Reformat CHANGELOG for auto

Author: jwodder

CHANGELOG.md

@@ -1,19 +1,13 @@
-# Changelog
-All notable changes to this project will be documented (for humans) in this file.
-
-The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
-and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
-
-## [0.10.0] - 2021-09-16
+# [0.10.0] - 2021-09-16
 
 Various improvements and compatibility/support (dcm2niix, datalad) changes.
 
-### Added
+## Added
 
 - Add "AcquisitionTime" to the seqinfo ([#487][])
 - Add support for saving the Phoenix Report in the sourcedata folder ([#489][])
 
-### Changed
+## Changed
 
 - Python 3.5 EOLed, supported (tested) versions now: 3.6 - 3.9
 - In reprorin heuristic, allow for having multiple accessions since now there is
@@ -22,7 +16,7 @@ Various improvements and compatibility/support (dcm2niix, datalad) changes.
   sub/ses (generates too many identical files) ([#507][])
 
 
-### Fixed
+## Fixed
 
 - Compatibility with DataLad 0.15.0. Minimal version is 0.13.0 now.
 - Try to open top level BIDS .json files a number of times for adjustment,
@@ -35,24 +29,24 @@ Various improvements and compatibility/support (dcm2niix, datalad) changes.
   and look for _bold only under sub-* directories ([#496][])
 - Ensure bvec/bval files are only created for dwi output ([#491][])
 
-### Removed
+## Removed
 
 - In reproin heuristic, old hardcoded sequence renamings and filters ([#508][])
 
 
-## [0.9.0] - 2020-12-23
+# [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
+## Added
 
 - #454 zenodo referencing in README.rst and support for ducredit for
   heudiconv and reproin heuristic
 - #445 more tutorial references in README.md
 
-### Changed
+## Changed
 
 - [#485][] placed files during conversion right away into the target
   directory (with a `_heudiconv???` suffix, renamed into ultimate target
@@ -66,21 +60,21 @@ target output directory during conversion.
 - [#442][] refactored code so there is now heudiconv.main.workflow for
   more convenient use as a Python module
 
-### Fixed
+## 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
+## Removed
 
 - #443 pathlib as a dependency (we are Python3 only now)
 
 
-## [0.8.0] - 2020-04-15
+# [0.8.0] - 2020-04-15
 
-### Enhancements
+## Enhancements
 
 - Centralized saving of .json files.  Indentation of some files could
   change now from previous versions where it could have used `3`
@@ -92,25 +86,25 @@ target output directory during conversion.
 - Provide an informative exception if command needs heuristic to be
   specified ([#437][])
 
-### Refactored
+## 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
+## 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][])
 
-## [0.7.0] - 2020-03-20
+# [0.7.0] - 2020-03-20
 
-### Removed
+## Removed
 
 - Python 2 support/testing
 
-### Enhancement
+## 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.
@@ -126,23 +120,23 @@ target output directory during conversion.
     naming (documentation is to come to http://github.com/ReproNim/reproin)
     ([#425][])
 
-### Fixed
+## 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][])
 
-## [0.6.0] - 2019-12-16
+# [0.6.0] - 2019-12-16
 
 This is largely a bug fix.  Metadata and order of `_key-value` fields in BIDS
 could change from the result of converting using previous versions, thus minor
 version boost.
 14 people contributed to this release -- thanks
 [everyone](https://github.com/nipy/heudiconv/graphs/contributors)!
 
-### Enhancement
+## Enhancement
 
 - Use [etelemetry](https://pypi.org/project/etelemetry) to inform about most
   recent available version of heudiconv. Please set `NO_ET` environment variable
@@ -168,7 +162,7 @@ version boost.
 - Log location of a bad .json file to ease troubleshooting ([#379][])
 - Add basic pypi classifiers for the package ([#380][])
 
-### Fixed
+## Fixed
 - Sorting `_scans.tsv` files lacking valid dates field should not cause a crash
   ([#337][])
 - Multi-echo files detection based number of echos ([#339][])
@@ -191,7 +185,7 @@ version boost.
 - Do not crash (with TypeError) while trying to sort absent file list ([#360][])
 - heudiconv requires nipype >= 1.0.0 ([#364][]) and blacklists `1.2.[12]` ([#375][])
 
-## [0.5.4] - 2019-04-29
+# [0.5.4] - 2019-04-29
 
 This release includes fixes to BIDS multi-echo conversions, the
 re-implementation of queuing support (currently just SLURM), as well as
@@ -201,17 +195,17 @@ Starting today, we will (finally) push versioned releases to DockerHub.
 Finally, to more accurately reflect on-going development, the `latest`
 tag has been renamed to `unstable`.
 
