| bcb23dc | Matt Newville | 02 December 2019, 21:45:31 UTC | Merge pull request #611 from lmfit/v0.9.15 announce end of support for Python 2.7 | 02 December 2019, 21:45:31 UTC |
| 832aa80 | reneeotten | 01 December 2019, 21:32:30 UTC | DOC: updates and release notes for v0.9.15 | 02 December 2019, 00:51:57 UTC |
| 565bfcb | reneeotten | 01 December 2019, 21:19:57 UTC | STY: fix import orders - update .pre-commit-config.yaml and isort configuration | 02 December 2019, 00:51:00 UTC |
| fb133d9 | Matthew Newville | 01 December 2019, 23:25:26 UTC | announce end of suport for Python 2.7 | 01 December 2019, 23:25:26 UTC |
| f763980 | Matt Newville | 21 November 2019, 15:33:29 UTC | Merge pull request #600 from lmfit/emcee_improvements Fixes for use of emcee v3 (remove PTsampler), and allow iter_cb to be run and abort fit | 21 November 2019, 15:33:29 UTC |
| 8a1a5f6 | Till Stensitzki | 21 November 2019, 11:37:52 UTC | Fix and refactor prob_func (#604) * Fix and refactor prob_func * Fix style issues, improve test * TST: make test_confidenc.py compatible with PY2 The keywword "nonlocal" is PY3 only, we can switch back to this more explicit testing once we drop PY2. | 21 November 2019, 11:37:52 UTC |
| 7dc09a2 | Renee Otten | 20 November 2019, 14:31:29 UTC | Merge pull request #609 from Tillsten/sync_setup Add [flake8] to setup.cfg, remove flake8 args from pre-commit | 20 November 2019, 14:31:29 UTC |
| 8323f78 | tillsten | 20 November 2019, 13:24:20 UTC | Add [flake8] to setup.cfg, remove from pre-commit | 20 November 2019, 13:27:18 UTC |
| 9f32edf | Matt Newville | 20 November 2019, 02:20:33 UTC | Merge pull request #608 from lmfit/params_add fix for adding parameters with user-defined symbols | 20 November 2019, 02:20:33 UTC |
| 0c17a7c | Matthew Newville | 20 November 2019, 02:07:25 UTC | add '.' to end of docstring | 20 November 2019, 02:07:25 UTC |
| 14187cb | Matthew Newville | 19 November 2019, 20:52:31 UTC | fix typos | 19 November 2019, 20:52:31 UTC |
| d001938 | Matthew Newville | 19 November 2019, 19:57:49 UTC | fix adding Parameters with custom user-defined symbols | 19 November 2019, 19:57:49 UTC |
| bd05970 | Matthew Newville | 19 November 2019, 19:56:21 UTC | add test for adding Parameters with user-defined symbols | 19 November 2019, 19:56:21 UTC |
| de48201 | reneeotten | 19 November 2019, 13:37:31 UTC | STY: end-of-file-fixer for example_detect_outliers.py | 19 November 2019, 13:37:31 UTC |
| 2b50080 | reneeotten | 17 November 2019, 22:51:16 UTC | DEP: add DeprecationWarning when attempting to use the PTSampler | 19 November 2019, 13:35:13 UTC |
| 80e0c80 | Matthew Newville | 11 November 2019, 18:05:46 UTC | DOC: add make debug as non-default option for building doc | 19 November 2019, 13:35:13 UTC |
| f09c24c | Matthew Newville | 10 November 2019, 03:36:22 UTC | TST: update tests for emcee v3 | 19 November 2019, 13:35:13 UTC |
| 1b90261 | Matthew Newville | 10 November 2019, 03:34:40 UTC | MAINT, DOC: require emcee version 3 - update link for emcee homepage and minimum version requirement - set 'progress=False' in the examples to work correctly with sphinx-gallery | 19 November 2019, 13:35:13 UTC |
| b77e781 | Stensitzki | 14 November 2019, 17:23:07 UTC | Merge branch 'master' of https://github.com/lmfit/lmfit-py | 14 November 2019, 17:23:07 UTC |
| d54d9c3 | Matt Newville | 09 November 2019, 13:38:14 UTC | Merge pull request #599 from reneeotten/python38 officially support Python 3.8 | 09 November 2019, 13:38:14 UTC |
