CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

[2.13.0] - 2024-11-03

Added

• Allow providing lower triangular matrix constructed from a Cholesky decomposition in least squares function for correlated fits.

Fixed

• Corrected bug that prevented combined fits with multiple x-obs in some cases.

[2.12.0] - 2024-08-22

Changed

• Support for numpy 2 was added via a new autograd release
• Support for python<3.9 was dropped and dependencies were updated.

Fixed

• Minor bug fixes in input.sfcf

[2.11.1] - 2024-04-25

Fixed

• Fixed a bug in error computation when combining two Obs from the same ensemble and fluctuations on one replicum are not part of one of the Obs.

[2.11.0] - 2024-04-01

Added

• New special function module.

Fixed

• Various bug fixes in input module.

[2.10.0] - 2023-11-24

Added

• More efficient implementation of read_sfcf
• added support for addition and multiplication of complex numbers to Corr objects
• the Corr.GEVP method can now also propagate the errors for the eigenvectors

Fixed

• Fixed bug in combined fit with multiple independent variables
• Check for invalid set of configuration numbers added when initializing an Obs object.
• Fixed a bug in hadrons.read_hdf5

[2.9.0] - 2023-07-20

Added

• Vectorized gamma_method added which can be applied to lists or arrays of pyerrors objects.
• Wrapper for numerical integration of Obs valued functions with Obs valued intervals.
• Bootstrap import and export added.
• matmul overloaded for Corr class.
• More options for initializing Corr objects added.
• General Hadrons hdf5 reader added.
• New variant of second_derivative.
• CObs formatting added.
• Comparisons for Corr class added.

Changed

• support for python<3.8 was dropped and dependencies were updated.

[2.8.2] - 2023-06-02

Fixed

• Another bug appearing in an edge case of _compute_drho fixed.

[2.8.1] - 2023-06-01

Fixed

• input.pandas can now deal with columns that only have None entries.
• Bug in f-string conversion of Obs fixed.
• Bug in edge case of _compute_drho fixed.
• Several numpy 1.25 deprecations fixed.

[2.8.0] - 2023-05-21

Added

• pyerrors can now deal with replica with different gapsizes.
• String formatting method for Obs added.
• t0 can now be extracted from hadrons files.
• w0 can now be extracted from openQCD files.
• pandas SQL export can now deal with None entries in columns with pyerrors datatypes.

Fixed

• dobs submodule is now correctly imported.
• Bug in merging of Obs fixed.
• Bug in rapidjson dict output fixed.
• String conversion of Obs can now handle special dvalues
• Bug in sfcf name sorting fixed.

[2.7.0] - 2023-03-21

Added

• Alternative way of specifying priors in least_squares added.
• Correlated fits now also work with priors.
• Lists of Obs can now be serialized and deserialized in pandas.to_sql
• print_config function for debugging purposes added.
• Corr.show can now visualize results of combined fits.

Changed

• Fit routines refactored and simplified.
• sfcf input routines refactored.
• drho is not automatically computed for all windows in the automatic windowing procedure. This change speeds up the gamma_method for very long Monte Carlo histories.
• __slots__ added to Corr class.

[2.6.0] - 2023-02-07

Added

• The fit module now has a new interface to deal with combined fits.
• pyerrors wrapper for matplotlib errorbar method added for Obs valued lists/arrays.
• roots module can now determine roots of multi parameter Obs valued functions.

Fixed

• Bug in treatment of error propagation of non-overlapping configurations fixed.
• Corr.symmetric can now deal with None entries.
• Fix in ms5_xsf input routines.
• Bug in dobs output format fixed.

[2.5.0] - 2023-01-07

Added

• Alias gm for Obs.gamma_method added.
• Hotelling t-squared p-value added for correlated fits.
• String conversion of numpy arrays containing Obs improved.
• Input routine for xSF measurement program added.

Fixed

• Complex valued Corr objects fixed.
• Small bug in qtop_projection fixed.
• Bug in Corr.spaghetti_plot fixed which appeared in connection with replica separators.

