Docs available from http://refl1d.readthedocs.org
- fixed PolarizedQProbe.calc_Q (should not call PolarizedNeutronProbe._calculate_union)
- added self-extracting self-contained folder install for Windows (see releases page)
- added Error-in-Variables examples (see doc/examples/eiv folder)
- fixed shouldn't show unpolarized data in spin-asymmetry (SA) view (thanks, purnimab)
- preliminary support for theta_offset in PolarizedNeutronProbe
- preserve manual zoom view on R during fits
- fix wx and matplotlib bug (setTitle)
- use numba JIT for reflectometry kernel, convolve, etc (replacing all uses of C/C++ extensions)
- (this results in a pure Python wheel)
- use magnetic_smooth_profile in "record_point", same as is done for non-magnetic profiles
- FunctionalLayer can now accept lists of parameters
- oversampling helper added (currently called refl1d.check_oversampling)
- much faster "Model Uncertainty" view calculation for large profiles
- update to bumps 0.8.1
- numba included in windows zipped executable
- use numba rather than C++ for fast polymer calculations
- wheels now built with stable ABI (one wheel per platform for all Python > 3.2)
- drop py27 support for compiled modules
- tolerance adjusted on polymer_test to account for sensitivity to input parameters
- display of chisq in plot window works again
- fix selection mask for load4 to work on theta and lambda as well as Q and R
- use github actions to build wheels and deploy
- update to bumps 0.8.0, with DREAM outlier removal and convergence tests
- allow garefl to work with DREAM again
- support uniform resolution in addition to gaussian resolution
- implement oversample() and critical_edge() for QProbe
- support variable wavelength probes for materials mixtures
- add irho to the profile contour plots
- save magnetic twist contour in output directory; it is not yet plotted
- simplify realignment usage to 'refl1d align ...'
- improve support for complex amplitude (beam corrections, interpolation)
- restore DREAM fitter efficiency (it should now require fewer burn-in steps)
- restore parallel processing for GUI
- reenable python 2.7 support
- support list values for angle and wavelength in column data format
- use dQ from datafile rather than calculating it from dL and dT
- adjust dQ with sample broadening rather than calculating it from dL and dT
- fix json output so saving the fit doesn't raise an error
- fix functional magnetic profile so [rho, rho] is not treated as rho, theta.
- fix plots to show magnetic angle when not the standard magnetic angle
- fix legends when show magnetic angles on plots
- wxpython is now an optional dependency
- bumps: support limits=(min, max) for pm and pmp parameter ranges
- bumps: fix --entropy command line option
- bumps: parallel fitting suppressed in GUI for now---need to reuse thread pool
BREAKING CHANGE: default thetaM for functional magnetism changed from 0 to 270
- add --checkpoint=n to save mcmc state every n hours.
- hide resolution bars using Probe.show_resolution = False in your model.py
- fix residuals, fresnel, logfresnel, and q4 plots when interpolation is used
- fix error contour save function: rhoM was not being written
- fix simulation error: theory and simulated data were sharing the same vector
- fix doc generation: now builds with sphinx 2.4.0 and matplotlib 3.1.0.
- python 3.8 support requires bumps v0.7.14 (released 2020-01-03)
BREAKING CHANGE: old-style data loader with sample_broadening set
- sample_broadening was applied twice: once to the base Δθ from when the probe was created and again whenever ΔQ was computed; this is not a problem with the new load4 function. The code was fixed, which may cause difficulties when reloading old fits.
- json save: material and magnetism are now json objects
- json save: include non-parameter data in save file
- load4: accept 2 and 3 column data
- load4: override resolution and uncertainty given (or missing) from file
- load4: accept multi-entry data as Q probe without knowing theta/lambda
- load4: set the data slice to load
- load4: set default radiation to 'neutron'
- allow fit by number density for materials
- fix interpolation when plotting reflectivity between measured data points
- fix bug in dQ when sample_broadening is initialized to non-zeros
- revised installer: embedded python in zip file
- functions to compute transmission and reflection at each layer
- allow simulation with uncertainty from data
- force minimum uncertainty in data to 1e-11
- change default data view from Fresnel to log10
- apply resolution to saved Fresnel curve
- improved python 3 support
- fix json save for MixedExperiments
- save smooth magnetic profiles
- fix abeles code to choose correct branch cut below critical edge
- force absorption to be 0 or positive
- make sample broadening a fittable parameter
- allow model + data to be loaded from zip file (bumps 0.7.12 and up)
- improve serialization support
- added serialization support
- added option to supply uncertainties when simulating data
- fix for plotting spin asymmetry when data is not present (model-only)
- added requirements to setup.py so that pip install refl1d suffices
- full support for python 3 in GUI
- allow
--pars=parfilewith extra or missing parameters
- fix saved magnetic profiles
- include new entry points: run program by typing
refl1dat prompt
- allow alternate column order, such as
load4(..., columns="Q dQ R dR") - include resolution effects in Fresnel reflectivity normalization
- allow magnetic profile to be saved
- incoherent cross sections now calculated as total minus coherent
- make sure displayed chisq is consistent with negative log likelihood
- allow blending across multiple interfaces
- allow Nevot-Croce calculations for magnetic models
- support magnetic substrate
- load 4-column data: Q, R, dR, dQ, with dQ using 1-sigma resolution
- support Zeeman/Felcher effect for spin-flip in large applied fields
- fix Fresnel calculation
- add --view option from command line to select plot format
- add end-tethered and mushroom models for polymers
- support magnetic incident and substrate media
- support Microsoft Visual C compiler
- allow stop after a maximum amount of time (useful in batch queues)
- add entropy calculator
- add levenberg-marquardt to available fitting engines
- display constraints info on graph
- estimate parameter uncertainty from covariance matrix
- fix windows binary
- read magnetic models from reflpak
- demonstrate functional profiles in examples/profile/flayer.py
- add MPI support
- add stopping condition for DE
- support python 2.6, 2.7 and 3.3+
- fix confidence intervals (old confidence intervals are 2x too small)
- R0.7.2 broke parallel fitting
- support new NCNR reflectometers PBR and Magik
- better labelling of data sets
- monospline fixes
- allow fit interrupt from GUI
- simplify contrast variation fits with free variables shared between models
- add FASTA sequence reader with support for labile hydrogen substitution
- redo magnetic profiles so magnetism is a property of nuclear layers
- use material name or layer number to reference model layers
- fix density calculations for natural density
- add support for density and mixtures into chemical formulas
- split bumps into its own package
- allow Q probes and oversampling
- allow penalty constraints
- resume a fit from last saved point
- fix garefl and staj file loaders
- fix polarization cross section identifiers
- simulate reflectivity from existing Q,dQ,R,dR data
- show chisq variation in variable histogram
First public release