Merge tag 'v0.6.0' into debian

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

- Use [etelemetry](https://pypi.org/project/etelemetry) to inform about most
  recent available version of heudiconv. Please set `NO_ET` environment variable
  if you want to disable it ([#369][])
- BIDS:
  - `--bids` flag became an option. It can (optionally) accept `notop` value
    to avoid creation of top level files (`CHANGES`, `dataset_description.json`,
    etc) as a workaround during parallel execution to avoid race conditions etc.
    ([#344][])
  - Generate basic `.json` files with descriptions of the fields for
    `participants.tsv` and `_scans.tsv` files ([#376][])
  - Use `filelock` while writing top level files. Use
    `HEUDICONV_FILELOCK_TIMEOUT` environment to change the default timeout value
    ([#348][])
  - `_PDT2` was added as a suffix for multi-echo (really "multi-modal")
    sequences ([#345][])
- Calls to `dcm2niix` would include full output path to make it easier to
  discern in the logs what file it is working on ([#351][])
- With recent [datalad]() (>= 0.10), created DataLad dataset will use
  `--fake-dates` functionality of DataLad to not leak data conversion dates,
  which might be close to actual data acquisition/patient visit ([#352][])
- Support multi-echo EPI `_phase` data ([#373][] fixes [#368][])
- Log location of a bad .json file to ease troubleshooting ([#379][])
- Add basic pypi classifiers for the package ([#380][])

 Fixed
- Sorting `_scans.tsv` files lacking valid dates field should not cause a crash
  ([#337][])
- Multi-echo files detection based number of echos ([#339][])
- BIDS
  - Use `EchoTimes` from the associated multi-echo files if `EchoNumber` tag is
    missing ([#366][] fixes [#347][])
  - Tolerate empty ContentTime and/or ContentDate in DICOMs ([#372][]) and place
    "n/a" if value is missing ([#390][])
  - Do not crash and store original .json file is "JSON pretification" fails
    ([#342][])
- ReproIn heuristic
  - tollerate WIP prefix on Philips scanners ([#343][])
  - allow for use of `(...)` instead of `{...}` since `{}` are not allowed
    ([#343][])
  - Support pipolar fieldmaps by providing them with `_epi` not `_magnitude`.
    "Loose" BIDS `_key-value` pairs might come now after `_dir-` even if they
    came first before ([#358][] fixes [#357][])
- All heuristics saved under `.heudiconv/` under `heuristic.py` name, to avoid
  discrepancy during reconversion ([#354][] fixes [#353][])
- 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][])

* tag 'v0.6.0': (60 commits)
  Version boost to 0.6.0
  DOC: populate detailed changelog for 0.6.0 and tune up formatting in previous one
  Fix miscellaneous typos in ReproIn heuristic file.
  BF: fix check for the sbatch (SLURM) not being available
  ENH: make test-compare-two-versions take any two worktrees, and just show diff if results already known
  Update heudiconv/convert.py
  apply @mgxd 's suggestions, adding a warning and a timeout environment variable
  need str typecast
  Use empty string not None
  Empty acq_time results in empty cell not 'n/a'
  DOC: Clarify tarball session handling
  remove repetitive import statement
  respond to review - add explicit py2 check - change file saving strategy - use logger instead of print
  fix remaning py2 errors
  MNT: Add Python support metadata to package
  fix some python2/3 incompatibilities
  add return data (accidently removed return)
  make content unicode
  test that load_json provides filename if invalid
  explicitly name invalid json
  ...

Author: yarikoptic

.travis.yml

@@ -2,9 +2,9 @@
 language: python
 python:
   - 2.7
-  - 3.4
   - 3.5
   - 3.6
+  - 3.7
 
 cache:
   - apt

CHANGELOG.md

@@ -4,15 +4,72 @@ 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).
 
+## [0.6.0] - 2019-12-05
+
+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
+
+- Use [etelemetry](https://pypi.org/project/etelemetry) to inform about most
+  recent available version of heudiconv. Please set `NO_ET` environment variable
+  if you want to disable it ([#369][])
+- BIDS:
+  - `--bids` flag became an option. It can (optionally) accept `notop` value
+    to avoid creation of top level files (`CHANGES`, `dataset_description.json`,
+    etc) as a workaround during parallel execution to avoid race conditions etc.
+    ([#344][])
+  - Generate basic `.json` files with descriptions of the fields for
+    `participants.tsv` and `_scans.tsv` files ([#376][])
+  - Use `filelock` while writing top level files. Use
+    `HEUDICONV_FILELOCK_TIMEOUT` environment to change the default timeout value
+    ([#348][])
+  - `_PDT2` was added as a suffix for multi-echo (really "multi-modal")
+    sequences ([#345][])
+- Calls to `dcm2niix` would include full output path to make it easier to
+  discern in the logs what file it is working on ([#351][])
+- With recent [datalad]() (>= 0.10), created DataLad dataset will use
+  `--fake-dates` functionality of DataLad to not leak data conversion dates,
+  which might be close to actual data acquisition/patient visit ([#352][])
+- Support multi-echo EPI `_phase` data ([#373][] fixes [#368][])
+- Log location of a bad .json file to ease troubleshooting ([#379][])
+- Add basic pypi classifiers for the package ([#380][])
+
+### Fixed
+- Sorting `_scans.tsv` files lacking valid dates field should not cause a crash
+  ([#337][])
+- Multi-echo files detection based number of echos ([#339][])
+- BIDS
+  - Use `EchoTimes` from the associated multi-echo files if `EchoNumber` tag is
+    missing ([#366][] fixes [#347][])
+  - Tolerate empty ContentTime and/or ContentDate in DICOMs ([#372][]) and place
+    "n/a" if value is missing ([#390][])
+  - Do not crash and store original .json file is "JSON pretification" fails
+    ([#342][])
+- ReproIn heuristic
+  - tollerate WIP prefix on Philips scanners ([#343][])
+  - allow for use of `(...)` instead of `{...}` since `{}` are not allowed
+    ([#343][])
+  - Support pipolar fieldmaps by providing them with `_epi` not `_magnitude`.
+    "Loose" BIDS `_key-value` pairs might come now after `_dir-` even if they
+    came first before ([#358][] fixes [#357][])
+- All heuristics saved under `.heudiconv/` under `heuristic.py` name, to avoid
+  discrepancy during reconversion ([#354][] fixes [#353][])
+- 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
 
