THzTools v0.5.5 (beta)

Added

• Add list of related software to README

THzTools v0.5.4 (beta)

Added

• Add CITATION.cff file
• Add citation information to README
• Add links to README that point to online documentation examples
• Add usage information and example code to README
• Add Attributes section to each dataclass docstring
• Add support for Python 3.13

Removed

• Remove support for Python 3.8

Full Changelog: v0.4.1...v0.5.4

THzTools v0.5.3 (beta)

Fixed

• Fix documentation error in the Contributing section (#59)
• Fix typographical errors in JOSS paper

Added

• Add repostatus.org badge (#58)
• Add documentation on type checking in the Contributing section (#59)
• Add student acknowledgements to JOSS paper

v0.5.2

Changed

• Replace Black badge with Ruff badge in README.md

Fixed

• Fix documentation error in fit

THzTools v0.5.1 (beta)

Added

• Add CONTRIBUTING.md file
• Add Installation section to README.md

Fixed

• Fix error in bug_report issue template

THzTools v0.5.0 (beta)

Changed

• Change development status to beta
• Change mu_var attribute of FitResult to mu_err
• Change p_var attribute of FitResult to p_cov
• Revise example of simulating noise
• Revise example of simulating a waveform
• Complete draft JOSS paper
• Rename transfer as apply_frf
• Revise docstrings for consistency and clarity
• Apply bias correction to noise model parameter estimates
• Reorganize tests

Added

• Add configuration file for doctests with PyTest
• Add example of appling a frequency response function
• Add example of estimating noise model parameters
• Add example of fitting a parameterized frequency response function model
• Add example of rescaling and shifting a waveform
• Add diagnostic, dof, frfun_opt, p_err, and psi_opt attributes to
  FitResult
• Add frequency bounds to fit
• Add tests for new functionality

Removed

• Remove examples directory from top level
• Remove unused lint options from pyproject.toml

Fixed

• Correct total least-squares residual computation

THzTools v0.4.2 (alpha)

Changed

• Revise docstrings for NoiseModel methods
• Refactor noisefit code to improve readability
• Set tolerance parameter in minimize function used in noisefit
• Change fft_sign options to numpy_sign_convention
• Restore factor of 0.5 in cost function computation and gradient
• Replace scale_sigma_* parameters (which simply adds a constant to the log)
  with scale_logv_* parameters
• Refactor noisefit to encapsulate cost function computations in separate
  functions, _nll_noisefit, _jac_noisefit, and _hess_noisefit

Added

• Add reset_option, set_option
• Rename simulate-ideal-waveform example to simulate-waveform
• Add conftest.py file to ensure that global options are reset with each test
• Add doctest to test-pip action
• Add doctest script and dependencies to pyproject.toml
• Add test to verify noise parameter estimates in TestNoiseFit
• Add _nll_noisefit, _jac_noisefit, and _hess_noisefit

Fixed

• Fix error in wave docstring example
• Fix scaling error in noisefit estimate for sigma_tau
• Fix noisefit docstring example
• Fix error in fit covariance estimate output

THzTools v0.4.1 (alpha)

Changed

• Refactor options
• Use explicit dt keyword option instead of global option in examples
• Change hatch doctest script from Sphinx to PyTest
• Change signature of fit
• Revise documentation for fit, FitResult, get_option, set_option,
  transfer
• Refactor _costfuntls

Added

• Add version badges for pip and Anaconda
• Add conda installation instructions
• Add FitResult dataclass and use it to return fit output
• Add autouse fixture to reset sampling_time option to default before each
  test
• Add Python 3.12 to testing workflow
• Add global doctest imports explicitly to docstrings
• Add numpy_sign_convention parameter to fit

Fixed

• Fix scaling error in _parse_noisefit_output

THzTools v0.4.0 (alpha)

Changed

• Rename module constant global_options as options
• Rename tdnoisefit as noisefit
• Rename NoiseModel attributes alpha, beta and tau as sigma_alpha,
  sigma_beta and sigma_tau, respectively
• Rename NoiseModel methods amplitude, noise, and variance as
  noise_amp, noise_sim, and noise_var, respectively
• Revise noisefit and associated functions to treat each of the 3 noise
  parameters separately instead of as a 3-component array, so that each may
  fixed independently in the optimization process
• Adjust internal scaling in noisefit
• Reorganize NoiseResult class as output for noisefit
• Revise NoiseResult docstring
• Rename transfer_out as transfer
• Rename fft_sign parameter as numpy_sign_convention in transfer
• Make dt and t0 keyword-only arguments in wave and set defaults
• Change position of dt in scaleshift, tdnoisefit, transfer docstrings
  and change defaults
• Revise defaults for wave
• Change default value for dt in fit
• Improve type annotations
• Update tests
• Update dependencies in environment-dev.yml and pyproject.toml
• Revise Getting Started page
• Revise documentation, including Sphinx format and project-specific layout

Added

• Add R. P. Hall, Laleh Mohtashemi and Naod Yimam to the author list
• Add missing ORCID IDs
• Add get_option and set_option functions to handle global options
• Add attributes to NoiseResult class
• Add timebase function
• Add seed parameter in NoiseModel.noise_sim
• Add NoiseResult class to documentation
• Add doctests
• Add warnings
• Add paper directory with bib-file and stub for JOSS paper
• Add draft-pdf.yml GitHub Action to autogenerate JOSS paper; update
  deprecated upload-artifact Action in workflow
• Add Contributing and Examples pages to documentation
• Add Code of Conduct
• Add gallery of Jupyter notebook examples to documentation using nbsphinx

Fixed

• Fix error in units of NoiseModel.sigma_tau in noisefit
• Fix bug related to eta scaling in noisefit

THzTools v0.3.6 (alpha)

Changed

• Reorganized NoiseResult dataclass
• Initialize tests with thztools.global_options.sampling_time = None

Added

• Add Zenodo badge to README
• Internal _validate_sampling_time function to handle sampling time input
• Tests for _validate_sampling_time