Renamed many classes. by coltonbh · Pull Request #90 · atomsforhumanity/qcdata

coltonbh · 2025-10-03T19:15:32Z

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Copilot

Pull Request Overview

This PR renames many classes throughout the codebase to better reflect their purpose and usage patterns. The primary changes focus on improving clarity by renaming "Program" prefixed classes to "Calc" (calculation) prefixed classes, and "Results" to "Data" for attributes that represent computed values.

Key changes include:

Renamed core classes like ProgramOutput → Results, ProgramInput → CalcInput
Updated attribute names like .results → .data, .stdout → .logs
Added backwards compatibility shims with deprecation warnings
Updated documentation and visualization code to use new naming

Reviewed Changes

Copilot reviewed 37 out of 39 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/test_view.py	Updated imports and variable names to use new class names
tests/test_serialization.py	Changed parameter names and class references
tests/test_results.py	New file with tests for renamed Results class and data structures
tests/test_qcel.py	Updated parameter names to use new naming convention
tests/test_outputs.py	File removed (tests moved to test_results.py)
tests/test_optimization_data.py	Updated to use new OptimizationData class name
tests/test_conformer_search_data.py	Updated to use new ConformerSearchData class name
tests/test_calc_input.py	Updated to use new CalcInput class name
tests/conftest.py	Updated fixture names and class references
src/qcio/view.py	Updated class names in visualization code
src/qcio/qcel.py	Updated import and function parameter types
src/qcio/models/structure.py	Updated base class name
src/qcio/models/results.py	Major refactor with class renames and compatibility shims
src/qcio/models/inputs.py	Updated class names with compatibility aliases
src/qcio/models/base_models.py	Renamed QCIOModelBase to QCIOBaseModel
src/qcio/models/init.py	Updated import reference
mkdocs.yml	Updated documentation structure and references
docs/...	Updated documentation files to reflect new naming

Comments suppressed due to low confidence (2)

tests/test_results.py:1

Duplicate Results class in the list. Based on the TODO comment above, this should likely be [Results, ProgramOutput] to register both the new and backwards compatibility classes.

import pickle

src/qcio/view.py:718

Should use po.data instead of po.results to access the data attribute directly rather than through the deprecated backwards compatibility property.

                results_html = generate_results_table(po.results)

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Copilot · 2025-10-03T22:45:33Z

+    assert deserialized.data == results.results
+    assert deserialized.input_data == results.input_data
+    assert deserialized.provenance.program == "qcio-test-suite"
+    assert deserialized.logs == results.logs
+    assert deserialized.extras == results.extras
+    # assert deserialized.return_result == prog_output.return_result
+    assert deserialized.data.energy == results.results.energy
+    assert np.array_equal(deserialized.data.gradient, results.results.gradient)
+    assert np.array_equal(deserialized.data.hessian, results.results.hessian)


Inconsistent attribute access: deserialized.data should be compared to results.data, not results.results. The .results attribute is the deprecated backwards compatibility property.

Suggested change

assert deserialized.data == results.results

assert deserialized.input_data == results.input_data

assert deserialized.provenance.program == "qcio-test-suite"

assert deserialized.logs == results.logs

assert deserialized.extras == results.extras

# assert deserialized.return_result == prog_output.return_result

assert deserialized.data.energy == results.results.energy

assert np.array_equal(deserialized.data.gradient, results.results.gradient)

assert np.array_equal(deserialized.data.hessian, results.results.hessian)

assert deserialized.data == results.data

assert deserialized.input_data == results.input_data

assert deserialized.provenance.program == "qcio-test-suite"

assert deserialized.logs == results.logs

assert deserialized.extras == results.extras

# assert deserialized.return_result == prog_output.return_result

assert deserialized.data.energy == results.data.energy

assert np.array_equal(deserialized.data.gradient, results.data.gradient)

assert np.array_equal(deserialized.data.hessian, results.data.hessian)

Copilot · 2025-10-03T22:45:34Z

+    assert deserialized.provenance.program == "qcio-test-suite"
+    assert deserialized.logs == results.logs
+    assert deserialized.extras == results.extras
+    # assert deserialized.return_result == prog_output.return_result


This commented-out assertion should either be uncommented and fixed to use the new variable names, or removed entirely if it's no longer needed.

