Rename json to json_qcschema

[tovrstra]

This is one of the cleanups listed in #204.

There are several JSON schemas that could be relevant for IOData, and so we should rename our current one to something more specific, so we don't have to revise the API when adding a second JSON schema. The ones I'm aware of include:

• NOMAD has a json schema for QC jobs. https://nomad-lab.eu/prod/v1/docs/howto/plugins/schema_packages.html (See also Support for NOMAD JSON? #223)
• ASE has its own JSON schema: https://wiki.fysik.dtu.dk/ase/ase/io/formatoptions.html#json)
• There is also CJSON: https://wiki.openchemistry.org/Chemical_JSON

I've also removed the *.json pattern, so one has to specify explicitly which JSON schema to use.

It seemed better to use json_qcshema.py than qcschema_json.py. When another JSON schema module is added, it will be alphabetically close, making it easier to spot in the list of modules.

Edit: I've added some tests suggested by sourcery AI, but then also had to fix some error handingling in the api module to make the tests pass.

Summary by Sourcery

This pull request renames the existing JSON schema module to 'json_qcschema' to facilitate the addition of other JSON schemas in the future. It also updates the test cases to use the new format explicitly.

• Enhancements:
  • Renamed the JSON schema module to 'json_qcschema' to allow for future additions of other JSON schemas without revising the API.
  • Updated test cases to use the new 'json_qcschema' format explicitly.

[sourcery-ai]

Reviewer's Guide by Sourcery

This pull request renames the JSON schema to json_qcschema to avoid future conflicts with other potential JSON schemas. The changes include updating test cases to explicitly specify the JSON schema format and removing the generic *.json pattern to enforce explicit schema specification.

File-Level Changes

Files	Changes
iodata/test/test_json.py	Updated test cases to specify the JSON schema format explicitly using fmt="json_qcschema".
iodata/formats/json.py	Removed the generic *.json pattern to enforce explicit specification of JSON schema formats.

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[deepsource-io]

Here's the code health analysis summary for commits f520645..a3a3a6a. View details on DeepSource ↗.

Analysis Summary

Analyzer	Status	Summary	Link
Shell	✅ Success		View Check ↗
Python	❌ Failure	❗ 11 occurences introduced 🎯 11 occurences resolved	View Check ↗

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[sourcery-ai]

Hey @tovrstra - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟡 General issues: 1 issue found
• 🟢 Security: all looks good
• 🟡 Testing: 2 issues found
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[tovrstra]

I checked the deepsource issues. Some of them should be fixed eventually, but they are not related to this PR. I'm not fixing them now to keep this PR manageable.

[PaulWAyers]

Seems good to me.

I think that it isn't worth working too hard on this, as I think QCSchema may be basically dead (no activity in >3 years).

https://github.com/MolSSI/QCSchema

[tovrstra]

Thanks for checking. I agree, I'm just keeping it alive for now and avoid that it blocks us from doing other JSON-related things in the future.

[berquist]

Seems good to me.

I think that it isn't worth working too hard on this, as I think QCSchema may be basically dead (no activity in >3 years).

MolSSI/QCSchema

There was some recent activity in issues, but yes. The schema proper in this repository is also outdated; the latest version is generated on-the-fly from Pydantic models in QCElemental.

[tovrstra]

@berquist Thank you for the info. So, if I understand correctly, the following files are no longer the right ones?

https://github.com/MolSSI/QCSchema/tree/master/qcschema/data/v2

(If yes, is there another way to get up-to-date schema files? That would be useful.)

[berquist]

@berquist Thank you for the info. So, if I understand correctly, the following files are no longer the right ones?

MolSSI/QCSchema@master/qcschema/data/v2

(If yes, is there another way to get up-to-date schema files? That would be useful.)

That's correct. This should give you what you want if you comment out all the qcschema lines:

"""dump_schemas.py: Save the JSON representation of each schema stored in QCSchema and QCElemental."""

from pathlib import Path
import json

# This requires https://github.com/MolSSI/QCSchema/pull/81
from qcschema.dev import dev_schema
import qcelemental as qcel

base_dir = Path(__file__).parent.resolve()
schema_dir = base_dir / "schemas"
schema_dir.mkdir(mode=0o755, parents=True, exist_ok=True)

qcel_models = {
    "qcel_atomic_input": qcel.models.results.AtomicInput,
    "qcel_atomic_result": qcel.models.results.AtomicResult,
    "qcel_atomic_result_properties": qcel.models.results.AtomicResultProperties,
    "qcel_basis_set": qcel.models.basis.BasisSet,
    "qcel_molecule": qcel.models.molecule.Molecule,
    "qcel_provenance": qcel.models.common_models.Provenance,
}
for name, model in qcel_models.items():
    (schema_dir / f"{name}.json").write_text(json.dumps(model.schema(), indent=2), encoding="utf-8")

qcsk_models = {
    "qcsk_input": dev_schema.input_dev_schema,
    "qcsk_output": dev_schema.output_dev_schema,
    "qcsk_basis_set": dev_schema.basis_dev_schema,
    "qcsk_molecule": dev_schema.molecule_dev_schema,
}
for name, model in qcsk_models.items():
    (schema_dir / f"{name}.json").write_text(json.dumps(model, indent=2), encoding="utf-8")

[tovrstra]

@berquist Thank you for providing the script. I'll open a new issue, so we can keep track of it. I'm currently prioritizing API stability for IOData, so I will not be able to get on it in the short term.