snakemake: 8.14.0 -> 8.20.1 (#339931) (0df8ba52) · Commits · nix / nixpkgs

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

+53 −16

Original line number	Diff line number	Diff line
		{ lib
		, fetchFromGitHub
		, fetchPypi
		, fetchpatch
		, python3
		, runtimeShell
		, stress
		}:

		python3.pkgs.buildPythonApplication rec {
		pname = "snakemake";
		version = "8.14.0";
		version = "8.20.1";
		format = "setuptools";

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = pname;
		rev = "refs/tags/v${version}";
		hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y=";
		# https://github.com/python-versioneer/python-versioneer/issues/217
		postFetch = ''
		sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'
		'';
		src = fetchPypi {
		inherit pname version;
		hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";
		};

		postPatch = ''
		patchShebangs --build tests/
		patchShebangs --host snakemake/executors/jobscript.sh
		substituteInPlace snakemake/shell.py \
		--replace "/bin/sh" "${runtimeShell}"
		substituteInPlace tests/common.py \
		--replace-fail 'os.environ["PYTHONPATH"] = os.getcwd()' "pass" \
		--replace-fail 'del os.environ["PYTHONPATH"]' "pass"
		substituteInPlace snakemake/unit_tests/__init__.py \
		--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
		'';

		propagatedBuildInputs = with python3.pkgs; [
		@@ -41,6 +39,7 @@ python3.pkgs.buildPythonApplication rec {
		nbformat
		psutil
		pulp
		pygments
		pyyaml
		requests
		reretry
		@@ -66,16 +65,54 @@ python3.pkgs.buildPythonApplication rec {
		numpy
		pandas
		pytestCheckHook
		pytest-mock
		requests-mock
		snakemake-executor-plugin-cluster-generic
		snakemake-storage-plugin-fs
		stress
		];

		disabledTestPaths = [
		"tests/test_conda_python_3_7_script/test_script.py"
		pytestFlagsArray = [
		"tests/tests.py"
		"tests/test_expand.py"
		"tests/test_io.py"
		"tests/test_schema.py"
		"tests/test_executor_test_suite.py"
		"tests/test_api.py"
		];

		# Some will be disabled via https://github.com/snakemake/snakemake/pull/3074
		disabledTests = [
		# requires graphviz
		"test_filegraph"
		# requires s3
		"test_storage"
		"test_default_storage"
		"test_output_file_cache_storage"
		# requires peppy and eido
		"test_pep"
		"test_modules_peppy"
		# requires perl
		"test_shadow"
		# requires snakemake-storage-plugin-http
		"test_ancient"
		"test_modules_prefix"
		# requires snakemake-storage-plugin-s3
		"test_deploy_sources"
		# requires modules
		"test_env_modules"
		# issue with locating template file
		"test_generate_unit_tests"
		# weird
		"test_strict_mode"
		"test_issue1256"
		"test_issue2574"
		"test_github_issue1384"
		# future-proofing
		"conda"
		"singularity"
		"apptainer"
		"container"
		];

		pythonImportsCheck = [

pkgs/development/python-modules/snakemake-storage-plugin-fs/default.nix

0 → 100644

+44 −0

Original line number	Diff line number	Diff line
		{
		lib,
		buildPythonPackage,
		fetchFromGitHub,
		poetry-core,
		snakemake,
		snakemake-interface-storage-plugins,
		snakemake-interface-common,
		sysrsync,
		}:

		buildPythonPackage rec {
		pname = "snakemake-storage-plugin-fs";
		version = "1.0.6";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = pname;
		rev = "refs/tags/v${version}";
		hash = "sha256-9A2W+V0d9K1Ei4WXqIZfIcOYsWgpGVP7P/ANy8jOGu0=";
		};

		build-system = [ poetry-core ];

		dependencies = [
		snakemake-interface-storage-plugins
		snakemake-interface-common
		sysrsync
		];

		# The current tests are not worth dealing with cyclic dependency on snakemake
		doCheck = false;

		# Use nothing due to a cyclic dependency on snakemake
		pythonImportsCheck = [ ];

		meta = with lib; {
		description = "A Snakemake storage plugin that reads and writes from a locally mounted filesystem using rsync";
		homepage = "https://github.com/snakemake/snakemake-storage-plugin-fs";
		license = licenses.mit;
		maintainers = with maintainers; [ veprbl ];
		};
		}

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

0 → 100644

+45 −0

Original line number	Diff line number	Diff line
		{
		lib,
		buildPythonPackage,
		fetchFromGitHub,
		poetry-core,
		setuptools,
		rsync,
		toml,
		}:

		buildPythonPackage rec {
		pname = "sysrsync";
		version = "1.1.1";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "gchamon";
		repo = pname;
		rev = "refs/tags/${version}";
		hash = "sha256-2Sz3JrNmIGOnad+qjRzbAgsFEzDtwBT0KLEFyQKZra4=";
		};

		postPatch = ''
		substituteInPlace sysrsync/command_maker.py \
		--replace-fail "'rsync'" "'${rsync}/bin/rsync'"
		'';

		build-system = [
		poetry-core
		setuptools
		];

		dependencies = [
		toml
		];

		pythonImportsCheck = [ "sysrsync" ];

		meta = with lib; {
		description = "Simple and safe system's rsync wrapper for Python";
		homepage = "https://github.com/gchamon/sysrsync";
		license = licenses.mit;
		maintainers = with maintainers; [ veprbl ];
		};
		}

pkgs/top-level/python-packages.nix

+4 −0

Original line number	Diff line number	Diff line
		@@ -14384,6 +14384,8 @@ self: super: with self; {

		snakemake-interface-storage-plugins = callPackage ../development/python-modules/snakemake-interface-storage-plugins { };

		snakemake-storage-plugin-fs = callPackage ../development/python-modules/snakemake-storage-plugin-fs { };

		snakemake-storage-plugin-s3 = callPackage ../development/python-modules/snakemake-storage-plugin-s3 { };

		snakemake-storage-plugin-xrootd = callPackage ../development/python-modules/snakemake-storage-plugin-xrootd { };
		@@ -15065,6 +15067,8 @@ self: super: with self; {

		syslog-rfc5424-formatter = callPackage ../development/python-modules/syslog-rfc5424-formatter { };

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

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

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

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