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snakemake: 6.15.5 -> 7.5.0

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This commit is contained in:
Fabian Affolter 2022-05-01 10:15:10 +02:00
parent 2b27987edc
commit 8b176291d7
1 changed files with 27 additions and 13 deletions
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40
pkgs/applications/science/misc/snakemake/default.nix
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@ -1,10 +1,21 @@
{ lib, python3Packages, fetchFromGitHub }: { lib
, fetchFromGitHub
, python3
}:
python3Packages.buildPythonApplication rec { python3.pkgs.buildPythonApplication rec {
pname = "snakemake"; pname = "snakemake";
version = "6.15.5"; version = "7.5.0";
format = "setuptools";
propagatedBuildInputs = with python3Packages; [ src = fetchFromGitHub {
owner = "snakemake";
repo = pname;
rev = "v${version}";
hash = "sha256-KIKuV6DVHn3dDY/rJG1zNWM79tdDB6GGVH9/kYn6XaE=";
};
propagatedBuildInputs = with python3.pkgs; [
appdirs appdirs
configargparse configargparse
connection-pool connection-pool
@ -22,26 +33,21 @@ python3Packages.buildPythonApplication rec {
pyyaml pyyaml
ratelimiter ratelimiter
requests requests
retry
smart-open smart-open
stopit stopit
tabulate tabulate
toposort toposort
wrapt wrapt
yte
]; ];
src = fetchFromGitHub {
owner = "snakemake";
repo = pname;
rev = "v${version}";
sha256 = "sha256-i8C7gPLzUzSxNH9xwpr+fUKI1SvpYFsFBlspS74LoWU=";
};
# See # See
# https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99 # 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. Tibanna and Tes require extra
# setup. # setup.
checkInputs = with python3Packages; [ checkInputs = with python3.pkgs; [
pandas pandas
pytestCheckHook pytestCheckHook
requests-mock requests-mock
@ -53,7 +59,15 @@ python3Packages.buildPythonApplication rec {
"tests/test_linting.py" "tests/test_linting.py"
]; ];
pythonImportsCheck = [ "snakemake" ]; disabledTests = [
# Tests require network access
"test_github_issue1396"
"test_github_issue1460"
];
pythonImportsCheck = [
"snakemake"
];
meta = with lib; { meta = with lib; {
homepage = "https://snakemake.github.io"; homepage = "https://snakemake.github.io";