Releases: nipy/heudiconv
Releases · nipy/heudiconv
v0.11.5
🐛 Bug Fix
- Fix certificate issue as indicated in #595 #597 (@neurorepro)
- BF docker build: use python3.9 (not 3.7 which gets upgraded to 3.9) and newer dcm2niix #596 (@yarikoptic)
- Fixup miniconda spec for neurodocker so it produces dockerfile now #596 (@yarikoptic)
🏠 Internal
- Update GitHub Actions action versions #601 (@jwodder)
- Set action step outputs via $GITHUB_OUTPUT #600 (@jwodder)
📝 Documentation
- DOC: codespell fix a few typos in code comments #605 (@yarikoptic)
Authors: 3
- John T. Wodder II (@jwodder)
- Michael (@neurorepro)
- Yaroslav Halchenko (@yarikoptic)
v0.11.4
🐛 Bug Fix
- install dcmstack straight from github until it is released #593 (@yarikoptic)
- DOC: provide rudimentary How to contribute section in README.rst (@yarikoptic)
⚠️ Pushed to master
- Check out a full clone when testing (@jwodder)
- Convert Travis workflow to GitHub Actions (@jwodder)
- BF(docker): replace old -tipsy with -y -all for conda clean as neurodocker does now (@yarikoptic)
- adjusted script for neurodocker although it does not work (@yarikoptic)
🏠 Internal
- 0.9 of dcmstack was released, no need for github version #594 (@yarikoptic)
- Minor face-lifts to ReproIn: align doc and code better to BIDS terms, address deprecation warnings etc #569 (@yarikoptic)
Authors: 2
- John T. Wodder II (@jwodder)
- Yaroslav Halchenko (@yarikoptic)
v0.11.3
🏠 Internal
- BF: add recently tests data missing from distribution #567 (@yarikoptic)
Authors: 1
- Yaroslav Halchenko (@yarikoptic)
v0.11.2
🏠 Internal
- Make versioningit write version to file; make setup.py read version as fallback #566 (@jwodder)
- BF: add fetch-depth: 0 to get all tags into docker builds of master #566 (@yarikoptic)
Authors: 2
- John T. Wodder II (@jwodder)
- Yaroslav Halchenko (@yarikoptic)
v0.11.1
🏠 Internal
- Remove .git/ from .dockerignore so that versioning works while building docker image #564 (@yarikoptic)
Authors: 1
- Yaroslav Halchenko (@yarikoptic)
v0.11.0
🚀 Enhancement
- RF: drop Python 3.6 (EOLed), fix dcm2niix version in neurodocker script #555 (@yarikoptic)
- ENH: Adds populate_intended_for for fmaps #482 (@pvelasco @yarikoptic [email protected] @neurorepro)
🐛 Bug Fix
- bids_ME heuristic: add test for the dataset that raised #541, add support for MEGRE #547 (@pvelasco @yarikoptic)
- reproin heuristic: specify POPULATE_INTENDED_FOR_OPTS #546 (@yarikoptic)
- FIX: Convert sets to lists for filename updaters #461 (@tsalo)
- Added new infofilestyle compatible with BIDS #12 (@chrisgorgo)
- try a simple fix for wrongly ordered files in tar file #535 (@bpinsard)
- BF: Fix the order of the 'echo' entity in the filename #542 (@pvelasco)
- ENH: add HeudiconvVersion to sidecar .json files #529 (@yarikoptic)
- BF (TST): make anonymize_script actually output anything and map determinstically #511 (@yarikoptic)
- Rename DICOMCONVERT_README.md to README.md #4 (@satra)
⚠️ Pushed to master
- Dockerfile - use bullseye for the base and fresh dcm2niix (@yarikoptic)
🏠 Internal
- Run codespell on some obvious typos #563 (@yarikoptic)
- Set up auto #558 (@jwodder @yarikoptic)
🧪 Tests
- BF(TST): use caplog to control logging level, use python3 in shebang #553 (@yarikoptic)
- BF(TST): use caplog instead of capfd for testing if we log a warning #534 (@yarikoptic)
- Travis - Use bionic for the base #533 (@yarikoptic)
Authors: 9
- Basile (@bpinsard)
- Chris Gorgolewski (@chrisgorgo)
- DBIC BIDS Team ([email protected])
- John T. Wodder II (@jwodder)
- Michael (@neurorepro)
- Pablo Velasco (@pvelasco)
- Satrajit Ghosh (@satra)
- Taylor Salo (@tsalo)
- Yaroslav Halchenko (@yarikoptic)
v0.10.0
Various improvements and compatibility/support (dcm2niix, datalad) ch…
v0.9.0: ## [0.9.0] - 2020-12-23
Various improvements and compatibility/support (dcm2niix, datalad, duecredit) changes. Major change is placement of output files to the target output directory during conversion. ### Added - #454 zenodo referencing in README.rst and support for ducredit for heudiconv and reproin heuristic - #445 more tutorial references in README.md ### Changed - [#485][] placed files during conversion right away into the target directory (with a `_heudiconv???` suffix, renamed into ultimate target name later on), which avoids hitting file size limits of /tmp ([#481][]) and helped to avoid a regression in dcm2nixx 1.0.20201102 - #477 replaced `rec-<magnitude|phase>` with `part-<mag|phase>` now that BIDS supports the part entity - #473 made default for CogAtlasID to be a TODO URL - #459 made AcquisitionTime used for acq_time scans file field - #451 retained sub-second resolution in scans files - #442 refactored code so there is now heudiconv.main.workflow for more convenient use as a Python module ### Fixed - minimal version of nipype set to 1.2.3 to guarantee correct handling of DWI files ([#480][]) - `heudiconvDCM*` temporary directories are removed now ([#462][]) - compatibility with DataLad 0.13 ([#464][]) ### Removed - #443 pathlib as a dependency (we are Python3 only now)
v0.8.0: [0.8.0] - 2020-04-15
Enhancements - Centralized saving of .json files. Indentation of some files could change now from previous versions where it could have used `3` spaces. Now indentation should be consistently `2` for .json files we produce/modify ([#436][]) (note: dcm2niix uses tabs for indentation) - ReproIn heuristic: support SBRef and phase data ([#387][]) - Set the "TaskName" field in .json sidecar files for multi-echo data ([#420][]) - Provide an informative exception if command needs heuristic to be specified ([#437][]) Refactored - `embed_nifti` was refactored into `embed_dicom_and_nifti_metadata` which would no longer create `.nii` file if it does not exist already ([#432][]) Fixed - Skip datalad-based tests if no datalad available ([#430][]) - Search heuristic file path first so we do not pick up a python module if name conflicts ([#434][])
v0.7.0: [0.7.0] - 2020-03-20
Removed - Python 2 support/testing Enhancement - `-g` option obtained two new modes: `all` and `custom`. In case of `all`, all provided DICOMs will be treated as coming from a single scanning session. `custom` instructs to use `.grouping` value (could be a DICOM attribute or a callable)provided by the heuristic ([#359][]). - Stop before reading pixels data while gathering metadata from DICOMs ([#404][]) - reproin heuristic: - In addition to original "md5sum of the study_description" `protocols2fix` could now have (and applied after md5sum matching ones) 1). a regular expression searched in study_description, 2). an empty string as "catch all". This features could be used to easily provide remapping into reproin naming (documentation is to come to http://github.com/ReproNim/reproin) ([#425][]) Fixed - Use nan, not None for absent echo value in sorting - reproin heuristic: case seqinfos into a list to be able to modify from overloaded heuristic ([#419][]) - No spurious errors from the logger upon a warning about `etelemetry` absence ([#407][])