Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / AFM-SPM/TopoStats issues and pull requests

#957 - fix: docutils<0.21; unpin sphinx-autoapi

Pull Request - State: closed - Opened by ns-rse 4 months ago - 4 comments
Labels: documentation, CI/CD

#955 - ci(gh-pages): Bump Python version to 3.12 for gh-pages workflow

Pull Request - State: closed - Opened by ns-rse 4 months ago - 2 comments

#945 - Add topostats file helper class

Pull Request - State: open - Opened by SylviaWhittle 4 months ago - 14 comments
Labels: user experience

#944 - Improve documentation and perhaps warn users about GPU requirements

Issue - State: open - Opened by ns-rse 4 months ago - 1 comment
Labels: documentation, Low Priority, user experience, v2.5.0

#943 - Update notebooks for better tracing

Issue - State: open - Opened by SylviaWhittle 4 months ago - 2 comments
Labels: enhancement, v2.3.2

#921 - Improve automatic testing strategy

Issue - State: open - Opened by ns-rse 5 months ago
Labels: CI/CD, Epic, tests

#916 - Split ML functionality dependencies into optional-dependencies

Issue - State: open - Opened by ns-rse 5 months ago - 1 comment
Labels: Low Priority, user experience, v2.3.2

#906 - fix: reinstate grains try except

Pull Request - State: open - Opened by ns-rse 5 months ago

#905 - test: Adds pytest-icdiff to dev dependencies

Pull Request - State: open - Opened by ns-rse 5 months ago

#904 - Add pytest-icdiff to facilitate visualising differences in failed tests

Issue - State: open - Opened by ns-rse 5 months ago
Labels: tests

#903 - tests(processing): Improves logic and tests for check_run_steps()

Pull Request - State: open - Opened by ns-rse 5 months ago
Labels: tests

#901 - Move description of nodestats dictionary to documentation

Issue - State: open - Opened by ns-rse 5 months ago
Labels: documentation

#900 - chore: fix linting errors

Pull Request - State: open - Opened by ns-rse 5 months ago - 3 comments
Labels: CI/CD

#898 - Adds topological features into better tracing

Pull Request - State: open - Opened by MaxGamill-Sheffield 5 months ago - 2 comments

#897 - Add basic smoke tests for topology branch

Pull Request - State: open - Opened by SylviaWhittle 5 months ago - 3 comments

#896 - Incorporate tmate into CI to facilitate debugging

Issue - State: open - Opened by ns-rse 6 months ago

#895 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 6 months ago

#894 - Fix height profile tests for macOS

Pull Request - State: closed - Opened by SylviaWhittle 6 months ago

#893 - Add multi-class deep learning segmentation support

Pull Request - State: closed - Opened by SylviaWhittle 6 months ago - 6 comments

#892 - Add trace smoothing tests

Pull Request - State: open - Opened by SylviaWhittle 6 months ago

#891 - Adding RI code to handle and break odd crossings

Pull Request - State: closed - Opened by MaxGamill-Sheffield 6 months ago

#890 - Add U-Net grain segmentation option

Pull Request - State: closed - Opened by SylviaWhittle 6 months ago - 3 comments

#889 - Maxgamill sheffield/800 btr splining

Pull Request - State: closed - Opened by MaxGamill-Sheffield 6 months ago - 1 comment

#888 - Sylvia whittle/800 analyse nodes

Pull Request - State: closed - Opened by SylviaWhittle 6 months ago

#887 - [feature] : message in terminal that says which image causes an error when processing multiple files at the same time

Issue - State: closed - Opened by TFirth2 6 months ago - 6 comments
Labels: enhancement, v2.3.0

#886 - Seperate out Splining from dnaTracing

Pull Request - State: closed - Opened by MaxGamill-Sheffield 6 months ago - 1 comment

#885 - tests(ordered_tracing): Tests and fixes for ordered_trace_mask()

Pull Request - State: closed - Opened by ns-rse 6 months ago - 2 comments

#884 - Separate out Ordered Tracing from dnaTracing.py

Pull Request - State: closed - Opened by MaxGamill-Sheffield 7 months ago - 2 comments

#883 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 7 months ago

#882 - tests(plotting): revert molecule_number > grain_number in tests

Pull Request - State: closed - Opened by ns-rse 7 months ago - 1 comment
Labels: tests

