Commit graph

963 commits

Author SHA1 Message Date
Fabian Joswig
1fce785597 [Build] Version bumped to 2.11, CHANGELOG updated, numpy<2 requirement
added.
2024-04-01 16:13:48 +02:00
Justus Kuhlmann
254a19f321
Catch error if no replica are found in the geiven directory (#230) 2024-03-25 15:50:19 +01:00
Justus Kuhlmann
b930fab9c2
Fix keyword files with list of lists (#226)
* first impl. handle reps with list of lists

* implement explicit type checks
2024-02-18 13:39:35 +01:00
Justus Kuhlmann
df1873b5ac
Throw error when trying to only find idls that are not present (#224) 2024-01-11 17:48:51 +01:00
Fabian Joswig
5122e260ea
Special function module (#221)
* [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.
2024-01-07 17:22:05 +01:00
Fabian Joswig
1360942a7b [build] version bumped to 2.11.0-dev 2023-11-24 17:15:12 +01:00
Fabian Joswig
d0cfc67a43 [release] Version bumped to 2.10.0, CHANGELOG updated. 2023-11-24 17:05:11 +01:00
Fabian Joswig
728c2e55ee
[fix] fixed how the filestem is extracted in hadrons/read_hdf5. (#218) 2023-11-23 13:34:07 +01:00
JanNeuendorf
e1a4d0c218
Additional GEVP method with errors (#195)
* 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>
2023-11-17 18:57:18 +01:00
s-kuberski
d689959b1f
fix: Check if configs appears multiple times when creating an obs (#216) 2023-11-10 19:13:11 +01:00
s-kuberski
dc63142f8e
Fixed bugs for combined fits with multiple independent variables (#211) 2023-10-24 19:30:52 +02:00
Justus Kuhlmann
0ef8649031
Feat/read sfcf multi (#210)
* 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>
2023-10-20 19:22:55 +02:00
Fabian Joswig
957030cba0 fix: explicit type check replaced by isinstance in fits.least_squares. 2023-09-17 18:11:26 +02:00
Fabian Joswig
7f8c2ce33b
feat: added support for addition and multiplication of complex numbers (#209)
to Corr objects.
2023-07-21 14:15:41 +01:00
Fabian Joswig
7f5373d5e4
build: version bumped to 2.10.0-dev 2023-07-20 11:54:43 +01:00
Fabian Joswig
d768d355ac
build: version bumped to 2.9.0 2023-07-20 11:41:50 +01:00
Fabian Joswig
087a3f92eb
feat: short version of vectorized gamma_method simplified. 2023-07-20 11:31:20 +01:00
Fabian Joswig
af28f77ec5
__eq__ method for Corr class (#206)
* 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.
2023-07-19 15:06:19 +01:00
Fabian Joswig
1e438356fd
Vectorized gamma_method (#207)
* 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.
2023-07-19 12:13:20 +01:00
Fabian Joswig
6b7846486d
General hadrons hdf5 reader added (#205)
* feat: new general read_hd5 function added.

* feat: real or imaginary part can be specified in read_hd5.

* fix: spacing fixed.

* feat: Added the option to extract complex correlators in read_hd5.
2023-07-18 16:04:59 +01:00
Fabian Joswig
66d5f8be24
Corr array initialization generalized (#203)
* feat: corr array initialization generalized.

* feat: additional checks for three-dimensional arrays added.

* docs: Corr docstring improved.

* docs: typos corrected.

* docs: details about None padding added to Corr docstring.
2023-07-18 12:07:46 +01:00
Fabian Joswig
491c7bcb04
fix: split meson on last underscore in read_meson_hdf5. (#204) 2023-07-18 10:36:19 +01:00
Fabian Joswig
ad188acec4
docs: instruction for installing develop branch updated. 2023-07-17 15:34:25 +01:00
Fabian Joswig
bf1c762148
docs: read_meson docstring improved. 2023-07-17 13:34:39 +01:00
Fabian Joswig
f1150f09c8
Matmul overloaded for correlator class. (#199)
* 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>
2023-07-17 11:48:57 +01:00
Fabian Joswig
5c2a6de56f
fix: explicit Exception for combined fit constant edge case. (#202) 2023-07-14 14:26:54 +01:00
s-kuberski
6dcd0c3518
feat: Added numerical integration of generic functions (#201)
* feat: Added numerical integration of generic functions

* refactored integration routines

* tests: two trivial tests for integration added.

* docs: quad docstring corrected.

* Small bugfix for integration without obs

---------

Co-authored-by: Fabian Joswig <fabian.joswig@ed.ac.uk>
2023-07-14 14:21:59 +01:00
Fabian Joswig
8736d1cd3c
feat: CObs format added and complex Corr print improved. (#200) 2023-07-14 13:38:21 +01:00
Fabian Joswig
b62a18643e
Bootstrap export/import (#198)
* feat: export_bootstrap method added.

* feat: import_bootstrap function added.

* tests: first test for import/export bootstrap added.

* feat: bootstrap feature cleaned up.

* docs: boostrap docstrings improved.
2023-07-14 13:12:11 +01:00
Fabian Joswig
2cd076dbd7
docs: details in documentation clarified. 2023-07-10 16:33:09 +01:00
Justus Kuhlmann
94b0322f0b
new variant of second derivative, bigger stencil (#197)
* new variant of second derivative, bigger stencil

* better docstring dor second_deriv

* forgot to "r" in front of docstring

* flake8 compliance
2023-07-10 15:32:27 +01:00
Fabian Joswig
8381189708
refactor: plot_piechart slightly simplified. 2023-06-23 13:24:35 +01:00
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