Ecosyste.ms: Issues

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GitHub / akhanf/snakebids issues and pull requests

#350 - Fix formatting of empty zip lists

Pull Request - State: closed - Opened by pvandyken about 1 year ago
Labels: bug

#349 - Transition to versioned bids functions

Pull Request - State: open - Opened by pvandyken about 1 year ago - 2 comments

#348 - Preserve order of entries in expand method

Pull Request - State: closed - Opened by pvandyken about 1 year ago
Labels: bug

#347 - No test dataset in snakebids bootstrap app

Issue - State: open - Opened by pvandyken about 1 year ago

#346 - `BidsComponent.expand()` fails to preserve order

Issue - State: closed - Opened by pvandyken about 1 year ago
Labels: bug

#345 - Port forward 0.9.x changes into 0.10.x

Pull Request - State: closed - Opened by pvandyken about 1 year ago
Labels: maintenance, skip_changelog

#344 - Overhaul global filtering of participants

Pull Request - State: open - Opened by pvandyken over 1 year ago
Labels: bug

#343 - Cannot use `--participant-label` and `--exclude-participant-label` simultaneously

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

#342 - Remove myself from reviewer list

Pull Request - State: closed - Opened by tkkuehn over 1 year ago - 1 comment
Labels: skip_changelog

#341 - Refactor install steps into resusable workflow

Pull Request - State: open - Opened by pvandyken over 1 year ago - 1 comment
Labels: maintenance, blocked

#340 - Remove dependency upper-caps and update

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 4 comments
Labels: maintenance

#339 - `_format_zip_lists` breaks when formatting an empty zip list

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

#338 - Add pytest-split and pytest-xdist

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 4 comments
Labels: maintenance

#337 - Fix typo in BidsValidator plugin

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: bug

#336 - Overhaul `snakebids create`

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 6 comments
Labels: enhancement

#335 - Extension of `BidsComponent.filter` api

Issue - State: open - Opened by pvandyken over 1 year ago

#334 - Add deprecation mechanism to old pybidsdb vals

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: bug

#333 - `pybids_db_dir` was eliminated without warning, causing migration issues

Issue - State: closed - Opened by pvandyken over 1 year ago - 2 comments

#332 - Refactor filter_list to use RegexContainer

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: maintenance

#331 - Add poetry lock check

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: maintenance

#330 - Update dependencies and pyright version

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: maintenance

#329 - Port documentation changes

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: skip_changelog

#328 - Update docs dependencies

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

#327 - Port hotfixes from 0.9.x

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: bug

#326 - Fix version fetching in readthedocs build

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: bug, documentation

#325 - HOTFIX Fix pybidsdb path resolution

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: bug

#324 - Implement Bids Spec files

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: maintenance

#323 - Fix mistaken comparison of BidsEntity to str sets

Pull Request - State: closed - Opened by pvandyken over 1 year ago
Labels: bug, skip_changelog

#322 - Drop support for Python 3.7

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: breaking

#321 - SnakeBidsApp Assumes filters are present

Issue - State: open - Opened by pvandyken over 1 year ago
Labels: bug

#320 - Update scipy constraints for py3.8

Pull Request - State: closed - Opened by kaitj over 1 year ago - 3 comments
Labels: maintenance

#319 - Scipy dependency

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

#317 - fixing small virtual env activation typo in tutorial.md

Pull Request - State: closed - Opened by ataha24 over 1 year ago
Labels: documentation

#316 - Update cookiecutter

Pull Request - State: closed - Opened by kaitj over 1 year ago - 4 comments
Labels: maintenance

#315 - Drop Support for Py37

Issue - State: closed - Opened by pvandyken over 1 year ago - 1 comment
Labels: breaking

#314 - Allow Booleans in filter lists

Pull Request - State: closed - Opened by pvandyken over 1 year ago - 2 comments
Labels: bug

#313 - Use PEP 621-based pyproject.toml in snakebids create

Issue - State: open - Opened by tkkuehn over 1 year ago - 2 comments

#312 - Add plugin reference page to docs

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

#311 - Plugins page in docs

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

#310 - Always set SnakeBidsApp.args in run_snakemake

Pull Request - State: closed - Opened by tkkuehn over 1 year ago
Labels: maintenance

#309 - Boolean CLI filters

Pull Request - State: closed - Opened by tkkuehn over 1 year ago - 1 comment
Labels: enhancement

#308 - Save more provenance information

Pull Request - State: closed - Opened by tkkuehn over 1 year ago - 9 comments
Labels: enhancement

#307 - Update app creation instructions

Issue - State: closed - Opened by kaitj over 1 year ago - 2 comments
Labels: documentation

#306 - Update cookiecutter template

Pull Request - State: closed - Opened by kaitj over 1 year ago - 1 comment
Labels: maintenance

#305 - Test magic args

Pull Request - State: closed - Opened by tkkuehn over 1 year ago - 3 comments
Labels: test

#304 - `export_sourcedir` plugin

Issue - State: open - Opened by pvandyken over 1 year ago - 1 comment
Labels: enhancement, plugin

#302 - Expect plugins to be callable classes

Issue - State: open - Opened by tkkuehn over 1 year ago - 1 comment

#301 - Split bids into its own repository

Issue - State: open - Opened by tkkuehn over 1 year ago

#300 - Add DuplicateComponentError for more precision

Pull Request - State: closed - Opened by tkkuehn over 1 year ago
Labels: maintenance

