| 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 |
| c46944e | reneeotten | 23 July 2019, 21:48:09 UTC | MAINT: add corner and jupyter_sphinx to requirements-dev.txt | 23 July 2019, 21:48:09 UTC |
| 354de80 | reneeotten | 23 July 2019, 15:40:08 UTC | DOC: add uncertainty calculation using numdifftools in index.rst | 23 July 2019, 15:58:32 UTC |
| d4cf6bd | reneeotten | 23 July 2019, 15:20:16 UTC | DOC: small corrections in *.rst files - correct indentation - remove stray backticks - correct syntax for chapter title - correct typos | 23 July 2019, 15:58:32 UTC |
| e20d8c7 | reneeotten | 23 July 2019, 02:04:17 UTC | DOC: remove static images | 23 July 2019, 15:58:32 UTC |
| e815694 | reneeotten | 23 July 2019, 01:52:10 UTC | DOC: update layout indexsidebar.html | 23 July 2019, 15:58:32 UTC |
| 662756e | reneeotten | 20 July 2019, 02:10:49 UTC | DOC: update Makefile - copy data files to doc while generating the documentation - copy the correct extensions.py file | 23 July 2019, 15:58:32 UTC |
| db9a109 | reneeotten | 22 July 2019, 20:19:52 UTC | DOC: list corner package in installation.rst | 23 July 2019, 15:58:32 UTC |
| 7820a78 | reneeotten | 22 July 2019, 19:41:30 UTC | DOC: do not redefine built-in functions in intro.rst | 23 July 2019, 15:58:32 UTC |
| 3577ce2 | reneeotten | 19 July 2019, 18:53:44 UTC | MAINT: remove stray newline in Model.fit_report() | 23 July 2019, 15:58:31 UTC |
| b60f096 | reneeotten | 17 July 2019, 12:42:40 UTC | DOC: update doc_*.py examples | 23 July 2019, 15:58:31 UTC |
| 4ebfa56 | reneeotten | 17 July 2019, 12:29:42 UTC | DOC: use jupyter-execute in doc/*.rst - only for the code blocks where we use the output in the documentation | 23 July 2019, 15:58:31 UTC |
| baff0e7 | reneeotten | 16 July 2019, 11:41:00 UTC | ENH: use jupyter-sphinx for code in documentation - add dependency on jupyter_sphinx for building the documentation - configure Sphinx to use it - have rstcheck ignore the 'jupyter-execute' directive | 23 July 2019, 15:58:31 UTC |
| db9a8c2 | Matt Newville | 17 July 2019, 11:54:31 UTC | Merge pull request #572 from reneeotten/test-suite-jsonutils Add tests for lmfit/jsonutils.py | 17 July 2019, 11:54:31 UTC |
| bb24d7b | Matt Newville | 15 July 2019, 02:07:23 UTC | Merge pull request #571 from reneeotten/test-suite-printfuncs Add tests for lmfit/printfuncs.py | 15 July 2019, 02:07:23 UTC |
| 45a0bcd | reneeotten | 14 July 2019, 13:21:09 UTC | FIX: handling of pandas.Series in encode4js() - treat pandas.DataFrames and pandas.Series the same - no need to do "value=json.loads(obj.to_json())", just use "value=obj.to_json()" - for pandas.Series one needs to supply "typ='series' to the read_json call | 14 July 2019, 20:16:59 UTC |
| 4420338 | reneeotten | 13 July 2019, 14:33:43 UTC | DOC: update docstrings in jsonutils.py | 14 July 2019, 20:16:59 UTC |
| c883f7c | reneeotten | 13 July 2019, 14:14:33 UTC | TST: expand tests for jsonutils.py | 14 July 2019, 20:16:59 UTC |
| 25639ee | reneeotten | 13 July 2019, 01:29:02 UTC | MAINT: update pre-commit hooks (pyupgrade, flake8) | 13 July 2019, 02:24:17 UTC |
| d86299f | reneeotten | 11 July 2019, 20:53:19 UTC | TST: expand test for printfuncs.py - add additional tests for functions in lmfit/printfuncs.py - merge tests from test_fitreports.py into this file | 13 July 2019, 02:24:17 UTC |
