AFM-SPM/TopoStats issues and pull requests

#1087 - Added rough grainstats summary documentation and metric images

Pull Request - State: open - Opened by MaxGamill-Sheffield 10 days ago

#1086 - Update loading of `.topostats` now just data is returned

Issue - State: open - Opened by ns-rse 10 days ago
Labels: refactor

#1085 - [doc] Add reference to nanoAFMr in related software

Issue - State: open - Opened by ns-rse 11 days ago
Labels: documentation

#1084 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 12 days ago

#1083 - docs|style: line wrapping in adding_modules.md

Pull Request - State: closed - Opened by ns-rse 15 days ago
Labels: documentation

#1082 - Adds grains entry point

Pull Request - State: closed - Opened by ns-rse 18 days ago - 3 comments
Labels: Grains, refactor

#1081 - [Bug]: Get an error saving the height profiles when saving grains but not tracing (`disordered_tracing` set to `false`)

Issue - State: open - Opened by derollins 18 days ago
Labels: bug

#1080 - chore: correcting error in contributing.md

Pull Request - State: closed - Opened by ns-rse 24 days ago
Labels: documentation, Low Priority

#1079 - docs: Reworks documentation to use mkdocs

Pull Request - State: open - Opened by ns-rse 24 days ago - 2 comments
Labels: documentation

#1078 - docs: Clearer workflow overview

Pull Request - State: closed - Opened by ns-rse 24 days ago - 1 comment
Labels: documentation

#1077 - docs: how to add functions and modules

Pull Request - State: closed - Opened by ns-rse 24 days ago
Labels: documentation

#1076 - [Bug]: Minor issue: Running just the filter program with image_set=all produces plotting directory structure erroneously.

Issue - State: open - Opened by SylviaWhittle 25 days ago - 1 comment
Labels: bug

#1075 - Migrate documentation from Sphinx to Mkdocs

Issue - State: open - Opened by ns-rse 25 days ago
Labels: documentation, Low Priority, CI/CD

#1074 - Update Workflow diagram in docs

Issue - State: closed - Opened by ns-rse 25 days ago - 2 comments
Labels: good first issue, documentation

#1071 - feature: Adds filter sub-command

Pull Request - State: closed - Opened by ns-rse about 1 month ago - 3 comments
Labels: v2.4.0

#1070 - Combine grain crops rather than overwriting them

Pull Request - State: closed - Opened by llwiggins about 1 month ago

#1069 - [pre-commit.ci] pre-commit-autoupdate

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

#1068 - feature: expand objects returned by LoadScan.load_topostats()

Pull Request - State: closed - Opened by ns-rse about 1 month ago - 7 comments
Labels: IO

#1067 - Extract correct image data from `.topostats` file.

Issue - State: closed - Opened by ns-rse about 1 month ago
Labels: ui, v2.3.1

#1066 - [Bug]: Bounding boxes for grain masks seem to be disrupting other masks and traces

Issue - State: closed - Opened by tcatley about 1 month ago - 4 comments
Labels: bug

#1065 - Tidy up package and build with only necessary files

Pull Request - State: closed - Opened by ns-rse about 2 months ago
Labels: CI/CD

#1064 - Exclude unnecessary files from package build

Issue - State: closed - Opened by ns-rse about 2 months ago - 1 comment
Labels: v2.3.0

#1062 - ci(pypi): Moving permissions

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

#1060 - ci(pypi) adding write permissions to PyPI workflow

Pull Request - State: closed - Opened by ns-rse about 2 months ago
Labels: CI/CD

#1058 - feature: Adds --image-set as option to topostats

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: enhancement, ui

#1057 - Add `image_set` to `topostats` argparse

Issue - State: closed - Opened by ns-rse 2 months ago - 1 comment

#1056 - curvature images doesn't overwrite

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

#1055 - chore: Clarify request for log output in bug reports

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: enhancement

#1054 - [Bug]: "Curvature" image not generating per file in the processed folder

Issue - State: closed - Opened by tcatley 2 months ago - 4 comments
Labels: bug, v2.3.0

#1053 - style(notebooks): Ignore Flake8 complaints on Notebooks

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: v2.3.0

#1052 - refactor(disordered_tracing): Work with skan-0.12.2

Pull Request - State: closed - Opened by ns-rse 2 months ago - 2 comments
Labels: DNATracing, v2.3.0

#1051 - Refactor smooth_mask to take null values

Pull Request - State: closed - Opened by MaxGamill-Sheffield 2 months ago
Labels: enhancement, v2.3.0

#1050 - Added more info to cores-1 bug report label

Pull Request - State: closed - Opened by MaxGamill-Sheffield 2 months ago - 1 comment
Labels: enhancement, v2.3.0

#1049 - chore: Remove unused method, test and package dependencies

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: IO, tests, v2.3.0

#1048 - Adds nbQA to pre-commit hooks

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: CI/CD, v2.3.0

#1047 - Returns grainstats rows when tracing for a grain fails

Pull Request - State: closed - Opened by MaxGamill-Sheffield 2 months ago
Labels: bug, v2.3.0

#1046 - tests(unet_masking): Correct ids and add expected fail

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

#1045 - Remove index column from results plus some other tidying

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: v2.3.0

#1044 - Possibly using variable before assignment

Issue - State: open - Opened by ns-rse 2 months ago
Labels: v2.3.2

#1043 - Remove derivation of "circular" variable in tracing

Issue - State: open - Opened by ns-rse 2 months ago - 1 comment
Labels: v2.3.1

#1042 - Enables legacy unets to run

Pull Request - State: closed - Opened by MaxGamill-Sheffield 2 months ago - 1 comment
Labels: v2.3.0

