CHANGELOG

0.15.1
 - fix: properly deregister a model
 - ref: remove iterative "sneddon_spher" model in developer mode
 - setup: bump nanite from 4.0.0 to 4.1.1
0.15.0
 - BREAKING CHANGE: Due to the upgrade of nanite, the rating values,
   e.g. for the "zef18" dataset might change slightly (on average by
   about 0.1). If you are excluding curves from your analysis based on
   rating, please rerun your analysis.
 - setup: bump nanite from 3.7.0 to 4.0.0 (support training sets that
   contain nan-values for zero responses and infinity values; minor
   other fixes)
0.14.3
 - setup: bump afmformats from 0.16.7 to 0.18.0 (support for specifying
   custom metadata when opening JPK files)
 - ci: maintenance
0.14.2
 - enh: support mirroring the input directory structure in the data
   conversion tool (#29)
 - docs: add info about data conversion tool
0.14.1
 - maintenance release
0.14.0
 - feat: support baseline corrections with linear slope (drift or shift)
 - ref: generalize the view of preprocessing insights
 - ref: support multiple options for nanite preprocessors
 - setup: bump nanite from 3.5.2 to 3.7.0
 - setup: bump Python version to 3.10
0.13.4
 - ref: don't use deprecated matplotlib.cm.get_cmap
 - ref: use packaging.version.parse to compare versions
 - ref: fix matplotlib deprecation warning for set_data
 - tests: don't be so strict
0.13.3
 - setup: bump afmformats from 0.16.4 to 0.16.7
 - setup: bump nanite from 3.5.0 to 3.5.2
 - setup: require Python 3.9
 - ci: update build pipelines
 - tests: loosen allclose call
0.13.2
 - fix: model parameters defined via expressions were not exported
 - fix: only export hidden parameters in developer mode
 - enh: export ancillary parameters in autosave
0.13.1
 - fix: make sure fit parameters are identified by their label
   instead of by an index (which can be wrong, now that we have
   hidden parameters)
 - fix: do not show "sneddon_spher" model in expert mode
0.13.0
 - feat: allow to specify the geometrical correction factor for
   non-single-contact experiments (#16)
 - fix: export fitting method and method kwargs with initial
   parameters
 - enh: add expert mode which is just a parital developer mode (#22)
 - enh: add links to docs in two places (#19)
 - enh: show "Axes" in fitting tab only in developer mode (#21)
 - setup: bump nanite from 3.4.0 to 3.5.0 (#16)
0.12.1
 - build: fixed testing pipeline
0.12.0
 - feat: support loading nanite model files as extensions
 - feat: added automatic update check during startup
 - ref: add preferences dialog
 - setup: bump nanite from 3.3.1 to 3.4.0
0.11.2
 - maintenance release
0.11.1
 - fix: check for identical label when updating parameters
   (previously, a parameter that starts with the label of another
   parameter got assigned the wrong boundaries)
 - enh: allow to hide model parameters via key names (#20)
 - enh: show hidden parameters in developer mode
 - ref: code-cleanup and simplification using latest nanite version
 - setup: bump nanite from 3.2.1 to 3.3.1
0.11.0
 - feat: allow custom fit methods with custom keyword arguments
   in developer mode (#18)
 - fix: correctly handle dependencies in preprocessing tab
 - fix: set POC method when loading recommended preprocessing (#17)
 - setup: bump nanite from 3.1.3 to 3.2.1 (new POC estimation
   methods: Frechet distance and linear+polynomial fit)
0.10.1
 - enh: use human-readable units in missing-metadata entry dialogs
 - enh: change default unit for spring constant to mN/m
 - ref: IndentationPreprocessor is deprecated in nanite
 - setup: bump nanite to version 3.1.3 (ask for missing spring
   constant for tip position computation)
0.10.0
 - BREAKING CHANGE: The default contact point estimation method
   changed. This means that your fitted contact points and any
   E(delta)-related results will change!
