Merge tag 'v0.6.0' into debian

[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

- 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
  - tolerate 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':
  Boost perspective release date in changelog to today
  ENH(TST): Fix version to older pytest to ease backward compatibility testing
  RF: use tmpdir not tmp_path fixture
  FIX: minor typo in CHANGELOG.md

CHANGELOG.md

@@ -4,7 +4,7 @@ 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
+## [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
@@ -50,7 +50,7 @@ version boost.
   - Do not crash and store original .json file is "JSON pretification" fails
     ([#342][])
 - ReproIn heuristic
-  - tollerate WIP prefix on Philips scanners ([#343][])
+  - tolerate 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`.

dev-requirements.txt

@@ -1,4 +1,5 @@
 -r requirements.txt
-pytest
+# Fix version to older pytest to ease backward compatibility testing
+pytest==3.6.4
 tinydb
 inotify

heudiconv/tests/test_utils.py

@@ -67,11 +67,11 @@ def test_json_dumps_pretty():
     assert pretty({'WipMemBlock': tstr}) == '{\n  "WipMemBlock": "%s"\n}' % tstr
 
 
-def test_load_json(tmp_path, caplog):
+def test_load_json(tmpdir, caplog):
     # test invalid json
     ifname = 'invalid.json'
-    invalid_json_file = str(tmp_path / ifname)
-    create_tree(str(tmp_path), {ifname: u"I'm Jason Bourne"})
+    invalid_json_file = str(tmpdir / ifname)
+    create_tree(str(tmpdir), {ifname: u"I'm Jason Bourne"})
 
     with pytest.raises(JSONDecodeError):
         load_json(str(invalid_json_file))
@@ -81,7 +81,7 @@ def test_load_json(tmp_path, caplog):
     # test valid json
     vcontent = {"secret": "spy"}
     vfname = "valid.json"
-    valid_json_file = str(tmp_path / vfname)
+    valid_json_file = str(tmpdir / vfname)
     save_json(valid_json_file, vcontent)
 
     assert load_json(valid_json_file) == vcontent