Update pyiron_base to 0.7.12

[jan-janssen]

This bug is hopefully fixed in pyiron/pyiron_base#1399

[jan-janssen]

@pmrv Most likely this is related to pyiron/pyiron_base#1392 , pyiron/pyiron_base#1394 or pyiron/pyiron_base#1397 .

======================================================================
ERROR: test_dump_parser_water (lammps.test_base.TestLammps.test_dump_parser_water)
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Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_base.py", line 237, in test_dump_parser_water
    self.job.run()
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py", line 171, in decorated
    return function(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py", line 781, in run
    self._run_if_collect()
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py", line 1344, in _run_if_collect
    run_job_with_status_collect(job=self)
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py", line 223, in run_job_with_status_collect
    job.collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 509, in collect_output
    super(LammpsInteractive, self).collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/base.py", line 454, in collect_output
    data_dict=self.collect_output_parser(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/base.py", line 430, in collect_output_parser
    return parse_lammps_output(
           ^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/output.py", line 66, in parse_lammps_output
    np.array(dump_dict.pop("steps"), dtype=int), label="steps"
             ^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'steps'

======================================================================
ERROR: test_lammps_water (lammps.test_base.TestLammps.test_lammps_water)
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Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_base.py", line 189, in test_lammps_water
    self.job.run()
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py", line 171, in decorated
    return function(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py", line 781, in run
    self._run_if_collect()
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py", line 1344, in _run_if_collect
    run_job_with_status_collect(job=self)
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py", line 223, in run_job_with_status_collect
    job.collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/interactive.py", line 509, in collect_output
    super(LammpsInteractive, self).collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/base.py", line 454, in collect_output
    data_dict=self.collect_output_parser(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/base.py", line 430, in collect_output_parser
    return parse_lammps_output(
           ^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/lammps/output.py", line 66, in parse_lammps_output
    np.array(dump_dict.pop("steps"), dtype=int), label="steps"
             ^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'steps'

======================================================================
ERROR: test_load_guess_group (sphinx.test_base.TestSphinx.test_load_guess_group)
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Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/sphinx/test_base.py", line 442, in test_load_guess_group
    self.assertEqual(guess.rho.file, '"' + rho_file + '"')
                     ^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/storage/datacontainer.py", line 366, in __getattr__
    raise AttributeError(name) from None
AttributeError: file

======================================================================
ERROR: test_run_complete (vasp.test_vasp.TestVasp.test_run_complete)
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Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/vasp/test_vasp.py", line 330, in test_run_complete
    self.job_complete.run()
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/utils/deprecate.py", line 171, in decorated
    return function(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py", line 781, in run
    self._run_if_collect()
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/generic.py", line 1344, in _run_if_collect
    run_job_with_status_collect(job=self)
  File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_base/jobs/job/runfunction.py", line 223, in run_job_with_status_collect
    job.collect_output()
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/vasp/base.py", line 472, in collect_output
    data_dict=self.collect_output_parser(cwd=self.working_directory),
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/vasp/base.py", line 421, in collect_output_parser
    self._output_parser.collect(
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/pyiron_atomistics/vasp/base.py", line 2011, in collect
    raise IOError("Either the OUTCAR or vasprun.xml files need to be present")
OSError: Either the OUTCAR or vasprun.xml files need to be present

======================================================================
FAIL: test_calc_static (sphinx.test_base.TestSphinx.test_calc_static)
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Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/sphinx/test_base.py", line 331, in test_calc_static
    self.assertTrue("keepRho" in self.sphinx.input.sphinx.main.to_sphinx())
AssertionError: False is not true

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[coveralls]

Pull Request Test Coverage Report for Build 8444097232

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 93.256%

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Totals
Change from base Build 8440425487:	0.0%
Covered Lines:	14201
Relevant Lines:	15228

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