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Author SHA1 Message Date
Fabian Joswig
e0e2686142
 		fix: bug in _find_correlator fixed. (#193) 2023-06-02 15:46:27 +01:00
Fabian Joswig
525c61ed20
 		Fix another edge case in _compute_drho (#194) 
* 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.
 2023-06-02 15:04:15 +01:00
Fabian Joswig
bb43a8afb7
 		Fix Obs in f-strings without specifier (#190) 
* 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.
 2023-05-31 18:07:38 +01:00
Fabian Joswig
ca70c7571b
 		fix: Conversion of an array with ndim > 0 to a scalar deprecation fixed. (#186) 2023-05-31 16:59:27 +01:00
s-kuberski
34fe7f44fc
 		Bug fix for edge case in _compute_drho (#189) 2023-05-30 15:29:22 +01:00
Justus Kuhlmann
1a811b04f3
 		Feat/files idl xsf (#185) 
* added kwrg idl to ms5_xsf_read

* change output, warn user if expected idl not found
 2023-05-26 13:01:52 +01:00
Justus Kuhlmann
e97cc519a9
 		taking care of cols with only None values (#184) 2023-05-22 12:37:46 +01:00
Fabian Joswig
a443b4bb17
 		build: version bumped to 2.9.0-dev. 2023-05-21 17:10:40 +01:00
Fabian Joswig
dfe7de3a03
 		build: version bumped to 2.8.0 2023-05-21 17:06:09 +01:00
Fabian Joswig
e9e02749a0
 		fix: dobs import added to input/__init__.py (#181) 2023-05-21 16:56:56 +01:00
s-kuberski
81e4f37934
 		Restored JSON output of dicts with non-string keys (#179) 
* Restored JSON output of dicts with non-string keys

* Use numpy.integer instead of deprecated numpy.int
 2023-05-19 14:58:56 +01:00
Justus Kuhlmann
a5b6f69160
 		Slightly better Typechecking when exporting to SQL (#174) 
* 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
 2023-05-18 17:11:52 +01:00
Fabian Joswig
b75aa741a9
 		feat: color and zorder for prange indicator in Corr.show added. (#178) 2023-05-18 17:06:15 +01:00
s-kuberski
3198088f9c
 		Feat/flow (#176) 
* 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
 2023-05-16 18:29:13 +01:00
Justus Kuhlmann
5155effbbf
 		Fix/sort names (#177) 
* cosmetic fix in sort_names

* bug fix, more tests
 2023-05-16 18:28:32 +01:00
s-kuberski
15d07de87f
 		fix: String conversion of Obs can now handle a dvalue that is NaN or inf (#173) 2023-05-03 16:30:59 +02:00
Fabian Joswig
ccd911fd17
 		docs: citation info in documentation updated. 2023-04-29 11:09:05 +01:00
s-kuberski
65a9128a7d
 		Fix/merge idx (#172) 
* 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
 2023-04-28 18:14:51 +01:00
Fabian Joswig
1184a0fe76
 		t0 extractions for new Hadrons module (#171) 
* feat: first version of read flow observables for new hadrons module.

* feat: refactored t0 fit in seperate function and added extract_t0_hd5 to
hadrons submodule.
 2023-04-25 08:25:33 +01:00
Fabian Joswig
be061fdc23
 		Feat/str format (#170) 
* 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.
 2023-04-20 17:31:37 +01:00
s-kuberski
a214465413
 		Fix/gaps (#169) 
* fix: Fixed range detection in gamma_method

* Corrected test in dobsio

* Changed expansion paradigm in gamma_method

* Extended tests

* Updated docstrings

* Removed unnecessary intermediate variable

* Removed unnecessary code

* Fixed previously introduced bug in output in obs.details()

* Fixed previously introduced bug in window determination

* New criterion for matching gapped replica, fixed determination of w_max and fixed tau_exp analysis with gaps

* tests: split up consistency test for gamma method.

---------

Co-authored-by: Fabian Joswig <fabian.joswig@ed.ac.uk>
 2023-04-20 17:30:57 +01:00
Justus Kuhlmann
9d67738b32
 		extended extract_t0 by postfix argument, default stays .ms (#168) 
* extended extract_t0 by postfix argument, default stays .ms

* linting
 2023-03-24 11:10:26 +01:00
Fabian Joswig
af364cfd09
 		build: version bumped to 2.8.0-dev 2023-03-21 10:47:25 +01:00
Fabian Joswig
857540dbf8
 		build: version number bumped to 2.7.0 2023-03-21 10:29:03 +01:00
nils-ht
2363b755dd
 		NHT changes plots combined fit (#166) 
* NHT changes plots combined fit

* feat: Exception for illegal combination added and test fixed.

