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08 August 2024, 09:19:58 UTC
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1268177 Matt Newville 29 November 2018, 01:40:50 UTC Merge pull request #520 from reneeotten/pytest test-suite: use pytest features, improve coverage, fix mistakes 29 November 2018, 01:40:50 UTC
852685a reneeotten 26 November 2018, 20:42:18 UTC TST: update dependencies in .travis.yml - install pytest using pip - install emcee/numdifftools using pip and only when version == latest - use pip because conda does not have the latest versions for all Python releases 27 November 2018, 02:38:43 UTC
f243c9a reneeotten 26 November 2018, 16:55:14 UTC FIX: do not try to calculate cov_x after AbortFitException 27 November 2018, 02:31:41 UTC
404670f reneeotten 23 November 2018, 18:08:03 UTC TST: use pytest features and increase coverage in test_itercb.py 27 November 2018, 02:31:41 UTC
0a6e3ae reneeotten 22 November 2018, 02:12:39 UTC FIX: make logic explicit in show_candidates 27 November 2018, 02:31:41 UTC
d417d59 reneeotten 18 November 2018, 22:58:55 UTC TST: use pytest features and increase coverage in test_brute.py 27 November 2018, 02:31:41 UTC
fee80f3 reneeotten 18 November 2018, 19:04:06 UTC TST: use pytest features and increase coverage in test_basinhopping.py 27 November 2018, 02:31:41 UTC
4cdef62 reneeotten 13 November 2018, 15:16:27 UTC TST: use pytest features and increase coverage in test_ampgo.py 27 November 2018, 02:31:41 UTC
7fec373 Matt Newville 26 November 2018, 15:25:27 UTC Merge pull request #519 from reneeotten/PR512 updates to complement PR512 26 November 2018, 15:25:27 UTC
deff523 reneeotten 22 November 2018, 04:06:14 UTC MAINT: small fixes after merge of PR #512 22 November 2018, 15:48:35 UTC
f9e92d5 reneeotten 21 November 2018, 15:54:41 UTC TST: add simple test for using method='emcee' 22 November 2018, 15:48:35 UTC
92fa6d7 reneeotten 21 November 2018, 02:25:45 UTC DOC: update release notes 22 November 2018, 15:48:35 UTC
0a3396f reneeotten 21 November 2018, 02:18:45 UTC DOC: update text and output of emcee example - keep colors in the documents consistent 22 November 2018, 15:48:35 UTC
69dfd02 Matt Newville 21 November 2018, 21:22:18 UTC Merge pull request #512 from FaustinCarter/add_emcee Add emcee 21 November 2018, 21:22:18 UTC
33f6c13 Faustin Carter 19 November 2018, 00:00:46 UTC Add newline at end of file for PEP8 19 November 2018, 00:00:46 UTC
2debc53 Faustin Carter 18 November 2018, 23:50:09 UTC Remove orphan comment that was missed a few commits back. 18 November 2018, 23:58:40 UTC
a344d12 Faustin Carter 18 November 2018, 23:49:38 UTC Add emcee method to table in docs 18 November 2018, 23:58:00 UTC
9a5734e Faustin Carter 16 November 2018, 01:25:26 UTC Small color changes to make figures easier to parse. This will be followed with appropriate updates to the actual images that go in the docs 18 November 2018, 23:58:00 UTC
66d1b88 Faustin Carter 16 November 2018, 01:21:25 UTC Remove orphan comment left over from create-by-copy 18 November 2018, 23:57:36 UTC
2e1e9e2 Faustin Carter 16 November 2018, 01:17:57 UTC Rework emcee statistics calculation to use the standard method for the known cases and only explicitly calculate the special case. 16 November 2018, 01:17:57 UTC
a8d29f3 Matt Newville 12 November 2018, 03:30:00 UTC Merge pull request #515 from reneeotten/minor-code-maintenance Minor code maintenance 12 November 2018, 03:30:00 UTC
ef1bbfa reneeotten 11 November 2018, 16:37:31 UTC DOC: doc/docstring updates 12 November 2018, 03:02:28 UTC
34ea61f Faustin Carter 12 November 2018, 02:01:37 UTC fix spacing for PEP8 12 November 2018, 02:01:37 UTC
