* feat: corr_matrix kwargs as input for least squares fit
* feat/tests: inverse covariance matrix and correlation matrix kwargs as input for least squares function
* feat/tests/example: reduced new kwargs to 'inv_chol_cov_matrix' and outsourced the inversion & cholesky decomposition of the covariance matrix (function 'invert_corr_cov_cholesky(corr, covdiag)')
* tests: added tests for inv_chol_cov_matrix kwarg for the case of combined fits
* fix: renamed covdiag to inverrdiag needed for the cholesky decomposition and corrected its documentation
* examples: added an example of a correlated combined fit to the least_squares documentation
* feat/tests/fix(of typos): added function 'sort_corr()' (and a test of it) to sort correlation matrix according to a list of alphabetically sorted keys
* docs: added more elaborate documentation/example of sort_corr(), fixed typos in documentation of invert_corr_cov_cholesky()
* [fix] First version of a fix to cope with missing replica.
* [fix] added test for missing replica
* [fix] refactored fix for missing replica, modified tests
* [fix] refinement of tests
* [fix] Fixed intendation for flake8
* [feat] special module with Bessel functions added.
* [feat] init adapted.
* [tests] First test for special module added.
* [tests] Check kn special function derivative explicitly vs numerical
derivative of scipy function.
* [feat] Added remaining autograd scipy special functions to the special
module.
* [feat] Imports corrected, docstring added.
* Added the function error_gevp() to compute the gevp with statistical errors.
* Changed method name from error_gevp to error_GEVP and removed automatic gamma method
* added auto_gamma to error_GEVP
* Specified exceptions in Corr.error_GEVP
* Fixed a wrong path. It should be np.linalg.LinAlgError
* Added a test for error_GEVP
* The tests of error_gevp loads a test matrix
* Incorporated eigenvectors with uncertainties in GEVP routine
* Cleaned up GEVP routines
* Cleaned up breaking change from merge
* Released tolerance in test of GEVP
* Repaired broken GEVP test
---------
Co-authored-by: Simon Kuberski <simon.kuberski@uni-muenster.de>
* make template
* read_sfcf_multi running with compact format
* fix append mode, norrmal tests work
* improve readability
* add simple test for multi_read
* simple multi_test works
* add first method to check sfcf param hashes
* add docstring
* simple test for o format working
* use benedict to make loops easier
* introduce python-benedict as dep
* no nice_out, less error prone, found bug in tests
* Revert "introduce python-benedict as dep"
This reverts commit 9696d68b7a.
* Revert "use benedict to make loops easier"
This reverts commit fa3987479b.
* no nice output after reverts
* [build] Added jkuhl-uni as CODEOWNER for sfcf.
* refactor: flatten internal dicts
* very small test extension
* ...flake8
* docu
* Delete second sep init
---------
Co-authored-by: Fabian Joswig <fabian.joswig@uni-muenster.de>
* feat: implemented __eq__ method for Corr class.
* feat: __eq__ method now respects None entries in correlators.
* feat: Obs can now be compared to None, __ne__ method removed as it is
not required.
* feat: Corr.__eq__ rewritten to give a per element comparison.
* tests: additional test case for correlator comparison added.
* feat: comparison now also works for padding.
* feat: vectorized gamma_method function added.
* feat: vectorized gamma method generalized to also work on other objects
like Corr or Fit_result.
* feat: alias gamma_method for vectorized gamma_method added.
* docs: example 5 updated to include vectorized gamma_method.
* docs: output of example 5 updated.
* feat: matmul method added to correlator class.
* feat: corr, corr matmul and correlator matrix trace added.
* tests: tests for matmul and trace added.
* tests: slightly reduced tolerance and good guess bad guess test.
* feat: rmatmul added and __array_priority__ set.
* tests: additional tests for rmatmul added.
* tests: one more tests for rmatmul added.
* docs: docstring added to Corr.trace.
* tests: associative property test added for complex Corr matmul.
* fix: Corr.roll method now also works for correlator matrices by
explicitly specifying the axis.
Co-authored-by: Matteo Di Carlo <matteo.dicarlo93@gmail.com>
* feat: exception type for correlator trace of 1dim correlator changed.