Changed

• Merged Obs are no longer filtered as this lead to inconsistent idls in some edge cases. Error estimates are unaffected up to filter precision.

Removed

• Removed the Obs attribute is_merged as this information was only needed for the filtering. The change results in a ~1.15x speed up in the multiplication of two Obs.

[2.4.0] - 2022-12-01

Added

• Log-derivatives and symmetric log-effective mass added.
• Covariance for irregular Monte Carlo chains sped up.
• Additional checks in Corr.GEVP added.

Fixed

• Bug in Obs.details fixed which appeared when tau had zero error.
• Bug in input.json export in connection with numpy.int64 fixed.
• Small bug fixes in input.openQCD.

[2.3.1] - 2022-10-19

Fixed

• Integrated autocorrelation times are now correctly estimated for gapped irregular Monte Carlo chains.
• The output of Obs.details was improved and now contains information about the stepsize in configurations for which the integrated autocorrelation time was estimated.

[2.3.0] - 2022-10-13

Added

• least_squares and total_least_squares fits now have an optional keyword argument num_grad. If this argument is set to True the error propagation of the fit is performed via numerical instead of automatic differentiation. This options allows for fits functions which contain special functions or which are not analytically known.

Fixed

• Bug in Corr.show comp option fixed.

[2.2.0] - 2022-08-01

Added

• New submodule input.pandas added which adds the possibility to read and write pandas DataFrames containing Obs or Corr objects to csv files or SQLite databases.
• hash method for Obs objects added.
• Obs.reweight method added in analogy to Corr.reweight which allows for a more convenient reweighting of individual observables.
• Corr.show now has the additional argument title which allows to add a title to the figure. Figures are now saved with bbox_inches='tight'.
• Function for the extraction of the gradient flow coupling added (see 1607.06423 for details).
• Corr.is_matrix_symmetric added which efficiently checks whether a correlator matrix is symmetric. This is used to speed up the GEVP method.

Fixed

• Corr.m_eff can now deal with correlator entries which are exactly zero.
• Minor bugs in input.dobs fixed.

[2.1.3] - 2022-06-13

Fixed

• Further bugs in connection with correlator objects which have arrays with None entries as content fixed.

[2.1.2] - 2022-06-10

Fixed

• Bug in Corr.matrix_symmetric fixed which appeared when a time slice contained an array with None entries.

[2.1.1] - 2022-06-06

Fixed

• Bug in error propagation of correlated least square fits fixed.
• Fit_result.gamma_method can now be called with kwargs.

[2.1.0] - 2022-05-31

Added

• obs.covariance now has the option to smooth small eigenvalues of the matrix with the method described in hep-lat/9412087.
• Corr.prune was added which can reduce the size of a correlator matrix before solving the GEVP.
• Corr.show has two additional optional arguments. hide_sigma to hide data points with large errors and references to display reference values as horizontal lines.
• I/O routines for ALPHA dobs format added.
• input.hadrons functionality extended.

Changed

• The standard behavior of the Corr.GEVP method has changed. It now returns all eigenvectors of the system instead of only the specified ones as default. The standard way of sorting the eigenvectors was changed to Eigenvalue. The argument sorted_list was deprecated in favor of sort.
• Before performing a correlated fit the routine first runs an uncorrelated one to obtain a better guess for the initial parameters.

Fixed

• obs.covariance now also gives correct estimators if data defined on non-identical configurations is passed to the function.
• Rounding errors in estimating derivatives of fit parameters with respect to input data from the inverse hessian reduced. This should only make a difference when the magnitude of the errors of different fit parameters vary vastly.
• Bug in json.gz format fixed which did not properly store the replica mean values. Format version bumped to 1.1.
• The GEVP matrix is now symmetrized before solving the system for all sorting options not only the one with fixed ts.
• Automatic range estimation improved in fits.residual_plot.
• Bugs in input.bdio fixed.

