pythonPackage.nipype: fix build #37952

Ma27 · 2018-03-27T23:10:03Z

Motivation for this change

pythonPackages.prov has been bumped to 1.5.2, however nipype
pinned prov to 1.5.0. Patching nipype/info.py fixes this issue by
bumping to the current prov version in nixpkgs.

See https://hydra.nixos.org/build/71817962/log
See ticket #36453

Things done

Tested using sandboxing (nix.useSandbox on NixOS, or option build-use-sandbox in nix.conf on non-NixOS)
Built on platform(s)
- NixOS
- macOS
- other Linux distributions
Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
Tested execution of all binary files (usually in ./result/bin/)
Fits CONTRIBUTING.md.

Mic92 · 2018-03-28T00:12:30Z

pkgs/development/python-modules/nipype/default.nix

@@ -36,6 +36,10 @@ buildPythonPackage rec {
    sha256 = "47f62fda3d6b9a37aa407a6b78c80e91240aa71e61191ed00da68b02839fe258";
  };

+  postPatch = ''
+    substituteInPlace "nipype/info.py" --replace "PROV_VERSION = '1.5.0'" "PROV_VERSION = '1.5.2'"


Can you remove this pinning instead? https://github.com/nipy/nipype/blob/master/nipype/info.py#L142
This only ask for trouble in future.

do we really want to drop dependency constraints in upstream repos? I guess that this makes it easier to spot possible issues related to a hypotehtical bump of pythonPackages.prov.

At least something like < 1.6.0 or < 2. Also see #34775 (comment)

Ma27 · 2018-03-28T07:44:49Z

@Mic92 ACK, a loosened version constraint might be better, I patched the library accordingly :)

Mic92 · 2018-03-28T10:10:58Z

@GrahamcOfBorg build pythonPackage.nipype

GrahamcOfBorg · 2018-03-28T10:11:22Z

No attempt on x86_64-linux (full log)

The following builds were skipped because they don't evaluate on x86_64-linux: pythonPackage.nipype

Partial log (click to expand)

Cannot nix-instantiate `pythonPackage.nipype' because:
error: attribute 'pythonPackage' in selection path 'pythonPackage.nipype' not found

GrahamcOfBorg · 2018-03-28T10:11:23Z

No attempt on aarch64-linux (full log)

The following builds were skipped because they don't evaluate on aarch64-linux: pythonPackage.nipype

Partial log (click to expand)

Cannot nix-instantiate `pythonPackage.nipype' because:
�[31;1merror:�[0m attribute 'pythonPackage' in selection path 'pythonPackage.nipype' not found

GrahamcOfBorg · 2018-03-28T10:12:29Z

No attempt on x86_64-darwin (full log)

The following builds were skipped because they don't evaluate on x86_64-darwin: pythonPackage.nipype

Partial log (click to expand)

Cannot nix-instantiate `pythonPackage.nipype' because:
�[31;1merror:�[0m attribute 'pythonPackage' in selection path 'pythonPackage.nipype' not found

dotlambda · 2018-03-30T15:40:02Z

pkgs/development/python-modules/nipype/default.nix

@@ -36,6 +36,8 @@ buildPythonPackage rec {
    sha256 = "47f62fda3d6b9a37aa407a6b78c80e91240aa71e61191ed00da68b02839fe258";
  };

+  patches = [ ./prov-version.patch ];


Please add a comment that links to this issue: nipy/nipype#2240

`pythonPackages.prov` has been bumped to `1.5.2`, however `nipype` pinned `prov` to `1.5.0`. Patching `nipype/info.py` fixes this issue by bumping to the current `prov` version in nixpkgs. See https://hydra.nixos.org/build/71817962/log See ticket NixOS#36453

Ma27 · 2018-03-31T08:18:42Z

@dotlambda fine now? %)

dotlambda · 2018-03-31T15:22:24Z

@GrahamcOfBorg build python2.pkgs.nipype python3.pkgs.nipype

GrahamcOfBorg · 2018-03-31T15:25:05Z

Success on aarch64-linux (full log)

Attempted: python2.pkgs.nipype, python3.pkgs.nipype

Partial log (click to expand)

/build/nipype-1.0.1
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1
strip is /nix/store/3zq400fri5dv7d30lpxlqm2v9y1iis6j-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1/lib  /nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1/bin
patching script interpreter paths in /nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1
checking for references to /build in /nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1...
wrapping `/nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1/bin/nipypecli'...
/nix/store/62w565xs1qskzdy4gziw7gjvjkh458xj-python2.7-nipype-1.0.1
/nix/store/l41f81arx7lgcsq3ayxyfic45an93y8d-python3.6-nipype-1.0.1

GrahamcOfBorg · 2018-03-31T15:25:07Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.nipype, python3.pkgs.nipype

Partial log (click to expand)

