pyrox.dev
snakemake: 8.23.0 -> 8.29.0 (#385979)
Co-authored-by: emaryn <emaryn@users.noreply.github.com>
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pkgs/by-name/sn/snakemake/package.nix
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pkgs/by-name/sn/snakemake/package.nix
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{
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lib,
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stdenv,
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fetchPypi,
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fetchFromGitHub,
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python3Packages,
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stress,
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versionCheckHook,
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writableTmpDirAsHomeHook,
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}:
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python3Packages.buildPythonApplication rec {
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pname = "snakemake";
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version = "8.23.0";
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version = "8.29.0";
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pyproject = true;
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src = fetchPypi {
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inherit pname version;
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hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";
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src = fetchFromGitHub {
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owner = "snakemake";
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repo = "snakemake";
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tag = "v${version}";
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hash = "sha256-vGa0N5jbm+b4FH1rkvZI5yI005K0D5AP29JGK2wscps=";
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};
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postPatch = ''
···
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--replace-fail 'del os.environ["PYTHONPATH"]' "pass"
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substituteInPlace snakemake/unit_tests/__init__.py \
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--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
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substituteInPlace snakemake/assets/__init__.py \
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--replace-fail "raise err" "return bytes('err','ascii')"
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'';
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build-system = with python3Packages; [
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setuptools
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];
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build-system = with python3Packages; [ setuptools ];
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dependencies = with python3Packages; [
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appdirs
···
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# for the current basic test suite. Slurm, Tibanna and Tes require extra
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# setup.
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nativeCheckInputs = with python3Packages; [
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numpy
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pandas
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pytestCheckHook
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pytest-mock
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requests-mock
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snakemake-executor-plugin-cluster-generic
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snakemake-storage-plugin-fs
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stress
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versionCheckHook
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];
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nativeCheckInputs =
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(with python3Packages; [
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numpy
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pandas
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pytestCheckHook
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pytest-mock
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requests-mock
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snakemake-executor-plugin-cluster-generic
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snakemake-storage-plugin-fs
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stress
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versionCheckHook
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polars
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])
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++ [ writableTmpDirAsHomeHook ];
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versionCheckProgramArg = [ "--version" ];
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pytestFlagsArray = [
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"test_scopes_submitted_to_cluster"
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];
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pythonImportsCheck = [
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"snakemake"
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];
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preCheck = ''
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export HOME="$(mktemp -d)"
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'';
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pythonImportsCheck = [ "snakemake" ];
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meta = {
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homepage = "https://snakemake.github.io";