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ENH: Reuse config #2240

Merged
merged 5 commits into from
Aug 31, 2020
Merged

ENH: Reuse config #2240

merged 5 commits into from
Aug 31, 2020

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effigies
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@effigies effigies commented Aug 18, 2020 •
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Restart of #2107. Last comments were about restyling with black, so I restyled, and rebased all of #2107 on top of this, restyling in the process.

Closes #2187.

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pep8speaks commented Aug 18, 2020 •
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Hello @effigies! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-08-29 14:07:40 UTC

effigies
effigies commented Aug 18, 2020
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Some initial thoughts. I think we should make reusing a config file a CLI flag --config <config-file>, rather than search + disable with an environment variable.

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mgxd
mgxd reviewed Aug 19, 2020
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Thanks for reviving this - I can take a deeper look tomorrow and push on it again.

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Rebased into a small set of commits. This is ready for review.

mgxd
mgxd approved these changes Aug 29, 2020
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This looks good, and I agree explicit reuse is better than implicit. @oesteban and I briefly chatted about this during the standup, and we came to the conclusion this is the direction we'll go in.

@effigies effigies merged commit ffa5dc0 into nipreps:master Aug 31, 2020
@effigies effigies deleted the enh/reuse-config branch August 31, 2020 17:42
HippocampusGirl added a commit to HippocampusGirl/fmriprep that referenced this pull request Sep 16, 2020
@HippocampusGirl
Merge tag '20.2.0rc0' into halfpipe
8744ba9 
20.2.0 RC0 (September 04, 2020)

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Revise the reproducibility of CompCor masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: FreeSurfer license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure NiPype telemetry is just pinged once (nipreps#2168)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin NiPype with new Sphinx extension syntax (nipreps#2092)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence PyBIDS warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#2158)
HippocampusGirl added a commit to HippocampusGirl/fmriprep that referenced this pull request Sep 16, 2020
@HippocampusGirl
Merge tag '20.2.0rc1' into halfpipe
8a1ae2f 
20.2.0rc1

With this third minor release series of 2020,
the first *fMRIPrep LTS* (*long-term support*) is finally here!

This release contains a number of bug-fixes and enhancements mostly
related to easing the maintenance, anticipating patch-release breaking
changes to ensure a longstanding LTS, and addressing some run-to-run
repeatability problems of the CompCor implementation.

.. admonition:: Long-Term Support (LTS)

    *fMRIPrep* 20.2 LTS introduces the `long-term support program
    <https://www.nipreps.org/devs/releases/#long-term-support-series>`__.
    This LTS version will be kindly steered and maintained by
    the group of Dr. Basile Pinsard and Prof. Pierre Bellec at
    `CRIUGM <http://www.criugm.qc.ca/>`__, (Université de Montréal).
    The LTS is planned for a window of 4 years of support (i.e., until
    September 2024).

.. caution::

    As with all minor version increments, working directories
    from previous versions **should not be reused**.

Thank you for using *fMRIPrep*!
If you encounter any issues with this release, please let us know
by posting an issue on our GitHub page!

A full list of changes can be found below.

* FIX: Get missing ``probseg`` file from MNI152NLin2009cAsym (nipreps#2271)
* FIX: Restore ``--ignore t2w/flair`` options (nipreps#2260)
* FIX: Revise the reproducibility of *CompCor* masks (nipreps#2130)
* FIX: Simplify transform aggregation in resampling, pass identity transforms for multi-echo cases (nipreps#2239)
* FIX: Skip the T1w check if ``--anat-derivatives`` is provided. (nipreps#2201)
* FIX: Storing ``--bids-filters`` within config file (nipreps#2177)
* FIX: Revise multi-echo reference generation, permitting using SBRefs too (nipreps#1803)
* FIX: *FreeSurfer* license manipulation & canary
* ENH: Output CompCor masks if ``--debug compcor`` is passed (nipreps#2248)
* ENH: Conform to BIDS Derivatives as of BIDS 1.4.0 (nipreps#2223)
* ENH: Reuse config (nipreps#2240)
* ENH: Save BOLD-anatomical transforms to derivatives folder (nipreps#2233)
* ENH: Leverage BIDSLayout's ``database_path`` (nipreps#2203)
* ENH: Add ``--no-tty`` option to ``fmriprep-docker.py`` (nipreps#2204)
* ENH: Report number of echoes in BOLD summary. (nipreps#2184)
* ENH: Ensure *NiPype* telemetry is just pinged once (nipreps#2168)
* DOC: Add FAQ entry for using pre-indexed layouts (nipreps#2256)
* DOC: Update reference in "Refinement of Brain Mask" description (nipreps#2215)
* DOC: List *TemplateFlow* templates that need to be prefetched (nipreps#2196)
* DOC: Update references to https://github.com/nipreps (nipreps#2191)
* DOC: Pin *NiPype* with new Sphinx extension syntax (nipreps#2092)
* MAINT: Track nipreps#2269 and nipreps#2269, bug-fixes on the 20.1.x series
* MAINT: Remove derivatives from layout index ignores (nipreps#2258)
* MAINT: Track nipreps#2252 from 20.1.x series (nipreps#2253)
* MAINT: Silence *PyBIDS* warning by setting extension mode (nipreps#2250)
* MAINT: Drop CircleCI docs build (nipreps#2247)
* MAINT: Pin latest *NiPreps* (nipreps#2244)
* MAINT: Update ``setup.cfg`` (flake8 and pytest) (nipreps#2183)
* MAINT: Delete release-drafter (nipreps#2169)
* MAINT: Track bug-fix release on the 20.1.x series (nipreps#2165)
* MAINT: Remove auto-comment bot (nipreps#2166)
* MAINT: Improve the questions on the bug-report template (nipreps#2158)