f43cb1f Faustin Carter 11 November 2018, 21:57:57 UTC add vscode prefs to gitignore 11 November 2018, 21:57:57 UTC
4864268 Faustin Carter 11 November 2018, 21:56:38 UTC remove duplicate assign statement 11 November 2018, 21:56:38 UTC
12e87da Faustin Carter 11 November 2018, 21:23:36 UTC Properly reassign likelihood 11 November 2018, 21:23:36 UTC
d81ab26 Faustin Carter 10 November 2018, 22:48:45 UTC move custom emcee statstics handling back to emcee from calc stats. Also deal with some whitespace isses. 10 November 2018, 22:48:45 UTC
e334bfa reneeotten 10 November 2018, 22:46:23 UTC MAINT: remove Python shebang line 10 November 2018, 22:48:14 UTC
60cdcde reneeotten 10 November 2018, 22:24:19 UTC STY: unused variable 'info' (unused-variable) 10 November 2018, 22:48:14 UTC
f243681 reneeotten 10 November 2018, 22:19:40 UTC STY: reimport 'warnings' (reimported) 10 November 2018, 22:48:14 UTC
d08268e reneeotten 10 November 2018, 22:17:03 UTC STY: import alias does not rename original package (useless-import-alias) 10 November 2018, 22:48:14 UTC
3c30dd7 reneeotten 10 November 2018, 22:09:05 UTC MAINT: propagate kws to json.dumps 10 November 2018, 22:48:14 UTC
49f4d81 reneeotten 10 November 2018, 17:28:45 UTC MAINT: remove uncertainties import from __init__.py - reorder some imports as suggested by isort (cannot sort them alphabetically as they are not independent) 10 November 2018, 22:48:14 UTC
54bb538 reneeotten 10 November 2018, 17:10:23 UTC STY: wrong continued indentation 10 November 2018, 22:48:14 UTC
d7671be reneeotten 10 November 2018, 17:05:50 UTC STY: missing whitespace around modulo operator 10 November 2018, 22:48:14 UTC
b7c3418 reneeotten 10 November 2018, 17:01:53 UTC STY: too many blank lines 10 November 2018, 22:48:14 UTC
71232cd reneeotten 10 November 2018, 13:21:50 UTC MAINT: remove import of __future__.print_function - this is present in Python >= 2.7 10 November 2018, 22:48:11 UTC
a4da432 reneeotten 10 November 2018, 02:47:01 UTC DOC: update docstring of __init__.py 10 November 2018, 22:36:53 UTC
4b57b82 reneeotten 09 November 2018, 22:30:37 UTC MAINT: make use of numpy.isclose function - identical function present in numpy since version 1.7.0 10 November 2018, 22:36:49 UTC
cc3a224 Faustin Carter 10 November 2018, 00:14:44 UTC bad spelling of variable 10 November 2018, 00:14:44 UTC
a19cb39 Faustin Carter 09 November 2018, 23:47:57 UTC compare equals is different than assign equals... sigh 09 November 2018, 23:47:57 UTC
2051e72 Faustin Carter 05 November 2018, 15:06:10 UTC fix stupid thing I did that was dumb 05 November 2018, 15:06:10 UTC
0c08c77 Matt Newville 04 November 2018, 21:37:44 UTC Merge pull request #514 from lmfit/voigt_fwhm improved FWHM calculation for VoigtModel, especially for gamma!=sigma 04 November 2018, 21:37:44 UTC
e380007 Faustin Carter 04 November 2018, 15:33:55 UTC Update emcee routine and _calculate_statistics routine to properly handle calculating statsitics output for emcee runs 04 November 2018, 15:33:55 UTC
38bc05c Faustin Carter 04 November 2018, 15:33:09 UTC Update emcee example to use minimizer with residual function. Still need to update docs! 04 November 2018, 15:33:09 UTC
152524b Matthew Newville 03 November 2018, 14:27:15 UTC update test of Voigt FWHM to match new value 03 November 2018, 14:27:15 UTC
3a989c6 Matthew Newville 03 November 2018, 14:19:21 UTC improved FWHM calculation for VoigtModel, especially for gamma!=sigma 03 November 2018, 14:19:21 UTC
47fce05 Matt Newville 02 November 2018, 01:29:10 UTC Merge pull request #513 from lmfit/license_clarify clarify License to be more standard BSD-3, some doc updates 02 November 2018, 01:29:10 UTC
