Update for viewer monorepo#292
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- Implement DataAccess[T] and DataContext[T] in data_access.py - __call__ returns iterable of DataContext, supports (raw, ctx) tuple unpacking - from_data classmethod wraps raw data directly for testing/composition - Source resolution: parses selection, matches schema sources, strips token - Add 25 tests covering all paths (passthrough, source resolution, errors) - Update port-quantity SKILL.md to iteration pattern (for raw, _ in self._data():) - Update docs/architecture/calculation.rst to iteration pattern
… results - merge(generator) unwraps single results, combines multiple dicts, returns None for empty/all-None - Add 9 tests covering all merge paths including primary DataAccess usage patterns
…uantity skill update
…ispatch functions
… selection arg, type hints, to_dict)
…gap from_path/from_file/_path
…cher/Handler architecture
…TCAR to Dispatcher/Handler architecture
…al, current_density
…election from *args - dispatch.py: add _method_accepts_selection() which inspects whether a handler method's first positional parameter is named 'selection'. Modify _dispatch() to automatically prepend remaining_selection to method args when the handler accepts it, removing the need for callers to pass selection in *args. - New convention enforced by test_selection_convention.py: * Dispatcher has 'selection' param -> 3rd merge arg = selection * Dispatcher has no 'selection' param -> 3rd merge arg = None * 'selection' NEVER appears in *args (dispatch handles forwarding) - Quantity dispatcher fixes (remove selection from *args, fix 3rd arg): band, bandgap, current_density, density, dielectric_function, _dispersion, dos, effective_coulomb, electronic_minimization, energy, exciton_density, local_moment, nics, pair_correlation, partial_density, phonon_band, phonon_dos, potential, projector - density.py: rename DensityHandler.to_view/to_contour 'selection' parameter to 'component' to avoid accidental auto-forwarding (density uses self._selection_name for source routing, not the method parameter) - test_dispatch.py: update tests for new auto-forwarding behavior, add _FakeHandler.read_with_selection, remove selection from *args in test helpers, mock schema_selections where needed
…ue to unconfigured dispatcher
- @quantity decorator now auto-injects from_path(), from_file(), and _path property on all dispatcher classes via FileSource construction - Remove manually-defined from_path/from_file/pathlib imports from all dispatcher classes to avoid duplication (~21 files cleaned up) - Fix _dispatch() to distinguish handler selection params with defaults vs required: skip forwarding remaining_selection=None when default exists, always forward when selection is required - Fix __str__ on all dispatchers to accept selection=None and forward to merge_strings (~25 files) - Fix phonon_band.py: pass width as keyword arg to avoid positional collision with selection in _dispatch - Refactor conftest.py check_factory_methods: derive quantity name from _quantity_name attr, detect methods without selection param, relax selection forwarding assertions - Remove @pytest.mark.skip from all 38 test files; add skip_methods for kpoint (selections) and stoichiometry (to_mdtraj) - Fix test_electronic_minimization: uncomment test_factory_methods Result: 42/42 test_factory_methods pass, 2051 total tests pass (6 pre-existing failures require optional mdtraj package)
…erties dict - _DatabaseData now has only two fields: metadata and properties - properties keys use <quantity>_<selection> format, no leading underscore - CalculationMetaData has path (directory), schema_version, file presence flags; removed hdf5_original_path, tags, infer_none_files - _DBDataMixin no longer carries __schema_version__ per-instance field - Calculation._to_database() takes no arguments - _compute_database_data iterates _REGISTRY via _ensure_all_quantities_imported - Added _to_database(selection=None) to 30 dispatcher classes - Updated tests: new test_to_database_new.py (16 tests), dispatcher tests, and updated test_database.py to use new API
Group members like @quantity('self_energy', group='electron_phonon') were storing _quantity_name = 'self_energy' (short name). Group.__getattr__ then passed this short name to the dispatcher constructor, causing FileAccessError because the schema key is 'electron_phonon_self_energy'. Fix: store _quantity_name = f'{group}_{name}' when a group is given, so the full schema-compatible key is always used. Add two tests: - TestQuantityDecorator::test_stores_full_quantity_name_for_grouped_quantity - TestGroup::test_attribute_access_passes_full_quantity_name_for_decorated_group
All handler to_database() methods now return the DB object directly instead
of {"quantity": DB_object}. Update tests to drop the ["key"] subscript and
update dispatcher tests to expect the DB object at result["default"] rather
than result["default"]["key"].
Introduces merge_to_database in dispatch.py, which wraps _dispatch and remaps result keys from selection names to quantity-prefixed keys: the default selection maps to just the quantity name, non-default selections to quantity_selection. Leading underscores are stripped so private quantities like _CONTCAR appear without the prefix. All dispatcher _to_database methods are updated to use merge_to_database instead of _dispatch, and _collect_to_database in __init__.py is simplified to use the pre-built keys directly. Two placement bugs are also fixed: the Dos and Energy _to_database methods were previously unreachable dead code in the wrong scope.
