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Add python packages: pyensembl and its dependencies, gffutils, pyBigWig #87551

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moritzschaefer commented May 10, 2020

Motivation for this change

Both pyenseml and gffutils are commonly used python packages (> 100 stars on GitHub), so I added them to nix packages.

Things done
  • Built on platform(s)
    • NixOS
  • 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/) (only pyensembl has a supplemental binary)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • [-] Mostly Fits I designed the derivations 1:1 to existing ones.
Vizaxo and others added 5 commits May 27, 2019
Add config option services.xserver.windowManager.exwm.loadScript,
which is passed to Emacs (as the -l option) to load after the user's init file.
nixos/exwm: allow custom Emacs load script
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FRidh commented May 14, 2020

Please rebase, don't merge master.

@adisbladis adisbladis removed their request for review May 14, 2020
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FRidh left a comment

Please ensure the modules are somehow tested. Maybe supporting the unit tests is too much, but we have the pythonImportsCheckHook so you could do import checks at least.

Also, remove empty lists and strings.

Finally, will you maintain the new packages?

pybedtools = callPackage ../development/python-modules/pybedtools { };

pyBigWig = callPackage ../development/python-modules/pyBigWig { };

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FRidh May 30, 2020


normalized names (lowercase and dashes instead of underscores)

@moritzschaefer moritzschaefer changed the title Add python packages: pyensembl (and its dependencies) + gffutils Add python packages: pyensembl and its dependencies, gffutils, pyBigWig May 30, 2020
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moritzschaefer commented May 30, 2020

@FRidh thanks for pointing this out. The module 'pybigwig' already existed in the correct format (lowercase) so I just reverted that commit.

I cannot guarantee to maintain the packages in a timely manner, but will try to update their versions from time to time.

I'm rebasing to master now and will push then.

New rebase is here: #89213
I close this one.

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