#1041 - [Bug]: Older TopoStats U-Net Models Throw Error on Import

Issue - State: closed - Opened by MaxGamill-Sheffield 2 months ago - 1 comment
Labels: bug

#1040 - doc: Updates the data dictionary

Pull Request - State: closed - Opened by ns-rse 2 months ago
Labels: v2.3.0

#1039 - Remove index column from `all_statistics.csv`

Issue - State: closed - Opened by ns-rse 2 months ago
Labels: IO, v2.3.0

#1038 - Add nbQA pre-commit hook and lint existing notebooks

Issue - State: closed - Opened by ns-rse 2 months ago
Labels: CI/CD, linting, notebooks, v2.3.1

#1037 - [Bug]: Possibly need to pin AFMReader version?

Issue - State: closed - Opened by SylviaWhittle 2 months ago - 2 comments
Labels: bug, v2.3.0

#1036 - Remove `io.LoadScan._spm_px_to_nm_scaling()`

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

#1035 - style: Tidying calculate_dna_width()

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

#1034 - chore: Improves .gitignore to ignore more Python files

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

#1033 - Improve DNA width measurements

Issue - State: open - Opened by ns-rse 2 months ago
Labels: DNATracing

#1032 - [pre-commit.ci] pre-commit-autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 2 months ago

#1031 - refactor(io): Load files with AFMReader

Pull Request - State: closed - Opened by ns-rse 3 months ago - 4 comments

#1030 - Modifies the squaring bbox and tweaks PIL input shapes

Pull Request - State: closed - Opened by MaxGamill-Sheffield 3 months ago
Labels: v2.3.0

#1029 - [Bug]: Large crops using a U-Net aren't cropped correctly

Issue - State: closed - Opened by MaxGamill-Sheffield 3 months ago
Labels: bug, v2.3.0

#1028 - [Bug]: Information missing from all_stats file for some grains

Issue - State: closed - Opened by Marina1595 3 months ago - 1 comment
Labels: bug, v2.3.0

#1027 - docs: Adds Under/Over preprint link to Publications of README.md

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

#1026 - Add Under/Over preprint to README.md

Issue - State: closed - Opened by ns-rse 3 months ago
Labels: v2.3.0

#1025 - Expand usage of AFMReader for all file formats...

Issue - State: closed - Opened by ns-rse 3 months ago - 1 comment

#1024 - chore: Updates publication in README.md

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

#1023 - chore: Adds earlier contributors to CITATION.cff

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

#1022 - Refactor pipeline to use grain crop dictionaries

Pull Request - State: open - Opened by SylviaWhittle 3 months ago - 13 comments

#1021 - Expand CITATION.cff

Issue - State: closed - Opened by ns-rse 3 months ago - 3 comments

#1020 - Update paper linked under Publications in README.md

Issue - State: closed - Opened by ns-rse 3 months ago - 1 comment
Labels: enhancement, v2.3.0

#1019 - DOI for versioned releases

Issue - State: open - Opened by ns-rse 3 months ago - 1 comment
Labels: CI/CD, packaging, v2.3.2

#1018 - [feature] : Tip broadening measurement

Issue - State: open - Opened by SylviaWhittle 3 months ago - 1 comment
Labels: enhancement

#1017 - ci: group dependabot github-actions updates

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

#1016 - Build(deps): Bump codecov/codecov-action from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago - 1 comment
Labels: dependencies

#1015 - Build(deps): Bump actions/add-to-project from 0.5.0 to 1.0.2

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#1014 - ci: Adds pygrep-hooks and fixes errors

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

#1013 - config: Removes target-version from ruff configuration

Pull Request - State: closed - Opened by ns-rse 3 months ago
Labels: v2.3.0

#1012 - dependabot for GitHub Actions

Pull Request - State: closed - Opened by ns-rse 3 months ago
Labels: v2.3.0

#1011 - style: Changes prettier mirror used by pre-commit

Pull Request - State: closed - Opened by ns-rse 3 months ago
Labels: v2.3.0

#1010 - Curvatrure entry point

Issue - State: open - Opened by ns-rse 3 months ago
Labels: ui, v2.4.0

#1009 - Splining entry point

Issue - State: open - Opened by ns-rse 3 months ago
Labels: ui, v2.4.0

#1008 - [feature] : Follow PixelQuest guidelines

Issue - State: open - Opened by ns-rse 3 months ago
Labels: enhancement, Images

#1007 - RF002: Target version must be set. - You have both Ruff's target-version and project.requires-python. You only need the latter.

Issue - State: closed - Opened by ns-rse 3 months ago

#1006 - PC180: Uses a markdown formatter. - Use https://github.com/rbubley/mirrors-prettier instead of https://github.com/pre-commit/mirrors-prettier in .pre-commit-config.yaml

Issue - State: closed - Opened by ns-rse 3 months ago

#1005 - PC170: Uses PyGrep hooks (only needed if rST present) - Must have https://github.com/pre-commit/pygrep-hooks in .pre-commit-config.yaml

Issue - State: closed - Opened by ns-rse 3 months ago

GitHub / AFM-SPM/TopoStats issues and pull requests