bumps - v1.0.3rc2

What's Changed

Limit context for mpl.use(agg) to exported plots by @pkienzle in https://github.com/bumps/bumps/pull/317
Run the model uncertainty plugin during export by @pkienzle in https://github.com/bumps/bumps/pull/318
remove duplicate nllf_scale function by @pkienzle in https://github.com/bumps/bumps/pull/329
Bump actions/download-artifact from 4 to 5 by @dependabot[bot] in https://github.com/bumps/bumps/pull/331
Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/bumps/bumps/pull/332
make legend draggable on convergence plot by @bmaranville in https://github.com/bumps/bumps/pull/333
Match requires-python and test coverage by @bmaranville in https://github.com/bumps/bumps/pull/334

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.3rc0...v1.0.3rc2

- Python
Published by bmaranville 10 months ago

bumps - v1.0.3rc0

What's Changed

Export data from custom plots by @hoogerheide in https://github.com/bumps/bumps/pull/323

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.3b1...v1.0.3rc0

- Python
Published by bmaranville 10 months ago

bumps - v1.0.3b1

What's Changed

Allow loading of the dream state from an export directory into webview by @pkienzle in https://github.com/bumps/bumps/pull/316
use cloudpickle rather than dill by @pkienzle in https://github.com/bumps/bumps/pull/308
Update outliers handling by @pkienzle in https://github.com/bumps/bumps/pull/310
Allow model file to control num parameters in correlation plot by @pkienzle in https://github.com/bumps/bumps/pull/315
refactor chisq calculations by @pkienzle in https://github.com/bumps/bumps/pull/313
Use --session rather than --store by @pkienzle in https://github.com/bumps/bumps/pull/322

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.3b0...v1.0.3b1

- Python
Published by bmaranville 10 months ago

bumps - v1.0.3b0

What's Changed

Fix vue-tsc check by @bmaranville in https://github.com/bumps/bumps/pull/319
Convergence show burn and control cutoff with slider by @bmaranville in https://github.com/bumps/bumps/pull/290
Use msgpack for websocket comms with webview client by @bmaranville in https://github.com/bumps/bumps/pull/291
Fix shutdown dialog by @bmaranville in https://github.com/bumps/bumps/pull/320

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.2...v1.0.3b0

- Python
Published by bmaranville 11 months ago

bumps - v1.0.2

What's Changed

BUGFIX prevent overwriting fit state in currently active history item after loading a session file and then reloading a different history item
Fix running client in dev mode by @bmaranville in https://github.com/bumps/bumps/pull/304
Fix summary panel issues by @bmaranville in https://github.com/bumps/bumps/pull/303
Add --export to the fitter check so that it runs during CI by @pkienzle in https://github.com/bumps/bumps/pull/300
don't reorder contours in form_quantiles by @bmaranville in https://github.com/bumps/bumps/pull/305
Create socket object in main.js, pass to App.vue by @bmaranville in https://github.com/bumps/bumps/pull/268
Handle user deleting "active" history item in session by @bmaranville in https://github.com/bumps/bumps/pull/307

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.1...v1.0.2

- Python
Published by bmaranville 12 months ago

bumps - v1.0.2rc0

Bug fix

fixes a bug where reloading further history items overwrites the contents (item.fitting.convergence and item.fitting.fit_state) of item.fitting for the item that is "active" on session load. (load sets state.fitting = item.fitting for the active item, but reload didn't do the same)

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.2a0...v1.0.2rc0

- Python
Published by bmaranville 12 months ago

bumps - v1.0.2a0

What's Changed

Fix running client in dev mode by @bmaranville in https://github.com/bumps/bumps/pull/304
Fix summary panel issues by @bmaranville in https://github.com/bumps/bumps/pull/303
Add --export to the fitter check so that it runs during CI by @pkienzle in https://github.com/bumps/bumps/pull/300
don't reorder contours in form_quantiles by @bmaranville in https://github.com/bumps/bumps/pull/305
Create socket object in main.js, pass to App.vue by @bmaranville in https://github.com/bumps/bumps/pull/268

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.1...v1.0.2a0

- Python
Published by bmaranville 12 months ago

bumps - v1.0.1

What's Changed

fix saving serialized problem from webview menu (is string now) by @bmaranville in https://github.com/bumps/bumps/pull/299

