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FIX: Blacklist nipype 1.2.1, 1.2.2 in Python 2.7 to avoid TraitError #375

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merged 3 commits into from
Sep 18, 2019
Merged

FIX: Blacklist nipype 1.2.1, 1.2.2 in Python 2.7 to avoid TraitError #375

merged 3 commits into from
Sep 18, 2019

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effigies
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@effigies effigies commented Sep 18, 2019 •
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First checking whether we've already fixed this in nipype master.

Fixes #374
Related nipy/nipype#3037

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codecov bot commented Sep 18, 2019 •
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Codecov Report

Merging #375 into master will increase coverage by 0.03%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #375      +/-   ##
==========================================
+ Coverage   74.26%   74.29%   +0.03%     
==========================================
  Files          35       35              
  Lines        2708     2708              
==========================================
+ Hits         2011     2012       +1     
+ Misses        697      696       -1
Impacted Files Coverage Δ
heudiconv/info.py 100% <ø> (ø) ⬆️
heudiconv/utils.py 90.49% <0%> (+0.45%) ⬆️

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@effigies
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K. Have to patch something quickly over at nipype, but this should be resolved for the next release.

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mgxd commented Sep 18, 2019

thanks, we'll leave the pin until the next release is out. just making a note here that we'll have to exclude nipype 1.2.2 for py2

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I think you need to exclude 1.2.1 as well.

mgxd
mgxd reviewed Sep 18, 2019
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heudiconv/info.py Outdated Show resolved Hide resolved
@effigies effigies changed the title FIX: TraitError FIX: Blacklist nipype 1.2.1, 1.2.2 in Python 2.7 to avoid TraitError Sep 18, 2019
@mgxd mgxd merged commit fe0f2c8 into nipy:master Sep 18, 2019
@yarikoptic
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Thank you guys!

@yarikoptic yarikoptic added this to the 0.6 milestone Nov 22, 2019
yarikoptic added a commit that referenced this pull request Dec 16, 2019
@yarikoptic
Merge tag 'v0.6.0' into debian
e6c5e1b 
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
  ...
yarikoptic added a commit that referenced this pull request Dec 16, 2019
@yarikoptic
Merge tag 'v0.6.0' into debian
abac818 
[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
@effigies effigies deleted the fix/traiterror branch May 31, 2023 19:37
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tests on python 2.7 started to fail within the past month
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