| fc13374 | Matt Newville | 07 November 2019, 18:13:30 UTC | Merge pull request #595 from reneeotten/parameter_repr changes to the Parameter class and increase coverage | 07 November 2019, 18:13:30 UTC |
| 89d6023 | reneeotten | 07 November 2019, 04:34:22 UTC | DOC: turn all Sphinx warnings into errors The warning for the syntax error introduced in PR #596 did not fail the build and, therefore, went unnoticed. Now Sphinx will error out on warnings and the build would fail. - fix the doctree warning - add "building the documentation" to the PR checklist | 07 November 2019, 13:36:36 UTC |
| 7434adb | reneeotten | 07 November 2019, 02:56:48 UTC | DOC: remove trailing-whitespace; fix syntax error, use jupyter-execute | 07 November 2019, 12:30:39 UTC |
| b3defbf | reneeotten | 07 November 2019, 02:56:07 UTC | MAINT: update pre-commit hooks | 07 November 2019, 12:30:39 UTC |
| c4145a0 | reneeotten | 23 October 2019, 16:43:57 UTC | MAINT, TST: officially support Python 3.8 - on Travis CI switch to Python 3.8 stable, add nightly | 07 November 2019, 12:30:35 UTC |
| dbf46ea | Stensitzki | 06 November 2019, 13:12:58 UTC | Add outlier detection example | 06 November 2019, 13:12:58 UTC |
| b9676dd | reneeotten | 31 October 2019, 18:40:19 UTC | TST: rework tests for Parameter class and improve coverage | 05 November 2019, 21:54:10 UTC |
| dd1f554 | reneeotten | 31 October 2019, 17:52:13 UTC | DEP: conversion from uncertainties.core.Variable to value in _getval | 05 November 2019, 21:54:10 UTC |
| 41748c8 | reneeotten | 31 October 2019, 16:58:49 UTC | DEP: add FutureWarning for isParameter ahead of deprecation | 05 November 2019, 21:54:10 UTC |
| a65c06e | reneeotten | 22 October 2019, 03:24:30 UTC | MAINT: update magic methods for Python 3 There are a few differences between PY2 and PY3: - __nonzero__ has been renamed to __bool__ - __div__ related magic methods are obsolete as division defaults to truedivision in Python 3 Already change the names of the functions defining the magic methods, and add a note to remove the obsolete ones when we change to PY3 only. | 05 November 2019, 21:54:10 UTC |
| 85e535a | reneeotten | 21 October 2019, 20:25:46 UTC | MAINT: always show label 'value' in Parameter.__repr__ | 05 November 2019, 21:54:10 UTC |
| 024f936 | reneeotten | 21 October 2019, 20:22:35 UTC | MAINT: make 'name' required positional argument of Parameter class Loading of Parameters or ModelResult from a JSON string requires the initialization of a Parameter class. In that case just, initialize with: _par = Parameter(name='') and switch to used named Parameters in example_Model_interface.py | 05 November 2019, 21:54:06 UTC |
| a19f526 | reneeotten | 23 October 2019, 12:38:41 UTC | MAINT, TST: require asteval >=0.9.16 - this version works with all supported Python versions | 05 November 2019, 20:39:39 UTC |
| 6b1f2d7 | Till Stensitzki | 05 November 2019, 20:35:43 UTC | FIX: nvars count and bound handling in confidence interval (#598) | 05 November 2019, 20:35:43 UTC |
| 9e66389 | Till Stensitzki | 05 November 2019, 20:19:27 UTC | DOC: workaround for missing stderr in CI calculations (#596) | 05 November 2019, 20:19:27 UTC |
| 449c6ed | Julius Zimmermann | 16 October 2019, 00:43:24 UTC | ENH: add more information about emcee fit (#593) Adds the following two attributes to the MinimizerResult when using the emcee method: - acor: an array containing the autocorrelation time for each parameter (where possible) - acceptance_fraction: an array of the fraction of steps accepted for each walker | 16 October 2019, 00:43:24 UTC |
