datalad/datalad-ukbiobank issues and pull requests

#102 - Missing mappings for connectome bulk files

Issue - State: open - Opened by psadil about 1 year ago - 3 comments

#101 - Support FreeSurfer data records

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

#100 - Tests fail due to deprecated module import

Issue - State: closed - Opened by loj almost 2 years ago

#99 - Add support for FreeSurfer data record

Issue - State: closed - Opened by loj almost 2 years ago

#98 - Bring test suite back in operation

Pull Request - State: closed - Opened by mih over 2 years ago - 1 comment

#97 - Adjust for config API deprecation

Issue - State: closed - Opened by mih over 2 years ago

#96 - Adjust for status API deprecation

Issue - State: closed - Opened by mih over 2 years ago

#95 - Adjust for API deprecation

Issue - State: closed - Opened by mih over 2 years ago

#94 - Adjust for deprecated module import

Issue - State: closed - Opened by mih over 2 years ago

#93 - Unpin git-annex in tests

Pull Request - State: closed - Opened by mih over 2 years ago - 1 comment

#92 - Test failure `test_drop`

Issue - State: closed - Opened by mih over 2 years ago - 1 comment

#91 - datalad-extensions FAILs in test_base

Issue - State: open - Opened by yarikoptic over 2 years ago - 1 comment

#90 - Make test output less noisy

Pull Request - State: closed - Opened by mih over 2 years ago - 1 comment

#89 - `ukb-update` broken with `git-annex >= 10.20220526`

Issue - State: closed - Opened by mih over 2 years ago - 2 comments

#88 - Internal command calls should yield and not render results

Issue - State: open - Opened by mih over 2 years ago

#87 - Switch to pytest, and bump dependency on Python (3.7) and datalad (0.17)

Pull Request - State: closed - Opened by mih over 2 years ago - 1 comment

#86 - Replacement for https://github.com/datalad/datalad-ukbiobank/pull/84

Pull Request - State: closed - Opened by mih over 2 years ago

#85 - BF: introduce helper to ensure newline characters in .gitattributes

Pull Request - State: closed - Opened by adswa over 2 years ago - 2 comments

#84 - MNT: Remove eval_file_type (removed from core) from code base

Pull Request - State: closed - Opened by adswa over 2 years ago - 5 comments

#83 - DOC: Set language in Sphinx config to en

Pull Request - State: closed - Opened by adswa over 2 years ago - 2 comments

#82 - failing tests in datalad-extensions runs

Issue - State: closed - Opened by yarikoptic almost 3 years ago - 10 comments

#81 - Missing json files for BIDS layout

Issue - State: closed - Opened by ltetrel about 3 years ago - 2 comments

#80 - Adding ukbfetch dependency and ukbfetch_surrogate information

Pull Request - State: closed - Opened by ltetrel about 3 years ago - 2 comments

#79 - Using with pre-downloaded data

Issue - State: closed - Opened by ltetrel about 3 years ago - 2 comments

#78 - CI: Enable new codecov uploader in Appveyor CI, fixes #77

Pull Request - State: closed - Opened by adswa over 3 years ago - 1 comment

#77 - Update Appveyor config to use new codecov uploader

Issue - State: closed - Opened by jwodder over 3 years ago

#76 - document removal of subjects

Issue - State: open - Opened by loj over 3 years ago

#75 - AnnexBatchCommandError: 'addurl' [Error, annex reported failure for addurl

Issue - State: closed - Opened by m-petersen over 3 years ago - 2 comments

#74 - Implement name prefix support for managed branches?

Issue - State: open - Opened by mih over 3 years ago
Labels: enhancement

#73 - Upgrade versioneer to 0.19 - might be more robust etc

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

#72 - TEMP: make git give us some info

Pull Request - State: closed - Opened by yarikoptic almost 4 years ago

#71 - Do apt-get update before apt-get install

Pull Request - State: closed - Opened by yarikoptic almost 4 years ago - 3 comments

#70 - Fix update --drop extracted crash (missing archives SR)

Pull Request - State: closed - Opened by mih almost 4 years ago - 6 comments

#69 - `ukb-update` fails with `--drop extracted` if only non-zip data types

Issue - State: closed - Opened by loj almost 4 years ago

#68 - Still usage of hard-coded 'master' branch

Issue - State: closed - Opened by mih almost 4 years ago

#67 - Update git-annex package URL to point to a stable place

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

#66 - DOCS: update with additional content

Pull Request - State: closed - Opened by loj almost 4 years ago - 8 comments

#65 - git-annex 8.20210223+git33-gee4fd38ec breaks things

Issue - State: closed - Opened by mih almost 4 years ago - 4 comments
Labels: bug

#64 - [ERROR] dataset containing given paths is not underneath the reference dataset

Issue - State: closed - Opened by fredrmag almost 4 years ago - 9 comments

#63 - Zenodo release

Issue - State: closed - Opened by adswa about 4 years ago - 2 comments

#62 - Rectify dependencies, now that 0.14rc1 is on PyPi

Pull Request - State: closed - Opened by mih about 4 years ago

#61 - no update tests on windows

Issue - State: open - Opened by bpoldrack about 4 years ago

#60 - RF: _run_annex_* is deprecated in datalad core

Pull Request - State: closed - Opened by bpoldrack about 4 years ago - 3 comments

#59 - TST: Replace travis-ci with a cross-platform appveyor setup

Pull Request - State: closed - Opened by mih about 4 years ago - 2 comments

#58 - tests started to fail against datalad master

Issue - State: closed - Opened by yarikoptic about 4 years ago - 1 comment

#57 - hardlink issue with datalad, datalad-ukbiobank (likely a git-annex issue)