| 0e92070 | reneeotten | 10 July 2019, 03:15:02 UTC | MAINT: align 'Non Numeric Value?' in fit_report | 12 July 2019, 01:43:04 UTC |
| d059561 | reneeotten | 09 July 2019, 15:06:47 UTC | FIX: compare par.value to par.min and par.max | 12 July 2019, 01:42:11 UTC |
| 083ea8d | reneeotten | 05 July 2019, 19:44:19 UTC | DOC: docstring updates in printfuncs.py | 11 July 2019, 21:06:04 UTC |
| b26c793 | reneeotten | 05 July 2019, 19:37:19 UTC | DEP: deprecate 'report_errors' in printfuncs.py This function is identical to 'report_fit' and, therefore, redundant. | 11 July 2019, 20:55:24 UTC |
| a17c5b4 | Renee Otten | 08 July 2019, 12:48:59 UTC | Merge pull request #565 from reneeotten/deprecate_missing_drop Remove deprecated "missing" and "drop" | 08 July 2019, 12:48:59 UTC |
| 2ae2fc9 | Matt Newville | 02 July 2019, 19:31:16 UTC | Splitloren hints with prefix (#569) * param_hints need to use prefix * add test for SplitLorentzianModel with/without prefix * fix typos (thanks @dimapu) Fixes: #566 | 02 July 2019, 19:31:16 UTC |
| 6ada323 | Matt Newville | 28 June 2019, 03:05:11 UTC | Merge pull request #567 from lmfit/models_need_prefixes make sure all parameters in Model.guess() use prefixes | 28 June 2019, 03:05:11 UTC |
| 4f22686 | Matt Newville | 28 June 2019, 03:04:43 UTC | Merge pull request #568 from reneeotten/PyPI_packaging Explicitly add install_requires in setup.py | 28 June 2019, 03:04:43 UTC |
| ae213b7 | reneeotten | 27 June 2019, 12:39:10 UTC | REL: explicitly add install_requires in setup.py Currently, the requirements do not end up in the json meta-data on PyPI which limits the usability of tools that rely on it. For example, the tool upt (https://framagit.org/upt/upt) that we are currently exploring to help with packaging for MacPorts does not report any dependencies. Apparently, the information is computed locally when generating the PyPI package and, therefore, might depend on how this is exactly done. Nevertheless, explicitly listing the dependencies should resolve this. | 27 June 2019, 12:57:39 UTC |
| c5efd5c | Matthew Newville | 27 June 2019, 00:46:44 UTC | make sure all parameters in Model.guess() use prefixes | 27 June 2019, 00:46:44 UTC |
| 7d99a32 | reneeotten | 22 June 2019, 03:22:11 UTC | TST: update tests to remove deprecated "missing" and "drop" arguments - test for possible values of nan_policy (should raise ValueError if not allowed) | 22 June 2019, 03:59:17 UTC |
| 829d14b | reneeotten | 22 June 2019, 03:09:18 UTC | DEP: remove "missing" and "drop", deprecated since 0.9.8 - "missing" argument of Model class was deprecated in favor of "nan_policy" - the option "drop" was deprecated in favor of "omit" In lmfit version 0.9.13 an explicit FutureWarning was added when these deprecated options were used. Now, we remove them completely as well as the redundant compatibility code. | 22 June 2019, 03:49:50 UTC |
| 4b5c701 | Renee Otten | 22 June 2019, 03:02:20 UTC | Merge pull request #564 from reneeotten/brute-parallelization Parallellization of brute force method | 22 June 2019, 03:02:20 UTC |
| 17b670c | reneeotten | 21 June 2019, 01:00:35 UTC | ENH: add parallelization to brute method - feature was added in SciPy v1.3 | 21 June 2019, 19:26:12 UTC |
| 7ee03cc | reneeotten | 21 June 2019, 00:40:28 UTC | MAINT: update pyupgrade pre-commit hook | 21 June 2019, 00:40:57 UTC |