| 7dedbc8 | Matt Newville | 09 October 2019, 15:44:24 UTC | Merge pull request #589 from ezwelty/support-all-jacobian-types Add support for non-array Jacobian types in least_squares | 09 October 2019, 15:44:24 UTC |
| 149d4d4 | ezwelty | 26 September 2019, 18:24:46 UTC | Add support for non-array Jacobian types in least_squares Add docstring to new test Replace assert_array_almost_equal with assert_allclose Clarify comment about scipy version in Jacobian transpose calculation Fix flake8 errors Use imported assert_allclose | 08 October 2019, 04:00:15 UTC |
| ffe550c | Matt Newville | 02 October 2019, 20:18:59 UTC | Merge pull request #592 from reneeotten/fixes_Travis_PY38 fixes for Travis CI and PY38 | 02 October 2019, 20:18:59 UTC |
| 55c888f | reneeotten | 01 October 2019, 15:43:53 UTC | TST: fix DeprecationWarning from unittest The function assertRaisesRegexp was renamed in Python 3.2 (DeprecationWarning: Please use assertRaisesRegex instead.) | 01 October 2019, 18:25:11 UTC |
| 472d628 | reneeotten | 01 October 2019, 15:40:39 UTC | TST: check for RuntimeWarning in test_ampgo.py | 01 October 2019, 18:25:11 UTC |
| 8cf1ed5 | reneeotten | 01 October 2019, 15:26:41 UTC | MAINT: add missing codecov dependency | 01 October 2019, 18:25:11 UTC |
| 40ba3bc | reneeotten | 01 October 2019, 14:38:00 UTC | MAINT: require emcee<3.0.0 for now - the PTSampler has been removed from the v3.0.0 release and forked to the ptemcee project. See: https://emcee.readthedocs.io/en/v3.0.0/user/upgrade/ Not sure yet whether we need to use this fork or if we can rewrite to use only the emcee package. | 01 October 2019, 18:25:11 UTC |
| f2de5f0 | reneeotten | 01 October 2019, 14:20:19 UTC | MAINT: test asteval fixes for Python 3.8 see: https://github.com/newville/asteval/issues/62 | 01 October 2019, 18:25:11 UTC |
| 5fbb89f | reneeotten | 01 October 2019, 13:59:20 UTC | MAINT: upgrade pyupgrade pre-commit hook | 01 October 2019, 18:25:11 UTC |
| 9dcfb71 | Matt Newville | 28 September 2019, 18:03:00 UTC | Merge pull request #591 from reneeotten/bump_dependencies Bump dependency versions and update Travis CI | 28 September 2019, 18:03:00 UTC |
| d7bc8b4 | reneeotten | 29 August 2019, 22:27:39 UTC | TST: update .travis.yml Use the Travis CI Python versions in combination with pip for testing; this has a few advantages: - it is slightly faster than using conda - with pip we can more easily install the *exact* minimum required versions of dependences - allows for testing of Python development versions (i.e., 3.8) Only potential drawback is that we do not necessarily the latest (micro) version of Python, but for our testing that shouldn't matter. | 27 September 2019, 15:44:38 UTC |
| 9a8906e | reneeotten | 04 September 2019, 02:09:04 UTC | DEP: drop support for Python 3.4 Support for Python 3.4 was dropped already in version 0.9.13; now also remove it from the classifiers and python_requires in setup.py | 27 September 2019, 15:44:38 UTC |
| a5f4fa8 | reneeotten | 04 September 2019, 02:01:28 UTC | DOC: updates for newer SciPy requirement | 27 September 2019, 15:44:38 UTC |
| c3aa693 | reneeotten | 04 September 2019, 01:59:20 UTC | TST: updates for newer SciPy requirement | 27 September 2019, 15:44:38 UTC |
| 49b32eb | reneeotten | 04 September 2019, 01:57:16 UTC | MAINT: clean-up code for newer SciPy requirement | 27 September 2019, 15:44:38 UTC |
