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python3Packages.nipype: disable neurdflib by default to avoid package collision #99971

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merged 2 commits into from Nov 27, 2020
Merged

python3Packages.nipype: disable neurdflib by default to avoid package collision #99971

merged 2 commits into from Nov 27, 2020

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bcdarwin
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@bcdarwin bcdarwin commented Oct 7, 2020 •
edited

Prior to this change, any closure containing python3Packages.rdflib causes a conflict with NIpype. Additionally, the patched rdflib (neurdflib) is an optional dependency of Nipype anyway (see nipy/nipype#2888) and our policy is not to include optdepends by default.

I also removed Python 2 support since Nipype doesn't support Python 2 (and python2Packages.nipype wouldn't even be attempted since dependency nibabel is disabled for that interpreter anyway).

Motivation for this change
Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • 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 nixpkgs-review --run "nixpkgs-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@ofborg ofborg bot requested a review from ashgillman October 7, 2020 18:57
drewrisinger
drewrisinger approved these changes Oct 8, 2020
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  • Diff LGTM
  • Commits LGTM
  • Builds via nix-review
3 packages built:
python37Packages.heudiconv python37Packages.nipype python38Packages.nipype

@jonringer
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diff LGTM

I would still like to see what @FRidh thinks about the switch

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https://github.com/NixOS/nixpkgs/pull/99971
3 packages built:
python37Packages.heudiconv python37Packages.nipype python38Packages.nipype

@SuperSandro2000
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Result of nixpkgs-review pr 99971 run on x86_64-linux 1

3 packages built:
  • python37Packages.heudiconv
  • python37Packages.nipype
  • python38Packages.nipype

@SuperSandro2000 SuperSandro2000 merged commit d26aa32 into NixOS:master Nov 27, 2020
@bcdarwin bcdarwin deleted the nipype-disable-neurdflib-by-default branch November 27, 2020 22:44
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@drewrisinger drewrisinger drewrisinger approved these changes

@FRidh FRidh Awaiting requested review from FRidh

@jonringer jonringer Awaiting requested review from jonringer

@ashgillman ashgillman Awaiting requested review from ashgillman

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6.topic: python 10.rebuild-darwin: 1-10 10.rebuild-linux: 1-10
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