#881 - Separate out NodeStats in 800-better-tracing-refactor

Pull Request - State: closed - Opened by MaxGamill-Sheffield 7 months ago - 1 comment

#880 - Changes to test files from PR #876

Pull Request - State: open - Opened by llwiggins 7 months ago - 4 comments

#879 - Re-add changes for connect_nodes_nearest

Pull Request - State: closed - Opened by SylviaWhittle 7 months ago - 2 comments

#878 - Refactor and test connect_extended_nodes_nearest

Pull Request - State: open - Opened by SylviaWhittle 7 months ago - 4 comments

#877 - Separates out the NodeStats statistics from dnatracing

Pull Request - State: closed - Opened by MaxGamill-Sheffield 7 months ago - 1 comment

#876 - Separated Disordered Tracing into own module

Pull Request - State: closed - Opened by MaxGamill-Sheffield 7 months ago - 5 comments

#875 - Height profiles for line perpendicular to maximum feret

Issue - State: open - Opened by ns-rse 7 months ago
Labels: Low Priority, GrainStats

#874 - Fixing broken tests (Part I)

Pull Request - State: closed - Opened by ns-rse 7 months ago - 3 comments
Labels: DNATracing, tests

#873 - Document updating HDF5 test files

Issue - State: open - Opened by ns-rse 8 months ago
Labels: good first issue, documentation, Low Priority

#872 - fix: Removes saving of plots to pickles

Pull Request - State: closed - Opened by ns-rse 8 months ago - 1 comment

#871 - Incorporating height profile into GrainStats

Pull Request - State: closed - Opened by ns-rse 8 months ago - 3 comments

#869 - DeprecationWarning: Pickle, copy, and deepcopy support will be removed from itertools in Python 3.14.

Issue - State: closed - Opened by ns-rse 8 months ago - 1 comment
Labels: deprecations

#868 - Refactor using functools.partial

Issue - State: open - Opened by ns-rse 8 months ago
Labels: Low Priority, refactor

#867 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago

#866 - [Bug]: Igor2 cannot be imported using Python 3.12

Issue - State: closed - Opened by SylviaWhittle 8 months ago - 2 comments
Labels: bug

#865 - [Bug]: Matplotlib 3.9.0 register_cmap deprecation

Issue - State: closed - Opened by SylviaWhittle 8 months ago - 2 comments
Labels: bug, duplicate

#864 - Bound aspect ratio between 0 and 1

Pull Request - State: closed - Opened by llwiggins 8 months ago - 2 comments

#863 - [feature] : Ferret ratio metric

Issue - State: open - Opened by MaxGamill-Sheffield 8 months ago
Labels: enhancement

#862 - [feature] : Surface RMS roughness metric

Issue - State: open - Opened by MaxGamill-Sheffield 8 months ago - 1 comment
Labels: enhancement

#861 - [feature] : Bound aspect ratio between 0 and 1

Issue - State: closed - Opened by MaxGamill-Sheffield 8 months ago
Labels: enhancement

#860 - [feature] : Circularity Metric

Issue - State: open - Opened by MaxGamill-Sheffield 8 months ago - 2 comments
Labels: enhancement, GrainStats

#859 - feature(measure): Adds the height_profiles sub-module

Pull Request - State: closed - Opened by ns-rse 8 months ago - 3 comments
Labels: GrainStats, Plotting, tests, measure

#858 - Processing .ibw images

Issue - State: open - Opened by ns-rse 8 months ago - 1 comment

#857 - chore(workflows): updating to setup-python@v5

Pull Request - State: closed - Opened by ns-rse 9 months ago

#855 - add orig err msg in broad channel try/except

Pull Request - State: closed - Opened by MaxGamill-Sheffield 9 months ago - 1 comment

#854 - chore: Update dependency to AFMReader

Pull Request - State: closed - Opened by MaxGamill-Sheffield 9 months ago - 1 comment

#853 - [Bug]: asd available channels not logged

Issue - State: closed - Opened by MaxGamill-Sheffield 9 months ago - 2 comments
Labels: bug

#852 - chore: Update dependency to AFMReader

Pull Request - State: closed - Opened by ns-rse 9 months ago - 2 comments

#851 - [Bug]: Update topofileformats dependency to AFMReader [URGENT]

Issue - State: closed - Opened by SylviaWhittle 9 months ago - 5 comments
Labels: bug