| aa0510e | Matt Newville | 19 June 2019, 03:10:47 UTC | more careful adding of parameters to handle out-of-order constraint expressions (#561) * add test for adding parameters with out-of-order expressions * look for NameErrors when adding parameters and try again, at least a few times, to handle out-of-order constraints * use param._delay_asteval in add_many() to better safeguard against not-yet-viable constraint expressions | 19 June 2019, 03:10:47 UTC |
| e96adc6 | Matt Newville | 29 May 2019, 02:58:13 UTC | clean up parameter html table (#559) * clean up parameter html table | 29 May 2019, 02:58:13 UTC |
| b0d9ac6 | Renee Otten | 24 May 2019, 02:37:02 UTC | Merge pull request #558 from reneeotten/emcee-set-method FIX: always set result.method for emcee | 24 May 2019, 02:37:02 UTC |
| 350e05e | Matt Newville | 24 May 2019, 01:02:09 UTC | Merge pull request #552 from aaristov/master Fix Division by Zero problem | 24 May 2019, 01:02:09 UTC |
| 52ef525 | reneeotten | 23 May 2019, 17:23:42 UTC | FIX: always set result.method for emcee If is_weighted=False, "result = self.prepare_fit(params)" gets called again, which reinitializes the ModelResult causing the method attribute not to be present anymore. | 23 May 2019, 17:24:49 UTC |
| 6d92d38 | Renee Otten | 23 May 2019, 02:48:37 UTC | Merge pull request #557 from reneeotten/fix-brute-test Fix brute method/test | 23 May 2019, 02:48:37 UTC |
| 707993b | reneeotten | 22 May 2019, 16:44:49 UTC | MAINT: update pre-commit hooks | 22 May 2019, 16:59:05 UTC |
| f6353dc | reneeotten | 22 May 2019, 16:29:06 UTC | FIX: no correction for nfev in brute method for scipy >= 1.3 | 22 May 2019, 16:29:06 UTC |
| ca4f853 | Renee Otten | 22 May 2019, 15:35:45 UTC | Merge pull request #556 from reneeotten/dual_annealing Add dual_annealing algorithm | 22 May 2019, 15:35:45 UTC |
| b1a6413 | aaristov | 20 May 2019, 13:13:19 UTC | update string format | 20 May 2019, 13:13:19 UTC |
| 208d62f | aaristov | 20 May 2019, 13:06:19 UTC | change if to try-except ZeroDivisionError | 20 May 2019, 13:06:19 UTC |
| 63369d3 | reneeotten | 18 May 2019, 20:35:27 UTC | TST: add tests for dual_annealing algorithm | 19 May 2019, 15:40:16 UTC |
| 7960821 | reneeotten | 18 May 2019, 20:34:54 UTC | DOC: add dual_annealing method to documentation | 19 May 2019, 15:40:16 UTC |
| a9892f4 | reneeotten | 18 May 2019, 20:34:26 UTC | ENH: add dual_annealing algorithm | 19 May 2019, 15:40:16 UTC |
| 76537d1 | Matt Newville | 13 May 2019, 16:31:31 UTC | Merge pull request #554 from lmfit/savemodel_fixes Savemodel fixes | 13 May 2019, 16:31:31 UTC |
| 8ae2c22 | Matthew Newville | 10 May 2019, 20:02:51 UTC | fix typo in test | 10 May 2019, 20:02:51 UTC |
| cf44a34 | Matthew Newville | 10 May 2019, 18:12:01 UTC | explicitly look for, import, and load unique symobls in parameter __setstate__ | 10 May 2019, 18:12:01 UTC |
| c6659fa | Matthew Newville | 10 May 2019, 18:10:02 UTC | add test for save/lood modelresult with VoigtModel | 10 May 2019, 18:10:02 UTC |
| 404866f | aaristov | 07 May 2019, 12:10:13 UTC | add params html teable test | 07 May 2019, 12:10:13 UTC |
| f2ce73d | aaristov | 07 May 2019, 12:07:18 UTC | check for zero | 07 May 2019, 12:07:18 UTC |
| 579f2a5 | aaristov | 03 May 2019, 10:00:52 UTC | Fix Division by Zero problem | 03 May 2019, 10:00:52 UTC |
| aa642a8 | Renee Otten | 02 May 2019, 14:07:43 UTC | Merge pull request #550 from zobristnicholas/params-eval Params eval | 02 May 2019, 14:07:43 UTC |