[2.0.0] - 2022-03-31

Added

• The possibility to work with Monte Carlo histories which are evenly or unevenly spaced was added.
• cov_Obs added as a possibility to propagate the error of non Monte Carlo data together with Monte Carlo data.
• CObs class added which can handle complex valued Markov chain Monte Carlo data and the corresponding error propagation.
• Matrix to matrix operations like the matrix inverse now also work for complex matrices and matrices containing entries that are not Obs but float or int.
• Support for a new json.gz file format was added.
• The Corr class now has additional methods like reverse, T_symmetry, correlate and reweight.
• Corr.m_eff can now cope with periodic and anti-periodic correlation functions.
• Forward, backward and improved variants of the first and second derivative were added to the Corr class.
• GEVP functionality of the Corr class was reworked and improved.
• The linalg module now has explicit functions inv, cholesky and det.
• Obs objects now have methods is_zero and is_zero_within_error as well as overloaded comparison operations.
• Functions to convert Obs data to or from jackknife was added.
• Alternative matrix multiplication routines einsum and jack_matmul were added to linalg module which make use of the jackknife approximation and are much faster for large matrices.
• Additional input routines for npr data added to input.hadrons.
• The sfcf and openQCD input modules can now handle all recent file type versions.
• extract_t0 can now visualize the extraction on the fly.
• Module added which provides the Dirac gamma matrices in the Grid convention.
• Version number added.

Changed

• The internal bookkeeping system for ensembles/replica was changed. The separator for replica is now |.
• The fit functions were renamed to least_squares and total_least_squares.
• The output of the fit functions is now a dedicated results class which keeps track of all relevant information.
• The fit functions can now deal with provided covariance matrices.
• covariance can now operate on a list or array of Obs and returns a matrix. The covariance estimate by pyerrors is now always positive semi-definite (within machine precision. Various warnings and exceptions were added for cases in which estimated covariances are close to singular.
• The convention for the fit range in the Corr class has been changed.
• Various method of the Corr class were renamed.
• Obs.print was renamed to Obs.details and the output was improved.
• The default value for Corr.prange is now None.
• The input module was restructured to contain one submodule per data source.
• Performance of Obs.init improved.

Removed

• The function plot_corrs was deprecated as all its functionality is now contained within Corr.show.
• fits.covariance_matrix was removed as it is now redundant with the functionality of covariance.
• The kwarg bias_correction in derived_observable was removed.
• Obs no longer have an attribute e_Q.
• Removed fits.fit_exp.
• Removed jackknife module.

[1.1.0] - 2021-10-11

Added

• Corr class added
• roots module added which can find the roots of a function that depends on Monte Carlo data via pyerrors Obs
• input/hadrons module added which can read hdf5 files written by Hadrons
• read_rwms can now read reweighting factors in the format used by openQCD-2.0.

[1.0.1] - 2020-11-03

Fixed

• Bug in pyerrors.covariance fixed that appeared when working with several replica of different length.

[1.0.0] - 2020-10-13

Added

• Compatibility with the BDIO Native format outlined here. Read and write function added to input.bdio
• new function input.bdio.read_dSdm which can read the bdio output of the program dSdm by Tomasz Korzec
• Expected chisquare implemented for fits with xerrors
• New implementation of the covariance of two observables which employs the arithmetic mean of the integrated autocorrelation times of the two observables. This new procedure has proven to be less biased in simulated data and is also much faster to compute as the computation time is of O(N) whereas the evaluation of the full correlation function is of O(Nlog(N)).
• Added function gen_correlated_data to misc which generates a set of observables with given covariance and autocorrelation.

Fixed

• Bias correction hep-lat/0306017 eq. (49) is no longer applied to the exponential tail in the critical slowing down analysis, but only to the part which is directly estimated from rho. This can lead to slightly smaller errors when using the critical slowing down analysis. The values for the integrated autocorrelation time tauint now include this bias correction (up to now the bias correction was applied after estimating tauint). The errors resulting from the automatic windowing procedure are unchanged.

[0.8.1] - 2020-06-09

Fixed

• Bug in fits.standard_fit fixed which occurred when attempting a fit with zero degrees of freedom.