#849 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 9 months ago

#848 - tests(pruning): Tests TopoStatsPrune and convPrune

Pull Request - State: closed - Opened by ns-rse 9 months ago - 14 comments

#847 - Bending Angle Calculations

Issue - State: open - Opened by ns-rse 9 months ago - 2 comments
Labels: curvature

#846 - chore(init): Update registration of colormaps

Pull Request - State: closed - Opened by ns-rse 9 months ago
Labels: Plotting, configuration

#845 - Update colormap registration

Issue - State: closed - Opened by ns-rse 9 months ago
Labels: Plotting, configuration

#844 - tests: Moves dummy skeleton & heights fixtures to tests/conftest.py

Pull Request - State: closed - Opened by ns-rse 9 months ago

#843 - [tests] Consolidate fixtures from pruning and height profiles

Issue - State: closed - Opened by ns-rse 9 months ago - 1 comment
Labels: tests

#842 - ci: Peg sphinx-autoapi-3.1.0b0

Pull Request - State: closed - Opened by ns-rse 9 months ago
Labels: documentation, CI/CD

#841 - Documentation fails to build

Issue - State: closed - Opened by ns-rse 9 months ago - 2 comments

#840 - ci(gh-pages): Build docs on PRs to main branch only

Pull Request - State: closed - Opened by ns-rse 9 months ago
Labels: CI/CD

#839 - ci(gh-pages): Build docs on PRs to main branch only

Pull Request - State: closed - Opened by ns-rse 9 months ago

#838 - Restrict GitHub Pages building to PRs on main branch

Issue - State: closed - Opened by ns-rse 9 months ago
Labels: documentation

#835 - tests(utils/pruning): Tests for utils and some of the pruning classes

Pull Request - State: closed - Opened by ns-rse 10 months ago - 9 comments

#834 - [feature] : Add support for legacy Bruker .spm.### files

Issue - State: open - Opened by ns-rse 10 months ago
Labels: enhancement, IO

#833 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago

#832 - [Bug]: Gwy file not loading

Issue - State: closed - Opened by SylviaWhittle 10 months ago - 1 comment
Labels: bug

#831 - chore: Update codecov version used in test workflow

Pull Request - State: closed - Opened by ns-rse 10 months ago
Labels: CI/CD

#830 - bug: Addresses importlib.resources.open_text() deprecation

Pull Request - State: closed - Opened by ns-rse 10 months ago
Labels: IO

#829 - [doc] Add nanosurf to listed of related software

Issue - State: open - Opened by ns-rse 10 months ago
Labels: documentation, Low Priority

#827 - chore(tracing,skeleton): Line length linting; correcting tpyos

Pull Request - State: closed - Opened by ns-rse 10 months ago

#826 - Update dnatracing docstrings

Pull Request - State: closed - Opened by MaxGamill-Sheffield 10 months ago

#824 - test(grainstats): Removes min/max feret co-ordinates from output

Pull Request - State: closed - Opened by ns-rse 10 months ago

#823 - refactor(grainstats): GrainStats.get_max_min_feret() > measure.feret

Pull Request - State: closed - Opened by ns-rse 10 months ago - 1 comment

#822 - tests: Adapts get_skeleton() tests to the getSkeleton() class

Pull Request - State: closed - Opened by ns-rse 11 months ago - 6 comments
Labels: linting, tests

#821 - tests: Adapts get_skeleton() tests to the getSkeleton() class

Pull Request - State: closed - Opened by ns-rse 11 months ago
Labels: linting, tests

#820 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago - 1 comment

#819 - Improve licensing compliance

Issue - State: open - Opened by ns-rse 11 months ago
Labels: Licensing

#818 - Tests for Skeletonisation and Pruning

Issue - State: open - Opened by ns-rse 11 months ago - 3 comments
Labels: testing

#817 - Typo correction to default_config.yaml

Pull Request - State: closed - Opened by derollins 12 months ago - 1 comment

#816 - Adds numpydoc-validation hook to pre-commit

Pull Request - State: closed - Opened by ns-rse 12 months ago - 1 comment
Labels: documentation, linting

#815 - Fixes for height-biasing of skeletons

Pull Request - State: closed - Opened by llwiggins 12 months ago

#814 - Document HDF5 image format

Issue - State: open - Opened by ns-rse 12 months ago
Labels: IO

#813 - Extract metadata from images and make available for saving

Issue - State: open - Opened by ns-rse 12 months ago
Labels: Images, IO