Repository: nipy/nipype

Issue:
REL: 1.5.0
## Summary

Prep for new feature release 1.5.0, targeting release on Monday, February 24.

Given that we just released 1.4.2 about a week ago, I'm inclined to hold this one off for any feature PRs that would like to shoot for inclusion.

Require merge or postponement decision on all issues/PRs in https://github.com/nipy/nipype/milestone/38:

* [x] ENH: Add a ``Bandpass`` filter interface under ``algorithms.filters`` #2915 (@oesteban)
* [x] [WIP/ENH] Adds a new interface for AFNI's ``3dMEMA`` command #2953 (@JesseyWright / @oesteban)
* [x] ENH: Add interface for fslorient #2955 (@felixsc1)
* [x] [FIX] Mrtrix3 usedefault issue (#3004) (@matteomancini)
* [x] [DOC] SelectFiles docstring corrected #3041 (@AKSoo)
* [ ] FIX Ants N4BiasFieldCorrection rescale_intensities bug #3139 (@salma1601)
* [x] CI: Test Python 3.8 #3154 (@effigies)
* [x] ENH: Detect values for EulerNumber interface #3173 (@mgxd)

Will try review the open PRs and see if anything is close enough to push on, tomorrow.

## Release checklist

* [ ] Merge pending PRs
* [x] Update changelog
* [x] Update .mailmap
* [x] Update .zenodo.json
* [x] Set release number in `nipype/info.py`
* [x] Update `doc/interfaces.rst` with previous releases
* [x] Check conda-forge feedstock build (conda-forge/nipype-feedstock#67)
* [ ] Tutorial tests (https://circleci.com/workflow-run/be312bea-8273-47cf-9e52-54257d969422)

## Uncredited authors

The following authors have contributed, but not added themselves to the [`.zenodo.json`](https://github.com/nipy/nipype/blob/master/.zenodo.json) file. If you would like to be an author on Zenodo releases, please add yourself or comment with your preferred publication name, affiliation and [ORCID](https://orcid.org/). If you would like to stop being spammed whenever I'm the one doing releases, let me know, and I'll add you to a blacklist.

No entry to sort: cdla (@cdla)
No entry to sort: Gio Piantoni (@gpiantoni)
No entry to sort: Victor Férat (@vferat)
No entry to sort: Niklas Förster (@niklasfoe)
~~No entry to sort: Adam Kimbler (@adamkimbler)~~
No entry to sort: Kirstie Whitaker (@KirstieJane)
No entry to sort: Pablo Polosecki (@polosecki)
No entry to sort: Ami Tsuchida
No entry to sort: Daniel Brenner (@brennerd11)
No entry to sort: Isaiah Norton (@ihnorton)
No entry to sort: Kevin Sitek (@sitek)
No entry to sort: Luke Bloy (@bloyl)
No entry to sort: Martin Luessi (@mluessi)
No entry to sort: steve (@steve19922)
No entry to sort: Charl Linssen (@turingbirds)
No entry to sort: Félix C. Morency (@fmorency)
~~No entry to sort: Jonathan R. Williford (@williford)~~
No entry to sort: Michiel Cottaar (@MichielCottaar)
No entry to sort: Regina Kim (@reginakim)
No entry to sort: Valentin Haenel (@esc)
No entry to sort: Xu Wang
No entry to sort: maedoc (@maedoc)

I am unable to find GitHub handles for Ami Tsuchida or Xu Wang.

Apologies also to anybody who may have 

## Acknowledgment

- [x] \(Mandatory\) I acknowledge that this contribution will be available under the Apache 2 license.


Discussion:
# [Codecov](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=h1) Report
> Merging [#3174](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=desc) into [master](https://codecov.io/gh/nipy/nipype/commit/c37fcfb2ce46c7918ae73c2af391f64f2e123616?src=pr&el=desc) will **decrease** coverage by `0.01%`.
> The diff coverage is `62.5%`.

[![Impacted file tree graph](https://codecov.io/gh/nipy/nipype/pull/3174/graphs/tree.svg?width=650&token=Tu0EnSSGVZ&height=150&src=pr)](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=tree)

```diff
@@            Coverage Diff             @@
##           master    #3174      +/-   ##
==========================================
- Coverage   65.07%   65.06%   -0.02%     
==========================================
  Files         301      301              
  Lines       39624    39624              
  Branches     5247     5247              
==========================================
- Hits        25786    25781       -5     
- Misses      12771    12776       +5     
  Partials     1067     1067
```

| Flag | Coverage Δ | |
|---|---|---|
| #unittests | `65.06% <62.5%> (-0.02%)` | :arrow_down: |