#298 - Update README

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

#297 - Raise error on missing `custom_path` and invalid `bids_dir`

Pull Request - State: closed - Opened by kaitj over 1 year ago
Labels: maintenance

#296 - Update pybids_db parameters

Pull Request - State: closed - Opened by kaitj over 1 year ago - 1 comment
Labels: maintenance, deprecation

#295 - Make the target easier to override in plugins

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

#294 - Allow builtins as types

Issue - State: open - Opened by pvandyken over 1 year ago

#293 - Mandatory vs Optional components in `pybids_inputs`

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

#292 - Improve implementation of `get()` in `MultiSelectDict`

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

#291 - Add BidsValidator Plugin

Pull Request - State: closed - Opened by kaitj almost 2 years ago - 4 comments
Labels: enhancement

#290 - Ignore deadlines for hypothesis tests on pr

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 2 comments
Labels: maintenance, test

#289 - Fix `--filter_{input_type}`

Pull Request - State: closed - Opened by kaitj almost 2 years ago - 11 comments
Labels: bug

#288 - Update pybids py37, py38+ constraints

Pull Request - State: closed - Opened by kaitj almost 2 years ago - 4 comments
Labels: maintenance

#287 - `--filter_{input_type}` ValueError

Issue - State: closed - Opened by kaitj almost 2 years ago - 5 comments
Labels: bug

#286 - Pybids version

Issue - State: closed - Opened by kaitj almost 2 years ago - 5 comments
Labels: maintenance

#285 - Implement extension support

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 3 comments
Labels: enhancement

#284 - Implement `BidsPartialComponent`

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 5 comments
Labels: enhancement

#283 - Restrict pybids bug check to python 3.7

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 6 comments
Labels: maintenance

#282 - Final documentation fixes before release

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: documentation

#281 - Remove unnecessary `use_bids_inputs = True`

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: maintenance

#280 - Change default of allow_missing

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: enhancement

#279 - `BidsComponent.filter`

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: enhancement

#278 - Switch from pylint/flake8 to ruff

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 1 comment
Labels: maintenance

#277 - Complete type hints and add pyright to CI

Pull Request - State: closed - Opened by tkkuehn almost 2 years ago - 7 comments
Labels: maintenance

#276 - Create migration guide for v0.8

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

#275 - Switch default of use_bids_inputs to True

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 2 comments
Labels: breaking

#274 - Support multiple selection in `BidComponent.wildcards`, `zip_lists`, and `entities`

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: enhancement

#273 - Implement `BidsComponent.expand()`

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 3 comments
Labels: enhancement

#272 - Update glob_wildcards to return ZipLists

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: maintenance

#271 - Remove add_plugins method from SnakeBidsApp

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: enhancement

#270 - Why is `pybids_db_dir` commented in the boilerplate config?

Issue - State: closed - Opened by pvandyken almost 2 years ago - 1 comment
Labels: maintenance

#269 - Confusing menagerie of names for pybids database

Issue - State: closed - Opened by pvandyken almost 2 years ago
Labels: breaking

#268 - Update deprecation dependency to own package

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: maintenance

#267 - Major updates to documentation

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 3 comments
Labels: documentation

#266 - Implement pretty printing for dataset objects

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 4 comments
Labels: enhancement

#265 - Move target_rule to beginning of snakemake call

Pull Request - State: closed - Opened by pvandyken almost 2 years ago
Labels: bug

#264 - Expose `args` on `SnakeBidsApp` for plugins

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

#262 - Deprecate `participant_label` and `exclude_participant_label` args

Issue - State: open - Opened by pvandyken almost 2 years ago - 3 comments
Labels: deprecation, blocked

#261 - Implement first pass at simple plugins

Pull Request - State: closed - Opened by tkkuehn almost 2 years ago - 1 comment
Labels: enhancement

#260 - Basic Plugin Architecture

Issue - State: closed - Opened by pvandyken almost 2 years ago - 5 comments
Labels: enhancement

#259 - BIDS validation

Pull Request - State: closed - Opened by kaitj almost 2 years ago - 8 comments
Labels: enhancement

#258 - Extend boolean filtering to cli

Issue - State: closed - Opened by pvandyken almost 2 years ago - 1 comment
Labels: enhancement

#257 - Allow specification of `snakebids` config file

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

#256 - Automatically create pybidsdb

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

#254 - Elaborate on warning for empty components

Pull Request - State: closed - Opened by tkkuehn almost 2 years ago
Labels: enhancement

#253 - Make some cookiecutter variables optional

Pull Request - State: closed - Opened by tkkuehn almost 2 years ago
Labels: enhancement

#252 - Introduce PybidsError for cryptic pybids errors

Pull Request - State: closed - Opened by tkkuehn almost 2 years ago - 2 comments
Labels: enhancement

#251 - Add deprecation warnings to `BidsDataset` properties slated for change

Pull Request - State: closed - Opened by pvandyken almost 2 years ago - 3 comments
Labels: enhancement

#250 - Consistently document argument and return types using type annotations

Issue - State: closed - Opened by pvandyken almost 2 years ago
Labels: documentation

#249 - Incorporate `pyright` checks

Issue - State: closed - Opened by pvandyken almost 2 years ago
Labels: maintenance

#248 - Method to find entity combinations "missing" from dataset

Issue - State: open - Opened by pvandyken almost 2 years ago - 1 comment
Labels: enhancement