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ENH: Finalizing the API overhaul #132

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@oesteban oesteban force-pushed the feat/gen-workflow-from-estimation-object branch from 282aee2 to d2ce402 Compare November 27, 2020 13:15
@oesteban oesteban force-pushed the feat/gen-workflow-from-estimation-object branch from d2ce402 to 75c4d07 Compare November 27, 2020 13:30
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codecov bot commented Nov 27, 2020

Codecov Report

Merging #132 (debce89) into dev/1.4.0 (5588e11) will increase coverage by 3.07%.
The diff coverage is 95.61%.

Impacted file tree graph

@@              Coverage Diff              @@
##           dev/1.4.0     #132      +/-   ##
=============================================
+ Coverage      88.44%   91.51%   +3.07%     
=============================================
  Files             15       17       +2     
  Lines            926      943      +17     
  Branches         109      121      +12     
=============================================
+ Hits             819      863      +44     
+ Misses            75       49      -26     
+ Partials          32       31       -1     
Flag Coverage Δ
travis ?
unittests 91.51% <95.61%> (+3.10%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
sdcflows/utils/phasemanip.py 91.30% <ø> (ø)
sdcflows/workflows/base.py 95.00% <ø> (ø)
sdcflows/fieldmaps.py 84.90% <91.66%> (+3.16%) ⬆️
sdcflows/utils/epimanip.py 96.15% <96.15%> (ø)
sdcflows/interfaces/epi.py 100.00% <100.00%> (+17.46%) ⬆️
sdcflows/utils/misc.py 100.00% <100.00%> (ø)
sdcflows/workflows/apply/correction.py 100.00% <100.00%> (ø)
sdcflows/workflows/apply/registration.py 92.00% <100.00%> (+9.85%) ⬆️
sdcflows/workflows/fit/fieldmap.py 98.30% <100.00%> (+0.12%) ⬆️
sdcflows/workflows/fit/pepolar.py 83.58% <100.00%> (+20.06%) ⬆️
... and 5 more

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@oesteban oesteban force-pushed the feat/gen-workflow-from-estimation-object branch 2 times, most recently from d38cf9d to 4c41428 Compare November 27, 2020 20:43
@oesteban oesteban force-pushed the feat/gen-workflow-from-estimation-object branch 2 times, most recently from 3ed7829 to 91ed4ff Compare November 28, 2020 01:48
@pep8speaks
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pep8speaks commented Nov 28, 2020

Hello @oesteban, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 sdcflows.

Comment last updated at 2020-11-28 15:16:29 UTC

This commit makes a deep revisiting of our total readout time implementation.
Most of the relevant details about this commit are included within the
documentation.

With thanks to @neurolabusc because this wouldn't have been possible without
his thorough work, to @parekhpravesh for the thread he opened at
Neurostars, to @Gilles86 for making us aware of these issues on the *fMRIPrep*
repo, and to @treanus for reporting nipreps#5.

Resolves: nipreps#5.
@oesteban oesteban force-pushed the feat/gen-workflow-from-estimation-object branch from 91ed4ff to debce89 Compare November 28, 2020 15:16
@oesteban oesteban marked this pull request as ready for review November 28, 2020 15:47
@oesteban oesteban merged commit 4f28ed3 into nipreps:dev/1.4.0 Nov 28, 2020
@oesteban oesteban deleted the feat/gen-workflow-from-estimation-object branch November 29, 2020 10:40
oesteban added a commit that referenced this pull request Dec 24, 2020
2.0.0rc4

* FIX: Convert SEI fieldmaps given in rad/s into Hz (#127)
* FIX: Limit ``3dQwarp`` to maximum 4 CPUs for stability reasons (#128)
* ENH: Generate a simple mask after correction (#161)
* ENH: Increase unit-tests coverage of ``sdcflows.fieldmaps`` (#159)
* ENH: Optimize tensor-product B-Spline kernel evaluation (#157)
* ENH: Add a memory check to dynamically limit interpolation blocksize (#156)
* ENH: Massage TOPUP's fieldcoeff files to be compatible with ours (#154)
* ENH: Add a simplistic EPI masking algorithm (#152)
* ENH: Utility that returns the ``B0FieldSource`` of a given potential EPI target (#151)
* ENH: Write ``fmapid-`` entity in Derivatives (#150)
* ENH: Multiplex fieldmap estimation outputs into a single ``outputnode`` (#149)
* ENH: Putting the new API together on a base workflow (#143)
* ENH: Autogenerate ``B0FieldIdentifiers`` from ``IntendedFor`` (#142)
* ENH: Finalizing the API overhaul (#132)
* ENH: Keep a registry of already-used identifiers (and auto-generate new) (#130)
* ENH: New objects for better representation of fieldmap estimation (#114)
* ENH: Show FieldmapReportlet oriented aligned with cardinal axes (#120)
* ENH: New estimation API (featuring a TOPUP implementation!) (#115)
* DOC: Minor improvements to the literate workflows descriptions. (#162)
* DOC: Fix typo in docstring (#155)
* DOC: Enable NiPype's sphinx-extension to better render Interfaces (#131)
* MAINT: Drop Python 3.6 (#160)
* MAINT: Enable Git-archive protocol with setuptools-scm-archive (#153)
* MAINT: Migrate TravisCI -> GH Actions (completion) (#138)
* MAINT: Migrate TravisCI -> GH Actions (#137)
* MAINT: Minimal unit test and refactor of pepolar workflow node (#133)
* MAINT: Collect code coverage from tests on Circle (#122)
* MAINT: Test minimum dependencies with TravisCI (#96)
* MAINT: Add FLIRT config files to prepare for TOPUP integration (#116)
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Susceptibility Distortion Correction - effective echo-spacing and total-readout time for Philips data
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