| 9f3f2d1 | reneeotten | 29 August 2019, 22:20:03 UTC | MAINT: bump minimum versions for dependencies Require the LTS version of both SciPy and NumPy that works for Python 2.7 and above. Also bump the six requirement to 1.11 (released on Sep 17, 2017) and uncertainties to 3.0.1 (released on Aug 15, 2016), and add missing coverage development dependency. | 27 September 2019, 15:44:38 UTC |
| 489f0e8 | Matt Newville | 26 September 2019, 22:01:14 UTC | Merge pull request #587 from lmfit/getval2setval Getval2setval | 26 September 2019, 22:01:14 UTC |
| 6a2cbd8 | Matthew Newville | 09 September 2019, 01:26:41 UTC | add comment for checking for overflow | 09 September 2019, 01:26:41 UTC |
| f21a204 | Matthew Newville | 06 September 2019, 20:02:05 UTC | avoid overflowing exp() | 06 September 2019, 20:02:05 UTC |
| 438176a | Matthew Newville | 06 September 2019, 20:01:39 UTC | apply bounds on set-param-value, not get-param-value | 06 September 2019, 20:01:39 UTC |
| d7b408b | Matt Newville | 29 August 2019, 17:07:38 UTC | Merge pull request #586 from reneeotten/nan_policy_message Nan policy message | 29 August 2019, 17:07:38 UTC |
| d76a546 | reneeotten | 29 August 2019, 11:51:35 UTC | REL: update release notes for 0.9.14 | 29 August 2019, 11:51:35 UTC |
| 46cee03 | reneeotten | 29 August 2019, 11:01:18 UTC | TST: add test for new warning messages for NaN values | 29 August 2019, 11:40:23 UTC |
| cc12c8e | reneeotten | 28 August 2019, 17:15:05 UTC | ENH: add check for NaN values in Model._residual() - only raise the ValueError with message if nan_policy is set to 'raise' | 29 August 2019, 10:48:35 UTC |
| a7e20eb | reneeotten | 28 August 2019, 12:43:26 UTC | MAINT: update pyupgrade pre-commit hook | 28 August 2019, 12:43:26 UTC |
| 12d8f91 | reneeotten | 28 August 2019, 12:33:56 UTC | ENH: improve message if ValueError is raised by _nan_policy The original message ("ValueError: The input contains nan values") seems often -incorrectly- imply to users that their input data contains NaN values. The "input" here is referring to the input data of the _nan_policy function. Clarify that it can either be caused by the input data or, more likely, by the output of the objective/model function. Additionally, include a link to the FAQ on the documentation website. | 28 August 2019, 12:34:02 UTC |
| 6478b7d | Matt Newville | 26 August 2019, 14:47:12 UTC | Merge pull request #585 from lmfit/doctests914 docstring fixes and the addition of tests for v0.9.14. Fixes #584 | 26 August 2019, 14:47:12 UTC |
| edad977 | Matthew Newville | 26 August 2019, 02:02:40 UTC | style tweaks to tests | 26 August 2019, 02:12:40 UTC |
| b33de90 | Matthew Newville | 25 August 2019, 13:21:33 UTC | tests: add test for parameter printing | 26 August 2019, 02:12:40 UTC |
| fb9a3f7 | Matthew Newville | 25 August 2019, 13:20:11 UTC | tests: add some tests for model.plot* | 26 August 2019, 02:12:40 UTC |
| 21be941 | Matthew Newville | 25 August 2019, 13:08:37 UTC | tests: add tests for guess() methods | 26 August 2019, 02:12:40 UTC |
| fb5daed | Matthew Newville | 25 August 2019, 13:05:04 UTC | fix split_lorentzian docstring, and doc, simplify code, fixing github #584 | 26 August 2019, 02:12:04 UTC |
| 7b664fc | Matt Newville | 25 August 2019, 00:51:29 UTC | Merge pull request #583 from lmfit/gallery_tweaks Tweaks to generating the examples gallery | 25 August 2019, 00:51:29 UTC |
| 76f9575 | Matthew Newville | 23 August 2019, 20:04:32 UTC | doc: Examples replacing Gallery | 23 August 2019, 20:04:32 UTC |
| a6408d3 | Matthew Newville | 23 August 2019, 17:36:26 UTC | ignore temp data files needed to generate gallery | 23 August 2019, 17:36:26 UTC |
