Unverified Commit 9d1a27e2 authored by Renato Garcia's avatar Renato Garcia Committed by GitHub
Browse files

snakemake: 7.14.2 -> 7.25.3 (#230524)

parent 6c3e79e0

pkgs/applications/science/misc/snakemake/default.nix

+7 −8
Original line number Diff line number Diff line
@@ -5,14 +5,14 @@ 


python3.pkgs.buildPythonApplication rec {

  pname = "snakemake";

  version = "7.14.2";

  version = "7.25.3";

  format = "setuptools";



  src = fetchFromGitHub {

    owner = "snakemake";

    repo = pname;

    rev = "refs/tags/v${version}";

    hash = "sha256-4XduybmDmlux3zvjbN1ouaJ1PkNO8h6vHuxgZ3YLBrw=";

    hash = "sha256-KrstajTocVX5Tw7aiPoJ9vxJ0nKF+jqJcYJKrJvBt0Q=";

  };



  propagatedBuildInputs = with python3.pkgs; [
@@ -21,22 +21,20 @@ python3.pkgs.buildPythonApplication rec { 
    connection-pool

    datrie

    docutils

    filelock

    gitpython

    humanfriendly

    jinja2

    jsonschema

    nbformat

    networkx

    psutil

    pulp

    pygraphviz

    pyyaml

    ratelimiter

    requests

    retry

    reretry

    smart-open

    stopit

    tabulate

    throttler

    toposort

    wrapt

    yte
@@ -44,7 +42,7 @@ python3.pkgs.buildPythonApplication rec { 


  # See

  # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99

  # for the current basic test suite. Tibanna and Tes require extra

  # for the current basic test suite. Slurm, Tibanna and Tes require extra

  # setup.



  nativeCheckInputs = with python3.pkgs; [
@@ -54,6 +52,7 @@ python3.pkgs.buildPythonApplication rec { 
  ];



  disabledTestPaths = [

    "tests/test_slurm.py"

    "tests/test_tes.py"

    "tests/test_tibanna.py"

    "tests/test_linting.py"

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

0 → 100644
+18 −0
Original line number Diff line number Diff line 
{ lib, buildPythonPackage, fetchPypi }:



buildPythonPackage rec {

  pname = "reretry";

  version = "0.11.8";



  src = fetchPypi {

    inherit pname version;

    hash = "sha256-8nkfzr5RLqLx0VOih0d4UjqAZIYLWRzZCvwhqL7UMuM=";

  };



  meta = with lib; {

    description = "An easy to use retry decorator.";

    homepage = "https://github.com/leshchenko1979/reretry";

    license = licenses.asl20;

    maintainers = with maintainers; [ renatoGarcia ];

  };

}

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

0 → 100644
+42 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, pytestCheckHook

, aiohttp

, codecov

, flake8

, pytest

, pytest-asyncio

, pytest-cov

}:



buildPythonPackage rec {

  pname = "throttler";

  version = "1.2.2";



  src = fetchFromGitHub {

    owner = "uburuntu";

    repo = pname;

    rev = "refs/tags/v${version}";

    hash = "sha256-fE35zPjBUn4e1VRkkIUMtYJ/+LbnUxnxyfnU+UEPwr4=";

  };



  checkInputs = [

    aiohttp

    codecov

    flake8

    pytest

    pytest-asyncio

    pytest-cov

    pytestCheckHook

  ];



  pytestFlagsArray = [ "tests/" ];



  meta = with lib; {

    description = "Zero-dependency Python package for easy throttling with asyncio support.";

    homepage = "https://github.com/uburuntu/throttler";

    license = licenses.mit;

    maintainers = with maintainers; [ renatoGarcia ];

  };

}

pkgs/top-level/python-packages.nix

+4 −0
Original line number Diff line number Diff line
@@ -10366,6 +10366,8 @@ self: super: with self; { 


  requirements-parser = callPackage ../development/python-modules/requirements-parser { };



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



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



  resolvelib = callPackage ../development/python-modules/resolvelib { };
@@ -11881,6 +11883,8 @@ self: super: with self; { 


  thriftpy2 = callPackage ../development/python-modules/thriftpy2 { };



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



  thumborPexif = callPackage ../development/python-modules/thumborpexif { };



  tkinter = callPackage ../development/python-modules/tkinter {