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python36Packages.nibabel: 2.3.0 -> 2.3.1 #49976

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merged 1 commit into from Nov 10, 2018
Merged

python36Packages.nibabel: 2.3.0 -> 2.3.1 #49976

merged 1 commit into from Nov 10, 2018

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r-ryantm
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@r-ryantm r-ryantm commented Nov 9, 2018

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/python3.6-nibabel/versions.

meta.description for python36Packages.nibabel is: '"Access a multitude of neuroimaging data formats"'.

Checks done (click to expand)
  • built on NixOS
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.nib-dicomfs-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-dicomfs passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.nib-diff-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-diff passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.nib-ls-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-ls passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.nib-nifti-dx-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-nifti-dx passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.nib-tck2trk-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-tck2trk passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.nib-trk2tck-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-trk2tck passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/.parrec2nii-wrapped passed the binary check.
  • /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/parrec2nii passed the binary check.
  • 14 of 14 passed binary check by having a zero exit code.
  • 10 of 14 passed binary check by having the new version present in output.
  • found 2.3.1 with grep in /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1
  • directory tree listing: https://gist.github.com/a770d8dca32fefd06fb1817e31b1688f
  • du listing: https://gist.github.com/f9c73b0434e2768efdde53cfe5beaa61
Outpath report (click to expand)

Outpath difference report
30 total rebuild paths

8 package rebuilds

8 x86_64-linux rebuilds
6 i686-linux rebuilds
8 x86_64-darwin rebuilds
8 aarch64-linux rebuilds

First ten rebuilds by attrpath
python27Packages.nibabel
python27Packages.nilearn
python27Packages.nipy
python27Packages.nipype
python36Packages.nibabel
python36Packages.nilearn
python36Packages.nipy
python36Packages.nipype

Instructions to test this update (click to expand)

Either download from Cachix:

nix-store -r /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1 \
  --option binary-caches 'https://cache.nixos.org/ https://r-ryantm.cachix.org/' \
  --option trusted-public-keys '
  r-ryantm.cachix.org-1:gkUbLkouDAyvBdpBX0JOdIiD2/DP1ldF3Z3Y6Gqcc4c=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(r-ryantm's Cachix cache is only trusted for this store-path realization.)

Or, build yourself:

nix-build -A python36Packages.nibabel https://github.com/r-ryantm/nixpkgs/archive/8c666a0a457b719993db63ceeff013fefd58e7d9.tar.gz

After you've downloaded or built it, look at the files and if there are any, run the binaries:

ls -la /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1
ls -la /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin

cc @ashgillman for testing.

@r-ryantm r-ryantm requested a review from FRidh as a code owner November 9, 2018 04:03
@GrahamcOfBorg
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Success on x86_64-linux (full log)

Attempted: python36Packages.nibabel

Partial log (click to expand)

stripping (with command strip and flags -S) in /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/lib  /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin
patching script interpreter paths in /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1
checking for references to /build in /nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-diff'...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-dicomfs'...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-trk2tck'...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-nifti-dx'...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-tck2trk'...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/nib-ls'...
wrapping `/nix/store/2l6plj18pfjxvvrwxlmjk8ffp0m4aaxd-python3.6-nibabel-2.3.1/bin/parrec2nii'...

@GrahamcOfBorg
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Success on x86_64-darwin (full log)

Attempted: python36Packages.nibabel

Partial log (click to expand)

strip is /nix/store/g5r4apl0za012ffs6ladinwa5w0m1l3k-cctools-binutils-darwin/bin/strip
stripping (with command strip and flags -S) in /nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/lib  /nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin
patching script interpreter paths in /nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/nib-dicomfs'...
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/nib-diff'...
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/nib-ls'...
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/nib-nifti-dx'...
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/nib-tck2trk'...
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/nib-trk2tck'...
wrapping `/nix/store/w50yda0djw4z17v325g8jfyrq1gl733j-python3.6-nibabel-2.3.1/bin/parrec2nii'...

@GrahamcOfBorg
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Success on aarch64-linux (full log)

Attempted: python36Packages.nibabel

Partial log (click to expand)

patching script interpreter paths in /nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1
checking for references to /build in /nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/nib-dicomfs'...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/nib-diff'...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/nib-ls'...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/nib-nifti-dx'...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/nib-tck2trk'...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/nib-trk2tck'...
wrapping `/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1/bin/parrec2nii'...
/nix/store/5zdz954p7hhsn20hyw3l79qf06dn1jn1-python3.6-nibabel-2.3.1

@ashgillman
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I submitted an issue upstream inquiring about the failing tests

nipy/nibabel#691

In the mean-time, is there a recommended way to skip tests with Nose? A quick grep looks like most packages do some ad-hoc patching - I thought there might be a nicer way?

@ryantm
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ryantm commented Nov 9, 2018

@ashgillman I think the only way is to skip all the tests with doCheck = false;

@Mic92
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Mic92 commented Nov 10, 2018

Nosetests accept the several arguments to whitelist/blacklist files or tests:

  -I REGEX, --ignore-files=REGEX
                        Completely ignore any file that matches this regular
                        expression. Takes precedence over any other settings
                        or plugins. Specifying this option will replace the
                        default setting. Specify this option multiple times to
                        add more regular expressions [NOSE_IGNORE_FILES]
  -e REGEX, --exclude=REGEX
                        Don't run tests that match regular expression
                        [NOSE_EXCLUDE]
  -i REGEX, --include=REGEX
                        This regular expression will be applied to files,
                        directories, function names, and class names for a
                        chance to include additional tests that do not match
                        TESTMATCH.  Specify this option multiple times to add
                        more regular expressions [NOSE_INCLUDE]

@Mic92 Mic92 merged commit 7104f01 into NixOS:master Nov 10, 2018
@r-ryantm r-ryantm deleted the auto-update/python3.6-nibabel branch November 17, 2018 23:05
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