Docs/api documentation update for release-3.1.0#202

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jeipollack wants to merge 135 commits intodevelopfrom

docs/api-documentation-update

Commits on Feb 2, 2026

Correct doc string, format errors, unused imports, type hints, etc
Jennifer Pollack
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Update documentation for v3.0.0: replace modules.rst with api.rst, clean up submodule docs, update conf.py, and update pyproject.toml version
Jennifer Pollack
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Update API reference and clean up package/module docstrings
Jennifer Pollack
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Remove auto-generated _autosummary from repo; will be built in CD
Jennifer Pollack
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Add arduino formatting to directory structure example
Jennifer Pollack
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Revise WaveDiff how-to guide in doc (part 1)
Jennifer Pollack
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Fix myst error with invalid code format
Jennifer Pollack
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Correct syntax in docstring and generalise exception message
Jennifer Pollack
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Add inference and test_inference packages
Jennifer Pollack
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Refactor: Encapsulate logic in psf_models package with subpackages: models and tf_modules, add/rm modules, update import statements and tests
Jennifer Pollack
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Remove unused module with duplicate zernike_generator function
Jennifer Pollack
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Correct syntax in docstrings and logger messages
Jennifer Pollack
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Refactor file structure; update import statements in tests; remove unit test due to refactoring
Jennifer Pollack
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Update package name in import statement
Jennifer Pollack
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Reorder imports; Refactor MetricsConfigHandler class attributes, methods and variable names|
Jennifer Pollack
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Move psf_model weights loader to psf_model_loader.py module
Jennifer Pollack
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Add psf_model_loader module
Jennifer Pollack
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Remove weights_path arg from evaluate_model method; Update logger.info statement and comment

jeipollack
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Jennifer Pollack
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Update variable name and logger statement

jeipollack
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Jennifer Pollack
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Add import logging and create logger object

jeipollack
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Jennifer Pollack
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Create psf_inference.py module
Jennifer Pollack
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Remove arg from evaluate_model unit test
Jennifer Pollack
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Refactor: reorganise modules, relocate utility functions, rename modules, update import statements and unit tests
Jennifer Pollack
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Update import statements to new module names
Jennifer Pollack
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Update DataHandler class docstring to include option for inference dataset handling
Jennifer Pollack
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Refactor data_handler with new utility functions to validate and process datasets and update docstrings
Jennifer Pollack
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Update unit tests associated to changes in data_handler.py
Jennifer Pollack
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Change exception handling in DataConfigHandler; modify args to DataHandler
Jennifer Pollack
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Add data and psf_model_imports into inference and sketch out methods
Jennifer Pollack
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add base psf inference

tobias-liaudat
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Jennifer Pollack
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add common call interface through PSF models

tobias-liaudat
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Jennifer Pollack
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add handling of inference params

tobias-liaudat
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Jennifer Pollack
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automatic formatting

tobias-liaudat
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Jennifer Pollack
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add first completed class draft

tobias-liaudat
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Jennifer Pollack
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add inference config file

tobias-liaudat
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Jennifer Pollack
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remove unused code

tobias-liaudat
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Jennifer Pollack
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update params

tobias-liaudat
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Jennifer Pollack
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update params

tobias-liaudat
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Jennifer Pollack
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update inference

tobias-liaudat
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Jennifer Pollack
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reduce arguments and add compute psfs when appropiate

tobias-liaudat
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Jennifer Pollack
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add config handler class

tobias-liaudat
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Jennifer Pollack
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set up inference config handler and simplify PSFInferenc init

tobias-liaudat
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Jennifer Pollack
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remove unused imports

tobias-liaudat
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Jennifer Pollack
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update inference

tobias-liaudat
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Jennifer Pollack
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Add single-space lines to improve readability; Remove duplicated static method
Jennifer Pollack
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Add additional PSFInference class attributes; update set_source_parameters to use class attributes; assign variable names in get_trained_psf_model; Update class and __init__ docstrings
Jennifer Pollack
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Add checks to convert to np.ndarray and expand dimensions if needed

jeipollack
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Jennifer Pollack
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Update pyproject.toml with numpy dependency limits - sdc-uk