Issue - State: closed - Opened by satra over 4 years ago - 6 comments

#56 - Fix two inconveniences re dataset maintenance

Pull Request - State: closed - Opened by mih over 4 years ago - 7 comments

#55 - Detection of BIDS-mode does not work with fresh clones

Issue - State: closed - Opened by mih over 4 years ago - 1 comment

#54 - incoming branch is not using standard .gitattributes from `datalad create`

Issue - State: closed - Opened by mih over 4 years ago

#53 - Juelich / Montreal UKB project todo list

Issue - State: closed - Opened by jbpoline over 4 years ago - 2 comments

#52 - Performance anecdotes

Issue - State: closed - Opened by mih over 4 years ago - 1 comment

#51 - Document how pre-downloaded content can be used as a permanent data source

Issue - State: open - Opened by mih over 4 years ago

#50 - Prevent inclusion of build helpers in binary packages

Pull Request - State: closed - Opened by mih over 4 years ago

#49 - Rename build helper location to avoid conflict with datalad itself

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#48 - Apply package setup updates from the revised extension-template

Pull Request - State: closed - Opened by mih over 4 years ago - 2 comments

#47 - Label data records properly

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#46 - ukb-update --drop {extracted|archives}

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#45 - Rename `update --force-update` -> `update --force`

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#44 - Ability to drop files from annex

Issue - State: closed - Opened by mih over 4 years ago

#43 - Rename `update --force-update` -> `update --force`

Issue - State: closed - Opened by mih over 4 years ago

#42 - Maintain BIDS and native dataset layout in parallel

Pull Request - State: closed - Opened by mih over 4 years ago - 2 comments

#41 - More complete unit tests

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#40 - Consolidate BIDS mapping code into a single invokation per update

Pull Request - State: closed - Opened by mih over 4 years ago - 2 comments

#39 - Support interactive entry of UKB access key file location

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#38 - Have BIDS in non-BIDS layout in different branch

Issue - State: closed - Opened by mih over 4 years ago

#37 - add all fields but fetch some

Issue - State: open - Opened by satra over 4 years ago - 1 comment

#36 - Release v0.3

Issue - State: closed - Opened by mih over 4 years ago - 3 comments

#35 - Basic setup to mock UKB updates

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#34 - Some initial unittests

Pull Request - State: closed - Opened by mih over 4 years ago - 1 comment

#33 - Add unittests

Issue - State: closed - Opened by mih over 4 years ago - 2 comments
Labels: good first issue

#32 - Avoid leakage of absolute paths into the ukbfetch run record

Pull Request - State: closed - Opened by mih over 4 years ago - 2 comments

#31 - Change non-BIDS dataset layout

Pull Request - State: closed - Opened by mih almost 5 years ago - 23 comments

#30 - WIP: add freesurfer recon fields

Pull Request - State: closed - Opened by satra almost 5 years ago - 8 comments

#29 - Add data record subdirectory for any ZIP file content in non-BIDS mode

Issue - State: closed - Opened by mih almost 5 years ago

#28 - Support for data types not downloaded as zip files

Pull Request - State: closed - Opened by mih almost 5 years ago - 1 comment

#27 - Add example replacement for ukbfetch

Pull Request - State: closed - Opened by mih almost 5 years ago - 1 comment

#26 - creating datalad-ukb dataset in a non empty directory

Issue - State: closed - Opened by djarecka almost 5 years ago - 12 comments

#25 - BIDS validation issues: Incorrect slice timing values?

Issue - State: open - Opened by adswa almost 5 years ago - 5 comments

#24 - BIDS validation issues: Unsupported BEP004?

Issue - State: open - Opened by adswa almost 5 years ago - 1 comment

#23 - BIDS validation issues: Non-compliant non-bids directory

Issue - State: open - Opened by adswa almost 5 years ago - 1 comment

#22 - support for data types not downloaded as zip files

Issue - State: closed - Opened by loj almost 5 years ago - 7 comments

#21 - Release 0.2 to PyPi (as well)

Issue - State: closed - Opened by mih almost 5 years ago - 1 comment

#20 - Support multi-instance data records

Pull Request - State: closed - Opened by mih almost 5 years ago - 3 comments

#19 - Do not fail on re-init due to deleted .ukbbatch file

Pull Request - State: closed - Opened by mih almost 5 years ago

#18 - adding new DATARECORD-IDs to the dataset

Issue - State: closed - Opened by djarecka almost 5 years ago - 3 comments

#17 - Overwrite error when downloading two data instances of one participant with ukb-update

Issue - State: closed - Opened by Hoda1394 almost 5 years ago - 12 comments

#16 - IDs used by datalad-ukb

Issue - State: closed - Opened by djarecka almost 5 years ago - 7 comments

#15 - Rename to datalad-ukbiobank

Issue - State: closed - Opened by yarikoptic almost 5 years ago - 1 comment

#14 - modify swi file names according to BEP004

Pull Request - State: closed - Opened by loj about 5 years ago

#13 - BIDS filename mapping

Pull Request - State: closed - Opened by mih about 5 years ago - 1 comment

#12 - ukb-update command

Pull Request - State: closed - Opened by mih about 5 years ago - 1 comment

#11 - ukb-init command

Pull Request - State: closed - Opened by mih about 5 years ago

#10 - Skeleton of a DataLad extension

Pull Request - State: closed - Opened by mih about 5 years ago

#9 - added BIDS conversion scripts as submodule

Pull Request - State: closed - Opened by AlexandreHutton about 5 years ago - 1 comment

#8 - download of 1000 subject subset with condor

Issue - State: closed - Opened by loj about 5 years ago - 5 comments

GitHub / datalad/datalad-ukbiobank issues and pull requests