ffcde29 Faustin Carter 01 November 2018, 18:00:49 UTC Move updated example to new location in prep for restoring old example 01 November 2018, 18:00:49 UTC
e0682e6 Faustin Carter 01 November 2018, 17:59:05 UTC Cast generator to list for python 3 compat 01 November 2018, 17:59:05 UTC
dabb061 Matthew Newville 01 November 2018, 02:35:48 UTC more acknowledgments of prior work 01 November 2018, 02:35:48 UTC
fe4e645 Matthew Newville 01 November 2018, 01:17:07 UTC make copyright be a true sub-section of installation doc 01 November 2018, 01:17:07 UTC
85ef355 Matthew Newville 01 November 2018, 01:13:27 UTC fix many typos 01 November 2018, 01:13:27 UTC
982fe81 Matthew Newville 01 November 2018, 01:13:06 UTC restore scipy license to LICENSE file 01 November 2018, 01:13:06 UTC
e1fabc7 Faustin Carter 31 October 2018, 21:12:09 UTC Update emcee example to use lmfit.Model interface 31 October 2018, 21:12:09 UTC
4df4923 Matthew Newville 31 October 2018, 02:55:53 UTC add FAQ entry on NaNs 31 October 2018, 02:55:53 UTC
3d95b08 Matthew Newville 31 October 2018, 02:55:37 UTC some minorish doc updates 31 October 2018, 02:55:37 UTC
17f54b9 Matthew Newville 31 October 2018, 02:55:24 UTC udpate THANKS.txt 31 October 2018, 02:55:24 UTC
db1b340 Matthew Newville 31 October 2018, 02:54:46 UTC update LICENSE to clarify BSD-3 31 October 2018, 02:54:46 UTC
f9b1b12 Faustin Carter 30 October 2018, 16:58:16 UTC fix typo in docstrings 30 October 2018, 16:58:16 UTC
eb56b1f Faustin Carter 29 October 2018, 17:54:44 UTC Remove unrelated unused variable 29 October 2018, 17:55:02 UTC
b2be396 Faustin Carter 28 October 2018, 19:21:36 UTC Add 'emcee' as method kwarg to both Minimizer.minimize and minimize. 29 October 2018, 17:55:01 UTC
1b70f92 Matt Newville 24 October 2018, 21:29:48 UTC Merge pull request #511 from reneeotten/build-tests-documentation updates for building, tests, and documentation 24 October 2018, 21:29:48 UTC
b3a1291 reneeotten 23 October 2018, 04:39:58 UTC ENH: add all arguments to the minimize wrapper function 24 October 2018, 15:47:58 UTC
a8ddc0b reneeotten 23 October 2018, 04:25:13 UTC DOC: update whatsnew.rst 24 October 2018, 15:47:58 UTC
787ac9a reneeotten 23 October 2018, 03:40:49 UTC DOC: update installation.rst - update supported Python versions - remove references to nose, tests should be run with pytest 24 October 2018, 15:47:58 UTC
b9d0296 reneeotten 22 October 2018, 21:41:01 UTC BLD/STY: add isort section to setup.cfg and run on source 24 October 2018, 15:47:58 UTC
cd3fc38 reneeotten 22 October 2018, 14:38:22 UTC TST/STY: fixes in tests prompted by flake8 / pylint 24 October 2018, 15:47:58 UTC
0c9fe1c reneeotten 22 October 2018, 14:29:54 UTC TST: remove redundant __main__ statements 24 October 2018, 15:47:57 UTC
7a40947 reneeotten 22 October 2018, 14:25:22 UTC TST: merge unused _test_ci.py into test_confidence.py 24 October 2018, 15:47:57 UTC
f9b2647 reneeotten 22 October 2018, 14:19:55 UTC TST: remove unused _test_make_paras_and_func.py 24 October 2018, 15:47:57 UTC
37cbc1b reneeotten 23 October 2018, 17:20:19 UTC BLD/TST: use https for conda website 24 October 2018, 15:47:57 UTC
75ede2a reneeotten 24 October 2018, 15:32:28 UTC BLD: update setup.py - correct typo --> tests_require - explicitly add Python versions - add license to classifiers as recommended - add keywords 24 October 2018, 15:47:57 UTC
e278951 Matthew Newville 23 October 2018, 11:48:40 UTC use inspect.getfullargspec for Python3 23 October 2018, 11:48:40 UTC
744cbd9 Matt Newville 22 October 2018, 23:56:51 UTC Merge pull request #506 from reneeotten/numdifftools add numdifftools to estimate parameter uncertainties/correlations 22 October 2018, 23:56:51 UTC