jeipollack
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Jennifer Pollack
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Correct name of psf_inference_test module to follow repo naming convention
Jennifer Pollack
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Correct config subkey names for defining trained_model_path and trained_model_config_path
Jennifer Pollack
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Refactor psf_inference adding PSFInferenceEngine to separate concerns, enabling isolated testing; implement lazy loaders for config handling, model loading, and inference
Jennifer Pollack
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Add unit tests for psf_inference
Jennifer Pollack
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Bugfix: Ensure updated training_config.training.model_params are passed to simPSF
Jennifer Pollack
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test(simPSF): add unit test to verify updated model_params are passed
Jennifer Pollack
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Bug: replace self.data_conf with self.data_config

jeipollack
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Jennifer Pollack
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Change logger.warnings to ValueErrors for missing fields in datasets & remove redundant check
Jennifer Pollack
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Update unit tests with changes to data_handler.py
Jennifer Pollack
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Refactor: reorganise modules, relocate utility functions, rename modules, update import statements and unit tests
Jennifer Pollack
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Refactor data_handler with new utility functions to validate and process datasets and update docstrings
Jennifer Pollack
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Update unit tests associated to changes in data_handler.py
Jennifer Pollack
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automatic formatting

tobias-liaudat
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Jennifer Pollack
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Refactor: add ZernikeInputs dataclass, ZernikeInputsFactory, helper methods for assembling zernike contributions according to run_type mode: training, simulation, or inference
Jennifer Pollack
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Update docstring describing data_conf types permitted
Jennifer Pollack
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Move imports to method to avoid circular imports
Jennifer Pollack
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Remove batch_size arg from ZernikeInputsFactory ; raise ValueError to check Zernike contributions have the same number of samples
Jennifer Pollack
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Add and set run_type attribute to DataConfigHandler object in TrainingConfigHandler constructor
Jennifer Pollack
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Add and set run_type attribute ; Replace var name end with end_sample in PSFInferenceEngine
Jennifer Pollack
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Refactor TFPhysicalPolychromaticField to lazy load property objects and attributes dynamically at run-time according to the run_type: training or inference
Jennifer Pollack
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Update/Add unit tests to test refactoring changes to psf_model_physical_polychromatic.py and data_zernike_utils.py
Jennifer Pollack
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Replace arg: data in compute_ccd_misalignment with positions
Jennifer Pollack
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Correct object attributes for DataConfigHandler in ZernikeInputsFactory

jeipollack
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Jennifer Pollack
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Add missing return for tf_physical_layer property

jeipollack
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Jennifer Pollack
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Add tf_utils.py module to tf_modules subpackage

jeipollack
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Jennifer Pollack
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Use ensure_tensor method from tf_utils.py to check/convert to tensorflow type; Remove get_obs_positions and replace with ensure_tensor method; add property tf_positions

jeipollack
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Jennifer Pollack
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Refactor: Add eager-mode helpers and avoid lazy-loading obscurations in graph mode

jeipollack
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Jennifer Pollack
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Replace deprecated get_obs_positions with get_np_obs_positions and apply ensure_tensor to convert obs_pos to tensorflow float32

jeipollack
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Jennifer Pollack
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Remove tf.convert_to_tensor from all Zernike list contributors

jeipollack
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Jennifer Pollack
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Add and set self.data_conf.run_type value to 'metrics' in MetricsConfigHandler

jeipollack
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Jennifer Pollack
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Eagerly precompute Zernike components; add support for 'metrics' run_type

jeipollack
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Jennifer Pollack
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Correct value error: train in dataset_type with training

jeipollack
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Jennifer Pollack
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fix: pass random seed to TFNonParametricPolynomialVariationsOPD constructor in psf_model_physical_polychromatic.py

jeipollack
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Jennifer Pollack
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Refactor to suppress TensorFlow debug msgs: replace lambda in call method with a proper function: find_position_indices enable batch processing for better graph optimization

jeipollack
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Jennifer Pollack
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Match old behaviour with conditional and float64 accumulation

jeipollack
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Jennifer Pollack
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Add helper to stack x/y field coordinates into (N, 2) positions array

jeipollack
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Jennifer Pollack
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Add helper method to prepare dataset for inference & handle empty/None fields