-### Added
+## Added
 - Readthedocs documentation ([#327][])
 
-### Changed
+## Changed
 - Update Docker dcm2niix to v.1.0.20190410 ([#334][])
 - Allow usage of `--files` with basic heuristics. This requires
   use of `--subject` flag, and is limited to one subject. ([#293][])
 
-### Deprecated
+## Deprecated
 
-### Fixed
+## Fixed
 - Improve support for multiple `--queue-args` ([#328][])
 - Fixed an issue where generated BIDS sidecar files were missing additional
   information - treating all conversions as if the `--minmeta` flag was
@@ -222,24 +216,24 @@ tag has been renamed to `unstable`.
   before '.nii.gz'. Previously would have lead to absent additional metadata
   extraction etc ([#310][])
 
-### Removed
+## Removed
 - `--sbargs` argument was renamed to `--queue-args` ([#304][])
 
-### Security
+## Security
 
 
-## [0.5.3] - 2019-01-12
+# [0.5.3] - 2019-01-12
 
 Minor hot bugfix release
 
-### Fixed
+## Fixed
 - Do not shorten spaces in the dates while pretty printing .json
 
-## [0.5.2] - 2019-01-04
+# [0.5.2] - 2019-01-04
 
 A variety of bugfixes
 
-### Changed
+## Changed
 - Reproin heuristic: `__dup` indices would now be assigned incrementally
   individually per each sequence, so there is a chance to properly treat
   associate for multi-file (e.g. `fmap`) sequences
@@ -250,7 +244,7 @@ A variety of bugfixes
   csa.tProtocolName header field if not present in public one
 - nipype>=0.12.0 is required now
 
-### Fixed
+## Fixed
 - Multiple files produced by dcm2niix are first sorted to guarantee
   correct order e.g. of magnitude files in fieldmaps, which otherwise
   resulted in incorrect according to BIDS ordering of them
@@ -259,23 +253,23 @@ A variety of bugfixes
   those files were not regenerated after an initial conversion
 - Unicode handling in anonimization scripts
 
-## [0.5.1] - 2018-07-05
+# [0.5.1] - 2018-07-05
 Bugfix release
 
-### Added
+## Added
 - Video tutorial / updated slides
 - Helper to set metadata restrictions correctly
 - Usage is now shown when run without arguments
 - New fields to Seqinfo
   - series_uid
 - Reproin heuristic support for xnat
-### Changed
+## Changed
 - Dockerfile updated to use `dcm2niix v1.0.20180622`
 - Conversion table will be regenerated if heurisic has changed
 - Do not touch existing BIDS files
   - events.tsv
   - task JSON
-### Fixed
+## Fixed
 - Python 2.7.8 and older installation
 - Support for updated packages
   - `Datalad` 0.10
@@ -286,10 +280,10 @@ Bugfix release
   - ensure phasediff exists
   - support for single magnitude acquisitions
 
-## [0.5] - 2018-03-01
+# [0.5] - 2018-03-01
 The first release after major refactoring:
 
-### Changed
+## Changed
 - Refactored into a proper `heudiconv` Python module
   - `heuristics` is now a `heudiconv.heuristics` submodule
   - you can specify shipped heuristics by name (e.g. `-f reproin`)
@@ -301,7 +295,7 @@ The first release after major refactoring:
 - Logging verbosity reduced
 - Increased leniency with missing DICOM fields
 - `dbic_bids` heuristic renamed into reproin
-### Added
+## Added
 - [LICENSE](https://github.com/nipy/heudiconv/blob/master/LICENSE)
   with Apache 2.0 license for the project
 - [CHANGELOG.md](https://github.com/nipy/heudiconv/blob/master/CHANGELOG.md)
@@ -311,11 +305,11 @@ The first release after major refactoring:
   `reproin` heuristic shipped with heudiconv
 - [utils/test-compare-two-versions.sh](utils/test-compare-two-versions.sh)
   helper to compare conversions with two different versions of heudiconv
-### Removed
+## Removed
 - Support for converters other than `dcm2niix`, which is now the default.
   Explicitly specify `-c none` to only prepare conversion specification
   files without performing actual conversion
-### Fixed
+## Fixed
 - Compatibility with Nipype 1.0, PyDicom 1.0, and upcoming DataLad 0.10
 - Consistency with converted files permissions
 - Ensured subject id for BIDS conversions will be BIDS compliant
@@ -324,54 +318,41 @@ The first release after major refactoring:
   numeric precision issues
 - Many other various issues
 
-## [0.4] - 2017-10-15
+# [0.4] - 2017-10-15
 A usable release to support [DBIC][] use-case
-### Added
+## Added
 - more testing
-### Changes
+## Changes
 - Dockerfile updates (added pigz, progressed forward [dcm2niix][])
-### Fixed
+## Fixed
 - correct date/time in BIDS `_scans` files
 - sort entries in `_scans` by date and then filename
 
-## [0.3] - 2017-07-10
+# [0.3] - 2017-07-10
 A somewhat working release on the way to support [DBIC][] use-case
-### Added
+## Added
 - more tests
 - groupping of dicoms by series if provided
 - many more features and fixes
 
-## [0.2] - 2016-10-20
+# [0.2] - 2016-10-20
 An initial release on the way to support [DBIC][] use-case
-### Added
+## Added
 - basic Python project assets (`setup.py`, etc)
 - basic tests
 - [datalad][] support
 - dbic_bids heuristic
 - `--dbg` command line flag to enter `pdb` environment upon failure
-## Fixed
+# Fixed
 - Better Python3 support
 - Better PEP8 compliance
 
-## [0.1] - 2015-09-23
+# [0.1] - 2015-09-23
 
 Initial version
 
 ---
 
-Just a template for future records:
-
-## [Unreleased] - Date
-TODO Summary
-### Added
-### Changed
-### Deprecated
-### Fixed
-### Removed
-### Security
-
----
-
 ## References
 [DBIC]: http://dbic.dartmouth.edu
 [datalad]: http://datalad.org