 This release includes fixes to BIDS multi-echo conversions, the
- re-implementation of queuing support (currently just SLURM), as well as
- some bugfixes.
+re-implementation of queuing support (currently just SLURM), as well as
+some bugfixes.
 
- 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`.
+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
 - Readthedocs documentation ([#327][])
@@ -189,8 +246,37 @@ TODO Summary
 [DBIC]: http://dbic.dartmouth.edu
 [datalad]: http://datalad.org
 [dcm2niix]: https://github.com/rordenlab/dcm2niix
-[#293]: https://github.com/nipy/heudiconv/issues/293
 [#301]: https://github.com/nipy/heudiconv/issues/301
+[#353]: https://github.com/nipy/heudiconv/issues/353
+[#354]: https://github.com/nipy/heudiconv/issues/354
+[#357]: https://github.com/nipy/heudiconv/issues/357
+[#358]: https://github.com/nipy/heudiconv/issues/358
+[#347]: https://github.com/nipy/heudiconv/issues/347
+[#366]: https://github.com/nipy/heudiconv/issues/366
+[#368]: https://github.com/nipy/heudiconv/issues/368
+[#373]: https://github.com/nipy/heudiconv/issues/373
+[#293]: https://github.com/nipy/heudiconv/issues/293
 [#304]: https://github.com/nipy/heudiconv/issues/304
 [#306]: https://github.com/nipy/heudiconv/issues/306
 [#310]: https://github.com/nipy/heudiconv/issues/310
+[#327]: https://github.com/nipy/heudiconv/issues/327
+[#328]: https://github.com/nipy/heudiconv/issues/328
+[#334]: https://github.com/nipy/heudiconv/issues/334
+[#337]: https://github.com/nipy/heudiconv/issues/337
+[#339]: https://github.com/nipy/heudiconv/issues/339
+[#342]: https://github.com/nipy/heudiconv/issues/342
+[#343]: https://github.com/nipy/heudiconv/issues/343
+[#344]: https://github.com/nipy/heudiconv/issues/344
+[#345]: https://github.com/nipy/heudiconv/issues/345
+[#348]: https://github.com/nipy/heudiconv/issues/348
+[#351]: https://github.com/nipy/heudiconv/issues/351
+[#352]: https://github.com/nipy/heudiconv/issues/352
+[#360]: https://github.com/nipy/heudiconv/issues/360
+[#364]: https://github.com/nipy/heudiconv/issues/364
+[#369]: https://github.com/nipy/heudiconv/issues/369
+[#372]: https://github.com/nipy/heudiconv/issues/372
+[#375]: https://github.com/nipy/heudiconv/issues/375
+[#376]: https://github.com/nipy/heudiconv/issues/376
+[#379]: https://github.com/nipy/heudiconv/issues/379
+[#380]: https://github.com/nipy/heudiconv/issues/380
+[#390]: https://github.com/nipy/heudiconv/issues/390

README.md

@@ -4,7 +4,7 @@
 
 `a heuristic-centric DICOM converter`
 
-.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:unstable-brightgreen.svg?logo=docker&style=flat
+.. image:: https://img.shields.io/badge/docker-nipy/heudiconv:0.5.4-brightgreen.svg?logo=docker&style=flat
   :target: https://hub.docker.com/r/nipy/heudiconv/tags/
   :alt: Our Docker image
 

README.rst

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ''
 # The full version, including alpha/beta/rc tags
-release = '0.5.4'
+release = '0.6.0'
 
 
 # -- General configuration ---------------------------------------------------

docs/conf.py

@@ -26,7 +26,7 @@ If `Docker <https://docs.docker.com/install/>`_ is available on your system, you
 can visit `our page on Docker Hub <https://hub.docker.com/r/nipy/heudiconv/tags>`_ 
 to view available releases. To pull the latest release, run::
 
-    $ docker pull nipy/heudiconv:0.5.4
+    $ docker pull nipy/heudiconv:0.6.0
 
 
 Singularity
@@ -35,4 +35,4 @@ If `Singularity <https://www.sylabs.io/singularity/>`_ is available on your syst
 you can use it to pull and convert our Docker images! For example, to pull and 
 build the latest release, you can run::
 
-    $ singularity pull docker://nipy/heudiconv:0.5.4
+    $ singularity pull docker://nipy/heudiconv:0.6.0