Open
Conversation
…ls and black for dev
Collaborator
Author
|
@tanghaibao was there a reason that numpy version was fixed as < 2 ? |
Owner
I don't recall. Introduced in 2eae789 Maybe some weird interaction between numpy version and cython. |
* Added new option "--annotation-boxes" that takes a bedfile input and draws a highlight box over the chrm track. * Fixed formatting of optional ribbon edge highlights * Added vscode pytest config file and recommends extensions config * Changed supported Python range to 3.9 - 3.12 --------- Co-authored-by: Adam Taranto <taranto.a@wehi.edu.au> Co-authored-by: Adamtaranto <2160099+Adamtaranto@users.noreply.github.com>
* Add option to use hex codes for ribbon colours * Style fixes by Black --------- Co-authored-by: Adam Taranto <taranto.a@wehi.edu.au> Co-authored-by: Adamtaranto <2160099+Adamtaranto@users.noreply.github.com>
* update gff.gtf() * Style fixes by Black * update testcase
* update FileMerger * Fix formats.pdf
* Add action linting, black formatting, yaml formatting, and bump versions * update latest version * OSX ARM64 env no longer required * Add black to dev env deps * formatting * formatting * update dep action versions * Add cff validation and update actions * isort imports * Add isort pre-commit hook * prettier no longer supported
[skip ci] - Version: 1.5.7 → 1.5.8 - Date: 2025-08-21 → 2025-11-09 Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* Initial plan * Fix ValueError when setting p.usage with %prog after OptionParser init * Update test docstring to remove placeholder issue number Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: tanghaibao <106987+tanghaibao@users.noreply.github.com>
[skip ci] - Version: 1.5.8 → 1.5.9 - Date: 2025-11-09 → 2025-11-30 Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Prevents AttributeError when a blank line or indented comment appears at the beginning, end or in between track and edge sections in layout files. Adds: - strip+skip for empty lines - line-based matching for "#" and "e" - only append non-empty LayoutLine instances This makes the layout parser more robust to formatting variations.
…809) * Initial plan * Implement memory-efficient BLAST processing for liftover operation
[skip ci] - Version: 1.5.9 → 1.5.10 - Date: 2025-11-30 → 2025-12-17 Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* remove numpy<2 * use int/float in place of np.int/np.float * update license
[skip ci] - Version: 1.5.10 → 1.5.11 - Date: 2025-12-17 → 2025-12-20 Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* bump pre-commit hooks * bump 3rd part action versions
* replace brewer2mpl with palettable * Style fixes by Black * fix where get_map() was imported from base --------- Co-authored-by: Adamtaranto <2160099+Adamtaranto@users.noreply.github.com>
[skip ci] - Version: 1.5.11 → 1.6.1 - Date: 2025-12-20 → 2026-02-15 Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
Collaborator
Author
|
Note: See if we can trim any non essential imports out of 'run' section in bioconda recipe to improve testing time: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/jcvi/meta.yaml |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Tidying up the codebase. Do not merge yet.