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][])