Various deprecation warnings

[sphuber]

• aiida.restapi.translator.nodes.node.NodeTranslator._get_subclasses uses the deprecated imp module.
• aiida.orm.nodes.data.structure.ase_refine_cell passes ASE object to spglib.refine_cell which is deprecated.
• aiida/backends/tests/test_dataclasses.py::TestKpointsData::test_path_wrapper_legacy gets warning: object of type <class 'numpy.float64'> cannot be safely interpreted as an integer.

[ltalirz]

As for the warning

 /opt/hostedtoolcache/Python/3.8.2/x64/lib/python3.8/site-packages/spglib/spglib.py:895: DeprecationWarning: ASE Atoms-like input is deprecated.
    warnings.warn("ASE Atoms-like input is deprecated.",

See here for the fix
https://atztogo.github.io/spglib/python-spglib.html#ase-atoms-like-input-is-deprecated

[CasperWA]

There was another deprecation warning in the REST API module aiida.restapi.common.identifiers:

DeprecationWarning: Using or importing the ABCs from 'collections' instead of from collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working

This will be fixed in #3974.

[DirectriX01]

I've created a pull request for aiida.restapi.translator.nodes.node.NodeTranslator._get_subclasses I'm not sure on how to work on the aiida.orm.nodes.data.structure.ase_refine_cell warning, the ASE structure is used by various functions, such as

aiida-core/aiida/orm/nodes/data/cif.py

Line 49 in dc9ec6f

def cif_from_ase(ase, full_occupancies=False, add_fake_biso=False):

[ltalirz]

thanks @DirectriX01

I'm not sure on how to work on the aiida.orm.nodes.data.structure.ase_refine_cell warning

Haven't looked into it in detail, but I guess you'll need to extract the "tuple input data"
described in https://atztogo.github.io/spglib/python-spglib.html#ase-atoms-like-input-is-deprecated

here

aiida-core/aiida/orm/nodes/data/structure.py

Line 636 in 4b7febe

cell, positions, numbers = refine_cell(aseatoms, **kwargs)

[unkcpz]

To show the deprecated message, just run the correspondence test cases. After having aiida environment set, run:

$ pytest -v tests/test_dataclasses.py::TestCifData::test_get_structure
$ pytest -v tests/test_dataclasses.py::TestKpointsData::test_path_wrapper_legacy
$ pytest -v pytest tests/restapi/test_translator.py

There are more deprecated message outputs than you can find as described in this issue.
Better to fix them all.

[sphuber]

This is very outdated. Some reported have since been addressed, many others have been added. No point in keeping this around