Snakebids

- Snakebids is now available on Conda!
- We've expanded the regex filtering capability from the CLI. You can now use syntax like: `--filter-T1w suffix:match=T1w?`
- This version still supports python 3.8. This will be dropped in future releases. No explicit testing yet on 3.13, but shouldn't be any issues.

Changes

🚀 Features

- Support for conda Dhananjhay (459)
- Add compatibility for urls in `generate_inputs` Karl5766 (452)
- Allow regex from the cli pvandyken (442)
- Add CLI argument in BidsValidator plugin pvandyken (443)

🐛 Bug Fixes

- remove the leading ./ from paths created in snakebids akhanf (462)
- Deduplicate wildcards when parsing components pvandyken (455)
- Update dependencies in template documentation pvandyken (453)

🧰 Maintenance

- Pass CI tests on main Dhananjhay (465)
- Add codespell support (config, workflow to detect/not fix) and make it fix few typos yarikoptic (449)
- Add pattern to coverage upload action pvandyken (441)
- Update dependencies pvandyken (439)

Changes

🐛 Bug Fixes

- Prevent bids values with leading 0s in tests pvandyken (427)
- Update argument handling for --derivatives pvandyken (425)
- Remove return from run method on Runner pvandyken (424)
- Add converters to SnakeBidsApp pvandyken (421)

🧰 Maintenance

- Add skip\_changelog label to test timing update PRs pvandyken (426)
- Run tests only when snakebids or scripts folder updated pvandyken (430)
- Move upload\_coverage to seperate workflow pvandyken (429)
- Add labeller action pvandyken (428)
- Update dependencies pvandyken (420)

Changes

- Another fix to test counting pvandyken (419)

🚀 Features

- Add hook to update and read argv before parsing pvandyken (417)

🐛 Bug Fixes

- Add missing spaces to default help for bidsargs pvandyken (416)

🧰 Maintenance

- Update maximum python version in template pvandyken (415)
- Fix test-counting code pvandyken (414)

Changes

`bidsapp` module

This version introduces a new `bidsapp` module, which moving forward will provide a much more flexible, extensible interface for bids apps. At this time, the module has yet to be completely documented, but new apps generated with `snakebids create` will automatically use the new api. Old apps can be updated using the [migration guide](https://snakebids.readthedocs.io/en/stable/migration/0.11_to_0.12.html).

Note that the old `run.py` api will still work fine, for most users this release does not have any breaking changes. The only apps that will be affected were those that used custom plugins: they will no longer work.

🚀 Features

- Add support for snakemake > 8.0 pvandyken (406)
- Major update to bidsapp pvandyken (362)
- Allow simult. use of partic incl and excl flags pvandyken (404)

🐛 Bug Fixes

- Fix flaky template tests pvandyken (405)
- Pin attrs to 22.2.0 pvandyken (403)
- Prevent installation of docutils==0.21.post1 pvandyken (402)
- Correctly activate virtualenv in readthedocs build pvandyken (394)

🧰 Maintenance

- Add codecov badge pvandyken (409)

📝 Documentation

- Update tutorial for new bidsapp pvandyken (408)

Changes

- Update the warning format to be more readable pvandyken (390)

🐛 Bug Fixes

- Fix docs template so that it builds pvandyken (392)
- Eliminate initial "\_" when suffix is only entity pvandyken (389)

Changes

🐛 Bug Fixes

- Prevent custom entities from drawing standard ent pvandyken (382)
- Expand paths unaltered when comp has no wcards pvandyken (378)
- Fix warning messages pvandyken (377)

🧰 Maintenance

- Move codecoverage upload to seperate job pvandyken (380)
- Allow custom snakebids version in app template pvandyken (376)