TopoStats v2.2.post0

The tag v2.2.0 appears to have already been used on PyPI (although no trace of it remains) and its impossible to make releases with versions that have already been used. This is therefore post0 as the release is identical and complies with such minor changes as described in the Python packaging post-releases page.

Please refer to v2.2.0 release notes for details of changes.

v2.2.0

User Interface

• Switched to topostats <action> and removed original run_topostats, for more details please refer to the usage documentation.
• Introduces a complete matplotlibrc params file for customising plots en-masse
  • Added topostats create-matplibrc command (with options) for generating user customisable figures.
• .asd file support @SylviaWhittle

Bugs

• Plotting of images that touch the border are now fixed @MaxGamill-Sheffield
• Improved linear splinning @SylviaWhittle
• Flattening runs when scar removal is disabled (which is now the default).

Miscellaneous

• Various minor updates to make the package compliant with Scientific Python Repository Review (still a few more steps to go though).

Development

• Adds snoop to aid with debugging.
• Additional pre-commit hooks are now included that prevent accidental commits to main.
• Issue templates have been improved to use Issue Forms.

Full Changelog: v2.1.2...v2.2.0

v2.1.2

Various small changes fixing aspects of plotting with regards to DPI and axis scales. Dependencies are updated and improved and igor2 instead of the unmaintained igor is now used for loading .ibw. Linting is improved and considerably faster in the pre-commit pipeline courtesy with ruff rather than flake8 and introducing pydocstyle linting.

Importantly scar removal is now disabled by default, its a time consuming step and should only be enable if you know you have scars in your scans that you want removing.

What's Changed

• Switched to igor2 instead of igor for loading .ibw files which allows unpinning of numpy dependency #685
• Added ruff and pydocstyle to the pre-commit configuration and removed flake8 (ruff covers the same issues) by @ns-rse in #670
• Moves DPI configuration from default_config to plotting_dictionary
• Fix broken reference to 'image', now 'image_original' by @SylviaWhittle in #654
• Updates violin plots to work with Seaborn-0.13 and adds legend only to plots with multiple images by @ns-rse in #680
• Disable scars by default and fix KDE plotting bug by @SylviaWhittle in #678
• Add a zeroing step to filters by @SylviaWhittle in #688
• Fix plotting in pixels for topostats files by @SylviaWhittle in #658
• Adds details for image_stats.csv by @ns-rse in #664
• Changed dict crop_size -1 names to match processing by @MaxGamill-Sheffield in #665
• Lower default DPI of individual molecule plots by @SylviaWhittle in #667
• Remove redundant test by @ns-rse in #689

Full Changelog: v2.1.1...v2.1.2

v2.1.1

A broad overview of what has changed...

Technical

• Dramatically speed up tests
• Nonlinear polynomial and edge intersecting grains.
• Set scale for cropped grains.
• Various improvements of tests.
• Refactoring of DNATracing to process individual grains rather than the whole image.

User Facing

• User facing channel names have been updated.
• Introduces images statistics in addition to grains statistics.
• DNA traces are now overlaid on plots

In Detail...

• Sylvia whittle/550 replace imghdr by @SylviaWhittle in #579
• Sylvia whittle/486 area unit tests by @SylviaWhittle in #578
• Quotes around installation of extra requirements by @ns-rse in #586
• Sylvia whittle/582 channel not found by @SylviaWhittle in #587
• Make channel a free text field by @SylviaWhittle in #590
• Include comments in config files generated with --create-config-file by @SylviaWhittle in #588
• Sylvia whittle/581 group plots by dir by @SylviaWhittle in #584
• Adds unit-tests for dnatracing methods by @ns-rse in #593
• Fixing tpyo's adding in image by @ns-rse in #599
• Improves processing of multiple grains during dnatracing by @ns-rse in #600
• Sylvia whittle/ 517 swiss army knife by @SylviaWhittle in #540
• Fix typo "contour_lengths" -> "contour_length" by @SylviaWhittle in #603
• Sylvia whittle/596 zscale grains by @SylviaWhittle in #597
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in #602
• Correcting padding of test grains for tracing by @ns-rse in #609
• Sylvia whittle/plotting traces new by @SylviaWhittle in #611
• Sylvia whittle/image stats by @SylviaWhittle in #556
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in #614
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in #618
• Update notebooks to fix dnatracing issue by @SylviaWhittle in #625
• Updating CITATION.cff by @ns-rse in #623
• User facing channel names swapped for bts channel names by @derollins in #622
• Nonlinear polynomial and edge intersecting grains by @SylviaWhittle in #626
• Add parameter for test_trace_mask for pad_width = 2 by @ns-rse in #628
• Sylvia whittle/601 further modularisation by @SylviaWhittle in #613
• Adds pytest exts to dev dependencies; disables some pytest warnings by @ns-rse in #635
• Speed up tests by @SylviaWhittle in #633
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in #637