Suggested change

# assert deserialized.return_result == prog_output.return_result

Copilot · 2025-10-03T22:45:34Z

        final_html.append(generate_output_table(po))

-        if isinstance(po.results, ConformerSearchResults):
+        if isinstance(po.results, ConformerSearchData):


Should use po.data instead of po.results since the Results class attribute was renamed from .results to .data. The .results property exists for backwards compatibility but emits deprecation warnings.

Copilot · 2025-10-03T22:45:34Z


                # Determine the Structure to use
-                if isinstance(po.results, OptimizationResults):
+                if isinstance(po.results, OptimizationData):


Multiple instances where po.results should be po.data to use the new attribute name instead of the deprecated backwards compatibility property.

Copilot · 2025-10-03T22:45:34Z

                        title_extra += " (Final Structure)"

-                elif isinstance(po.results, SinglePointResults):
+                elif isinstance(po.results, SinglePointData):


Multiple instances where po.results should be po.data to use the new attribute name instead of the deprecated backwards compatibility property.

Copilot · 2025-10-03T22:45:34Z


            # Create results table or plot
-            if isinstance(po.results, OptimizationResults):
+            if isinstance(po.results, OptimizationData):


Multiple instances where po.results should be po.data to use the new attribute name instead of the deprecated backwards compatibility property.

Copilot · 2025-10-03T22:45:34Z

   "source": [
-    "# Inspect a single frame. This will be ProgramOutput for a single point calculation\n",
+    "# Inspect a single frame. This will be Results for a single point calculation\n",
    "view.view(xtb_opt.results.trajectory[-1], width=400, height=350)"


Should use xtb_opt.data.trajectory[-1] instead of xtb_opt.results.trajectory[-1] to access the data attribute directly rather than through the deprecated backwards compatibility property.

Copilot

Pull Request Overview

Copilot reviewed 37 out of 39 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (1)

src/qcio/view.py:457

Should use the new .data attribute instead of the deprecated .results attribute for consistency with the renaming.

    energies = prog_output.results.energies * constants.HARTREE_TO_KCAL_PER_MOL

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Copilot

Pull Request Overview

Copilot reviewed 40 out of 42 changed files in this pull request and generated 5 comments.

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Copilot · 2025-10-06T20:16:06Z

 import numpy as np

-from qcio import ProgramInput, SinglePointResults, Wavefunction
+from qcio import CalcSpec, SinglePointResults, Wavefunction


Import still references the old class name SinglePointResults instead of the new SinglePointData.

Copilot · 2025-10-06T20:16:07Z

-            setattr(this_module, name, _class)
+    for input_type, results_type in product(get_args(Specs), get_args(Data)):
+        # TODO: Remove ProgramOutput when compatibility is no longer needed
+        for ClassType in [Results, Results]:


The loop iterates over [Results, Results] (duplicated), but the comment suggests it should include ProgramOutput for backward compatibility.

Suggested change

for ClassType in [Results, Results]:

for ClassType in [Results, ProgramOutput]:

Copilot · 2025-10-06T20:16:07Z

+@deprecated_class("CoreSpec")
+class ProgramArgs(CoreSpec):
+    """Deprecated alias for CalcArgs.
+
+    This class is deprecated and will be removed in a future release. Please use
+    `CoreSpec` instead.
+    """


Corrected class name in docstring from 'CalcArgs' to 'CoreSpec'.

Copilot · 2025-10-06T20:16:07Z

    model: Optional[Model] = None
    subprogram: str
-    subprogram_args: ProgramArgs
+    subprogram_spec: CoreSpec


The docstring still refers to 'ProgramArgs' instead of 'CoreSpec' for the subprogram_spec attribute type.

Copilot · 2025-10-06T20:16:08Z

 - [`Structure`](./structure.md) objects represent a collection of atoms, a molecule, or any super molecular structure in 3D cartesian space.
- [`Input`](./inputs.md) objects define the input parameters for a calculation.
- [`ProgramOutput`](./outputs.md) objects store computed values and output files (collectively called [`Results`](./outputs.md#qcio.Results)) from a calculation. `ProgramOutput` also stores the exact input data (`.input_data`) used for a calculation, relevant metadata, and [`Provenance`](./provenance.md) information so you have full visibility of how every result was generated.
+- [`Calculation Specification`](./calculation_specificaions.md) objects define the parameters for a calculation.