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0...v1.0.1

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0

Major changes in 1.0.0 release

a new web-based GUI (webview) has been added as the default GUI
- (the WXPython GUI is deprecated)
a dataclass-based JSON serialization is available for bumps classes (and the serializer can be used for model classes as well, falling back to dill)
FitProblem class was refactored to support simultaneous fitting of multiple models, and MultiFitProblem is deprecated (currently an alias to FitProblem)
Fitness is a Protocol class defining the interface for models
FitProblem.models is now a generator that returns Fitness-compatible objects
Parameter was refactored and has an indirection attribute slot:
- Parameter.value now returns float(Parameter.slot)
- this allows Parameter to be a wrapper of other Parameter or Expression or Calculation or Constant objects
Expression is a new class that replaces Operation for combining Parameter objects in expressions (can be used in Parameter slots, and in a model)
Use Parameter.equals(Expression|Parameter) for equality constraints. This preserves bounds and limits on the parameter imposed by the model. Calling Parameter.unlink() clears the constraint.
Calculation is a new class to represent a calculable property of a class, which can be used in Expression instances (e.g. the total thickness of a stack of layers)
new Constraint class that can be created with e.g. constraints = [par1 < par2, par2 < par3] and passed directly to FitProblem
the DE stepper (also used by dream) is now fully accelerated with numba when numba is present (C DLL is still faster)
setup.py removed and the package is now defined in pyproject.toml
when using trim option in dream, the calculated stable portion is stored in the Dream state (MCMCDraw.portion),
- this portion is used by default in MCMCDraw.draw() and plotting methods

What's Changed: (all pull requests)

