AFM-SPM/TopoStats issues and pull requests

#601 - Further Modularisation

Issue - State: open - Opened by SylviaWhittle over 1 year ago - 3 comments
Labels: enhancement

#600 - Improves processing of multiple grains during dnatracing

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

#599 - Fixing tpyo's adding in `image`

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

#598 - Clarify documentation on standard deviation thresholds/abstract below

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

#597 - Sylvia whittle/596 zscale grains

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

#596 - Z range of cropped images not set by config file

Issue - State: closed - Opened by derollins over 1 year ago - 11 comments
Labels: enhancement

#595 - Write trace co-ordinates to file

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

#594 - Different processing success rates with different numbers of cores

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

#593 - Adds unit-tests for dnatracing methods

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

#592 - Dummy PR

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

#591 - Maxgamill sheffield/cats

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

#590 - Make channel a free text field

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

#589 - Make channel a free string field

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

#588 - Include comments in config files generated with --create-config-file

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

#587 - Sylvia whittle/582 channel not found

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

#586 - Quotes around installation of extra requirements

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

#585 - Update instructions on notebook installation to account for zsh globbing

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

#584 - Sylvia whittle/581 group plots by dir

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

#583 - Initial dnatracing refactor

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

#582 - Topostats crashes when a file without a set channel is found

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

#581 - Toposums default output should group by folder, and not by image

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

#580 - Pull new main changes into height_traces branch

Pull Request - State: closed - Opened by MaxGamill-Sheffield almost 2 years ago - 1 comment

#579 - Sylvia whittle/550 replace imghdr

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#578 - Sylvia whittle/486 area unit tests

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#576 - Updating package build to work with Debian System

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

#574 - Sylvia whittle/431 ignore high grains

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 9 comments

#572 - Removing blank line from pyproject.toml & versioneer from workflow

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#569 - Make pypi workflow dispatchable

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

#566 - Adding missing setuptools_scm dependency

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

#562 - Corrects alignment/merging of grainstats and tracing_stats dataframes

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: bug

#561 - Laura wiggins pull request

Pull Request - State: closed - Opened by MaxGamill-Sheffield almost 2 years ago

#560 - Revert "Laura's push"

Pull Request - State: closed - Opened by MaxGamill-Sheffield almost 2 years ago

#559 - Laura's push

Pull Request - State: closed - Opened by llwiggins almost 2 years ago

#558 - Only create filters, grains dirs when image_set is "all"

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#557 - Adds Mermaid diagram describing extensions to DNA Tracing

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

#556 - Sylvia whittle/image stats

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#555 - Fix no grains found crash

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#554 - Clarifying documentation for zrange

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: documentation

#553 - Fixing markdownlint-cli2 errors

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

#552 - Fix failing markdownlint-cli2

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: CI/CD

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 1 comment

#550 - Remove deprecated imghdr dependency

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: Low Priority, deprecations

#549 - Sylvia whittle/pandas reset index error

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 4 comments

#548 - Updating documentation

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 2 comments
Labels: documentation

#547 - Take .npy arrays as inputs for reprocessing without filters step.

Issue - State: open - Opened by derollins almost 2 years ago - 2 comments
Labels: enhancement

#546 - Move contributing guidelines to website

Issue - State: open - Opened by ns-rse almost 2 years ago
Labels: documentation

#545 - Sylvia whittle/507 svd nonconverging

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 3 comments

#544 - Ns rse/514 suggestions

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 3 comments

#543 - Future Milestones

Issue - State: closed - Opened by ns-rse almost 2 years ago

#542 - Split config file into advanced and basic setting

Issue - State: closed - Opened by derollins almost 2 years ago - 3 comments
Labels: enhancement, user experience

#541 - Empty grains and filters folders produced when 'image_set' is 'core'

Issue - State: closed - Opened by derollins almost 2 years ago
Labels: bug, Low Priority

#540 - Sylvia whittle/ 517 swiss army knife

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 2 comments

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 1 comment

#538 - Fix summary_config undefined in completion message

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#537 - Completion message fails when summary stats option is disabled

Issue - State: closed - Opened by SylviaWhittle almost 2 years ago
Labels: bug

#536 - Include field descriptors in autogenerated config file

Issue - State: closed - Opened by derollins almost 2 years ago - 7 comments
Labels: enhancement