 - feat: allow to select point of contact method (#15)
 - enh: restructure preprocessing tab and avoid situations where
   preprocessing dependencies are not met (#15)
 - enh: visualize contact point estimation algorithms in
   preprocessing tab
 - setup: bump nanite from 2.0.0 to 3.1.1 (improved preprocessing)
0.9.4
 - enh: only show exact sneddon model "sneddon_spher" in developer
   mode to avoid confusion
 - setup: bump afmformats from 0.15.0 to 0.16.0 (improve support for
   AFM workshop data)
 - setup: bump nanite from 1.7.6 to 2.0.0
0.9.3
 - fix: possible fix for TypeError in InfDoubleSpinBox
 - setup: bump afmformats from 0.14.3 to 0.15.0 as well as
   nanite from 1.7.6 to 1.7.8 (requirement for #14)
0.9.2
 - ref: improve speed when displaying QMap data
 - enh: add developer mode for loading creep-compliance data (#14)
 - setup: bump afmformats from 0.13.3 to 0.14.3 (mostly speed,
   support AFM workshop maps)
 - setup: bump nanite from 1.7.4 to 1.7.6 (mostly speed)
 - ref: speed-up QMap visualization by caching nanite.QMap instances
0.9.1
 - docs: minor update
 - fix: regression where left fitting range could not be set
 - fix: improved checks for InfDoubleSpinBox which acted up when
   entering absolutely sane floating point values
0.9.0
 - feat: allow users to enter missing metadata during loading
   of data files (#5)
 - fix: automatically append .h5 suffix when rating datasets
 - enh: add busy cursor where applicable
 - ref: directory for importing training datasets for rating changed
   (but I think this currently affects nobody)
 - setup: dump appdirs dependency (moved to QSettings)
 - setup: bump afmformats from 0.12.5 to 0.13.3 (mostly #5 and speed)
 - setup: bump nanite from 1.7.3 to 1.7.4 (mostly #5)
 - tests: increase coverage
0.8.8
 - fix: handle bad curves properly when running bulk analysis (#13)
 - ref: make sure there are no duplicate files when loading data
   (possibly fixes #12)
 - ref: cleanup - call overloaded processEvents
 - ref: properly decorate pyqtSlots
 - tests: add helper function for setting up datasets
0.8.7
 - fix: add workaround for macOS where the non-native PyQt5 dialogs
   did not allow browsing to "/Volumes" (it is now added to the sidebar)
 - build: bump afmformats from 0.12.4 to 0.12.5 (OSError:
   "Too many files open" with the JPK file format)
 - build: bump nanite from 1.6.2 to 1.7.3
 - build: pin PyQt5 for GitHub releases
 - tests: don't used deprecated weight_cp function from nanite
0.8.6
 - build: bump afmformats from 0.12.2 to 0.12.4 (AttributeError
   when reading HDF5 files)
 - tests: deprecate setup.py test
0.8.5
 - build: migrate from travisCI to GitHub Actions
 - build: overhauled build pipeline (#9)
0.8.4
 - build: add pyinstaller hooks for afmformats
0.8.3
 - fix: main window not focused after startup
 - fix: Windows installation location was confusing and did
   not coincide configuration file location
 - fix: files are sorted before batch loading
 - fix: change visualization of fitting region by gray
   wraparound instead of yellow highlight (not visible
   on all screens)
 - setup: bump afmformats from 0.11.0 to 0.12.2
   (improved JPK file format speed)
0.8.2
 - setup: bump matplotlib to >=3
   (NavigationToolbar2QT modifications)
0.8.1
 - fix: correctly handle lmfit models with expressions
 - setup: bump nanite from 1.6.0 to 1.6.2 (improve contact point
   retrieval for bad data, check models during registration)
0.8.0
 - fix: exclude misplaced 'available' method from preprocessors
 - setup: bump nanite from 1.5.5 to 1.6.0 (improved contact point
   estimation - this may introduce small changes in the fit result
   which should not be significant, but which justify a new minor
   version)
0.7.6
 - maintenance release (fix macOS build)
 - setup: bump afmformats from 0.10.2 to 0.11.0
 - setup: bump nanite from 1.5.4 to 1.5.5
0.7.5
 - maintenance release (fix build)
0.7.4
 - setup: bump afmfomats from 0.10.0 to 0.10.2
 - setup: bump nanite from 1.5.2 to 1.5.4
 - build: add command-line option --version to just print the
   version and exit
0.7.3
 - fix: update initial parameters when the user edits the left
   fitting interval boundary
 - fix: conical indenter model did not work, because of a wrong
   (and unnecessary) entry in the `human_units` scheme.