restructure parameter and expression handling by @pkienzle in https://github.com/bumps/bumps/pull/56
Webview: separate API from server logic by @bmaranville in https://github.com/bumps/bumps/pull/126
Add set_model() by @mdoucet in https://github.com/bumps/bumps/pull/130
Webview serialize v2 by @bmaranville in https://github.com/bumps/bumps/pull/133
bumps webview update by @pkienzle in https://github.com/bumps/bumps/pull/148
Refactor serialization by @pkienzle in https://github.com/bumps/bumps/pull/59
Coerce individual bounds by @krzywon in https://github.com/bumps/bumps/pull/155
Some light cleanup (similar to refl1d) by @glass-ships in https://github.com/bumps/bumps/pull/152
Publish package in pypi by @jmborr in https://github.com/bumps/bumps/pull/154
Get version number from tag using versioningit by @backmari in https://github.com/bumps/bumps/pull/153
Remove to_dict from Fitness by @glass-ships in https://github.com/bumps/bumps/pull/158
install node and build webview client before wheel by @bmaranville in https://github.com/bumps/bumps/pull/157
Fix bug preventing warning message from displaying correctly by @tsole0 in https://github.com/bumps/bumps/pull/143
FIX: added support for Constant class by @acaruana2009 in https://github.com/bumps/bumps/pull/159
adding mystic to packages to install by @bmaranville in https://github.com/bumps/bumps/pull/163
Fix mystic import by @bmaranville in https://github.com/bumps/bumps/pull/165
get correct link to server in macos jupyter lab, which uses 127.0.0.1… by @bmaranville in https://github.com/bumps/bumps/pull/156
Custom plots rebase by @bmaranville in https://github.com/bumps/bumps/pull/167
Custom plot table by @hoogerheide in https://github.com/bumps/bumps/pull/171
Trace plot update by @hoogerheide in https://github.com/bumps/bumps/pull/170
Add build scripts for creating distributable bumps apps by @bmaranville in https://github.com/bumps/bumps/pull/162
Webview: Ensure fit complete handler runs after uncertainty_final event handled by @bmaranville in https://github.com/bumps/bumps/pull/173
Optional persistent path by @bmaranville in https://github.com/bumps/bumps/pull/174
fall back to current working directory if state.base_path does not exist by @bmaranville in https://github.com/bumps/bumps/pull/175
add count of displayed parameters to 'Fit Parameter' heading by @bmaranville in https://github.com/bumps/bumps/pull/178
Add extension to session file if none provided by @glass-ships in https://github.com/bumps/bumps/pull/177
Fix session update only in session menu save by @glass-ships in https://github.com/bumps/bumps/pull/180
Fix bug where you can't initialize (frozen) Normal distribution dataclass instance by @bmaranville in https://github.com/bumps/bumps/pull/182
separate the generation of error points to calculate from the calculation call by @bmaranville in https://github.com/bumps/bumps/pull/183
allow fitter_settings to be empty (e.g. if undefined in session file) by @bmaranville in https://github.com/bumps/bumps/pull/186
adding helper script to build or remove stepper dll in deployed bumps by @bmaranville in https://github.com/bumps/bumps/pull/184
numba implementation of dream stepper by @pkienzle in https://github.com/bumps/bumps/pull/151
catch error returned on first run of lmfit (TypeError) by @bmaranville in https://github.com/bumps/bumps/pull/161
Remove bootstrap js by @bmaranville in https://github.com/bumps/bumps/pull/188
Various minor changes by @glass-ships in https://github.com/bumps/bumps/pull/185
Random123 to optional external build-time dependency by @bmaranville in https://github.com/bumps/bumps/pull/195
Add linting and formatting for webview client by @glass-ships in https://github.com/bumps/bumps/pull/191
Remove client cdn rebase by @bmaranville in https://github.com/bumps/bumps/pull/200
Update vite.config.js by @glass-ships in https://github.com/bumps/bumps/pull/203
Webview Client - add type testing with vue-tsc by @glass-ships in https://github.com/bumps/bumps/pull/202
Disable ruff in pre-commit by @glass-ships in https://github.com/bumps/bumps/pull/205
Fix gaussian mixture example by @pkienzle in https://github.com/bumps/bumps/pull/201
Add application schema to serialized metadata, helps with application model migration by @bmaranville in https://github.com/bumps/bumps/pull/204
fix function to get all libraries with versions for models by @bmaranville in https://github.com/bumps/bumps/pull/206
Add head and body tags to log table by @glass-ships in https://github.com/bumps/bumps/pull/209
Add Ruff, pre-commit, and a Makefile by @glass-ships in https://github.com/bumps/bumps/pull/193
Pre-commit eslint and prettier using node language by @bmaranville in https://github.com/bumps/bumps/pull/214
Generic fitproblem by @bmaranville in https://github.com/bumps/bumps/pull/217
Remove deprecated div by @bmaranville in https://github.com/bumps/bumps/pull/211
Fix model select in webview data panel by @bmaranville in https://github.com/bumps/bumps/pull/223
Binary installers by @bmaranville in https://github.com/bumps/bumps/pull/221
clear uncertainty plots if returned plottable is null by @bmaranville in https://github.com/bumps/bumps/pull/228
scroll behavior on sliders is more harmful than helpful by @bmaranville in https://github.com/bumps/bumps/pull/227
Default install client dependencies by @bmaranville in https://github.com/bumps/bumps/pull/229
Dark mode by @bmaranville in https://github.com/bumps/bumps/pull/225
remove unused dependencies by @bmaranville in https://github.com/bumps/bumps/pull/234
Webview cli fit options by @bmaranville in https://github.com/bumps/bumps/pull/176
Autohide panels by @bmaranville in https://github.com/bumps/bumps/pull/231
try preferred port (5148) first before selecting random port, if no p… by @bmaranville in https://github.com/bumps/bumps/pull/235
Disconnected dialog refactor by @bmaranville in https://github.com/bumps/bumps/pull/236
Modify plugin api so refl1d doesn't need to monkey-patch bumps by @pkienzle in https://github.com/bumps/bumps/pull/237
Restore check against overall χ² value for all fitters by @pkienzle in https://github.com/bumps/bumps/pull/239
Ensure unique names for session history items by @bmaranville in https://github.com/bumps/bumps/pull/238
Shared memory for populating MPMapper workers by @bmaranville in https://github.com/bumps/bumps/pull/218
synchronize CLI fit options with the webview interface by @bmaranville in https://github.com/bumps/bumps/pull/241
fix using_mpi test by @pkienzle in https://github.com/bumps/bumps/pull/248
Add max time option to fitters by @pkienzle in https://github.com/bumps/bumps/pull/242
Show final step on console and rename near_best to jump by @pkienzle in https://github.com/bumps/bumps/pull/245
Webview resume dream by @pkienzle in https://github.com/bumps/bumps/pull/246
Add optional fig argument to plottrace and plottraces by @bmaranville in https://github.com/bumps/bumps/pull/250
Client fit fields from server by @bmaranville in https://github.com/bumps/bumps/pull/251
Add store/export to simple fit interface by @pkienzle in https://github.com/bumps/bumps/pull/249
Coerce dream integer attributes on load by @bmaranville in https://github.com/bumps/bumps/pull/255
Use nllf() rather than sum-squared residuals for lm return value by @pkienzle in https://github.com/bumps/bumps/pull/257
Prevent caching webview index page by @bmaranville in https://github.com/bumps/bumps/pull/256
Fix start fit button in webview client by @bmaranville in https://github.com/bumps/bumps/pull/258
Allow an app using bumps cli to specify a version by @bmaranville in https://github.com/bumps/bumps/pull/259
create public property to access FitProblem._parameters by @bmaranville in https://github.com/bumps/bumps/pull/261
Fix can't run multiple instances of webview without specifying new port by @bmaranville in https://github.com/bumps/bumps/pull/262
improve dream resume support by @pkienzle in https://github.com/bumps/bumps/pull/266
Remove unused bumps.vfs module by @bmaranville in https://github.com/bumps/bumps/pull/271
Remove custom number formatter (existed because of broken Windows number formatting) by @bmaranville in https://github.com/bumps/bumps/pull/270
add a helper function to simplify usage of Calculation in models by @bmaranville in https://github.com/bumps/bumps/pull/272
Set default alpha to zero for no convergence test by @pkienzle in https://github.com/bumps/bumps/pull/277
Relax type checks in HDF5 read/write methods for bumps dream state by @bmaranville in https://github.com/bumps/bumps/pull/274
Show errors from --pars option in batch mode by @pkienzle in https://github.com/bumps/bumps/pull/281
Store user-controlled 'portion' setting in Dream state by @bmaranville in https://github.com/bumps/bumps/pull/289
add chisq() method to FitProblem by @bmaranville in https://github.com/bumps/bumps/pull/283
Fix method for starting webview server in jupyter by @bmaranville in https://github.com/bumps/bumps/pull/292
Serialize curvefit with generic function pickling by @pkienzle in https://github.com/bumps/bumps/pull/253
Documentation for v1.0.0 full release by @bmaranville in https://github.com/bumps/bumps/pull/207
bugfix: cli flags converted to dashes but not updated in distributables by @bmaranville in https://github.com/bumps/bumps/pull/293
fix linting by @glass-ships in https://github.com/bumps/bumps/pull/295
Fix parsing of model serialization in client by @bmaranville in https://github.com/bumps/bumps/pull/294
Install webview dependencies by default by @bmaranville in https://github.com/bumps/bumps/pull/296
Hard link root fitting group to active item in session HDF5 by @bmaranville in https://github.com/bumps/bumps/pull/297
Fix issue with export: model serialization is now a string by @pkienzle in https://github.com/bumps/bumps/pull/298

