THzTools - THzTools v0.5.5.post0

Added

• Add pyOpenSci badge to README.md
• Add JOSS badge to README.md

Changed

• Update CITATION.cff
• Change citation information in README.md

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 1 year ago

THzTools - THzTools v0.5.5 (beta)

Added

• Add list of related software to README

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 1 year ago

THzTools - 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: https://github.com/dodge-research-group/thztools/compare/v0.4.1...v0.5.4

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 1 year ago

THzTools - 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

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools -

Changed

• Replace Black badge with Ruff badge in README.md

Fixed

• Fix documentation error in fit

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools - THzTools v0.5.1 (beta)

Added

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

Fixed

• Fix error in bug_report issue template

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools - 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

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools - 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

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools - 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

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools - 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

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 1 year ago

THzTools - 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

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 2 years ago

THzTools - THzTools v0.3.5 (alpha)

Added

• GlobalOptions class
• global_options module constant

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 2 years ago

THzTools - THzTools v0.3.4 (alpha)

Changed

• Fix bug in NoiseModel example
• Replace tuple return value in tdnoisefit with NoiseResult

Added

• NoiseResult class

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 2 years ago

THzTools - THzTools v0.3.3 (alpha)

Changed

• Prune and update notebooks
• Fix error in noiseamp docstring example (now amplitude method of NoiseModel class)
• Darken text color for logo in dark mode
• Move make-logo script into default hatch environment
• Rename sampling time variable from ts to dt
• Rename thzgen as wave
• Revise conf.py in Sphinx documentation
• Add SciPy templates for attributes.rst, class.rst and method.rst
• Refactor code to decouple computations from sampling time
• Make dt parameter optional in most functions
• Set default dt to None, to indicate that time units are unspecified

Added

• NoiseModel class
• transfer_out function
• Example for scaleshift function
• Specify logo based on light/dark theme

Removed

• noiseamp and noisevar functions

Scientific Software - Peer-reviewed - Python
Published by jsdodge about 2 years ago

THzTools - THzTools 0.3.2 (alpha)

0.3.2 - 2023-10-11

Changed

• Point logo link to raw image file on GitHub

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 2 years ago

THzTools - THzTools 0.3.1 (alpha)

0.3.1 - 2023-10-11

Changelog introduced.

Changed

• Use internal scaling parameters to tdnoisefit (Steve)

Added

• Add changelog (Steve)
• Add frequency bounds to fit function (#27) (Alireza)
• Add Notes, References, and Examples docstring sections to noisevar, noiseamp, and thzgen (Steve)
• Add scaling parameters to tdnll (now _tdnll_scaled) (Steve)
• Add logo (Steve)

Removed

• Remove costfunlsq
• Remove costfuntls, tdnll from public functions (rename as _costfuntls and _tdnll_scaled)

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 2 years ago

THzTools - THzTools 0.3.0 (alpha)

This release is alpha software. Some of the planned functionality remains unfinished.

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 2 years ago

THzTools - THzTools 0.2.2 (alpha)

This release is alpha software, and the purpose of the release is mainly to test the continuous integration pipeline for publishing to PyPI.

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 2 years ago

THzTools - Test release

Test release workflow

Scientific Software - Peer-reviewed - Python
Published by jsdodge over 2 years ago