#535 - Error when `colorbar` is turned off

Issue - State: closed - Opened by derollins almost 2 years ago - 2 comments
Labels: bug

#534 - Add sphinx-autoapi; removing pre-generated API .rst files

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

#533 - Removing pre-generated API .rst files

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

#532 - Missing Documentation

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: documentation

#531 - Disabling if statement within sphinx step

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#530 - Disabling Sphinx doc builds only on tagged commits

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

#529 - Correcting workflow_dispatch configuration

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

#528 - Enabling multiple versions of documentation

Pull Request - State: closed - Opened by ns-rse almost 2 years ago
Labels: documentation, CI/CD

#527 - Makes DPI configurable via default_config.yaml

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 5 comments
Labels: Images

#526 - Make DPI configurable

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: Images

#525 - ORDA GitHub Action

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 2 comments
Labels: CI/CD

#524 - Consistent bin-width in histograms summarising multiple images

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 2 comments
Labels: Plotting

#523 - Move creation of output directory to after config file generation

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#522 - Creating a config file leads to the generation of an output directory

Issue - State: closed - Opened by Jean-Du almost 2 years ago - 1 comment
Labels: bug, Low Priority

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 1 comment

#520 - Removing errant pkl

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 2 comments

#519 - 504 Notebook for plotting image arrays

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: Plotting

#518 - Remove _version.py from version control as per advice

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#517 - Remodel entry points and Command Line Interface to use "Swiss Army knife" approach

Issue - State: open - Opened by ns-rse almost 2 years ago - 4 comments
Labels: IO, user experience, v2.4.0

#516 - Apply typehints consistently across the code base

Issue - State: open - Opened by ns-rse almost 2 years ago - 3 comments
Labels: enhancement, CI/CD, linting

#515 - Sylvia whittle/514 grainstats assignment

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 3 comments

#514 - grainstats_df variable assignment error

Issue - State: closed - Opened by derollins almost 2 years ago
Labels: bug

#513 - GitHub Actions fail on Windows systems

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: CI/CD

#512 - Adds pyupgrade to pre-commit and lints code

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#511 - Clarifying running analyses sequentially

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#510 - Update bug report template to run with 1 core

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: bug, documentation, admin

#509 - Add pyupgrade to pre-commit

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: CI/CD

#508 - Speed up tests

Issue - State: closed - Opened by ns-rse almost 2 years ago - 4 comments
Labels: CI/CD, testing

#507 - Not all .spm files generate a processed image in specified file

Issue - State: closed - Opened by LHolmes2 almost 2 years ago - 3 comments
Labels: bug

#506 - Sylvia whittle/documentation improvements

Pull Request - State: closed - Opened by SylviaWhittle almost 2 years ago - 1 comment

#505 - Suggesting how to share documents; tidying some erroneous characters

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#504 - Save z-thresholded numpy array & add Notebook demonstrating how to plot.

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: notebooks

#503 - Update Notebook 00 to work with updated grain arrays.

Issue - State: open - Opened by ns-rse almost 2 years ago
Labels: Grains, notebooks

#502 - Empty commit to undo mistaken push to main

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#501 - Updating bug report template

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#500 - Additional pre-commit checks

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#499 - Lint Markdown with pre-commit

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: CI/CD

#498 - Add roughness measurements

Issue - State: closed - Opened by SylviaWhittle almost 2 years ago
Labels: enhancement

#497 - Corrects pprint usage; tidies up runtime arguments

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#496 - pprint() show output; -q flag no longer silent

Issue - State: closed - Opened by ns-rse almost 2 years ago - 1 comment
Labels: bug

#495 - Update Bug Report issue template

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: Medium Priority, admin, user experience

#494 - Publish to conda-forge?

Issue - State: open - Opened by stavrina almost 2 years ago - 4 comments
Labels: Low Priority, CI/CD, user experience

#492 - 457 Investigations

Pull Request - State: closed - Opened by ns-rse almost 2 years ago - 1 comment

#490 - Additional hooks for pre-commit

Issue - State: closed - Opened by ns-rse almost 2 years ago
Labels: CI/CD

GitHub / AFM-SPM/TopoStats issues and pull requests