AFM-SPM/TopoStats issues and pull requests

#707 - Adds a complete custom matplotlibrc params file

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 2 comments

#706 - Add unit tests for `topostats.tracing.tracinfuncs.orderTrace`

Issue - State: open - Opened by ns-rse over 1 year ago
Labels: testing, DNATracing

#705 - TopoStats Logo

Issue - State: open - Opened by ns-rse over 1 year ago - 5 comments
Labels: help wanted, good first issue, documentation, Images

#704 - Expand plotting defaults and option for users to load their own mplstyle

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: Plotting, user experience

#703 - Annotate plots with a footer referencing TopoStats

Issue - State: open - Opened by ns-rse over 1 year ago - 1 comment
Labels: enhancement, Low Priority, Plotting

#702 - Move all cropped images to folder inside processed

Issue - State: open - Opened by MaxGamill-Sheffield over 1 year ago - 1 comment
Labels: enhancement, Low Priority

#701 - Maxgamill sheffield/692 standardised images

Pull Request - State: closed - Opened by MaxGamill-Sheffield over 1 year ago - 3 comments

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

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

#699 - Remove broad Exception catch surrounding dnatracing

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 3 comments
Labels: enhancement, v2.3.0

#698 - Explicit request of Python packages in Bug Reports

Pull Request - State: closed - Opened by ns-rse over 1 year ago

#697 - Add pytest-github-actions-annotate-failures

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment

#696 - Dnatracing fails when one molecule spline fails

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 7 comments
Labels: bug

#695 - Sylvia whittle/height trace redo

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 8 comments

#694 - Move Notebooks to run on JupyterLite

Issue - State: closed - Opened by ns-rse over 1 year ago - 2 comments
Labels: notebooks

#692 - Standardised plotting format

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: Plotting

#691 - Adding 3.12 to workflow test matrix

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 4 comments

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

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

#689 - Remove redundant test

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: testing

#688 - Add a zeroing step to filters

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 2 comments

#687 - Add test for processing when scar removal is disabled

Issue - State: open - Opened by ns-rse over 1 year ago - 1 comment
Labels: testing, scars

#686 - Support Python 3.12

Issue - State: closed - Opened by ns-rse over 1 year ago - 3 comments
Labels: CI/CD

#685 - Switch to igor2 for .ibw and unpeg NumPy

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: IO

#684 - Switch to igor2 for .ibw and unpeg NumPy dependency

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: IO

#683 - Switch to igor2 for .ibw and unpeg NumPy dependency

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: IO

#682 - Unpeg numpy==1.23.4 by switching to igor2

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: bug, IO

#681 - Missed line 45 noqa and hadn't corrected class name

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: linting

#680 - Legend plotted on single image violin plots; update to Seaborn 0.13

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: CI/CD, testing, Plotting

#679 - Violin plots changed as of Seaborn 0.13. [Tests broken].

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 2 comments
Labels: bug, testing, Plotting

#678 - Disable scars by default and fix KDE plotting bug

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 4 comments

#677 - Disable scar removal by default

Issue - State: closed - Opened by SylviaWhittle over 1 year ago
Labels: enhancement

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

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

#675 - Add .asd file support

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 5 comments
Labels: enhancement

#674 - No nm scaling when no config file used

Issue - State: closed - Opened by derollins over 1 year ago - 2 comments
Labels: bug

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

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

#672 - Remove `tests/tracing/test_dnatracing_single_grain.py::test_purge_obvious_crap_exceptions()

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: testing

#671 - Maxgamill sheffield/cats window

Pull Request - State: closed - Opened by MaxGamill-Sheffield over 1 year ago - 2 comments

#670 - Adding Ruff and pydocstyle to pre-commit

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 3 comments
Labels: CI/CD, linting, configuration

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#668 - Add codecov to CI pipeline

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: CI/CD

#667 - Lower default DPI of individual molecule plots

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment

#666 - Add upper limit to thresholding

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 10 comments
Labels: enhancement

#665 - Changed dict crop_size -1 names to match processing

Pull Request - State: closed - Opened by MaxGamill-Sheffield over 1 year ago - 1 comment

#664 - Adds details for image_stats.csv

Pull Request - State: closed - Opened by ns-rse over 1 year ago
Labels: documentation

#663 - Add pydocstyle to pre-commit checks

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: enhancement, documentation, CI/CD

#662 - Moves DPI configuration from default_config to plotting_dictionary

Pull Request - State: closed - Opened by ns-rse over 1 year ago

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#660 - Add pydocstyle to pre-commit hooks

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: CI/CD

#659 - Conversion factors from um to nanometre added in load_gwy in io.py

Pull Request - State: closed - Opened by iobataya over 1 year ago - 4 comments

#658 - Fix plotting in pixels for topostats files

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago

#657 - .topostats file plotting in pixels not nanometres

Issue - State: closed - Opened by SylviaWhittle over 1 year ago
Labels: bug

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

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

#655 - Document Statistics in all_statistics.csv and image_stats.csv

Issue - State: closed - Opened by SylviaWhittle over 1 year ago
Labels: enhancement, Low Priority

