Changelog

List of changes in-between nanite releases.

version 2.0.1

  • enh: implement ‘require_steps’ in preprocessing to make sure that steps are executed in the correct order

  • enh: add several helper functions for preprocessing

version 2.0.0

  • BREAKING CHANGE: segment in FitProperties is now an integer

  • setup: bump afmformats from 0.15.0 to 0.16.0

  • docs: update doc strings for the “sneddon_spher_approx” model

  • docs: remove duplcate docs for model functions

version 1.7.8

  • ref: introduce preprocessing_step decorator for managing preprocessing steps

  • ref: explicitly request “force-distance” data from afmformats (can be lifted by setting nanite.read.DEFAULT_MODALITY to None)

  • setup: bump afmformats from 0.14.3 to 0.15.0 (initial support for loading creep-compliance data)

version 1.7.7

  • docs: fix build

version 1.7.6

  • setup: bump afmformats from 0.14.1 to 0.14.3 (adjust tests, speed)

version 1.7.5

  • ref: migrate QMap and Group code to afmformats 0.14.1

  • ref: Indentation is now a subclass for afmformats.AFMForceDistance

  • ref: QMap is now a subclass for afmformats.AFMQMap

  • ref: Group is now a subclass for afmformats.AFMGroup

version 1.7.4

  • enh: allow passing metadata to the IndentationGroup initializer

  • setup: bump afmformats from 0.10.2 to 0.13.2

  • ref: deprecate get_data_paths in favor of afmformats.find_data

version 1.7.3

  • build: move windows pipeline to GH Actions

  • ref: better warning traceback for deprecated weight_cp method

  • ref: DeprecationWarning: np.int from numpy 1.20

version 1.7.2

  • build: use oldest-supported-numpy in pyproject.toml

version 1.7.1

  • build: migrate to GitHub Actions

version 1.7.0

  • enh: simplified writing new model functions by introducing default modeling and residual wrappers

  • ref: improve code readability

version 1.6.3

  • tests: fix fails due to tifffile upgrade

  • setup: lift historic pinning of lmfit==0.9.5

version 1.6.2

  • tests: improve coverage

  • enh: add sanity checks for models during registration (#5)

version 1.6.1

  • enh: if the contact point estimate is not possible, use a fit with a partially constant and linear function

version 1.6.0

  • enh: improve contact point estimation by computing the gradient first; resolves issues with tilted baselines (#6) (This may affect fitting results slightly, hence the new minor release)

version 1.5.5

  • setup: make tkinter optional for frozen applications

version 1.5.4

  • setup: bump scikit-learn from 0.18.0 to 0.23.0 (different model results due to bugfixes, enhancements, or random sampling procedures; the tests have been updated accordingly)

  • setup: bump afmformats from 0.10.0 to 0.10.2

version 1.5.3

  • setup: new builds for Python 3.8

version 1.5.2

  • enh: be more verbose when tip position cannot be computed

  • setup: bump afmformats from 0.7.0 to 0.10.0

version 1.5.1

  • setup: bump afmformats from 0.6.0 to 0.7.0 (metadata fixes)

version 1.5.0

  • feat: IndentationGroup.get_enum returns a curve from an enum value

  • setup: bump afmformats from 0.5.0 to 0.6.0 (hdf5 export, improved tab export)

version 1.4.1

  • enh: set parameter baseline to “vary” for all models

  • fix: make sure that model_key is set before params_initial when fitting with kwargs (otherwise, params_initial might reset)

version 1.4.0

  • feat: add function Indentation.get_rating_parameters

  • feat: compute additional ancillary parameter “Maximum indentation”

  • feat: new functions model.get_parm_unit and updated model.get_parm_name to work with ancillary parameters as well

version 1.3.0

  • feat: allow to define ancillary parameters for models and use them during fitting by default

  • feat: Indentation.get_initial_fit_parameters now automatically computes common and model-related ancillary parameters if no initial parameters are present

  • enh: allow to set the model_key in more functions of Indentation

  • ref: use idnt to represent Indentation instances

  • fix: preprocessing steps not stored in Indentation.preprocessing

  • setup: bump afmformats from 0.4.1 to 0.5.0

version 1.2.4

  • enh: update boundaries and default values for model parameters

version 1.2.3

  • fix: FitProperties did not detect changes in “params_initial”

version 1.2.2

  • setup: bump afmformats version from 0.3.0 to 0.4.1

version 1.2.1

  • enh: skip computation of tip position if it is already in the dataset and cannot be computed e.g. due to missing spring constant

  • fix: typo in get_data_paths_enum

  • setup: bump afmformats version from 0.2.0 to 0.3.0

version 1.2.0

  • tests: np.asscalar is deprecated

  • ref: migrate to afmformats (#1)

  • docs: minor improvements

version 1.1.2

  • fix: add __version__ property

  • tests: use time.perf_counter for timing tests

  • docs: improved LaTeX rendering

version 1.1.1

  • setup: migrate to PEP 517 (pyproject.toml)

  • docs: minor update

version 1.1.0

  • feat: add contact point to available features in qmap visualization

  • fix: avoid two invalid operations when computing features

version 1.0.1

  • fix: invalid operation when loading data with a callback function

version 1.0.0

  • docs: minor update

version 0.9.3

  • enh: store nanite and h5py library versions in rating container

  • enh: update hyperparameters of rating regressors

  • ref: deprecation in h5py: replace dataset.value by dataset[…]

version 0.9.2

  • ref: renamed the mode model_hertz_parabolic to model_hertz_paraboloidal to be consistent

  • docs: updat code reference and other minor improvements

version 0.9.1

  • fix: preprocessing keyword not working in Indentation.fit_model

  • docs: add another scripting example and minor improvements

  • tests: increase coverage

version 0.9.0

  • ref: remove legacy “discrete” feature type

  • ref: renamed kwargs for Indetation.rate_quality

  • ref: new method nanite.load_group for loading experimental data

  • ref: new class read.data.IndentationData for managing data

  • ref: replace dataset.IndentationDataSet with group.IndentationGroup to avoid ambiguities

  • fix: add missing “zef18” training set

  • fix: sample weight computation failed when a rating level was missing

  • enh: add nanite-generate-training-set command line program

  • tests: reduce warnings and increase coverage

  • cleanup: old docs in nanite.rate.io

  • docs: major update using helper extensions

version 0.8.0

  • initial release