Bump pyiron-atomistics from 0.3.0 to 0.3.3

[dependabot]

Bumps pyiron-atomistics from 0.3.0 to 0.3.3.

Release notes

Sourced from pyiron-atomistics's releases.

pyiron_atomistics-0.3.3

What's Changed

• Bump mp-api from 0.34.3 to 0.35.1 by @​dependabot in pyiron/pyiron_atomistics#1145
• Fix selective dynamics for LAMMPS by @​jan-janssen in pyiron/pyiron_atomistics#1146
• Refactor lammps output parser by @​liamhuber in pyiron/pyiron_atomistics#1143
• Bump pandas from 2.0.3 to 2.1.0 by @​dependabot in pyiron/pyiron_atomistics#1148
• Structure toolkit update 0.0.9 by @​jan-janssen in pyiron/pyiron_atomistics#1149
• Update structuretoolkit to 0.0.7 by @​jan-janssen in pyiron/pyiron_atomistics#1119
• Add empty line again to main by @​jan-janssen in pyiron/pyiron_atomistics#1153
• Use phonopy interface from structure toolkit by @​jan-janssen in pyiron/pyiron_atomistics#1152
• Merge main by @​jan-janssen in pyiron/pyiron_atomistics#1155
• Update atomistics to 0.0.2 by @​jan-janssen in pyiron/pyiron_atomistics#1154
• Only structuretoolkit depends on pymatgen not pyiron_atomistics by @​jan-janssen in pyiron/pyiron_atomistics#1151
• Update atomstics and structuretoolkit by @​jan-janssen in pyiron/pyiron_atomistics#1156
• Bump pyiron-base from 0.6.4 to 0.6.5 by @​dependabot in pyiron/pyiron_atomistics#1163
• Bump atomistics from 0.0.3 to 0.0.5 by @​dependabot in pyiron/pyiron_atomistics#1164
• Bump mp-api from 0.35.1 to 0.36.1 by @​dependabot in pyiron/pyiron_atomistics#1168
• Bump base by @​niklassiemer in pyiron/pyiron_atomistics#1170

Full Changelog: pyiron/pyiron_atomistics@pyiron_atomistics-0.3.2...pyiron_atomistics-0.3.3

pyiron_atomistics-0.3.2

What's Changed

• Bump pymatgen from 2023.6.28 to 2023.7.17 by @​dependabot in pyiron/pyiron_atomistics#1115
• Bump pymatgen from 2023.7.17 to 2023.7.20 by @​dependabot in pyiron/pyiron_atomistics#1117
• Bump structuretoolkit from 0.0.5 to 0.0.6 by @​dependabot in pyiron/pyiron_atomistics#1116
• Use the conversion from pymatgen to ase defined in structure toolkit by @​jan-janssen in pyiron/pyiron_atomistics#1118
• Supply default, in case of loading old murnaghans by @​pmrv in pyiron/pyiron_atomistics#1120
• Small fixes to Vasp.calc_minimize by @​pmrv in pyiron/pyiron_atomistics#1125
• [minor] Refactor potential setter by @​samwaseda in pyiron/pyiron_atomistics#1126
• Bump pymatgen from 2023.7.20 to 2023.8.10 by @​dependabot in pyiron/pyiron_atomistics#1129
• Bump structuretoolkit from 0.0.6 to 0.0.8 by @​dependabot in pyiron/pyiron_atomistics#1128
• Bump mp-api from 0.33.3 to 0.34.3 by @​dependabot in pyiron/pyiron_atomistics#1138
• Bump scipy from 1.11.1 to 1.11.2 by @​dependabot in pyiron/pyiron_atomistics#1137
• Use atomistics package - alternative implementation by @​jan-janssen in pyiron/pyiron_atomistics#1135
• Lammps drop 2016 by @​jan-janssen in pyiron/pyiron_atomistics#1132
• Refactor the VASP collect_output() parser by @​jan-janssen in pyiron/pyiron_atomistics#1131
• Refactor the lammps collect_output() parser by @​jan-janssen in pyiron/pyiron_atomistics#1130
• Update base 0.6.4 by @​niklassiemer in pyiron/pyiron_atomistics#1141

Full Changelog: pyiron/pyiron_atomistics@pyiron_atomistics-0.3.1...pyiron_atomistics-0.3.2

pyiron_atomistics-0.3.1

What's Changed

• Use remove_jobs() rather than remove_jobs_silently() by @​jan-janssen in pyiron/pyiron_atomistics#1079
• flux calculator support for VASP by @​jan-janssen in pyiron/pyiron_atomistics#1080
• Update pyiron_base to 0.6.1 by @​jan-janssen in pyiron/pyiron_atomistics#1081
• Bump mendeleev from 0.13.1 to 0.14.0 by @​dependabot in pyiron/pyiron_atomistics#1082

... (truncated)

Commits

• 5fcc87b Merge pull request #1170 from pyiron/bump_base
• c004bdc Update setup.py
• 65841a3 Update environment.yml
• 3146560 Merge pull request #1168 from pyiron/dependabot/pip/mp-api-0.36.1
• 4565d47 [dependabot skip] Update environment
• 4b9e475 Bump mp-api from 0.35.1 to 0.36.1
• dd00bf8 Merge pull request #1164 from pyiron/dependabot/pip/atomistics-0.0.4
• 87ee630 Update thermo_bulk.py
• 03e519d Update setup.py
• 8c7109f Update environment.yml
• Additional commits viewable in compare view

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[github-actions]

👈 Launch a binder notebook on branch pyiron/pyiron_contrib/dependabot/pip/pyiron-atomistics-0.3.3

[liamhuber]

The daily tests started to fail because of an upstream problem when we from pyiron_atomistics.atomistics.structure.factory import StructureFactory, where there is some further-up-stream problem with MaterialsProjectFactory and mp_api expecting something in pydantic that doesn't exist.

I double-checked, and the difference between our version of atomistics and the latest does indeed include a version update to the mp_api version, so it's plausible to me that getting this PR merged will solve the trouble with the daily tests.

This is failing now because:

Looking for: ['coverage', "coveralls[version='>=3.3.1']", 'codacy-coverage', 'ase=3.22.1', 'cloudpickle', 'matplotlib=3.7.2', 'numpy=1.24.3', 'pyiron_base=0.6.3', 'pyiron_atomistics=0.3.3', 'pyparsing=3.0.9', 'scipy=1.11.1', 'seaborn=0.12.2', 'scikit-image=0.21.0', 'toposort', 'randspg=0.0.1', 'boto3=1.28.25', 'moto=4.1.14', 'pycp2k=0.2.2', 'python-graphviz', 'typeguard=4.1.0', 'aws-sam-translator=1.71.0', 'pympipool=0.6.2', 'distributed=2023.8.0']

Could not solve for environment specs
The following package could not be installed
└─ pyiron_atomistics 0.3.3**  does not exist (perhaps a typo or a missing channel).

I suspect this is just the conda repo and pypi getting out of sync, so I'm going to try simply restarting this PR.

[liamhuber]

@dependabot rebase

[dependabot]

Looks like this PR is already up-to-date with main! If you'd still like to recreate it from scratch, overwriting any edits, you can request @dependabot recreate.

[liamhuber]

@dependabot recreate

[liamhuber]

Could not solve for environment specs
The following packages are incompatible
├─ pyiron_atomistics 0.3.3**  is installable and it requires
│  └─ scipy >=1.11.2  with the potential options
│     ├─ scipy [1.11.2|1.11.3], which can be installed;
│     ├─ scipy [1.11.1|1.11.2|1.11.3] would require
│     │  └─ python >=3.11,<3.12.0a0 , which can be installed;
│     └─ scipy [1.11.1|1.11.2|1.11.3] would require
│        └─ python >=3.9,<3.10.0a0 , which can be installed;
└─ scipy 1.11.1**  is installable with the potential options
   ├─ scipy [1.11.1|1.11.2|1.11.3], which can be installed (as previously explained);
   ├─ scipy [1.11.1|1.11.2|1.11.3], which can be installed (as previously explained);
   └─ scipy 1.11.1 conflicts with any installable versions previously reported.

I guess scipy needs to get updated first

[liamhuber]

@dependabot rebase

[liamhuber]

Well I'm a bit confused now. The install error stems from

Looking for: ['coverage', "coveralls[version='>=3.3.1']", 'codacy-coverage', 'ase=3.22.1', 'cloudpickle', 'matplotlib=3.7.2', 'numpy=1.24.3', 'pyiron_base=0.6.3', 'pyiron_atomistics=0.3.3', 'pyparsing=3.0.9', 'scipy=1.11.1', 'seaborn=0.12.2', 'scikit-image=0.21.0', 'toposort', 'randspg=0.0.1', 'boto3=1.28.25', 'moto=4.1.14', 'pycp2k=0.2.2', 'python-graphviz', 'typeguard=4.1.0', 'aws-sam-translator=1.71.0', 'pympipool=0.6.2', 'distributed=2023.8.0']

And yields the same error as before

The following packages are incompatible
├─ pyiron_atomistics 0.3.3**  is installable and it requires
│  └─ scipy >=1.11.2  with the potential options
│     ├─ scipy [1.11.1|1.11.2|1.11.3] would require
│     │  └─ python >=3.10,<3.11.0a0 , which can be installed;
│     ├─ scipy [1.11.2|1.11.3], which can be installed;
│     └─ scipy [1.11.1|1.11.2|1.11.3] would require
│        └─ python >=3.9,<3.10.0a0 , which can be installed;
└─ scipy 1.11.1**  is installable with the potential options
   ├─ scipy [1.11.1|1.11.2|1.11.3], which can be installed (as previously explained);
   ├─ scipy [1.11.1|1.11.2|1.11.3], which can be installed (as previously explained);
   └─ scipy 1.11.1 conflicts with any installable versions previously reported.

What's weird about this is where is that scipy=1.11.1 is coming from?! On the dependabot branch both setup.py and .ci_support/environment.yml are correctly specifying 1.11.2. And of course ditto for main.

Atomistics 0.3.3 does indeed want 1.11.2 as well, just as claimed in the error message.

I also don't see any evidence that it's a python version thing, as 1.11.2 is available in all those versions above.

I only hope that somehow the rebase command wasn't robust enough and had something wrongly cached (or similar)?

[liamhuber]

@dependabot recreate

[liamhuber]

Ok, we're slowly getting somewhere

Looking for: ['coverage', "coveralls[version='>=3.3.1']", 'codacy-coverage', 'ase=3.22.1', 'cloudpickle', 'matplotlib=3.7.2', 'numpy=1.24.3', 'pyiron_base=0.6.3', 'pyiron_atomistics=0.3.3', 'pyparsing=3.0.9', 'scipy=1.11.2', 'seaborn=0.12.2', 'scikit-image=0.21.0', 'toposort', 'randspg=0.0.1', 'boto3=1.28.25', 'moto=4.1.14', 'pycp2k=0.2.2', 'python-graphviz', 'typeguard=4.1.0', 'aws-sam-translator=1.71.0', 'pympipool=0.6.2', 'distributed=2023.8.0']

Could not solve for environment specs
The following packages are incompatible
├─ pyiron_atomistics 0.3.3**  is installable and it requires
│  └─ pyiron_base >=0.6.4  with the potential options
│     ├─ pyiron_base [0.6.4|0.6.5], which can be installed;
│     └─ pyiron_base 0.6.6 would require
│        └─ pysqa >=0.1.2 , which requires
│           └─ pympipool >=0.7.0 , which can be installed;
├─ pyiron_base 0.6.3**  is uninstallable because it conflicts with any installable versions previously reported;
└─ pympipool 0.6.2**  is uninstallable because it conflicts with any installable versions previously reported.

Unfortunately the base update PR #867 is also failing right now.

[dependabot]

Looks like pyiron-atomistics is up-to-date now, so this is no longer needed.