| 1ff5a45 | Matthew Newville | 23 August 2019, 17:35:48 UTC | update MANIFEST to include examples, but not generated gallery files | 23 August 2019, 17:35:48 UTC |
| f838dfd | Matthew Newville | 23 August 2019, 01:15:29 UTC | doc: add as Makefile directive so that gallery is not generated every time docs are generated, only after rm -rf _build/* rm -f extensions.py rm -f *.dat *.sav *.csv rm -rf examples/* rm -rf ../examples/documentation | 23 August 2019, 01:15:29 UTC |
| 0aefd3b | Matthew Newville | 23 August 2019, 01:14:39 UTC | doc: several tweaks to gallery gen script, including warning suppression | 23 August 2019, 01:14:39 UTC |
| 47616b1 | Matthew Newville | 23 August 2019, 01:12:35 UTC | doc: add Gallery and Support link to upper left of HTML doc | 23 August 2019, 01:12:35 UTC |
| 0c1e693 | Matthew Newville | 23 August 2019, 01:10:42 UTC | doc: add examples/ gallery to TOC | 23 August 2019, 01:10:42 UTC |
| 10afd00 | Matt Newville | 23 August 2019, 01:02:44 UTC | Merge pull request #582 from lmfit/asteval_maxtime remove deprecated max_time from asteval.Interpreter() creation | 23 August 2019, 01:02:44 UTC |
| 7ba1cc8 | Matthew Newville | 22 August 2019, 16:09:36 UTC | remove deprecated max_time from asteval.Interpreter() creation | 22 August 2019, 16:09:36 UTC |
| 60cf4ec | Matt Newville | 22 August 2019, 16:07:06 UTC | Merge pull request #581 from reneeotten/release-0.9.14 almost ready to release 0.9.14? | 22 August 2019, 16:07:06 UTC |
| b5f5518 | reneeotten | 22 August 2019, 12:57:05 UTC | REL: update release notes for 0.9.14 - link to the release notes in the installation instructions | 22 August 2019, 13:54:27 UTC |
| 37761fc | reneeotten | 22 August 2019, 12:54:26 UTC | DOC: add contributors to THANKS.txt | 22 August 2019, 13:38:40 UTC |
| 075e479 | Matt Newville | 21 August 2019, 20:27:11 UTC | Merge pull request #574 from reneeotten/examples Gallery with examples | 21 August 2019, 20:27:11 UTC |
| c3f3b64 | reneeotten | 16 August 2019, 21:46:16 UTC | Examples: review and update examples for gallery - all files that start with 'example_' will be executed, others will only be parsed - files should be "normal" Python code with embedded rST text in their source code (see https://sphinx-gallery.github.io/) TODO: - example_fit_multi_datasets.py: should use the Model interface - lmfit_emcee_model_selection.py: good example, but it does not seem to run correctly anymore - example_Model_interface.py: the section about "A Helpful Exception" does not seem accurate | 21 August 2019, 18:46:11 UTC |
| 28a43bc | reneeotten | 16 August 2019, 20:43:38 UTC | DOC: add comment about the failure of doc_model_loadresult.py For some reason the conversion by sphinx-gallery for doc_model_loadresult.py fails, even though execute the code in a Python shell or Jupyter notebook works fine. Error raised = NameError: name 'np' is not defined Add a note to the resulting example in the gallery and add this file to 'expected_failing_examples' to make sure the build finishes. | 21 August 2019, 12:18:48 UTC |
| 01d444d | reneeotten | 16 August 2019, 12:15:00 UTC | DOC: small updates to doc_*.py examples - remove plotting from doc_model_savemodelresult.py - remove leftover shebang line in doc_model_loadmodelresult2.py - generate new figure in doc_builtinmodels_peakmodels.py | 21 August 2019, 12:18:48 UTC |
