v0.2.1

A new release for dockerhub.

What's Changed

• [FIX] Fixed xnat_to_bids ignoring --clobber before pulling data by @slimnsour in #330
• Make datman easier to install and use by @DESm1th in #303
• [FIX] framewise displacement mis-calculation by @jerdra in #305
• FIX: Handle sessions (repeats) appropriately in matching algorithm by @jerdra in #331
• [ENH] Remove the static HTML QC pages by @DESm1th in #329
• Add kevin to auto assigned reviewers by @DESm1th in #325
• ENH: Update configuration options for defacing by @josephmje in #328
• [FIX] qc_report consuming all db connections + queue jobs timing out by @DESm1th in #332
• [FIX] address dm_qc_report edge case + db update issues by @DESm1th in #333
• add jerdra as a contributor by @allcontributors in #337
• add josephmje as a contributor by @allcontributors in #336
• add slimnsour as a contributor by @allcontributors in #339
• [ENH] Refactor dm_xnat_extract + allow nii folders to be replace with sym links to bids folders by @DESm1th in #334
• [ENH] Switch datman's CI config to github actions + update package configuration by @DESm1th in #335
• [FIX] Stop dm_xnat_extract from crashing on malformed series 'numbers' by @DESm1th in #340
• ENH: Add --match-series option to enforce that matches Series# is found by @jerdra in #342
• ENH: Enable XnatType key in ExportInfo by @jerdra in #345
• [FIX] Adjust pipeline permissions to stop jobs from failing by @DESm1th in #343
• [ENH] un-hardcode dm_blacklist_rm's list of directories to purge from by @DESm1th in #344
• [FIX] Stop nightly run log issues by @DESm1th in #346
• [FIX] Stop test failures, permissions issue, and failing auto-assign by @DESm1th in #347
• [FIX] Handle Split FMAP files by @DESm1th in #348
• [FIX] Fix REDCAP ID issue + linked scans missed by datman.exporters.DBExporter by @DESm1th in #349
• [FIX] Update xnat extract bids conversion to better handle repeat sessions by @DESm1th in #350
• [FIX] update xnat_extract NiiLink to stop repeats from being linked under multiple session numbers by @DESm1th in #351
• [FIX] Ensure tech notes are pushed if they arrive after scan data by @DESm1th in #352
• [Docs] Migrate contents from docs wiki + add missing config values by @DESm1th in #353
• [FIX] Update API URL retrieval, and documentation for the config val by @DESm1th in #354
• [FIX] Stop series download from failing silently by @DESm1th in #355
• [FIX] Collection of small bug fixes by @DESm1th in #356
• [FIX] Remove conversion error message from DB when no longer exists by @DESm1th in #357
• [ENH] Allow datman to handle linked XNAT sessions by @DESm1th in #358
• [ENH] Add better error messages + filter out noisy redcap messages by @DESm1th in #359
• [FIX] Update dependencies and dockerfile for release by @DESm1th in #360

Full Changelog: 0.2.0...0.2.1

0.2.0

Changes

• FIX: Fix/ea handle quit code (#327)
• MAINT: Docs build failures (#326)
• MAINT: Update circle ci ubuntu + python versions (#324)
• ENH: Create dm_parse_Nback_abcd.py (#315)
• FIX Fix errors from updating dashboard (#323)
• FIX: remove study invalid attribute access (#322)
• FIX: Update references to dashboard.queries function (#321)
• ENH: Updates and bug fixes for dm_parse_faces (#320)
• FIX: Wrapped dcm2bids import in exception message for better messaging (#319)
• ENH: Added inital xnat_to_bids function and error checking for it (#317)
• ENH: Add defacing script (#318)
• MAINT: Deal with circleci errors (#316)
• FIX: Fix dm_blacklist_rm not being able to run without a 'dcm' folder (#314)
• ENH: Updating dm_parse_faces onset timestamps (#312)
• FIX: Scan module fails trying to set dcm properties (#313)
• MAINT: Remove dependencies on the 'dcm' folder (#311)
• FIX: Added fix for SPN30/31 redcap issues (#310)
• ENH: Add dm_parse_faces (#307)
• FIX: Update how derived scans are handled (#306)
• ENH: Update dm_mripicture.py (#304)
• ENH: Create dm_mripicture.py (#302)
• ENH: Updated EA parse to remove button press during scan response (#298)
• FIX: Prevent error log messages from being lost (#295)
• FIX: Fix bidsify match algorithm associating the wrong fieldmaps (#294)
• FIX: Make config keys CamelCase (#296)
• FIX: Make the ea parser work without hardcoded stuff (#292)
• FIX: Update add_redcap function call (#293)
• ENH: Remove single fmap-type assumption for BIDSIFY, more flexible derivative specification (#291)
• ENH: Added parser for Nback and GNGo (#286)
• FIX: Small but fatal xnat.py errors (#273)
• FIX: Removed XNAT integration (was unused) (#288)
• ENH: Allow the subid field to be modified between naming conventions (#287)
• MAINT: update ssh key for auto-deploying docs (#285)
• DOCS: Update sphinx settings and requirements (#284)
• FIX: Ensure non-nifti resources get downloaded when downloading session as a zip (#283)
• FIX: Correctly convert KCNI IDs from the redcap form (#282)
• FIX: Update scanid ID regexes to handle date based KCNI Phantom IDs (#280)
• FIX: Bidsify fix - don't re-write dataset_description.json on every run (#281)
• FIX: Experiment renaming failures (#272)
• FIX: missed edge cases in dm_xnat_upload (#271)
• DOCS: Update .all-contributorsrc (#276)
• DOCS: Self-host docs using GitHub pages (#266)
• ENH: Add ability to rename xnat sessions (#263)
• FIX: Ensure database is available for datman (#264)
• REF: Allow multiple XNAT servers to be used for upload / extraction (#270)
• FIX: Bug fixes from adding KCNI name support (#267)
• DOC: Update dm_qc_report.py docstring with software versions (#269)
• FIX: Bug when SliceTiming length's don't match gold standard (#268)
• ENH: Add KCNI ID support (#265)
• FIX/MAINT: Only deploy on pypi when commits/PRs are made to the release branch (#262)
• ENH/MAINT: Implement CircleCI (#260)
• FIX: Fix to aggregate task files based on config (#261)
• REF: Clean up error messages (#258)
• MAINT/FIX: Remove nose dependency, fix issues with some tests (#256)
• FIX: BIDS requirements YAML (#259)
• FIX: dm_qc_report.py header diff related crashes (#255)
• MAINT: Update of package install features and coding contributions (#246)
• STY: PEP8 style changes and minor logging fixes (#253)
• FIX: Python3 conversion bug fix (Round 3) (#254)

0.2.0rc1

Release Notes

Upgrade Python version to 3.6 and above.

Changes

• [FIX] Python3 conversion bug fixes (Round 2) (#252)
• [FIX] Python3 conversion bug fixes (round 1) (#251)
• [FIX] Pull all subjects in dm_task_files.py instead of just checklisted ones. (#247)
• [FIX] Decode bytestring for version from REDCap (#250)
• [FIX] Modify scanid variable in dm_link.py (#248)
• [REF] Update code to Python 3 + PEP8 changes + remove deprecated scripts (#245)

0.1.0

This release is datman from BEFORE we:
1. Deleted old scripts from the bin folder (mostly old analysis pipelines we dont run anymore, or have better versions of)
2. Upgraded to python3

It's mostly here so that anyone needing a legacy pipeline has an easy way to jump back in time and grab the scripts we dropped.