.. admonition:: Author list for papers based on *fMRIPrep* 20.2 LTS series

    As described in the `Contributor Guidelines
    <https://www.nipreps.org/community/CONTRIBUTING/#recognizing-contributions>`__,
    anyone listed as developer or contributor may write and submit manuscripts
    about *fMRIPrep*.
    To do so, please move the author(s) name(s) to the front of the following list:

    Markiewicz, Christopher J. \ :sup:`1`\ ; Goncalves, Mathias \ :sup:`1`\ ; DuPre, Elizabeth \ :sup:`2`\ ; Kent, James D. \ :sup:`3`\ ; Salo, Taylor \ :sup:`4`\ ; Ciric, Rastko \ :sup:`1`\ ; Pinsard, Basile \ :sup:`5`\ ; Finc, Karolina \ :sup:`6`\ ; de la Vega, Alejandro \ :sup:`7`\ ; Feingold, Franklin \ :sup:`1`\ ; Tooley, Ursula A. \ :sup:`8`\ ; Benson, Noah C. \ :sup:`9`\ ; Urchs, Sebastian \ :sup:`2`\ ; Blair, Ross W. \ :sup:`1`\ ; Erramuzpe, Asier \ :sup:`10`\ ; Lurie, Daniel J. \ :sup:`11`\ ; Heinsfeld, Anibal S. \ :sup:`12`\ ; Jacoby, Nir \ :sup:`13`\ ; Jamison, Keith W. \ :sup:`14`\ ; Frederick, Blaise B. \ :sup:`15, 16`\ ; Valabregue, Romain \ :sup:`17`\ ; Sneve, Markus H. \ :sup:`18`\ ; Liem, Franz \ :sup:`19`\ ; Adebimpe, Azeez \ :sup:`20`\ ; Velasco, Pablo \ :sup:`21`\ ; Wexler, Joseph B. \ :sup:`1`\ ; Groen, Iris I. A. \ :sup:`22`\ ; Ma, Feilong \ :sup:`23`\ ; Amlien, Inge K. \ :sup:`18`\ ; Bellec, Pierre \ :sup:`5`\ ; Cieslak, Matthew \ :sup:`20`\ ; Devenyi, Grabriel A. \ :sup:`24`\ ; Ghosh, Satrajit S. \ :sup:`25, 26`\ ; Gomez, Daniel E. P. \ :sup:`27`\ ; Halchenko, Yaroslav O. \ :sup:`23`\ ; Isik, Ayse Ilkay \ :sup:`28`\ ; Moodie, Craig A. \ :sup:`1`\ ; Naveau, Mikaël \ :sup:`29`\ ; Rivera-Dompenciel, Adriana \ :sup:`3`\ ; Satterthwaite, Theodore D. \ :sup:`20`\ ; Sitek, Kevin R. \ :sup:`30`\ ; Stojić, Hrvoje \ :sup:`31`\ ; Thompson, William H. \ :sup:`1`\ ; Wright, Jessey \ :sup:`1`\ ; Ye, Zhifang \ :sup:`32`\ ; Gorgolewski, Krzysztof J. \ :sup:`1`\ ; Poldrack, Russell A. \ :sup:`1`\ ; Esteban, Oscar \ :sup:`33`\ .

    Affiliations:

      1. Department of Psychology, Stanford University
      2. Montreal Neurological Institute, McGill University
      3. Neuroscience Program, University of Iowa
      4. Department of Psychology, Florida International University
      5. SIMEXP Lab, CRIUGM, University of Montréal, Montréal, Canada
      6. Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń
      7. University of Texas at Austin
      8. Department of Neuroscience, University of Pennsylvania, PA, USA
      9. Department of Psychology, New York University
      10. Computational Neuroimaging Lab, BioCruces Health Research Institute
      11. Department of Psychology, University of California, Berkeley
      12. Child Mind Institute
      13. Department of Psychology, Columbia University
      14. Department of Radiology, Weill Cornell Medicine
      15. McLean Hospital Brain Imaging Center, MA, USA
      16. Consolidated Department of Psychiatry, Harvard Medical School, MA, USA
      17. CENIR, INSERM U1127, CNRS UMR 7225, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, F-75013, Paris, France
      18. Center for Lifespan Changes in Brain and Cognition, University of Oslo
      19. URPP Dynamics of Healthy Aging, University of Zurich
      20. Perelman School of Medicine, University of Pennsylvania, PA, USA
      21. Center for Brain Imaging, New York University
      22. Department of Psychology, New York University, NY, USA
      23. Dartmouth College: Hanover, NH, United States
      24. Department of Psychiatry, McGill University
      25. McGovern Institute for Brain Research, MIT, MA, USA
      26. Department of Otolaryngology, Harvard Medical School, MA, USA
      27. Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen
      28. Max Planck Institute for Empirical Aesthetics
      29. Cyceron, UMS 3408 (CNRS - UCBN), France
      30. Speech & Hearing Bioscience & Technology Program, Harvard University
      31. Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London
      32. State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University
      33. Department of Radiology, CHUV, Université de Lausanne
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Reuse of config file
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@effigies @pep8speaks @mgxd