[0.8.0] - 2020-06-05

Added

• merge_obs function added which allows to merge Obs which describe different replica of the same observable and have been read in separately. Use with care as there is no safeguard implemented which prevent you from merging unrelated Obs.
• standard fit and odr_fit can now treat fits with several x-values via tuples.
• Fit functions have a new kwarg dict_output which allows to change the output to a dictionary containing additional information.
• S_dict and tau_exp_dict added to Obs in which global values for individual ensembles can be stored.
• new function read_pbp added which reads dS/dm_q from pbp.dat files.
• new function extract_t0 added which can extract the value of t0 from .ms.dat files of openQCD v 1.2

Changed

• When creating an Obs object defined for multiple replica/ensembles, the given names are now sorted alphabetically before assigning the internal dictionaries. This makes sure that my_Obs has the same dictionaries as my_Obs * 1 (derived_observable always sorted the names). WARNING: Obs created with previous versions of pyerrors may not be completely identical to new ones (The internal dictionaries may have different ordering). However, this should not affect the inner workings of the error analysis.

Fixed

• Bug in covariance fixed which appeared when different ensemble contents were used.

[0.7.0] - 2020-03-10

Added

• New fit functions for fitting with and without x-errors added which use automatic differentiation and should be more reliable than the old ones.
• Fitting with Bayesian priors added.
• New functions for visualization of fits which can be activated via the kwargs resplot and qqplot.
• chisquare/expected_chisquared which takes into account correlations in the data and non-linearities in the fit function can now be activated with the kwarg expected_chisquare.
• Silent mode added to fit functions.
• Examples reworked.
• Changed default function to compute covariances.
• output of input.bdio.read_mesons is now a dictionary instead of a list.

Deprecated

• The function fit_general which is based on numerical differentiation will be removed in future versions as new fit functions based on automatic differentiation are now available.

[0.6.1] - 2020-01-14

Added

• mesons bdio functionality improved and accelerated, progress report added.
• added the possibility to manually supply a jacobian to derived_observable via the kwarg man_grad. This feature was not implemented for the user, but for internal optimization of most basic arithmetic operations which now do not require a call to the autograd package anymore. This results in a speed up of 2 to 3, especially relevant for the multiplication of large matrices.

Changed

• input.py and bdio.py moved into submodule input. This should not affect the user API.
• autograd.numpy was replaced by pure numpy wherever it was possible. This should result in a slight speed up.

Fixed

• fixed bias_correction which broke as a result of the vectorized derived_observable.
• linalg.eig does not give an error anymore if the eigenvalues are complex by just truncating the imaginary part.

[0.6.0] - 2020-01-06

Added

• Matrix pencil method for algebraic extraction of energy levels implemented according to Y. Hua, T. K. Sarkar, IEEE Trans. Acoust. 38, 814-824 (1990) in module mpm.py.
• Import API simplified. After import pyerrors as pe, some submodules can be accessed via pe.fits etc.
• derived_observable now supports functions which have single- or multi-dimensional numpy arrays as input and/or output (Works only with automatic differentiation).
• Matrix functions accelerated by using the new version of derived_observable.
• New matrix functions: Moore-Penrose Pseudoinverse, Singular Value Decomposition, eigenvalue determination of a general matrix (automatic differentiation included from autograd master).
• Obs can now be compared with < or >, a list of Obs can now be sorted.
• Numerical differentiation can now be controlled via the kwargs of numdifftools.step_generators.MaxStepGenerator.
• Tuned standard parameters for numerical derivative to base_step=0.1 and step_ratio=2.5.

Changed

• Matrix functions moved to new module linalg.py.
• Kolmogorov-Smirnov test moved to new module misc.py.

[0.5.0] - 2019-12-19

Added

• Numerical differentiation is now based on the package numdifftools which should be more reliable.

Changed

• kwarg h_num_grad changed to num_grad which takes boolean values (default False).
• Speed up of rfft calculation of the autocorrelation by reducing the zero padding.