New Contributors

@krzywon made their first contribution in https://github.com/bumps/bumps/pull/155
@jmborr made their first contribution in https://github.com/bumps/bumps/pull/154
@backmari made their first contribution in https://github.com/bumps/bumps/pull/153
@tsole0 made their first contribution in https://github.com/bumps/bumps/pull/143
@glass-ships made their first contribution in https://github.com/bumps/bumps/pull/152

Full Changelog: https://github.com/bumps/bumps/compare/v0.9.3...v1.0.0

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0rc3

What's Changed

Hard link root fitting group to active item in session HDF5 by @bmaranville in https://github.com/bumps/bumps/pull/297
Fix issue with export: model serialization is now a string by @pkienzle in https://github.com/bumps/bumps/pull/298

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0rc2...v1.0.0rc3

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0rc2

What's Changed

fix linting by @glass-ships in https://github.com/bumps/bumps/pull/295
Fix parsing of model serialization in client by @bmaranville in https://github.com/bumps/bumps/pull/294
Install webview dependencies by default by @bmaranville in https://github.com/bumps/bumps/pull/296

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0rc1...v1.0.0rc2

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0rc1

What's Changed

bugfix: cli flags converted to dashes but not updated in distributables by @bmaranville in https://github.com/bumps/bumps/pull/293
bugfix: update all shortcuts/scripts that start bumps webview gui to use python -m bumps instead of python -m bumps.webview.server

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0rc0...v1.0.0rc1

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0rc0

What's Changed

Fix method for starting webview server in jupyter by @bmaranville in https://github.com/bumps/bumps/pull/292
Serialize curvefit with generic function pickling by @pkienzle in https://github.com/bumps/bumps/pull/253
Documentation for v1.0.0 full release by @bmaranville in https://github.com/bumps/bumps/pull/207

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b8...v1.0.0rc0

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b8

What's Changed

Remove unused bumps.vfs module by @bmaranville in https://github.com/bumps/bumps/pull/271
Remove custom number formatter (existed because of broken Windows number formatting) by @bmaranville in https://github.com/bumps/bumps/pull/270
add a helper function to simplify usage of Calculation in models by @bmaranville in https://github.com/bumps/bumps/pull/272
Set default alpha to zero for no convergence test by @pkienzle in https://github.com/bumps/bumps/pull/277
Relax type checks in HDF5 read/write methods for bumps dream state by @bmaranville in https://github.com/bumps/bumps/pull/274
Show errors from --pars option in batch mode by @pkienzle in https://github.com/bumps/bumps/pull/281
Store user-controlled 'portion' setting in Dream state by @bmaranville in https://github.com/bumps/bumps/pull/289
add chisq() method to FitProblem by @bmaranville in https://github.com/bumps/bumps/pull/283