…r for monorepo architecture and refactoring, as well as new features; adjust tests accordingly
…WidgetConfig; apply black formatting
…urrent branch - the broken .gitlink seems to have accidentally added workshop as a git submodule, but the link is broken and is also broken on main (main does not have it as far as I can tell)
…]`; add `only_available` parameter to either constrain quantities/selections or not
…lse to respect method implementation
… whether all demo quantities implement .read()
# Conflicts: # src/py4vasp/_calculation/_CONTCAR.py # src/py4vasp/_calculation/__init__.py # src/py4vasp/_calculation/_dispersion.py # src/py4vasp/_calculation/_stoichiometry.py # src/py4vasp/_calculation/band.py # src/py4vasp/_calculation/bandgap.py # src/py4vasp/_calculation/born_effective_charge.py # src/py4vasp/_calculation/cell.py # src/py4vasp/_calculation/current_density.py # src/py4vasp/_calculation/density.py # src/py4vasp/_calculation/dielectric_function.py # src/py4vasp/_calculation/dielectric_tensor.py # src/py4vasp/_calculation/dispatch.py # src/py4vasp/_calculation/dos.py # src/py4vasp/_calculation/effective_coulomb.py # src/py4vasp/_calculation/elastic_modulus.py # src/py4vasp/_calculation/electronic_minimization.py # src/py4vasp/_calculation/energy.py # src/py4vasp/_calculation/exciton_density.py # src/py4vasp/_calculation/exciton_eigenvector.py # src/py4vasp/_calculation/force.py # src/py4vasp/_calculation/kpoint.py # src/py4vasp/_calculation/local_moment.py # src/py4vasp/_calculation/nics.py # src/py4vasp/_calculation/pair_correlation.py # src/py4vasp/_calculation/phonon_band.py # src/py4vasp/_calculation/phonon_dos.py # src/py4vasp/_calculation/phonon_mode.py # src/py4vasp/_calculation/piezoelectric_tensor.py # src/py4vasp/_calculation/polarization.py # src/py4vasp/_calculation/potential.py # src/py4vasp/_calculation/projector.py # src/py4vasp/_calculation/run_info.py # src/py4vasp/_calculation/stress.py # src/py4vasp/_calculation/structure.py # src/py4vasp/_calculation/velocity.py # src/py4vasp/_calculation/workfunction.py # tests/calculation/conftest.py # tests/calculation/test_band.py # tests/calculation/test_calculation_registry.py # tests/calculation/test_contcar.py # tests/calculation/test_dispatch.py # tests/calculation/test_partial_density.py # tests/calculation/test_phonon_mode.py # tests/calculation/test_run_info.py # tests/calculation/test_selection_convention.py # tests/calculation/test_stoichiometry.py # tests/calculation/test_structure.py
![github-code-quality[bot]](https://avatars.githubusercontent.com/u/9919?s=60&v=4){kind=small}
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| class _TensorReduction(index.Reduction): |
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| alpha_2d = (l_vacuum / (4.0 * np.pi)) * (eps_parallel - 1.0) | ||
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Remove unused imports flagged by the static-analysis bot: - _dispatch from _dispersion, band, bandgap, born_effective_charge - slice_steps from bandgap - pathlib and Optional from band - copy from current_density Remove a redundant duplicate `vickers_hardness = elastic_tensor.get_hardness()` in elastic_modulus._compute_elastic_properties: it was recomputed inside the "fracture" suppress block after already being computed in the dedicated "hardness" block. The two remaining bot findings were false positives and left unchanged: - nics._TensorReduction missing super().__init__(): the parent index.Reduction is an ABC whose __init__ is an empty abstractmethod, so there is no base setup. - dielectric_tensor "unreachable" return None: it is reached when error.suppress_and_record swallows an exception in the with-block.
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| from py4vasp._calculation.dispatch import ( | ||
| DataSource, | ||
| _dispatch, | ||
| merge_default, | ||
| merge_strings, | ||
| merge_to_database, | ||
| quantity, | ||
| ) |
| # Copyright © VASP Software GmbH, | ||
| # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) | ||
| import copy | ||
| import itertools |
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| from py4vasp._calculation.dispatch import ( | ||
| DataSource, | ||
| _dispatch, | ||
| merge_default, | ||
| merge_graphs, | ||
| merge_strings, | ||
| merge_to_database, | ||
| quantity, | ||
| ) |
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| from py4vasp._calculation.dispatch import ( | ||
| DataSource, | ||
| _dispatch, | ||
| merge_default, | ||
| merge_strings, | ||
| merge_to_database, | ||
| quantity, | ||
| ) |
| return "down" in name and "up" not in name and "total" not in name | ||
| # Copyright © VASP Software GmbH, | ||
| # Licensed under the Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0) | ||
| import pathlib |
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| from py4vasp._calculation.dispatch import ( | ||
| DataSource, | ||
| _dispatch, | ||
| merge_default, | ||
| merge_strings, | ||
| merge_to_database, | ||
| quantity, | ||
| ) |
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| from py4vasp._calculation.dispatch import ( | ||
| DataSource, | ||
| _dispatch, | ||
| merge_default, | ||
| merge_graphs, | ||
| merge_strings, | ||
| merge_to_database, | ||
| quantity, | ||
| ) |
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| from py4vasp._calculation.dispatch import ( | ||
| DataSource, | ||
| _dispatch, | ||
| merge_default, | ||
| merge_strings, | ||
| merge_to_database, | ||
| quantity, | ||
| ) |
The `only_available=True` example claimed density had a loadable `tau` source, but the demo data provides no loadable `tau` density, so the actual result is `'density': ['default']`. Corrected the expected output to match, consistent with the sibling `method="to_view", only_available=True` example that already showed `['default']`.
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Implemented utilities surrounding vasp.viewer and View functionality related to interface changes (mostly volume support)
Add Calculation.selections() to obtain loadable quantities (and method to check can be specified)
Add View.to_vasp_viewer_config() and refactor View.to_vasp_viewer()
Add support for adding up View instances (
__add__)Share additive logic between Graph and View
Add tests for all changes and features
Removed an unused submodule link to
workshopthat had no URL and prevented importing py4vasp on this branch as a dependency viauv; the link was likely added unintentionally?