0.7.2
 - fix: setting bad fit range lead to ValueError during plotting
0.7.1
 - fix: wrong SI units assigend to fit results parameters
 - setup: bump afmformats from 0.9.0 to 0.10.0
   (new formats: JPK (.jpk-qi-data), AFM workshop (.csv),
   NT-MDT (.txt exported by Nova))
 - setup: bump nanite from 1.4.1 to 1.5.2
0.7.0
 - feat: add data conversion tool
 - enh: allow to select multiple files when loading data
 - ref: changed order and clarified meaning of options in file menu
 - setup: bump afmformats from 0.7.0 to 0.9.0 (fix HDF5 export,
   support new file formats)
0.6.8
 - setup: bump afmformats from 0.5.1 to 0.7.0 (improved metadata view
   in info tab)
 - setup: bump nanite from 1.4.1 to 1.5.1 (compatibility to afmformats)
 - enh: fit results and parameter export dialog now supports new groups
   in afmformats 0.7.0
 - enh: autosave now only stores fit results and rating parameters
 - enh: remember scroll position in info tab
0.6.7
 - setup: bump nanite from 1.4.0 to 1.4.1
   (baseline is now a free parameter by default)
 - docs: add first tutorial (PAAm gels)
0.6.6
 - fix: typo lead to error when using rating threshold
0.6.5
 - build: macOS build failed due to PyInstaller issue 4626
0.6.4
 - fix: info tab did not display QMap metadata
 - fix: do not fit the entire dataset when applying a rating threshold
   but take the values from previous ratings
 - fix: deselecting curves of a qmap resulted in ValueError if QMap tab
   was selected
 - fix: set correct display range for residuals
 - docs: UI section for basics FD analysis
 - build: Windows build broken since 0.5.6
0.6.3
 - fix: support JPK data recorded in the "force-modulation" feedback mode
   (bump afmformats from 0.5.0 to 0.5.1)
 - fix: make sure ancillary parameters are computed from the initial
   parameters set in the user interface (not from the default model
   parameters)
0.6.2
 - enh: allow to select which metadata is exported
 - fix: do not apply and fit to all before exporting metadata
   (user may have performed individual fits)
 - setup: bump nanite from 1.3.0 to 1.4.0
0.6.1
 - build: workaround for Pyinstaller issue 4626
0.6.0
 - feat: initial support for ancillary parameters
 - fix: always display parameter units
 - fix: other minor UI bugs
 - setup: bump afmformats from 0.4.1 to 0.5.0
 - setup: bump nanite from 1.2.4 to 1.3.0
0.5.7
 - enh: allow to also set right part of fitting range individually
 - fix: improve layout of FD fitting panel
 - setup: bump nanite from 1.2.3 to 1.2.4 (improved default params)
0.5.6
 - setup: bump nanite from 1.2.2 to 1.2.3 (fixes issue with fits not
   being redone when the user changes an initial parameter)
 - fix: IndexError when editing the fitting range
0.5.5
 - maintenance release
0.5.4
 - enh: write maximum indentation to statistics file (#3)
 - fix: unicode characters were not read correctly from statistics
   file by libre office (added UTF-8 BOM)
0.5.3
 - enh: improved visualization of meta data parameters in the Info tab
 - setup: bump afmformats from 0.3.0 to 0.4.1
 - setup: bump nanite from 1.2.0 to 1.2.2
0.5.2
 - ref: bump nanite to 1.2.0
 - ref: migrate to afmformats (0.3.0)
0.5.1
 - fix: missing title in FD window and missing FD number in export menu
 - enh: add help menu with link to docs, about, and software used (#1)
 - docs: add quick guide for importing a nanite training set
 - docs: add black/white logo
0.5.0
 - feat: allow to import training sets produced with nanite
 - ref: major code refactoring of force-distance interface and cleanup
 - setup: bump nanite dependency to >=1.1.1
0.4.4
 - ci: pin 'joblib==0.11.0' on travis-CI (workaround for infinite loop
   in macOS build, https://github.com/pyinstaller/pyinstaller/issues/4067)
 - docs: add installation instructions
0.4.3
 - maintenance release (migrate to GitHub infrastructure)
 - experimental macOS builds
0.4.2
 - enh: merge training set and regressor selection into scheme selection
   (prevents confusion for users that are unsure what to choose)
 - enh: user rating is saved during rating, not afterwards
 - enh: rating containers for user rating can be reused explicitly
 - enh: qmap plot now better distinguishes between unavailable and
   invalid data
 - ref: migrate user rating output to nanite
0.4.1
 - fix: autoscaling according to fitting range did not work
 - fix: not possible to load .jpk-force-map files
 - ref: migrate qmap generation to nanite
0.4.0
 - migration to GitHub