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b7...v1.0.0b8

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b7

What's Changed

Allow an app using bumps cli to specify a version by @bmaranville in https://github.com/bumps/bumps/pull/259
create public property to access FitProblem._parameters by @bmaranville in https://github.com/bumps/bumps/pull/261
Fix can't run multiple instances of webview without specifying new port by @bmaranville in https://github.com/bumps/bumps/pull/262
improve dream resume support by @pkienzle in https://github.com/bumps/bumps/pull/266

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b6...v1.0.0b7

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b6

What's Changed

Use nllf() rather than sum-squared residuals for lm return value by @pkienzle in https://github.com/bumps/bumps/pull/257
Prevent caching webview index page by @bmaranville in https://github.com/bumps/bumps/pull/256
Fix start fit button in webview client by @bmaranville in https://github.com/bumps/bumps/pull/258

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b5...v1.0.0b6

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b5

What's Changed

Client fit fields from server by @bmaranville in https://github.com/bumps/bumps/pull/251
Add store/export to simple fit interface by @pkienzle in https://github.com/bumps/bumps/pull/249
Coerce dream integer attributes on load by @bmaranville in https://github.com/bumps/bumps/pull/255

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b4...v1.0.0b5

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b4

What's Changed

Add optional fig argument to plottrace and plottraces by @bmaranville in https://github.com/bumps/bumps/pull/250

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b3...v1.0.0b4

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b3

What's Changed

synchronize CLI fit options with the webview interface by @bmaranville in https://github.com/bumps/bumps/pull/241
fix using_mpi test by @pkienzle in https://github.com/bumps/bumps/pull/248
Add max time option to fitters by @pkienzle in https://github.com/bumps/bumps/pull/242
Show final step on console and rename near_best to jump by @pkienzle in https://github.com/bumps/bumps/pull/245
Webview resume dream by @pkienzle in https://github.com/bumps/bumps/pull/246

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0b2...v1.0.0b3

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0b2

What's Changed

remove unused dependencies by @bmaranville in https://github.com/bumps/bumps/pull/234
Webview cli fit options by @pkienzle in https://github.com/bumps/bumps/pull/176
Autohide panels by @bmaranville in https://github.com/bumps/bumps/pull/231
try preferred port (5148) first before selecting random port, if no p… by @bmaranville in https://github.com/bumps/bumps/pull/235
Disconnected dialog refactor by @bmaranville in https://github.com/bumps/bumps/pull/236
Modify plugin api so refl1d doesn't need to monkey-patch bumps by @pkienzle in https://github.com/bumps/bumps/pull/237
Restore check against overall χ² value for all fitters by @pkienzle in https://github.com/bumps/bumps/pull/239
Ensure unique names for session history items by @bmaranville in https://github.com/bumps/bumps/pull/238
Shared memory for populating MPMapper workers by @bmaranville in https://github.com/bumps/bumps/pull/218

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a15...v1.0.0b2

- Python
Published by bmaranville about 1 year ago

bumps - v1.0.0a15

What's Changed

clear uncertainty plots if returned plottable is null by @bmaranville in https://github.com/bumps/bumps/pull/228
scroll behavior on sliders is more harmful than helpful by @bmaranville in https://github.com/bumps/bumps/pull/227
Default install client dependencies by @bmaranville in https://github.com/bumps/bumps/pull/229
Dark mode by @bmaranville in https://github.com/bumps/bumps/pull/225

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a14...v1.0.0a15

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a14

What's Changed

Fix model select in webview data panel by @bmaranville in https://github.com/bumps/bumps/pull/223
Binary installers by @bmaranville in https://github.com/bumps/bumps/pull/221

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a13...v1.0.0a14

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a13

What's Changed

Add head and body tags to log table by @glass-ships in https://github.com/bumps/bumps/pull/209
Add Ruff, pre-commit, and a Makefile by @glass-ships in https://github.com/bumps/bumps/pull/193
Pre-commit eslint and prettier using node language by @bmaranville in https://github.com/bumps/bumps/pull/214
Generic fitproblem by @bmaranville in https://github.com/bumps/bumps/pull/217
Remove deprecated div by @bmaranville in https://github.com/bumps/bumps/pull/211

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a12...v1.0.0a13

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a12

What's Changed

fix function to get all libraries with versions for models by @bmaranville in https://github.com/bumps/bumps/pull/206

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a11...v1.0.0a12

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a11

What's Changed

Disable ruff in pre-commit by @glass-ships in https://github.com/bumps/bumps/pull/205
Fix gaussian mixture example by @pkienzle in https://github.com/bumps/bumps/pull/201
Add application schema to serialized metadata, helps with application model migration by @bmaranville in https://github.com/bumps/bumps/pull/204