6f62789 Matt Newville 22 October 2018, 20:42:29 UTC Merge pull request #510 from lmfit/params_usersyms Add `usersyms` to Parameters() initialization 22 October 2018, 20:42:29 UTC
fb34f7e reneeotten 08 October 2018, 20:39:13 UTC DOC: update documentation for numdifftools 21 October 2018, 00:27:15 UTC
453f584 reneeotten 07 October 2018, 21:08:10 UTC FIX: catch exception if numdifftools encounters NaN 21 October 2018, 00:27:15 UTC
11b8220 reneeotten 07 October 2018, 20:57:36 UTC FIX: numdifftools needs len(residual) > len(pars) Some tests (test_ampgo.py, test_basinhopping.py) were failing. To me it seems the reason is there we are trying to find the minimum of a function instead of fitting a function to data points. I *think* that numdifftools requires that the output of a function is an array with more elements than fitting parameters. Adding this requirement will not calculate a covariance_matrix when fitting a function, but probably not many people use lmfit for this anyway... 21 October 2018, 00:27:15 UTC
b05a90f reneeotten 17 September 2018, 22:49:55 UTC TST: add tests for numdifftools cov_x and uncertainties/correlations 21 October 2018, 00:27:15 UTC
1455b05 reneeotten 17 September 2018, 21:53:00 UTC ENH: calculate cov_x if not done by the minimizers - attempts to calculate the covariance matrix for minimizers other than (1) leastsq, least_square and emcee that already do this and (2) the brute force method - if successful, calculate parameter uncertainties and correlations 21 October 2018, 00:27:15 UTC
02f76e7 reneeotten 08 October 2018, 00:05:33 UTC ENH: add calc_covar to Model class 21 October 2018, 00:27:15 UTC
64b4c24 reneeotten 13 June 2018, 01:54:07 UTC ENH: add method to calculate the covariance matrix * calc_covar (default is True) added as an argument to the Minimizer class that determines whether or not to calculate the covariance matrix. * requires the numdifftools package to be installed 21 October 2018, 00:27:15 UTC
3a79237 reneeotten 07 October 2018, 15:42:07 UTC FIX: nfree cannot be < 0 21 October 2018, 00:27:15 UTC
e1f198b Matthew Newville 20 October 2018, 17:12:16 UTC pep8 / pylint cleanups 20 October 2018, 17:12:16 UTC
600257c Matthew Newville 14 October 2018, 23:52:15 UTC more uniform use of encode4js 14 October 2018, 23:52:15 UTC
b364a7e Matthew Newville 14 October 2018, 23:51:52 UTC add storing and retrieving of callables using import path of callable if dill is unavailable 14 October 2018, 23:51:52 UTC
803da4c Matthew Newville 14 October 2018, 23:48:32 UTC add test for Parameter usersyms 14 October 2018, 23:49:53 UTC
553488a Matthew Newville 14 October 2018, 23:47:55 UTC add usersyms keyword argument to Parameters() to populate symbol table 14 October 2018, 23:47:55 UTC
cac2d38 Matt Newville 14 October 2018, 14:32:40 UTC Merge pull request #508 from lmfit/small_fixes Small fixes 14 October 2018, 14:32:40 UTC
bc366ee Matt Newville 11 October 2018, 13:01:58 UTC Merge pull request #509 from lmfit/revert-503-plot-complex Revert "Handle plotting of complex-valued models in ModelResult class" 11 October 2018, 13:01:58 UTC
476bffc Matthew Newville 07 October 2018, 14:55:26 UTC numpy tests still require nose to be installed 10 October 2018, 23:03:26 UTC
1921a37 Matthew Newville 07 October 2018, 13:21:32 UTC ModelResult.eval() and .eval_components() should not permanently overwrite .userkws 10 October 2018, 23:03:26 UTC