/build/nipype-1.0.1
post-installation fixup
shrinking RPATHs of ELF executables and libraries in /nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1
strip is /nix/store/fzcs0fn6bb04m82frhlb78nc03ny3w55-binutils-2.28.1/bin/strip
stripping (with command strip and flags -S) in /nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1/lib  /nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1/bin
patching script interpreter paths in /nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1
checking for references to /build in /nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1...
wrapping `/nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1/bin/nipypecli'...
/nix/store/cri2jg0z0kxrmiq81w9n0phdngcxn9i1-python2.7-nipype-1.0.1
/nix/store/s1wbyclq6cc4152jlw9jh1phjicyaw7d-python3.6-nipype-1.0.1

dotlambda · 2018-03-31T18:46:43Z

@GrahamcOfBorg build python2.pkgs.nipype python3.pkgs.nipype

GrahamcOfBorg · 2018-03-31T18:57:45Z

Success on aarch64-linux (full log)

Attempted: python2.pkgs.nipype, python3.pkgs.nipype

Partial log (click to expand)

    warn('NO FSL found')

workflows/dmri/fsl/tbss.py::nipype.workflows.dmri.fsl.tbss.create_tbss_non_FA
  /build/nipype-1.0.1/nipype/workflows/dmri/fsl/tbss.py:550: UserWarning: NO FSL found
    warn('NO FSL found')

-- Docs: http://doc.pytest.org/en/latest/warnings.html
====== 2718 passed, 232 skipped, 7 xfailed, 19 warnings in 533.59 seconds ======
/nix/store/vqw5n3kf2h56izjz22c6g6xxdybdpy9s-python2.7-nipype-1.0.1
/nix/store/miv9y05nkpz8526lan0zz83ak7wc8s2y-python3.6-nipype-1.0.1

GrahamcOfBorg · 2018-03-31T18:59:44Z

Success on x86_64-linux (full log)

Attempted: python2.pkgs.nipype, python3.pkgs.nipype

Partial log (click to expand)

  /tmp/nix-build-python3.6-nipype-1.0.1.drv-0/nipype-1.0.1/nipype/workflows/dmri/fsl/tbss.py:550: UserWarning: NO FSL found
    warn('NO FSL found')


-- Docs: http://doc.pytest.org/en/latest/warnings.html

====== 2720 passed, 230 skipped, 7 xfailed, 20 warnings in 240.03 seconds ======

/nix/store/qvaisgyvfsrmnp6k5h3l4fs106kqf1xx-python2.7-nipype-1.0.1
/nix/store/lr57r3542ws3c057g42v3aq2fj8a9g96-python3.6-nipype-1.0.1

Ma27 · 2018-03-31T19:10:59Z

@dotlambda awesome! Thanks a lot for the feedback and support in the last time! %)

dotlambda · 2018-03-31T19:13:34Z

Backported in a7c0fdb and a2c57c5.

Ma27 requested a review from FRidh as a code owner March 27, 2018 23:10

GrahamcOfBorg added 6.topic: python 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10 labels Mar 27, 2018

Mic92 reviewed Mar 28, 2018

View reviewed changes

Ma27 force-pushed the fix-nipype branch from 377c871 to 47b2520 Compare March 28, 2018 07:43

dotlambda reviewed Mar 30, 2018

View reviewed changes

Ma27 force-pushed the fix-nipype branch from 47b2520 to db0fa06 Compare March 30, 2018 16:45

pythonPackages.nipype: enable tests

ee1896d

dotlambda merged commit 10e0295 into NixOS:master Mar 31, 2018

Ma27 deleted the fix-nipype branch March 31, 2018 19:10

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pythonPackage.nipype: fix build #37952

pythonPackage.nipype: fix build #37952

Ma27 commented Mar 27, 2018 •

edited

Mic92 Mar 28, 2018

Ma27 Mar 28, 2018

Mic92 Mar 28, 2018

Ma27 commented Mar 28, 2018

Mic92 commented Mar 28, 2018

GrahamcOfBorg commented Mar 28, 2018

GrahamcOfBorg commented Mar 28, 2018

GrahamcOfBorg commented Mar 28, 2018

dotlambda Mar 30, 2018

Ma27 commented Mar 31, 2018

dotlambda commented Mar 31, 2018

GrahamcOfBorg commented Mar 31, 2018

GrahamcOfBorg commented Mar 31, 2018

dotlambda commented Mar 31, 2018

GrahamcOfBorg commented Mar 31, 2018

GrahamcOfBorg commented Mar 31, 2018

Ma27 commented Mar 31, 2018

dotlambda commented Mar 31, 2018

pythonPackage.nipype: fix build #37952

pythonPackage.nipype: fix build #37952

Conversation

Ma27 commented Mar 27, 2018 • edited

Motivation for this change

Things done

Mic92 Mar 28, 2018

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Ma27 commented Mar 28, 2018

Mic92 commented Mar 28, 2018

GrahamcOfBorg commented Mar 28, 2018

GrahamcOfBorg commented Mar 28, 2018

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Ma27 commented Mar 31, 2018

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dotlambda commented Mar 31, 2018

GrahamcOfBorg commented Mar 31, 2018

GrahamcOfBorg commented Mar 31, 2018

Ma27 commented Mar 31, 2018

dotlambda commented Mar 31, 2018

Ma27 commented Mar 27, 2018 •

edited