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FIX: Update mne.WatershedBEM command line #3007

Merged
merged 7 commits into from
Sep 5, 2019
Merged

FIX: Update mne.WatershedBEM command line #3007

merged 7 commits into from
Sep 5, 2019

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vferat
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@vferat vferat commented Aug 23, 2019

Summary

Close #2995.

List of changes proposed in this PR (pull-request)

modified mne.WatershedBEM _cmd from mne_watershed_bem to mne watershed_bem see documentation

Acknowledgment

  • I acknowledge that this contribution will be available under the Apache 2 license.

@vferat
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vferat commented Aug 23, 2019

when first running make check-before-commit I got an error saying that no module named "bids" where found. I had to manually install pybids ( I setuped the testing environment using pip install -e ".[dev]" )

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Basicaly , it's the only change wanted here, do not know why so much files are changed

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This seems right, as watershed_bem was added in mne-tools/mne-python#2194, after the switch to an mne master command (mne-tools/mne-python#866).

Can you rebase or revert to reduce this PR to only the change you wanted to make and the tests?

@effigies effigies added this to the 1.2.2 milestone Aug 30, 2019
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codecov bot commented Aug 30, 2019

Codecov Report

Merging #3007 into master will decrease coverage by 0.29%.
The diff coverage is 41.66%.

Impacted file tree graph

@@           Coverage Diff            @@
##           master   #3007     +/-   ##
========================================
- Coverage    67.5%   67.2%   -0.3%     
========================================
  Files         344     344             
  Lines       44039   44134     +95     
  Branches     5554    5585     +31     
========================================
- Hits        29727   29659     -68     
- Misses      13560   13689    +129     
- Partials      752     786     +34
Flag Coverage Δ
#smoketests 49.03% <41.66%> (-1.37%) ⬇️
#unittests 65.02% <41.66%> (+0.07%) ⬆️
Impacted Files Coverage Δ
nipype/interfaces/mne/base.py 50.84% <41.66%> (ø) ⬆️
nipype/workflows/fmri/fsl/preprocess.py 72.67% <0%> (-13.39%) ⬇️
nipype/info.py 89.58% <0%> (-4.79%) ⬇️
nipype/utils/config.py 61.82% <0%> (-4.31%) ⬇️
nipype/pipeline/engine/utils.py 77.48% <0%> (-3.46%) ⬇️
nipype/workflows/fmri/fsl/estimate.py 61.97% <0%> (-2.82%) ⬇️
nipype/interfaces/fsl/model.py 77.91% <0%> (-2.71%) ⬇️
nipype/interfaces/fsl/preprocess.py 80.33% <0%> (-2.27%) ⬇️
nipype/scripts/cli.py 40.9% <0%> (-1.95%) ⬇️
nipype/pipeline/plugins/multiproc.py 82.71% <0%> (-1.86%) ⬇️
... and 13 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 23300e9...183ab88. Read the comment docs.

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codecov bot commented Aug 30, 2019

Codecov Report

Merging #3007 into master will decrease coverage by 0.29%.
The diff coverage is 41.66%.

Impacted file tree graph

@@           Coverage Diff            @@
##           master   #3007     +/-   ##
========================================
- Coverage    67.5%   67.2%   -0.3%     
========================================
  Files         344     344             
  Lines       44039   44134     +95     
  Branches     5554    5585     +31     
========================================
- Hits        29727   29659     -68     
- Misses      13560   13689    +129     
- Partials      752     786     +34
Flag Coverage Δ
#smoketests 49.03% <41.66%> (-1.37%) ⬇️
#unittests 65.02% <41.66%> (+0.07%) ⬆️
Impacted Files Coverage Δ
nipype/interfaces/mne/base.py 50.84% <41.66%> (ø) ⬆️
nipype/workflows/fmri/fsl/preprocess.py 72.67% <0%> (-13.39%) ⬇️
nipype/info.py 89.58% <0%> (-4.79%) ⬇️
nipype/utils/config.py 61.82% <0%> (-4.31%) ⬇️
nipype/pipeline/engine/utils.py 77.48% <0%> (-3.46%) ⬇️
nipype/workflows/fmri/fsl/estimate.py 61.97% <0%> (-2.82%) ⬇️
nipype/interfaces/fsl/model.py 77.91% <0%> (-2.71%) ⬇️
nipype/interfaces/fsl/preprocess.py 80.33% <0%> (-2.27%) ⬇️
nipype/scripts/cli.py 40.9% <0%> (-1.95%) ⬇️
nipype/pipeline/plugins/multiproc.py 82.71% <0%> (-1.86%) ⬇️
... and 13 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 23300e9...183ab88. Read the comment docs.

@effigies effigies changed the title [FIX] mne.WatershedBEM command FIX: Update mne.WatershedBEM command line Sep 5, 2019
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effigies commented Sep 5, 2019

Thanks for this.

@effigies effigies merged commit 2642799 into nipy:master Sep 5, 2019
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mne.WatershedBEM creates incorrect command line
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