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a10...v1.0.0a11

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a10

What's Changed

Random123 to optional external build-time dependency by @bmaranville in https://github.com/bumps/bumps/pull/195
Add linting and formatting for webview client by @glass-ships in https://github.com/bumps/bumps/pull/191
Remove client cdn rebase by @bmaranville in https://github.com/bumps/bumps/pull/200
Bump conda-incubator/setup-miniconda from 2 to 3 by @dependabot in https://github.com/bumps/bumps/pull/197
Bump actions/github-script from 6 to 7 by @dependabot in https://github.com/bumps/bumps/pull/199
Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/bumps/bumps/pull/198
Update vite.config.js by @glass-ships in https://github.com/bumps/bumps/pull/203
Webview Client - add type testing with vue-tsc by @glass-ships in https://github.com/bumps/bumps/pull/202

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a9...v1.0.0a10

- Python
Published by glass-ships over 1 year ago

bumps - v1.0.0a9

What's Changed

allow fitter_settings to be empty (e.g. if undefined in session file) by @bmaranville in https://github.com/bumps/bumps/pull/186
adding helper script to build or remove stepper dll in deployed bumps by @bmaranville in https://github.com/bumps/bumps/pull/184
numba implementation of dream stepper by @pkienzle in https://github.com/bumps/bumps/pull/151
catch error returned on first run of lmfit (TypeError) by @bmaranville in https://github.com/bumps/bumps/pull/161
Remove bootstrap js by @bmaranville in https://github.com/bumps/bumps/pull/188
Various minor changes by @glass-ships in https://github.com/bumps/bumps/pull/185

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a8...v1.0.0a9

- Python
Published by glass-ships over 1 year ago

bumps - v1.0.0a8

What's Changed

Fix bug where you can't initialize (frozen) Normal distribution dataclass instance by @bmaranville in https://github.com/bumps/bumps/pull/182
separate the generation of error points to calculate from the calculation call by @bmaranville in https://github.com/bumps/bumps/pull/183

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a7...v1.0.0a8

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a7

What's Changed

add count of displayed parameters to 'Fit Parameter' heading by @bmaranville in https://github.com/bumps/bumps/pull/178
Add extension to session file if none provided by @glass-ships in https://github.com/bumps/bumps/pull/177
Fix session update only in session menu save by @glass-ships in https://github.com/bumps/bumps/pull/180

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a6...v1.0.0a7

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a6

What's Changed

Webview: Ensure fit complete handler runs after uncertainty_final event handled by @bmaranville in https://github.com/bumps/bumps/pull/173
Optional persistent path by @bmaranville in https://github.com/bumps/bumps/pull/174
fall back to current working directory if state.base_path does not exist by @bmaranville in https://github.com/bumps/bumps/pull/175

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a5...v1.0.0a6

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a5

What's Changed

Trace plot update by @hoogerheide in https://github.com/bumps/bumps/pull/170
Add build scripts for creating distributable bumps apps by @bmaranville in https://github.com/bumps/bumps/pull/162

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a4...v1.0.0a5

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a4

What's Changed

Custom plot table by @hoogerheide in https://github.com/bumps/bumps/pull/171

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a3...v1.0.0a4

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a3

What's Changed

get correct link to server in macos jupyter lab, which uses 127.0.0.1… by @bmaranville in https://github.com/bumps/bumps/pull/156
Custom plots rebase by @bmaranville in https://github.com/bumps/bumps/pull/167

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a2...v1.0.0a3

- Python
Published by bmaranville over 1 year ago

bumps - v1.0.0a2

What's Changed

Fix mystic import by @bmaranville in https://github.com/bumps/bumps/pull/165

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a1...v1.0.0a2

- Python
Published by bmaranville almost 2 years ago

bumps - v1.0.0a1

What's Changed

Fix bug preventing warning message from displaying correctly by @tsole0 in https://github.com/bumps/bumps/pull/143
FIX: added support for Constant class by @acaruana2009 in https://github.com/bumps/bumps/pull/159
adding mystic to packages to install by @bmaranville in https://github.com/bumps/bumps/pull/163