| [Impacted Files](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=tree) | Coverage Δ | |
|---|---|---|
| [nipype/interfaces/base/traits\_extension.py](https://codecov.io/gh/nipy/nipype/pull/3174/diff?src=pr&el=tree#diff-bmlweXBlL2ludGVyZmFjZXMvYmFzZS90cmFpdHNfZXh0ZW5zaW9uLnB5) | `88.23% <ø> (ø)` | :arrow_up: |
| [nipype/pipeline/engine/workflows.py](https://codecov.io/gh/nipy/nipype/pull/3174/diff?src=pr&el=tree#diff-bmlweXBlL3BpcGVsaW5lL2VuZ2luZS93b3JrZmxvd3MucHk=) | `69.12% <0%> (ø)` | :arrow_up: |
| [nipype/interfaces/io.py](https://codecov.io/gh/nipy/nipype/pull/3174/diff?src=pr&el=tree#diff-bmlweXBlL2ludGVyZmFjZXMvaW8ucHk=) | `56.41% <0%> (ø)` | :arrow_up: |
| [nipype/info.py](https://codecov.io/gh/nipy/nipype/pull/3174/diff?src=pr&el=tree#diff-bmlweXBlL2luZm8ucHk=) | `92.3% <100%> (ø)` | :arrow_up: |
| [nipype/interfaces/freesurfer/utils.py](https://codecov.io/gh/nipy/nipype/pull/3174/diff?src=pr&el=tree#diff-bmlweXBlL2ludGVyZmFjZXMvZnJlZXN1cmZlci91dGlscy5weQ==) | `63.25% <100%> (ø)` | :arrow_up: |
| [nipype/utils/filemanip.py](https://codecov.io/gh/nipy/nipype/pull/3174/diff?src=pr&el=tree#diff-bmlweXBlL3V0aWxzL2ZpbGVtYW5pcC5weQ==) | `72.87% <0%> (-1.18%)` | :arrow_down: |

------

[Continue to review full report at Codecov](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=continue).
> **Legend** - [Click here to learn more](https://docs.codecov.io/docs/codecov-delta)
> `Δ = absolute <relative> (impact)`, `ø = not affected`, `? = missing data`
> Powered by [Codecov](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=footer). Last update [c37fcfb...47de76e](https://codecov.io/gh/nipy/nipype/pull/3174?src=pr&el=lastupdated). Read the [comment docs](https://docs.codecov.io/docs/pull-request-comments).

Hey, 

Sorry for the delay in submitting this.

{
     "affiliation": "Florida International University",
     "name": "Kimbler, Adam",
     "orcid": "0000-0001-5885-9596"
}
@miykael @djarecka Any chance one of you could have a look at https://circleci.com/workflow-run/6eba71d4-5cb8-4711-b95a-83d7393dd71c?

For reference, here's the diff between that branch and `master`: https://github.com/miykael/nipype_tutorial/compare/master...effigies:rel/1.4.1
Bump for @miykael and @djarecka, in case this got lost in your notifications last night.
It could be interesting to push #3180 into 1.5.0, wdyt @effigies ?
Sure. I don't see much prospect of fixing the tutorials soon, so the release is held up for now. Squeeze in as you like.
Mark,

Could you blacklist me? My contribution was insignificant and I give up any
rights to my contribution(s) (you can license or re-license however you
want).

Thanks!
Jonathan

On Sat, Feb 22, 2020 at 7:54 PM Chris Markiewicz <notifications@github.com>
wrote:

> Summary
>
> Prep for new feature release 1.5.0, targeting release on Monday, February
> 24.
>
> Given that we just released 1.4.2 about a week ago, I'm inclined to hold
> this one off for any feature PRs that would like to shoot for inclusion.
>
> Require merge or postponement decision on all issues/PRs in
> https://github.com/nipy/nipype/milestone/38:
>
>    - ENH: Add a Bandpass filter interface under algorithms.filters #2915
>    <https://github.com/nipy/nipype/pull/2915> (@oesteban
>    <https://github.com/oesteban>)
>    - [WIP/ENH] Adds a new interface for AFNI's 3dMEMA command #2953
>    <https://github.com/nipy/nipype/pull/2953> (@JesseyWright
>    <https://github.com/JesseyWright> / @oesteban
>    <https://github.com/oesteban>)
>    - ENH: Add interface for fslorient #2955
>    <https://github.com/nipy/nipype/pull/2955> (@felixsc1
>    <https://github.com/felixsc1>)
>    - [FIX] Mrtrix3 usedefault issue (#3004
>    <https://github.com/nipy/nipype/pull/3004>) (@matteomancini
>    <https://github.com/matteomancini>)
>    - [DOC] SelectFiles docstring corrected #3041
>    <https://github.com/nipy/nipype/pull/3041> (@AKSoo
>    <https://github.com/AKSoo>)
>    - FIX Ants N4BiasFieldCorrection rescale_intensities bug #3139
>    <https://github.com/nipy/nipype/pull/3139> (@salma1601
>    <https://github.com/salma1601>)
>    - CI: Test Python 3.8 #3154 <https://github.com/nipy/nipype/pull/3154>
>    (@effigies <https://github.com/effigies>)
>    - ENH: Detect values for EulerNumber interface #3173
>    <https://github.com/nipy/nipype/pull/3173> (@mgxd
>    <https://github.com/mgxd>)
>
> Will try review the open PRs and see if anything is close enough to push
> on, tomorrow.
> Release checklist
>
>    - Merge pending PRs
>    - Update changelog
>    - Update .mailmap
>    - Update .zenodo.json
>    - Set release number in nipype/info.py
>    - Update doc/interfaces.rst with previous releases
>    - Check conda-forge feedstock build (conda-forge/nipype-feedstock#65
>    <https://github.com/conda-forge/nipype-feedstock/pull/65>)
>    - Tutorial tests (
>    https://circleci.com/workflow-run/aa70a094-fd7f-4b80-b6a3-e573b1f5400d)
>
> Uncredited authors
>
> The following authors have contributed, but not added themselves to the
> .zenodo.json <https://github.com/nipy/nipype/blob/master/.zenodo.json>
> file. If you would like to be an author on Zenodo releases, please add
> yourself or comment with your preferred publication name, affiliation and
> ORCID <https://orcid.org/>. If you would like to stop being spammed
> whenever I'm the one doing releases, let me know, and I'll add you to a
> blacklist.
>
> No entry to sort: cdla (@cdla <https://github.com/cdla>)
> No entry to sort: Gio Piantoni (@gpiantoni <https://github.com/gpiantoni>)
> No entry to sort: Victor Férat (@vferat <https://github.com/vferat>)
> No entry to sort: Niklas Förster (@niklasfoe
> <https://github.com/niklasfoe>)
> No entry to sort: Adam Kimbler (@adamkimbler
> <https://github.com/adamkimbler>)
> No entry to sort: Kirstie Whitaker (@KirstieJane
> <https://github.com/KirstieJane>)
> No entry to sort: Pablo Polosecki (@polosecki
> <https://github.com/polosecki>)
> No entry to sort: Ami Tsuchida
> No entry to sort: Daniel Brenner (@brennerd11
> <https://github.com/brennerd11>)
> No entry to sort: Isaiah Norton (@ihnorton <https://github.com/ihnorton>)
> No entry to sort: Kevin Sitek (@sitek <https://github.com/sitek>)
> No entry to sort: Luke Bloy (@bloyl <https://github.com/bloyl>)
> No entry to sort: Martin Luessi (@mluessi <https://github.com/mluessi>)
> No entry to sort: steve (@steve19922 <https://github.com/steve19922>)
> No entry to sort: Charl Linssen (@turingbirds
> <https://github.com/turingbirds>)
> No entry to sort: Félix C. Morency (@fmorency
> <https://github.com/fmorency>)
> No entry to sort: Jonathan R. Williford (@williford
> <https://github.com/williford>)
> No entry to sort: Michiel Cottaar (@MichielCottaar
> <https://github.com/MichielCottaar>)
> No entry to sort: Regina Kim (@reginakim <https://github.com/reginakim>)
> No entry to sort: Valentin Haenel (@esc <https://github.com/esc>)
> No entry to sort: Xu Wang
> No entry to sort: maedoc (@maedoc <https://github.com/maedoc>)
>
> I am unable to find GitHub handles for Ami Tsuchida or Xu Wang.
>
> Apologies also to anybody who may have
> Acknowledgment
>
>    - (Mandatory) I acknowledge that this contribution will be available
>    under the Apache 2 license.
>
> ------------------------------
> You can view, comment on, or merge this pull request online at:
>
>   https://github.com/nipy/nipype/pull/3174
> Commit Summary
>
>    - NEP29+1y: Set minimum numpy to 1.13
>    - DOC: Update changelog
>    - MNT: Update Zenodo ordering
>    - MNT: 1.5.0
>
> File Changes
>
>    - *M* .zenodo.json
>    <https://github.com/nipy/nipype/pull/3174/files#diff-0> (30)
>    - *M* doc/changelog/1.X.X-changelog.rst
>    <https://github.com/nipy/nipype/pull/3174/files#diff-1> (17)
>    - *M* nipype/info.py
>    <https://github.com/nipy/nipype/pull/3174/files#diff-2> (4)
>
> Patch Links:
>
>    - https://github.com/nipy/nipype/pull/3174.patch
>    - https://github.com/nipy/nipype/pull/3174.diff
>
> —
> You are receiving this because you were mentioned.
> Reply to this email directly, view it on GitHub
> <https://github.com/nipy/nipype/pull/3174?email_source=notifications&email_token=AAHV53EVFGL6E4F4KJDKHM3REHCL5A5CNFSM4KZWEA2KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IPQTL2Q>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAHV53CD2B5AF6SMV7OC3XDREHCL5ANCNFSM4KZWEA2A>
> .
>

While we figure out the notebooks problem, could we maybe push an RC?
Sure.
@oesteban @satra I'm planning on releasing 1.5.0rc1 from this branch, once the feedstock build is fixed. Or, if we don't care about getting release candidates on conda, I can just go ahead...
I'm fine either way. I don't think we really need this RC other than in Pypi
Sorry, should have updated. Rerendering the feedstock worked. 1.5.0rc1 is on PyPI and conda-forge.

Resolving patch:
diff --git a/nipype/info.py b/nipype/info.py
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -5,7 +5,7 @@
 
 # nipype version information
 # Remove -dev for release
-__version__ = "1.5.0-rc1.post-dev"
+__version__ = "1.5.0"
 
 
 def get_nipype_gitversion():


Test patch: