Test docs examples

[liamhuber]

Rename the "notebooks" env more properly to reflect it is just pyiron_atomistics, and it is used for both docs and notebooks. Then format the README examples for doctest and test them.

[github-actions[bot]]

:point_left: Launch a binder notebook on branch _pyiron/pyiron_ontology/test_docsexamples

[codacy-production[bot]]

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
:white_check_mark: +3.92% (target: -1.00%)	:white_check_mark: 100.00%

Coverage variation details

| | Coverable lines | Covered lines | Coverage | | ------------- | ------------- | ------------- | ------------- | | Common ancestor commit (43e57167607af2ce57c6a803dc528b5ae9d3969a) | 459 | 400 | 87.15% | | | Head commit (594c6d2528a2fdfb030c63407f84608b2ad87c96) | 459 (+0) | 418 (+18) | 91.07% (**+3.92%**) | **Coverage variation** is the difference between the coverage for the head and common ancestor commits of the pull request branch: ` - `

Diff coverage details

| | Coverable lines | Covered lines | Diff coverage | | ------------- | ------------- | ------------- | ------------- | | Pull request (#35) | 1 | 1 | **100.00%** | **Diff coverage** is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: `/ * 100%`

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_{You may notice some variations in coverage metrics with the latest Coverage engine update. For more details, visit the documentation}

[liamhuber]

On windows:

Looking for: ['coverage', "coveralls[version='>=3.3.1']", 'codacy-coverage', 'numpy=1.26.3', 'openjdk', 'owlready2=0.45', 'pandas=2.1.4', 'pint=0.23', "python[version='>=3.8']", 'lammps', 'pyiron_atomistics', 'pyiron-data']

Could not solve for environment specs
The following package could not be installed
└─ lammps   does not exist (perhaps a typo or a missing channel).
Error: Process completed with exit code 1.

Riiight. The lammps package is architecture-specific and precludes windows. So I can't just dump the docs and notebooks envs together like that.

[liamhuber]

Doc test is failing, but it looks at first glance like the problem is up-stream:

File "/home/runner/work/pyiron_ontology/pyiron_ontology/tests/integration/../../docs/README.md", line 336, in README.md
Failed example:
    from pyiron_atomistics import Project
Exception raised:
    Traceback (most recent call last):
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/doctest.py", line 1353, in __run
        exec(compile(example.source, filename, "single",
      File "<doctest README.md[45]>", line 1, in <module>
        from pyiron_atomistics import Project
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_atomistics/__init__.py", line 1, in <module>
        from pyiron_atomistics.project import Project
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_atomistics/project.py", line 37, in <module>
        from pyiron_atomistics.atomistics.structure.factory import StructureFactory
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_atomistics/atomistics/structure/factory.py", line 40, in <module>
        from pyiron_atomistics.atomistics.structure.factories.materialsproject import (
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/pyiron_atomistics/atomistics/structure/factories/materialsproject.py", line 2, in <module>
        from mp_api.client import MPRester
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/mp_api/client/__init__.py", line 7, in <module>
        from .core import MPRestError
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/mp_api/client/core/__init__.py", line 3, in <module>
        from .client import BaseRester, MPRestError
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/mp_api/client/core/client.py", line 31, in <module>
        from mp_api.client.core.utils import api_sanitize, validate_ids
      File "/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/mp_api/client/core/utils.py", line 7, in <module>
        from maggma.utils import get_flat_models_from_model
    ImportError: cannot import name 'get_flat_models_from_model' from 'maggma.utils' (/usr/share/miniconda3/envs/my-env/lib/python3.11/site-packages/maggma/utils.py)

Installed versions in that stack:

pyiron_atomistics                 0.4.4  pyhd8ed1ab_0             conda-forge/noarch 
mp-api                           0.37.2  pyhd8ed1ab_0             conda-forge/noarch
maggma                           0.38.1  pyhd8ed1ab_0             conda-forge/noarch

[liamhuber]

Yeah, pyiron_atomistics 0.4.4 specifies mp-api =0.39.4 so I guess that's the problem. The conda package permits anything >=0.37

[liamhuber]

The latest version of mp-api (0.39.5) puts a hard lower limit of 0.57.1, so I guess this is pyiron's fault for permitting older versions of mp-api when their dependency control was suckier.