---------

Co-authored-by: Fabian Joswig <fabian.joswig@ed.ac.uk>
 2023-03-17 13:52:07 +00:00
Justus Kuhlmann
83204ce794
 		fixed appended mode reading (#165) 2023-03-16 13:12:03 +00:00
Justus Kuhlmann
41fec09816
 		Impr/fix refactor sfcf read (#164) 
* 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>
 2023-03-15 17:46:12 +00:00
Fabian Joswig
90c9ce9c73
 		refactor: unnecessary line in fit parameter detection removed. 
Iterator variable renamed.
 2023-03-14 09:50:35 +00:00
Fabian Joswig
5255f87d7d
 		docs: image resized. 2023-03-13 16:34:01 +00:00
Fabian Joswig
23fd00b4c2
 		docs: image resized. 2023-03-13 16:25:50 +00:00
Fabian Joswig
8530353d32
 		docs: xkcd 927 added to documentation of json.gz format. 2023-03-13 16:20:25 +00:00
Fabian Joswig
08197efe0f
 		docs: moved installation info for develop branch to documentation. 2023-03-13 13:30:43 +00:00
Fabian Joswig
a2a64146b0
 		docs: installation info also added to start page of the documentation. 2023-03-13 13:27:57 +00:00
Fabian Joswig
bafa6ce38d
 		feat: system added to print_config. 2023-03-11 21:31:21 +00:00
Fabian Joswig
0044f90315
 		feat: print_config moved to misc. 2023-03-11 21:22:03 +00:00
Fabian Joswig
8ed5ce9569
 		feat: print_config function added to help with debugging. 2023-03-11 21:17:09 +00:00
Fabian Joswig
3c942b380d
 		Serialize list of Obs in pandas.to_sql (#162) 
* 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.
 2023-03-10 14:17:20 +00:00
Fabian Joswig
a7a098b861
 		fix: chisquare, dof and p-value also calculated when dof is 0. Test for 
dof and chisquare_over_dof added.
 2023-03-09 15:32:27 +00:00
Fabian Joswig
99a1033703
 		refactor: refactored construction of prior Obs in least_squares. 2023-03-09 14:25:37 +00:00
Fabian Joswig
507fa7dbdc
 		chore: Duplicate check of y-errors removed and Exception made more 
explicit in least_squares.
 2023-03-08 16:52:21 +00:00
Fabian Joswig
80f4eef912
 		chore: Exception in least_squares specified. 2023-03-08 16:45:29 +00:00
Fabian Joswig
e6051d7ba0
 		docs: docstring of least_squares updated. 2023-03-07 16:39:37 +00:00
Fabian Joswig
839d9214ed
 		Improved prior fit (#161) 
* 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>
 2023-03-07 16:15:16 +00:00
Fabian Joswig
82cd2f11ea
 		fix: multi dim fits fixed in least squares. Test added. (#160) 
Co-authored-by: Simon Kuberski <simon.kuberski@uni-muenster.de>
 2023-03-03 16:35:26 +00:00
Fabian Joswig
cb289a55ec
 		Merge pull request #158 from fjosw/refactor/fits2 
Refactor chisquare function in least squares
 2023-03-03 16:34:28 +00:00
Fabian Joswig
9ef7e504a0
 		chore: Exceptions in Obs.__init__ made more explicit. 2023-03-02 18:54:08 +00:00
Fabian Joswig
2ac38515b6
 		refactor: logic in least square fits simplified. 
Co-authored-by: Simon Kuberski <simon.kuberski@uni-muenster.de>
 2023-03-02 18:42:55 +00:00
Fabian Joswig
a140b2ab39
 		refactor: removed redundant formulations of the chisquare function in 
least_squares.
 2023-03-01 16:29:59 +00:00
Fabian Joswig
ee2944d5b0
 		refactor: chisqfunc rewritten as sum over residuals. 2023-03-01 16:12:31 +00:00
Fabian Joswig
dc7033e51f
 		refactor: _standard_fit method made redundant. (#154) 
* 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.
 2023-03-01 10:00:35 +00:00