topostats - v2.3.0

What's Changed

• Fixes for height-biasing of skeletons by @llwiggins in https://github.com/AFM-SPM/TopoStats/pull/815
• tests: Adapts get_skeleton() tests to the getSkeleton() class by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/822
• chore: Linting dnatracing; setup skeletons for remaining tests; split pruning to submodule by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/825
• Update dnatracing docstrings by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/826
• chore(tracing,skeleton): Line length linting; correcting tpyos by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/827
• tests(utils/pruning): Tests for utils and some of the pruning classes by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/835
• tests: Moves dummy skeleton & heights fixtures to tests/conftest.py by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/844
• chore(workflows): updating to setup-python@v5 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/857
• feature(measure): Adds the height_profiles sub-module by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/859
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in https://github.com/AFM-SPM/TopoStats/pull/867
• tests(pruning): Tests TopoStatsPrune and convPrune by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/848
• Bound aspect ratio between 0 and 1 by @llwiggins in https://github.com/AFM-SPM/TopoStats/pull/864
• fix: Removes saving of plots to pickles by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/872
• Incorporating height profile into GrainStats by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/871
• Re-add changes for connectnodesnearest by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/879
• Fixing broken tests (Part I) by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/874
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in https://github.com/AFM-SPM/TopoStats/pull/883
• Sylvia whittle/800 analyse nodes by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/888
• Maxgamill sheffield/800 btr splining by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/889
• Add U-Net grain segmentation option by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/890
• Seperate out Splining from dnaTracing by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/886
• Fix height profile tests for macOS by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/894
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in https://github.com/AFM-SPM/TopoStats/pull/895
• Add multi-class deep learning segmentation support by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/893
• Adding RI code to handle and break odd crossings by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/891
• tests(plotting): revert moleculenumber > grainnumber in tests by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/882
• test: Adds pytest-icdiff to dev dependencies by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/905
• chore: fix linting errors by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/900
• tests(processing): Improves logic and tests for checkrunsteps() by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/903
• fix: reinstate grains try except by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/906
• test(utils): Fixing broken tests by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/907
• tests(plottingfuncs): fixes failing tests by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/909
• Add trace smoothing tests by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/892
• tests: Remove restriction on pytest<8.0.0 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/917
• tests: Remove restriction on pytest<8.0.0 (cherry pick) by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/918
• fix(plotting): remove dilation if images are large by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/914
• Add basic smoke tests for topology branch by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/897
• ci: Run tests workflow on all pull_request by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/925
• ci: Add local pytest --testmon to pre-commit by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/926
• ci: restrict supported python version to <3.12 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/931
• Adds topological features into better tracing by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/898
• ci: Explicit types of pull requests and paths to run CI tests by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/933
• style(tracing/nodestats): Fix all numpydoc-validation errors by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/937
• Fix processing tests by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/939
• 800 : Migrate / delete old dnatracing tests by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/941
• Fix Grainstats failing test on 800-better-tracing by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/940
• Fixes failing pruning tests on 800-better-tracing by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/938
• ci: Adds tmate to tests.yaml workflow by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/946
• fix(disorderedtracing): force branchtype to int64 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/949
• style(theme): RT01 Numpydoc Validation by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/952
• style(tracingfuncs): Numpydoc validation, PEP8 & tidying by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/948
• docs: Document refactored tracing by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/936
• 950 better tracing angle out of range by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/956
• ci: gh-pages building correctly by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/961
• ci: gh-pages building correctly by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/963
• docs: lower-case link by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/964
• ci(sphinx): Python 3.12 > 3.11 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/965
• Fixes the dictionary keys docs formation by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/968
• Adding the Better Tracing Suite into Main by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/932
• Remove Python 3.8 from pyproject.toml classifiers by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/971
• Removing errant notebook by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/970
• Fixes pd.concat error halting processing by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/972
• tests(utils): parameterise testcreateempty_dataframe() by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/977
• chore: Adds fair-software.eu badge to README.md by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/979
• Fixes None tracing outputs attempted to be concatenated by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/973
• tests(disordered_tracing): Bulks out missing unittests by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/978
• feature: Print 'art' above completion message by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/980
• General Cleanup and Following the Better Tracing Merger by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/976
• fix: Remove duplicate modification of TensorFlow log level by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/982
• refactor(entry_points): Removing legacy entry points by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/985
• Add support for partial config files by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/981
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in https://github.com/AFM-SPM/TopoStats/pull/991
• wip: Adding all configuration options as arguments by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/988
• Add documentation for flattening and grains by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/993
• update readme.md with new swiss army knife processing order by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/997
• refactor(run_modules): Move common setup to individual functions by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/996
• ci: Adds a Pull Request template by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1000
• Hariborings vetting to main by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/992
• tests(processing): Update regression test targets to include dna width by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1002
• package: Unpin topoly version by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/995
• doc: Reduce Python version to 3.11 in .readthedocs.yaml by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1004
• style: Changes prettier mirror used by pre-commit by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1011
• dependabot for GitHub Actions by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1012
• config: Removes target-version from ruff configuration by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1013
• ci: Adds pygrep-hooks and fixes errors by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1014
• Build(deps): Bump actions/add-to-project from 0.5.0 to 1.0.2 by @dependabot in https://github.com/AFM-SPM/TopoStats/pull/1015
• Build(deps): Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/AFM-SPM/TopoStats/pull/1016
• ci: group dependabot github-actions updates by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1017
• Add basic curvature by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/974
• chore: Updates publication in README.md by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1024
• chore: Adds earlier contributors to CITATION.cff by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1023
• docs: Adds Under/Over preprint link to Publications of README.md by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1027
• [pre-commit.ci] pre-commit-autoupdate by @pre-commit-ci in https://github.com/AFM-SPM/TopoStats/pull/1032
• refactor(io): Load files with AFMReader by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1031
• chore: Improves .gitignore to ignore more Python files by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1034
• style: Tidying calculatednawidth() by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1035
• Added average grain width measurement to disordered tracing by @tcatley in https://github.com/AFM-SPM/TopoStats/pull/999
• Remove index column from results plus some other tidying by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1045
• doc: Updates the data dictionary by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1040
• tests(unet_masking): Correct ids and add expected fail by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1046
• Modifies the squaring bbox and tweaks PIL input shapes by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/1030
• Enables legacy unets to run by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/1042
• Returns grainstats rows when tracing for a grain fails by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/1047
• Refactor smooth_mask to take null values by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/1051
• Adds nbQA to pre-commit hooks by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1048
• Added more info to cores-1 bug report label by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/1050
• chore: Remove unused method, test and package dependencies by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1049
• style(notebooks): Ignore Flake8 complaints on Notebooks by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1053
• refactor(disordered_tracing): Work with skan-0.12.2 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1052
• chore: Clarify request for log output in bug reports by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1055
• feature: Adds --image-set as option to topostats by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/1058
• curvature images doesn't overwrite by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/1056