* tests: trace N=1 exception tested.
---------
Co-authored-by: Matteo Di Carlo <matteo.dicarlo93@gmail.com>
* tests: failing test for compute_drho edge case added.
* tests: example file for failing compute_drho added.
* tests: assertion that dvalue stays the same added to compute drho test.
* fix: another edge case in computation of drho fixed.
* fix: Conversion of an array with ndim > 0 to a scalar deprecation fixed.
* fix: adjusted maximal value for rho in test_gamma_method_irregular.
* fix: obs in f-strings now work again when no specifier is provided.
* corret type clause
* add tests, changes in create_json_string
* create json-string now gives back None
* revert changes
* fix panda sql export
* add SQL test
* fixed None type export for csv and sql.gz
* move None parsing to json io
* alter regex
* revert changes
* only replace None with empty str when necessary
* fixed deserialze_df for python 3.7
* add more tesets
* fix case where gz was ignored
* hand voer gz explicitly
* replace nan by None in non-Obs columns
* moved warning to csv export, mroe tests
* only values able to be nan are put in np.isnan()
* added python float for warning
* fix: String conversion of Obs can now handle a dvalue that is NaN or inf
* Feat: Added extraction of w0/a from openQCD files
* Removed unnecessary round in w0 routine
* Improved error handling in fit_t0
* Allowed to change the reference flow time in t0 and w0 determinations.
* Added doc string to fit_t0
* Fix: Corrected merging of idls
* Fix: Computation of drho in cases where tau_int is large compared to the chain length
* Removed unnecessary imports
* Refactor list comparisons in obs.py
* feat: _format_uncertainty now accepts a significance.
* feat: __format__ now accepts significance.
* feat: explicit + sign added to format.
* fix: - option removed from format specifier.
* feat: space format added.
* refactor read_sfcf
* adding tests for find_corr and read_compact_file
* add necessary broken data for tests
* fixed appended mode reading
* factored out sort_names and find_files
* now also using sort_files in sfcf.py
* edited tests to fit with new structure
* added find_files function
* shifted helpfunctions to bottom of file
* removed some debug lines
* linting
* Fixed requested changes, added silent mode
* added Exception if correlator is not found by read_append_rep
* use tmp_path fixture
* linting silent keyword
* try to fix testing for a_bb
* tests: Exception testing in test_find_corr made more explicit.
---------
Co-authored-by: Fabian Joswig <fabian.joswig@ed.ac.uk>
* feat: Added serialization of list of Obs in pandas.to_sql.
* tests: test for list of Obs to sql added.
* feat: auto_gamma functionality added for deserialization of lists of
Obs.
* refactor: merged combined fit and prior fit without breaking the
routine. Fitting with priors does not work yet.
* refactor: correlated fits without priors work now.
* refactor: prior error propagation and dof fixed.
* refactor: old prior fit implementation moved to tests.
* refactor: moved _extract_val_and_dval out of least_squares.
* refactor: comment removed.
* tests: additional tests and exceptions added.
* tests: test for constrained prior fit added.
* docs: least_squares docstring extended.
* fix: linting errors fixed.
* feat: additional if cause for fits without priors added to achieve
original speed.
* tests: test_constrained_and_prior_fit fixed.
* fix: fix array cast of least_squares dict mode.
* tests: test for lists in dict fit added.
* fix: additional asarray added in resplot.
Co-authored-by: Simon Kuberski <simon.kuberski@uni-muenster.de>
* refactor: _standard_fit method made redundant.
* fix: xs and yz in Corr.fit promoted to arrays.
* fix: x promoted to array in _combined_fit if input is just a list.
* feat: residual_plot and qqplot now work with combined fits with
dictionary inputs.
* tests: test for combined fit resplot and qqplot added.
* docs: docstring of fits.residual_plot extended.
* wrote small test for ms5_xsf read method
* small bug in ms5_xsf found
* first version of refactoring with test
* built _find_files into openQCD module
* postfix can now be used as before
* altered test data to be smaller
* read_rwms throws better Exception now
* typo corrected
* better tests for postfixes, also added similar solution for ext variable
* added method to sort names of files and replica better