| 666a396 | reneeotten | 16 August 2019, 03:36:15 UTC | DOC: add examples from documentation to gallery For the gallery one needs a correct header/docstring for the conversion to work. We don't want this for our examples that are part of the documentation where we often just show the file content. So we copy the doc_*.py examples to a separate "documentation" folder and add a header. In this way they will also show up in a "sub-gallery". | 21 August 2019, 12:18:48 UTC |
| c8ad365 | reneeotten | 15 July 2019, 14:22:35 UTC | ENH: use sphinx-gallery to generate a gallery with examples - all files in the "examples" directory, with the exception of "doc_*.py", will be added to the main example gallery. | 21 August 2019, 12:18:48 UTC |
| d68dbe9 | Matt Newville | 15 August 2019, 16:42:25 UTC | Merge pull request #579 from reneeotten/fix_nfev_brute Fix nfev for brute with multiprocessing | 15 August 2019, 16:42:25 UTC |
| eafeaee | reneeotten | 15 August 2019, 03:13:21 UTC | MAINT: update pre-commit hooks | 15 August 2019, 03:13:21 UTC |
| 34334d1 | reneeotten | 14 August 2019, 18:42:34 UTC | FIX: only check if a parameter is at its initial value if an initial value is present Probably this is a rare occurence as most users will actually set an initial value when initializing the parameters. However, for algorithms like "brute" that is actually not required and this might happen. Added a regression test and updated the code to include the check whether an init_value is present. See: #578 | 15 August 2019, 03:09:10 UTC |
| 7e38291 | reneeotten | 14 August 2019, 18:06:12 UTC | FIX: correct value for nfev when using brute algorithm When using multiprocessing (i.e., workers != 1) the number of function evaluations in the MinimizerResult is incorrect. For the brute method we actually know beforehand how many evaluation will be performed as we have a pre-determined search-grid. So setting result.nfev = len(result.brute_Jout.ravel()) will always work correctly. Updated the test-suite accordingly. Fixes: #578 | 14 August 2019, 18:43:59 UTC |
| 41667df | Matt Newville | 02 August 2019, 18:55:21 UTC | Merge pull request #576 from lmfit/inspect_signature use `inspect.signature` for better support of Py3 and wrapped functions | 02 August 2019, 18:55:21 UTC |
| b06bb1c | Matthew Newville | 01 August 2019, 16:29:02 UTC | fix import order, simplify version test | 01 August 2019, 16:29:02 UTC |
| bb8674a | Matthew Newville | 31 July 2019, 03:30:04 UTC | skip wrapped_model_func test with Py2 | 31 July 2019, 03:30:04 UTC |
| a3c0939 | Matthew Newville | 31 July 2019, 03:11:09 UTC | add test of using a wrapped function as a model function | 31 July 2019, 03:11:09 UTC |
| ad71135 | Matthew Newville | 31 July 2019, 01:07:53 UTC | use inspect.signature to inspect model function (towards Py3 only) | 31 July 2019, 01:07:53 UTC |
| 0c8607f | Matt Newville | 26 July 2019, 12:23:05 UTC | Merge pull request #575 from reneeotten/fix_pdf_documentation Fix documentation in PDF format | 26 July 2019, 12:23:05 UTC |
| 997ed10 | reneeotten | 25 July 2019, 01:49:36 UTC | DOC: list extra dependencies for building the documentation | 25 July 2019, 03:08:24 UTC |
| 9d9cb9f | reneeotten | 25 July 2019, 00:04:11 UTC | FIX: building of documentation in PDF format Problem: SVG figures cannot be incorporated in LaTeX files Solution: add 'sphinx.ext.imgconverter' to the extensions - additionally, minor Makefile fixes | 25 July 2019, 03:08:24 UTC |
| 4d483ca | Matt Newville | 24 July 2019, 15:07:26 UTC | Merge pull request #573 from reneeotten/documentation Documentation updates | 24 July 2019, 15:07:26 UTC |