#654 - Fix broken reference to 'image', now 'image_original'

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment

#653 - Improve linear splining

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 11 comments

#652 - Improved binary masking to retain details from grains

Issue - State: closed - Opened by llwiggins over 1 year ago - 1 comment
Labels: enhancement

#649 - Notebook for DNA Tracing

Issue - State: open - Opened by ns-rse over 1 year ago
Labels: DNATracing, notebooks

#648 - Continue refactoring internals of processing.py

Issue - State: open - Opened by SylviaWhittle over 1 year ago - 1 comment
Labels: enhancement

#647 - Fork libasd and release to PyPI

Issue - State: closed - Opened by ns-rse over 1 year ago - 2 comments
Labels: IO

#646 - Script for constructing .topostats files out of images and masks.

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment
Labels: enhancement

#645 - Move DPI setting to plotting dictionary

Issue - State: closed - Opened by ns-rse over 1 year ago - 3 comments
Labels: Plotting, configuration

#644 - Handle duplicate statistics that arise from multiple molecules within a single grain

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: Plotting, DNATracing

#643 - Plotting Notebook should have examples of groupby

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: notebooks

#642 - Splined Traces Overlay Image

Issue - State: closed - Opened by MaxGamill-Sheffield over 1 year ago - 1 comment
Labels: enhancement

#641 - More prominent signposting for Notebooks in Documentation

Issue - State: open - Opened by ns-rse over 1 year ago
Labels: notebooks

#640 - Run Notebooks in Google Colab/Jupyter Lite

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: notebooks

#639 - Tests for Notebooks

Issue - State: open - Opened by ns-rse over 1 year ago
Labels: testing

#638 - Notebooks

Issue - State: open - Opened by ns-rse over 1 year ago
Labels: notebooks, Epic

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

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

#636 - TopoStats RoadMap

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment
Labels: planning

#635 - Adds pytest exts to dev dependencies; disables some pytest warnings

Pull Request - State: closed - Opened by ns-rse over 1 year ago
Labels: user experience

#634 - Resolve conflict of arguments between toposum and run_topostats

Issue - State: open - Opened by ns-rse over 1 year ago - 1 comment
Labels: bug, testing

#633 - Speed up tests

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 2 comments

#631 - Tidy up dataframe creation

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 2 comments
Labels: enhancement, v2.3.0

#630 - Cats branch intermittent thread crash & hang

Issue - State: closed - Opened by MaxGamill-Sheffield over 1 year ago - 8 comments
Labels: bug

#629 - Flattening: Zero the background height before masking

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment
Labels: bug

#628 - Add parameter for test_trace_mask for pad_width = 2

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 7 comments
Labels: testing

#627 - Expand testes for trace_mask() to cover padding > 1

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: testing

#626 - Nonlinear polynomial and edge intersecting grains

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 2 comments

#625 - Update notebooks to fix dnatracing issue

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment

#624 - Notebooks need updating to reflect DNAtracing changes

Issue - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment
Labels: bug

#623 - Updating CITATION.cff

Pull Request - State: closed - Opened by ns-rse over 1 year ago - 1 comment

#622 - User facing channel names swapped for bts channel names

Pull Request - State: closed - Opened by derollins over 1 year ago - 1 comment

#621 - Wrong channel error message incorrect (spms)

Issue - State: closed - Opened by MaxGamill-Sheffield over 1 year ago
Labels: bug

#620 - Update CITATION.cff

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: documentation

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago

#617 - Method of Quantifying Protein Location on DNA Strand

Issue - State: open - Opened by neumagen over 1 year ago - 6 comments
Labels: enhancement

#615 - Add support for .TIFF files

Issue - State: open - Opened by SylviaWhittle over 1 year ago - 2 comments
Labels: enhancement

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

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

#613 - Sylvia whittle/601 further modularisation

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment

#612 - Add option to not ignore errors

Issue - State: open - Opened by SylviaWhittle over 1 year ago - 1 comment
Labels: enhancement

#611 - Sylvia whittle/plotting traces new

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment

#610 - Prune skeletons

Issue - State: closed - Opened by ns-rse over 1 year ago - 3 comments
Labels: DNATracing

#609 - Correcting padding of test grains for tracing

Pull Request - State: closed - Opened by ns-rse over 1 year ago

#608 - Consider pytest-dev/pytest-github-actions-annotate-failures

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: CI/CD

#607 - Splining Linear Molecules

Issue - State: closed - Opened by ns-rse over 1 year ago - 1 comment

#606 - Correct single grain images for dnatracing tests and investigate padding

Issue - State: closed - Opened by ns-rse over 1 year ago
Labels: DNATracing

#605 - Sylvia whittle/plotting traces OLD

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 2 comments

#604 - Add extra image_set options

Issue - State: open - Opened by derollins over 1 year ago
Labels: enhancement

#603 - Fix typo "contour_lengths" -> "contour_length"

Pull Request - State: closed - Opened by SylviaWhittle over 1 year ago - 1 comment

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

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

GitHub / AFM-SPM/TopoStats issues and pull requests