Commit graph

1301 commits

Author SHA1 Message Date
Fabian Joswig
9bc9910f27
docs: citation file updated. 2023-04-29 10:56:23 +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
Fabian Joswig
edcb4de8aa
docs: DOI badge corrected. 2023-04-14 15:41:29 +01:00
Fabian Joswig
05d47a2540
docs: DOI badge added. 2023-04-14 15:40:00 +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
Fabian Joswig
64e8e4975e
docs: CHANGELOG updated. 2023-03-21 10:28:15 +01:00
Fabian Joswig
500690b266
build: .hypothesis added to gitignore. 2023-03-17 17:56:40 +00:00
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
991199a680
docs: README updated. 2023-03-14 14:27:51 +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
34981b6102
docs: conda-forge installation added to README. 2023-03-13 13:25:24 +00:00
Fabian Joswig
a1d6b95e9a
build: bug report default title changed again. 2023-03-11 21:38:29 +00:00
Fabian Joswig
031b048fa3
build: bug report default title changed. 2023-03-11 21:35:34 +00:00
Fabian Joswig
bafa6ce38d
feat: system added to print_config. 2023-03-11 21:31:21 +00:00
Fabian Joswig
caef8af988
build: bug report issue template added. 2023-03-11 21:30:14 +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
d8fb683262
docs: CONTRIBUTING.md extended. 2023-03-10 14:37:50 +00:00
Fabian Joswig
fe0f80b8c3
docs: README and CONTRIBUTING updated. 2023-03-10 14:25:17 +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
06ba2015be
tests: test for different methods in prior fit added. 2023-03-09 15:00:52 +00:00
Fabian Joswig
99a1033703
refactor: refactored construction of prior Obs in least_squares. 2023-03-09 14:25:37 +00:00
Fabian Joswig
e41f869d18
docs: version guard added to combined fit example. 2023-03-09 13:38:51 +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
Fabian Joswig
de35332a80
Merge pull request #157 from fjosw/fix/calc_rho_large_t
_calculate_drho for large time separations
2023-02-28 15:46:54 +00:00
Fabian Joswig
d81d6ea0b8
fix: loop range in standard windowing procedure adjusted by gapsize
- Test added

Co-authored-by: Simon Kuberski <simon.kuberski@uni-muenster.de>
2023-02-27 21:43:29 +00:00
Fabian Joswig
a33c0a205a
feat: added __slots__ to Corr class. (#155) 2023-02-27 10:23:02 +00:00