jeipollack
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Jennifer Pollack
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Update data_handler_test replacing "get_obs_positions" (deprecation) with "get_np_obs_positions"
Jennifer Pollack
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Remove deprecated code from rebase
Jennifer Pollack
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Remove duplicated checks on arg existance
Jennifer Pollack
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Improve Zernike prior handling in assemble_zernike_contributions
Jennifer Pollack
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Fix bug where Tensor zernike_prior was not appended after eager conversion
Jennifer Pollack
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Update unit tests with latest changes to fixtures and data_zernike_utils.py
Jennifer Pollack
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Set mock Zernike priors to None in test_data_utils.py helper module
Jennifer Pollack
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Remove -1.0 multiplicative factor applied to Zernike tip and tilt values
Jennifer Pollack
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Move TFPhysicalPolychromaticField.pad_zernikes to helper method pad_tf_zernikes in data_zernike_utils.py
Jennifer Pollack
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Correct bug in test_load_inference_model
Jennifer Pollack
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Revert sign change applied to compute_centroid_correction
Jennifer Pollack
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Refactor _prepare_positions_and_seds to enforce shape consistency and add validation
Jennifer Pollack
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Fix tensor handling in ZernikeInputsFactory

jeipollack
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Jennifer Pollack
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Reformat and remove unused import
Jennifer Pollack
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Correct zernike_prior extraction when dataset is a dict, reformat file
Jennifer Pollack
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Replace np.array with Tensorflow tensors in unit test and fixtures, reformat files
Jennifer Pollack
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Eagerly initialise trainable layers in physical poly model constructor required for evaluation/inference

jeipollack
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Jennifer Pollack
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fix: use expect_partial() when loading model weights for evaluation

jeipollack
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Jennifer Pollack
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Add memory cleanup after training completion

jeipollack
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Jennifer Pollack
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refactor: centralise PSF data extraction in data_handler

jeipollack
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Jennifer Pollack
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Add and options to inference_config.yaml (forgot to stage with previous commit)

jeipollack
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Jennifer Pollack
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Update PSFInference doc string with new optional attributes

jeipollack
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Jennifer Pollack
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Rename _get_inference_data to _get_direct_data

jeipollack
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Jennifer Pollack
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Reformat with black
Jennifer Pollack
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Correct type hint errors

jeipollack
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Jennifer Pollack
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Remove unused import

jeipollack
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Jennifer Pollack
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Replace call to deprecated get_np_obs_positions with get_data_array

jeipollack
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Jennifer Pollack
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Remove unused imports and reformat
Jennifer Pollack
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Update fixtures and unit tests
Jennifer Pollack
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Reformat with black
Jennifer Pollack
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Remove outdated back module
Jennifer Pollack
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Remove unused import left after rebase
Jennifer Pollack
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Update doc strings and cache handling
Jennifer Pollack
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Update psf_test_setup fixture for reusability and add unit tests for cache handling
Jennifer Pollack
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Remove unneeded mock of logger in evaluate_model
Jennifer Pollack
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Add wf_psf.inference to list of main packages
Jennifer Pollack
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Update version to 3.1.0
Jennifer Pollack
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docs: Correct syntax error and code-block formatting in doc string examples
Jennifer Pollack
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Remove weights_path references missed during rebase
Jennifer Pollack
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Add changelog fragment
Jennifer Pollack
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Fix logger formatting for relative RMSE metrics

jeipollack
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Jennifer Pollack
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Update changelog with entry under Bug Fixes

jeipollack
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Jennifer Pollack
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Correct rebase error in configuration.md
Jennifer Pollack
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Commits on Feb 10, 2026

Add new changelog fragment for deprecated import
Jennifer Pollack
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Commits on Feb 13, 2026

Fix Sphinx autosummary imports and improve comments
Jennifer Pollack
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Update .gitignore
Jennifer Pollack
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docs: Update API documentation for v3.1.0 release
Jennifer Pollack
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Uncomment tensorflow dependency
Jennifer Pollack
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Update cd manual workflow to use editable install and adjust sys.path in conf.py
Jennifer Pollack
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Correct pip install typo and fix path for uploading artifact
Jennifer Pollack
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