:213)
    161     if kw in self.arguments:
[213](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:214)
    162         warnings.warn(
[214](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:215)
    163             message_format.format(
[215](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:216)
    164                 "{}.{}({}={})".format(
[216](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:217)
   (...)
[217](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:218)
    169             stacklevel=2,
[218](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:219)
    170         )
[219](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:220)
--> 171 return function(*args, **kwargs)
[220](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:221)

[221](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:222)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/job/generic.py:704, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
[222](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:223)
    702     self._run_if_repair()
[223](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:224)
    703 elif status == "initialized":
[224](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:225)
--> 704     self._run_if_new(debug=debug)
[225](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:226)
    705 elif status == "created":
[226](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:227)
    706     self._run_if_created()
[227](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:228)

[228](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:229)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/job/generic.py:1238, in GenericJob._run_if_new(self, debug)
[229](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:230)
   1230 def _run_if_new(self, debug=False):
[230](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:231)
   1231     """
[231](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:232)
   1232     Internal helper function the run if new function is called when the job status is 'initialized'. It prepares
[232](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:233)
   1233     the hdf5 file and the corresponding directory structure.
[233](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:234)
   (...)
[234](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:235)
   1236         debug (bool): Debug Mode
[235](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:236)
   1237     """
[236](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:237)
-> 1238     run_job_with_status_initialized(job=self, debug=debug)
[237](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:238)

[238](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:239)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/job/runfunction.py:76, in run_job_with_status_initialized(job, debug)
[239](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:240)
     74 else:
[240](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:241)
     75     job.save()
[241](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:242)
---> 76     job.run()
[242](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:243)

[243](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:244)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/utils/deprecate.py:171, in Deprecator.__deprecate_argument.<locals>.decorated(*args, **kwargs)
[244](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:245)
    161     if kw in self.arguments:
[245](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:246)
    162         warnings.warn(
[246](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:247)
    163             message_format.format(
[247](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:248)
    164                 "{}.{}({}={})".format(
[248](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:249)
   (...)
[249](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:250)
    169             stacklevel=2,
[250](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:251)
    170         )
[251](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:252)
--> 171 return function(*args, **kwargs)
[252](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:253)

[253](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:254)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/job/generic.py:706, in GenericJob.run(self, delete_existing_job, repair, debug, run_mode, run_again)
[254](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:255)
    704     self._run_if_new(debug=debug)
[255](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:256)
    705 elif status == "created":
[256](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:257)
--> 706     self._run_if_created()
[257](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:258)
    707 elif status == "submitted":
[258](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:259)
    708     run_job_with_status_submitted(job=self)
[259](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:260)

[260](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:261)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/job/generic.py:1249, in GenericJob._run_if_created(self)
[261](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:262)
   1240 def _run_if_created(self):
[262](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:263)
   1241     """
[263](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:264)
   1242     Internal helper function the run if created function is called when the job status is 'created'. It executes
[264](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:265)
   1243     the simulation, either in modal mode, meaning waiting for the simulation to finish, manually, or submits the
[265](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:266)
   (...)
[266](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:267)
   1247         int: Queue ID - if the job was send to the queue
[267](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:268)
   1248     """
[268](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:269)
-> 1249     return run_job_with_status_created(job=self)
[269](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:270)

[270](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:271)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/job/runfunction.py:99, in run_job_with_status_created(job)
[271](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:272)
     97     job.run_if_manually(_manually_print=False)
[272](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:273)
     98 elif job.server.run_mode.modal:
[273](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:274)
---> 99     job.run_static()
[274](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:275)
    100 elif job.server.run_mode.srun:
[275](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:276)
    101     job.run_if_srun()
[276](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:277)

[277](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:278)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/master/flexible.py:94, in FlexibleMaster.run_static(self)
[278](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:279)
     92     if ind < max_steps:
[279](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:280)
     93         mod_funct = self._step_function_lst[ind - 1]
[280](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:281)
---> 94         mod_funct(prev_job, job)
[281](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:282)
     95     job._parent_id = prev_job.job_id
[282](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:283)
     96 job.run()
[283](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:284)

[284](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:285)
File ~/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/atomistics/master/parallel.py:208, in _structure_one_to_one(job_prev, job_next)
[285](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:286)
    200 def _structure_one_to_one(job_prev, job_next):
[286](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:287)
    201     """
[287](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:288)
    202     Copy final structure from previous job to the input structure of the next job
[288](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:289)
    203 
[289](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:290)
   (...)
[290](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:291)
    206         job_next (AtomisticGenericJob): next Job object
[291](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:292)
    207     """
[292](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:293)
--> 208     job_next.structure = job_prev.get_structure(iteration_step=-1)
[293](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:294)

[294](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:295)
File /usr/share/miniconda3/envs/my-env/lib/python3.10/site-packages/pyiron_base/jobs/master/generic.py:350, in GenericMaster.__getattr__(self, item)
[295](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:296)
    348     return item_from_get_item
[296](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:297)
    349 else:
[297](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:298)
--> 350     raise AttributeError(
[298](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:299)
    351         "{} tried to find child job {}, but getattr failed to find the item.".format(
[299](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:300)
    352             self.job_name, item
[300](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:301)
    353         )
[301](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:302)
    354     )
[302](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:303)

[303](https://github.com/pyiron/pyiron_atomistics/runs/9898467595?check_suite_focus=true#step:9:304)
AttributeError: struct_master tried to find child job get_structure, but getattr failed to find the item.

@jan-janssen jan-janssen marked this pull request as draft December 5, 2022 20:30
@jan-janssen
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The issues are presumably related to recent changes to the master job classes - pyiron/pyiron_base#927

@dependabot @github
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dependabot bot commented on behalf of github Dec 15, 2022

OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting @dependabot ignore this major version or @dependabot ignore this minor version. You can also ignore all major, minor, or patch releases for a dependency by adding an ignore condition with the desired update_types to your config file.

If you change your mind, just re-open this PR and I'll resolve any conflicts on it.

@jan-janssen jan-janssen reopened this Dec 15, 2022
@jan-janssen jan-janssen marked this pull request as ready for review December 15, 2022 06:09
Bumps [pyiron-base](https://github.com/pyiron/pyiron_base) from 0.5.29 to 0.5.30.
- [Release notes](https://github.com/pyiron/pyiron_base/releases)
- [Changelog](https://github.com/pyiron/pyiron_base/blob/main/CHANGELOG.md)
- [Commits](pyiron/pyiron_base@pyiron_base-0.5.29...pyiron_base-0.5.30)

---
updated-dependencies:
- dependency-name: pyiron-base
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot dependabot bot force-pushed the dependabot/pip/pyiron-base-0.5.30 branch from 332c4b5 to feb62ab Compare December 15, 2022 06:10
@jan-janssen jan-janssen merged commit 629207f into main Dec 15, 2022
@delete-merged-branch delete-merged-branch bot deleted the dependabot/pip/pyiron-base-0.5.30 branch December 15, 2022 07:03
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