Corrected spelling of 'specifications' in the link path.

Suggested change

- [`Calculation Specification`](./calculation_specificaions.md) objects define the parameters for a calculation.

- [`Calculation Specification`](./calculation_specifications.md) objects define the parameters for a calculation.

Copilot

Pull Request Overview

Copilot reviewed 40 out of 42 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (2)

src/qcio/view.py:1

[nitpick] Variable name po (likely short for 'program output') should be updated to result to match the new naming convention where the class is now called Results.

"""

src/qcio/view.py:435

The code is accessing .subprogram_args which has been renamed to .subprogram_spec. This should be po.input_data.subprogram_spec.model and po.input_data.subprogram_spec.keywords.

        if isinstance(po.input_data, CompositeCalcSpec):
            base_row += f"""
            <td>{po.input_data.subprogram}</td>
            <td>{po.input_data.subprogram_args.model}</td>
            <td>{generate_dictionary_string(po.input_data.subprogram_args.keywords)}</td>
            """

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Copilot · 2025-10-06T20:26:41Z

+
+@deprecated_class("OptimizationData")
+class OptimizationResults(OptimizationData):
+    """ "This class is deprecated and will be removed in a future release. Please use


Removed extra quote character at the beginning of the docstring.

Suggested change

""" "This class is deprecated and will be removed in a future release. Please use

"""This class is deprecated and will be removed in a future release. Please use

Copilot · 2025-10-06T20:26:42Z

+    assert opt_res.energies == [results.results.energy]
+    assert opt_res.structures == [results.input_data.structure]


The code is accessing .results attribute which has been renamed to .data. This should be results.data.energy to match the new naming convention.

coltonbh added 2 commits October 3, 2025 12:15

Renamed many classes.

035777e

Fixed typos.

49ccb5a

coltonbh force-pushed the feature-results-data-rename branch from e45a4f3 to 49ccb5a Compare October 3, 2025 19:21

coltonbh added 6 commits October 3, 2025 13:53

Updating test fixture and test names.

6736fa3

Added optimization viewer to docs assets.

95b6bf8

Updated README.md

73bb859

Updated names in docs.

13b3b0b

Updated docs.

58a5a8c

Remove more old references.

40c7821

coltonbh requested a review from Copilot October 3, 2025 22:43

Copilot AI reviewed Oct 3, 2025

View reviewed changes

Fix more names!

0d96fff

coltonbh requested a review from Copilot October 3, 2025 22:52

Copilot AI reviewed Oct 3, 2025

View reviewed changes

Renamed inputs to specs.

5387b62

coltonbh force-pushed the feature-results-data-rename branch from b3601a8 to 5387b62 Compare October 6, 2025 20:14

coltonbh requested a review from Copilot October 6, 2025 20:14

Copilot AI reviewed Oct 6, 2025

View reviewed changes

coltonbh requested a review from Copilot October 6, 2025 20:25

Copilot AI reviewed Oct 6, 2025

View reviewed changes

coltonbh force-pushed the feature-results-data-rename branch from 2835623 to 6511172 Compare October 6, 2025 20:27

tTypos

380bff4

coltonbh force-pushed the feature-results-data-rename branch from 6511172 to 380bff4 Compare October 6, 2025 20:29

coltonbh merged commit 753c589 into master Oct 6, 2025
5 checks passed

coltonbh deleted the feature-results-data-rename branch October 6, 2025 20:32

	for ClassType in [Results, Results]:
	for ClassType in [Results, ProgramOutput]:

	- [`Calculation Specification`](./calculation_specificaions.md) objects define the parameters for a calculation.
	- [`Calculation Specification`](./calculation_specifications.md) objects define the parameters for a calculation.

	""" "This class is deprecated and will be removed in a future release. Please use
	"""This class is deprecated and will be removed in a future release. Please use

		assert opt_res.energies == [results.results.energy]
		assert opt_res.structures == [results.input_data.structure]

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