New Contributors

@tsole0 made their first contribution in https://github.com/bumps/bumps/pull/143

Full Changelog: https://github.com/bumps/bumps/compare/v1.0.0a0...v1.0.0a1

- Python
Published by bmaranville almost 2 years ago

bumps - v1.0.0a0

What's Changed

restructure parameter and expression handling by @pkienzle in https://github.com/bumps/bumps/pull/56
Webview: separate API from server logic by @bmaranville in https://github.com/bumps/bumps/pull/126
Add set_model() by @mdoucet in https://github.com/bumps/bumps/pull/130
Webview serialize v2 by @bmaranville in https://github.com/bumps/bumps/pull/133
Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows by @dependabot in https://github.com/bumps/bumps/pull/147
bumps webview update by @pkienzle in https://github.com/bumps/bumps/pull/148
Refactor serialization by @pkienzle in https://github.com/bumps/bumps/pull/59
Coerce individual bounds by @krzywon in https://github.com/bumps/bumps/pull/155
Some light cleanup (similar to refl1d) by @glass-ships in https://github.com/bumps/bumps/pull/152
Publish package in pypi by @jmborr in https://github.com/bumps/bumps/pull/154
Get version number from tag using versioningit by @backmari in https://github.com/bumps/bumps/pull/153
Remove to_dict from Fitness by @glass-ships in https://github.com/bumps/bumps/pull/158
install node and build webview client before wheel by @bmaranville in https://github.com/bumps/bumps/pull/157

New Contributors

@dependabot made their first contribution in https://github.com/bumps/bumps/pull/147
@krzywon made their first contribution in https://github.com/bumps/bumps/pull/155
@glass-ships made their first contribution in https://github.com/bumps/bumps/pull/152
@jmborr made their first contribution in https://github.com/bumps/bumps/pull/154
@backmari made their first contribution in https://github.com/bumps/bumps/pull/153

Full Changelog: https://github.com/bumps/bumps/compare/v0.9.3...v1.0.0a0

- Python
Published by bmaranville almost 2 years ago

bumps - v0.9.3

v0.9.3 2024-07-09

fixed issues with numpy > = 2.0 (see #140, numpy.NaN deprecated and removed)
fixed issues with refactor of scipy.stats (see #139)

- Python
Published by bmaranville almost 2 years ago

bumps - v0.9.2

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.9.2 2024-03-05

added testing for python 3.12
fixed issue with matplotlib >= 3.8.0 (see #129)
added missing documents to dream manual (Convergence tests, Parallel coordinates plot)
added numba.njit-accelerated fallback bounds.apply methods to dream (still uses compiled C DLL if available)
provide MAXCORR attribute on the CorrelationView; clear the figure if the number of variables exceeds MAXCORR

- Python
Published by bmaranville over 2 years ago

bumps - Unstable

A persistent prerelease where build artifacts for the current tip will be deposited

Last updated: Tue Nov 21 2023

- Python
Published by bmaranville over 2 years ago

bumps - v0.9.1

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.9.1 2023-04-10

added support for python 3.11, scipy 1.10, numpy 1.24, wx 4.1.1
fixed covariance calculation for n-D datasets
fixed batch mode I/O redirection cleanup
fixed issue with DREAM bounds checker when running in parallel
default to single precision derivatives with lm (fixes issue in SasView where OpenCL models failed with Levenberg-Marquardt)
improved support for repeat fitting within scripts and notebooks (start_mapper should now work after stop_mapper)

- Python
Published by pkienzle about 3 years ago

bumps - v0.9.0

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.9.0 2022-03-15

use MPFit in place of scipy.leastsq for bounds-constrained Levenberg-Marquardt
weights are properly applied to models (nllf) in FitProblem

- Python
Published by pkienzle over 4 years ago

bumps - v0.8.1

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.8.1 2021-11-18

"apply parameters" action added to GUI menu (does the same as --pars flag in CLI)
operators refactored (no more eval)
BoundedNormal keywords renamed (sigma, mu) -> (std, mean)
support for numba usage in models
fixed Parameters view jumping to top after toggling fit (linux, Mac)
fixed Summary view sliders disappearing in linux
fixed uncertainty plots regenerating at each parameter update
improved documentation of uncertainty analysis

- Python
Published by bmaranville over 4 years ago

bumps - v0.8.0

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.8.0 2020-12-16

add stopping conditions to DREAM, using --alpha=p-value to reject convergence
require --overwrite or --resume when reusing a store directory
enable outlier trimming in DREAM with --outliers=iqr
add fitted slope and loglikelihood distribution to the loglikelihood plot
display seed value used for fit so it can be rerun with --seed
save MCMC files using gzip
remove R stat from saved state
restore --pars option, which was broken in 0.7.17
terminate the MPI session when the fit is complete instead of waiting for the allocation to expire
allow a series of fits in the same MPI session
support newest matplotlib

