List of changes in-between PyJibe releases.

version 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

version 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

version 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)

version 0.12.1

  • build: fixed testing pipeline

version 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

version 0.11.2

  • maintenance release

version 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

version 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)

version 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)

version 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)

version 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

version 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)

version 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

version 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

version 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

version 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

version 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

version 0.8.6

  • build: bump afmformats from 0.12.2 to 0.12.4 (AttributeError when reading HDF5 files)

  • tests: deprecate test

version 0.8.5

  • build: migrate from travisCI to GitHub Actions

  • build: overhauled build pipeline (#9)

version 0.8.4

  • build: add pyinstaller hooks for afmformats

version 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)

version 0.8.2

  • setup: bump matplotlib to >=3 (NavigationToolbar2QT modifications)

version 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)

version 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)

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

version 0.7.5

  • maintenance release (fix build)

version 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

version 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.

version 0.7.2

  • fix: setting bad fit range lead to ValueError during plotting

version 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

version 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)

version 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

version 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)

version 0.6.6

  • fix: typo lead to error when using rating threshold

version 0.6.5

  • build: macOS build failed due to PyInstaller issue 4626

version 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

version 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)

version 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

version 0.6.1

  • build: workaround for Pyinstaller issue 4626

version 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

version 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)

version 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

version 0.5.5

  • maintenance release

version 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)

version 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

version 0.5.2

  • ref: bump nanite to 1.2.0

  • ref: migrate to afmformats (0.3.0)

version 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

version 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

version 0.4.4

version 0.4.3

  • maintenance release (migrate to GitHub infrastructure)

  • experimental macOS builds

version 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

version 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

version 0.4.0

  • migration to GitHub