New Contributors

• @dependabot made their first contribution in https://github.com/AFM-SPM/TopoStats/pull/1015
• @tcatley made their first contribution in https://github.com/AFM-SPM/TopoStats/pull/999

Full Changelog: https://github.com/AFM-SPM/TopoStats/compare/v2.2.1...v2.3.0

- Python
Published by ns-rse about 1 year ago

topostats - v2.3.1

What's Changed

• Added average grain width measurement to disordered tracing by @tcatley in https://github.com/AFM-SPM/TopoStats/pull/999
• Combine grain crops rather than overwriting them by @llwiggins in https://github.com/AFM-SPM/TopoStats/pull/1070

New Contributors

• @dependabot made their first contribution in https://github.com/AFM-SPM/TopoStats/pull/1015
• @tcatley made their first contribution in https://github.com/AFM-SPM/TopoStats/pull/999

Full Changelog: https://github.com/AFM-SPM/TopoStats/compare/v2.2.1...v2.3.1

- Python
Published by ns-rse over 1 year ago

topostats - v2.2.1

Highlights

• Basic .tif file support (currently no metadata is included).
• Saves results in HDF5 file.
• Supports Python 3.12
• Improved .asd file format via AFMReader (nee topofileformats)
• New submodule for feret calculations.
• Support for very small (pm) and large (mm) scans.

What's Changed

• pytest<8.0.0 by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/788
• Add the option to save as a tif file by @derollins in https://github.com/AFM-SPM/TopoStats/pull/778
• Save grain trace data to HDF5 format by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/790
• Added 'pm' and 'mm' for very small and large scans by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/801
• Added 'pm' and 'mm' for very small and large scans by @MaxGamill-Sheffield in https://github.com/AFM-SPM/TopoStats/pull/796
• Remove saving of gaussian filtered arrays to .npy files by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/804
• Adding 3.12 to workflow test matrix by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/691
• Sets the type of all arguments that are files/paths to Path by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/809
• Fixing DPI settings by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/808
• Tidies up Images.plotandsave() by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/810
• Adds numpydoc-validation hook to pre-commit by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/816
• New submodule for feret calculations by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/755
• refactor(grainstats): GrainStats.getmaxmin_feret() > measure.feret by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/823
• chore: Update codecov version used in test workflow by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/831
• bug: Addresses importlib.resources.open_text() deprecation by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/830
• Resolve .gwy file not loading and add channel support for .gwy files by @SylviaWhittle in https://github.com/AFM-SPM/TopoStats/pull/837
• chore: Update dependency to AFMReader by @ns-rse in https://github.com/AFM-SPM/TopoStats/pull/852

Full Changelog: https://github.com/AFM-SPM/TopoStats/compare/v2.2.0...v2.2.1

- Python
Published by ns-rse almost 2 years ago

topostats - 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.

- Python
Published by ns-rse over 2 years ago

topostats - v2.2.0

User Interface

• Switched to topostats <action> and removed original run_topostats.
• 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: https://github.com/AFM-SPM/TopoStats/compare/v2.1.2...v2.2.0

- Python
Published by ns-rse over 2 years ago

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

Full Changelog: https://github.com/AFM-SPM/TopoStats/compare/v2.1.1...v2.1.2

- Python
Published by ns-rse over 2 years ago

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

Full Changelog: https://github.com/AFM-SPM/TopoStats/compare/v2.1.0...v2.1.1

- Python
Published by ns-rse almost 3 years ago

topostats - TopoStats v2.1.0

The TopoStats team are pleased to announce the release of v2.1.0 :tada: . 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: https://github.com/AFM-SPM/TopoStats/compare/v2.0.0...v2.1.0

- Python
Published by ns-rse about 3 years ago

topostats - 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

- Python
Published by ns-rse over 3 years ago