- Python
Published by pkienzle over 5 years ago

bumps - v0.7.18

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.18 2020-11-16

restore python 2.7 support

- Python
Published by pkienzle over 5 years ago

bumps - v0.7.17

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.17 2020-11-06

restore DREAM fitter efficiency (it should now require fewer burn-in steps)
errplot.reload_errors allows full path to model file
clip values within bounds at start of fit so constraints aren't infinite
allow --entropy=gmm|mvn|wnn|llf to specify entropy estimation algorithm
allow duplicate parameter names in model on reload
expand tilde in path names
GUI: restore parallel processing
GUI: suppress uncertainty updates during fit to avoid memory leak
disable broken fitters: particle swarm, random lines, snobfit
minor doc changes

- Python
Published by pkienzle over 5 years ago

bumps - v0.7.16

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.16 2020-06-11

improved handling of parameters for to_dict() json pickling

- Python
Published by pkienzle about 6 years ago

bumps - v0.7.15

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.15 2020-06-09

parallel fitting suppressed in GUI for now---need to reuse thread pool
support limits=(min, max) for pm and pmp parameter ranges
cleaner handling of single/multiple fit specification
fix --entropy command line option
better support for pathlib with virtual file system

- Python
Published by pkienzle about 6 years ago

bumps - v0.7.14

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.14 2020-01-03

support for --checkpoint=n, which updates the .mc files every n hours
fix bug for stuck fits on --resume: probabilities contain NaN
better error message for missing store directory
Python 3.8 support (time.clock no longer exists)

- Python
Published by pkienzle about 6 years ago

bumps - v0.7.13

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.13 2019-10-15

fix pickle problem for parameterized functions
support multi-valued functions in Curve, shown with a coupled ODE example
update support for newer numpy and matplotlib

- Python
Published by pkienzle about 6 years ago

bumps - v0.7.9

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.9 2018-06-14

full support for python 3 in wx GUI
allow added or missing parameters in reloaded .par file
add dream state to return from fit() call

- Python
Published by pkienzle almost 7 years ago

bumps - v0.7.10

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.10 2018-06-15

restructure parameter table in gui

- Python
Published by pkienzle almost 7 years ago

bumps - v0.7.12

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.12 2019-07-30

--parallel defaults to using one process per CPU.
--pop=-k sets population size to k rather than k times num parameters
--resume=- resumes from --store=/path/to/store
use expanded canvas for parameter histograms to make plots more readable
use regular spaced tics for parameter histograms rather than 1- and 2-sigma
improve consistency between values of cov, stderr and chisq
fix handling of degenerate ranges on parameter output
add entropy calculator using gaussian mixture models (default is still Kramer)
vfs module allows loading of model and data from zip file (not yet enabled)
warn when model has no fitted parameters
update mpfit to support python 3
support various versions of scipy and numpy

- Python
Published by pkienzle almost 7 years ago

bumps - v0.7.11

Documentation: http://bumps.readthedocs.org

v0.7.11 2018-09-24

Added partial support for parameter serialization

See release notes for complete history.

- Python
Published by mdoucet almost 8 years ago

bumps - v0.7.6

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.6 2016-08-05

add --view option to command line which gets propagated to the model plotter
add support for probability p(x) for vector x using VectorPDF(f,x0)
rename DirectPDF to DirectProblem, and allow it to run in GUI
data reader supports multi-part files, with parts separated by blank lines
add gaussian mixture and laplace examples
bug fix: plots were failing if model name contains a '.'
miscellaneous code cleanup

- Python
Published by pkienzle about 8 years ago

bumps - v0.7.7

Documentation: http://bumps.readthedocs.org

Release notes: https://github.com/bumps/bumps

v0.7.7 2018-05-17

merge in amdahl branch for improved performance
update plot so that the displayed "chisq" is consistent with nllf
slight modification to the DREAM DE crossover ratio so that no crossover weight ever goes to zero.
par.dev(std) now uses the initial value of the parameter as the center of the distribution for a gaussian prior on par, as stated in the documentation. In older releases it was incorrectly defaulting to mean=0 if the mean was not specified.
save parameters and uncertainties as JSON as well as text
convert discrete variables to integer prior to computing DREAM statistics
allow relative imports from model files
support latest numpy/matplotlib stack
initial support for wxPhoenix/python 4 GUI (fit ranges can't yet be set)

- Python
Published by pkienzle about 8 years ago

bumps - v0.7.5.10

Release notes: https://github.com/bumps/bumps

Documentation: http://bumps.readthedocs.org

- Python
Published by pkienzle about 10 years ago

bumps - v0.7.5.7

Release notes: https://github.com/bumps/bumps

Documentation: http://bumps.readthedocs.org

- Python
Published by pkienzle almost 11 years ago

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