Full Changelog: v2.1.0...v2.1.1

TopoStats v2.1.0

The TopoStats team are pleased to announce the release of v2.1.0 🎉 . A link to the full Changelog of the commits merged since v2.0.0 can be found at the bottom of this post.

Release Highlights

• Scar removal is now available and configurable (@SylviaWhittle)
• Support for .jpk files (@MaxGamill-Sheffield)
• Support for .gwy files (@SylviaWhittle)
• Improved logging verbosity (@ns-rse)
• Area thresholding of grains (@SylviaWhittle)
• Updated bug report templates (@ns-rse)
• Median flattening quantile configurable (@SylviaWhittle)
• Dots Per Inch (DPI) of scan plots is configurable (@ns-rse)
• Improvements to documentation which is now built for multiple versions and main branch (@SylviaWhittle , @ns-rse)
• Command line option to generate sample configuration files for subsequent customisation (@ns-rse)
• Processed arrays are saved as Numpy arrays for subsequent plotting (@SylviaWhittle)

Miscellaneous

• Citation File Format file is included (@ns-rse)
• Additional pre-commit hooks (markdownlint-cli2; ruff; pyupgrade; pylint) (@ns-rse)
• pre-commit.ci is now used on pull requests to ensure code passes all pre-commit hooks for linting code prior to merging. (@ns-rse)
• Updated bug report templates (@ns-rse)
• Switched to single pyproject.toml for package configuration (@ns-rse)
• Switched from versioneer to setuptools_scm for automatic versioning (@ns-rse)
• Output is now in SI units (i.e. metres rather than nanometres) (@SylviaWhittle)

Bug fixes

Thanks to all users who reported bugs, there were quite a few (19). @SylviaWhittle and @ns-rse have worked hard to track down and correct these and we hope to have squashed them all, but expect there to be more out there waiting for you to report. Please do not hesitate to start a discussion or open a new issue.

Notebooks

We also have a set of Jupyter Notebooks available from the GitHub repository. These take you through the steps in processing scans with TopoStats that run automatically, summarising the resulting statistics using Matplotlib, and plotting the scans which are now saved as Numpy arrays.

We are working on some Notebooks to run in Google Colab, for now though you can either save the Notebooks to your computer from GitHub and run them or clone the TopoStats repository and run them from the notebook directory.

Full Changelog: v2.0.0...v2.1.0

TopoStats v2.0.0

What's Changed

This is the first major release candidate of TopoStats v2. The code base has been completely re-written in Python 3 to remove the dependency on Gwyddion. Key features are...

• Refactoring of code to give classes which improves maintainability and extensibility.
• Filtering, flattening and grain detection performed via native code using NumPy and Scikit-Image functions.
• Configuration via YAML file(s).
• Re-written documentation on the website covering installation, usage and workflow.
• Unit and regression tests for refactored code run automatically via GitHub Actions.
• Linting of code to conform to PEP8 (via black and flake8).

Full Changelog: https://github.com/AFM-SPM/TopoStats/commits/v2.0.0-rc1

Contributors

The work has involved contributions from a number of the AFM-SPM team, in alphabetical order...

• @alicepyne
• @benthomasuos
• @bobturneruk
• @derollins
• @Jean-Du
• @JoeBeton
• @MaxGamill-Sheffield
• @ns-rse
• @SylviaWhittle