9efc6ed Faustin Carter 09 October 2018, 01:41:34 UTC Handle plotting of complex-valued models in ModelResult class (#503) * Update plot routines in ModelResult class to gracefully handle models that return vectors of complex numbers. Adds options to convert the complex vector to a real one via several standard methods. * Update dosctrings and also add a line to the FAQ that is relevant to complex fitting. * Fix error propagation to not be wrong for phase error estimation when magnitude is zero * Change phase error to pi for case where magnitude is zero * Make a vector valued comparison not crash by using all * Update docstrings to be more compliant and refactor input-checking assertions to all be in central location * More docstring tweaking * Remove superfluous assert statement since this is handled with a raise later * consistent labeling of default option in docstrings * Replace asserts and default logic raises with explicit parameter test/raise * normalize angle errors by the square of the magnitude so that units are correct. Missed this earlier... * trim trailing whitespace and remove newlines between docstring and code 09 October 2018, 01:41:34 UTC
6a945a6 Jonathan Fraine 07 October 2018, 21:25:09 UTC Added progress bar to emcee call (#496) * Add `sampler_kwargs` as kwarg to Minimizer.emcee By adding `sampler_kwargs` as a kwarg to `Minimizer.emcee`, we can now send kwargs directly to emcee that are not consider by default in the current Minimizer instance. Example: `emcee` was updated to use `tqdm` as a progress bar over the MCMC sampling; but this was not added into the `lmfit-py`. To avoid requiring `lmfit-py` to update itself with every new kwarg from `emcee`, passing a `sampler_kwargs` into the `Minimizer` instance allows users to access all `emcee` kwargs directly. * Deleted sampler_kwargs and added progress=True The opposite of what I hoped for, I had to manually add the flag `progress=True` (`line 879`) and `progress=progress` (`line 1200`), because the progress bar is allocated in the `self.sampler` method `self.sampler.run` (where `self.sampler = EnsembleSampler(...)`). It works great; but the precedent is that we need to add a new flag for each `.run` kwarg. * minimized the number of PR corrections * add tqdm to the dependencies * updated requirements for emcee * removed dependencies for sub features * include a emcee major version check Because the latest PYPI version of `emcee` does not include the `progress` kwarg -- to be released with v3.0.dev0 -- we added a version check to confirm that the `emcee` major version installed is >3. If it is, then `lmfit` with use progress with `progress=progress` on `line 1201`. The flag (`progress=True` `line 880`) can still be deactivated manually, even if `emcee.__version__ >= 3`. * Include emcee v3 check in self._lastpos line1200 * Configured EMCEE_VERSION Check and output Changes the variable name and behaviour of the EMCEE version check for version>=3, now it runs one set of 2 lines, as oppose to the default set of 2 lines 07 October 2018, 21:25:09 UTC
900095d Matthew Newville 07 October 2018, 13:17:54 UTC convert tests to not rely on nose, using pytest instead where needed 07 October 2018, 13:17:54 UTC
aabf1f7 Matthew Newville 07 October 2018, 13:16:43 UTC auto-convert independent var to array only if it is a list or tuple -- allow complex objects as independent vars 07 October 2018, 13:16:43 UTC
d4d8958 Matt Newville 05 October 2018, 21:51:27 UTC Merge pull request #501 from reneeotten/least_squares calculate uncertainties in least_squares method 05 October 2018, 21:51:27 UTC
a7ca476 reneeotten 02 October 2018, 18:51:17 UTC TST: fix DeprecationWarning random_integers --> randint 02 October 2018, 18:51:17 UTC
cc306ba reneeotten 24 September 2018, 18:05:01 UTC ENH: set result.errorbars to True in _calculate_uncertainties_correlations() 24 September 2018, 18:08:26 UTC
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