snakemake: 8.29.2 -> 9.1.10 (#398494) (08ea6efa) · Commits · nix / nixpkgs

pkgs/by-name/sn/snakemake/package.nix

+28 −5

Original line number	Diff line number	Diff line
		@@ -10,14 +10,14 @@

		python3Packages.buildPythonApplication rec {
		pname = "snakemake";
		version = "8.29.2";
		version = "9.1.10";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = "snakemake";
		tag = "v${version}";
		hash = "sha256-69NsbfHF29l92gwO8If9vp8Cdjac3BnO+hbY3b2bZ8E=";
		hash = "sha256-saEfclp6cRcBBUv/ssszr9Q8PGPapkSsjDwTUP9XOhg=";
		};

		postPatch = ''
		@@ -25,13 +25,13 @@ python3Packages.buildPythonApplication rec {
		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 \
		substituteInPlace src/snakemake/unit_tests/__init__.py \
		--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
		substituteInPlace snakemake/assets/__init__.py \
		substituteInPlace src/snakemake/assets/__init__.py \
		--replace-fail "raise err" "return bytes('err','ascii')"
		'';

		build-system = with python3Packages; [ setuptools ];
		build-system = with python3Packages; [ setuptools-scm ];

		dependencies = with python3Packages; [
		appdirs
		@@ -55,6 +55,7 @@ python3Packages.buildPythonApplication rec {
		smart-open
		snakemake-interface-executor-plugins
		snakemake-interface-common
		snakemake-interface-logger-plugins
		snakemake-interface-storage-plugins
		snakemake-interface-report-plugins
		stopit
		@@ -126,6 +127,20 @@ python3Packages.buildPythonApplication rec {
		"test_deploy_sources"
		"test_output_file_cache_storage"
		"test_storage"

		# Tries to access internet
		"test_report_after_run"

		# Needs stress-ng
		"test_benchmark"
		"test_benchmark_jsonl"

		# Needs unshare
		"test_nodelocal"

		# Requires snakemake-storage-plugin-http
		"test_keep_local"
		"test_retrieve"
		]
		++ lib.optionals stdenv.hostPlatform.isDarwin [
		# Unclear failure:
		@@ -144,6 +159,14 @@ python3Packages.buildPythonApplication rec {
		"test_queue_input_forceall"
		"test_resources_submitted_to_cluster"
		"test_scopes_submitted_to_cluster"

		# Issue with /dev/stderr in sandbox
		"test_protected_symlink_output"

		# Unclear issue:
		# pulp.apis.core.PulpSolverError: Pulp: cannot execute cbc cwd:
		# but pulp solver is not default
		"test_access_patterns"
		];

		pythonImportsCheck = [ "snakemake" ];

pkgs/development/python-modules/snakemake-interface-logger-plugins/default.nix

0 → 100644

+35 −0

Original line number	Diff line number	Diff line
		{
		lib,
		buildPythonPackage,
		fetchFromGitHub,
		hatchling,
		snakemake-interface-common,
		}:

		buildPythonPackage rec {
		pname = "snakemake-interface-logger-plugins";
		version = "1.2.3";
		format = "pyproject";

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = pname;
		tag = "v${version}";
		hash = "sha256-VHbta+R2a/K2L03IRu/Ya7dJzshIAvyK9cNIRbx8QqM=";
		};

		nativeBuildInputs = [ hatchling ];

		propagatedBuildInputs = [
		snakemake-interface-common
		];

		pythonImportsCheck = [ "snakemake_interface_logger_plugins" ];

		meta = with lib; {
		description = "A stable interface for interactions between Snakemake and its logger plugins";
		homepage = "https://github.com/snakemake/snakemake-interface-logger-plugins";
		license = licenses.mit;
		maintainers = with maintainers; [ veprbl ];
		};
		}

pkgs/development/python-modules/snakemake-interface-storage-plugins/default.nix

+4 −2

Original line number	Diff line number	Diff line
		@@ -3,6 +3,7 @@
		buildPythonPackage,
		fetchFromGitHub,
		poetry-core,
		humanfriendly,
		reretry,
		snakemake-interface-common,
		throttler,
		@@ -11,19 +12,20 @@

		buildPythonPackage rec {
		pname = "snakemake-interface-storage-plugins";
		version = "3.3.0";
		version = "4.2.1";
		format = "pyproject";

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = pname;
		tag = "v${version}";
		hash = "sha256-qjQZc7DIXIPmqXq+Fjslgrq2LbjbdRS/twGsp/jrxRY=";
		hash = "sha256-mGpKmKWWL4ue9Dddjs4fXCaITrC97yHC58Jh2vclXAY=";
		};

		nativeBuildInputs = [ poetry-core ];

		propagatedBuildInputs = [
		humanfriendly
		reretry
		snakemake-interface-common
		throttler

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

+2 −2

Original line number	Diff line number	Diff line
		@@ -10,14 +10,14 @@

		buildPythonPackage rec {
		pname = "snakemake-storage-plugin-fs";
		version = "1.0.6";
		version = "1.1.1";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = pname;
		tag = "v${version}";
		hash = "sha256-9A2W+V0d9K1Ei4WXqIZfIcOYsWgpGVP7P/ANy8jOGu0=";
		hash = "sha256-Y+Fofz4D/CWgdG3lOneadRu/VfJ23D4Dz751j9rUKNo=";
		};

		build-system = [ poetry-core ];

pkgs/development/python-modules/snakemake-storage-plugin-s3/default.nix

+2 −2

Original line number	Diff line number	Diff line
		@@ -13,14 +13,14 @@

		buildPythonPackage rec {
		pname = "snakemake-storage-plugin-s3";
		version = "0.3.1";
		version = "0.3.3";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = "snakemake-storage-plugin-s3";
		tag = "v${version}";
		hash = "sha256-WbGlXu6/7e9U2GfVd4IF86bRfulNxjP1Tw5pVHpEj/g=";
		hash = "sha256-jIz8Stx2Abd+xGx6kEwlgq3KGsFO13Lk2N8eLB8marA=";
		};

		build-system = [ poetry-core ];

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