snakemake: 8.20.1 -> 8.23.0 (#348616) (fba4f0f7) · Commits · nix / nixpkgs

pkgs/applications/science/misc/snakemake/default.nix→pkgs/by-name/sn/snakemake/package.nix

+170 −0

Original line number	Diff line number	Diff line
		{ lib
		, fetchPypi
		, python3
		, stress
		{
		lib,
		stdenv,
		fetchPypi,
		python3Packages,
		stress,
		versionCheckHook,
		}:

		python3.pkgs.buildPythonApplication rec {
		python3Packages.buildPythonApplication rec {
		pname = "snakemake";
		version = "8.20.1";
		format = "setuptools";
		version = "8.23.0";

		pyproject = true;

		src = fetchPypi {
		inherit pname version;
		hash = "sha256-adNwIA1z/TwWsa0gQb4hAsUvHInjd30sm1dYKXvvXy8=";
		hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";
		};

		postPatch = ''
		@@ -23,8 +27,13 @@ python3.pkgs.buildPythonApplication rec {
		--replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
		'';

		propagatedBuildInputs = with python3.pkgs; [
		build-system = with python3Packages; [
		setuptools
		];

		dependencies = with python3Packages; [
		appdirs
		conda-inject
		configargparse
		connection-pool
		datrie
		@@ -59,7 +68,7 @@ python3.pkgs.buildPythonApplication rec {
		# for the current basic test suite. Slurm, Tibanna and Tes require extra
		# setup.

		nativeCheckInputs = with python3.pkgs; [
		nativeCheckInputs = with python3Packages; [
		numpy
		pandas
		pytestCheckHook
		@@ -68,7 +77,9 @@ python3.pkgs.buildPythonApplication rec {
		snakemake-executor-plugin-cluster-generic
		snakemake-storage-plugin-fs
		stress
		versionCheckHook
		];
		versionCheckProgramArg = [ "--version" ];

		pytestFlagsArray = [
		"tests/tests.py"
		@@ -79,38 +90,54 @@ python3.pkgs.buildPythonApplication rec {
		"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
		disabledTests =
		[
		# FAILED tests/tests.py::test_env_modules - AssertionError: expected successful execution
		"test_ancient"
		"test_modules_prefix"
		# requires snakemake-storage-plugin-s3
		"test_deploy_sources"
		# requires modules
		"test_conda_create_envs_only"
		"test_env_modules"
		# issue with locating template file
		"test_generate_unit_tests"
		# weird
		"test_modules_prefix"
		"test_strict_mode"
		# Requires perl
		"test_shadow"
		# Require peppy and eido
		"test_peppy"
		"test_modules_peppy"
		"test_pep_pathlib"

		# CalledProcessError
		"test_filegraph" # requires graphviz
		"test_github_issue1384"

		# AssertionError: assert 127 == 1
		"test_issue1256"
		"test_issue2574"
		"test_github_issue1384"
		# future-proofing
		"conda"
		"singularity"
		"apptainer"
		"container"

		# Require `snakemake-storage-plugin-fs` (circular dependency)
		"test_default_storage"
		"test_default_storage_local_job"
		"test_deploy_sources"
		"test_output_file_cache_storage"
		"test_storage"
		]
		++ lib.optionals stdenv.isDarwin [
		# Unclear failure:
		# AssertionError: expected successful execution
		# `__darwinAllowLocalNetworking` doesn't help
		"test_excluded_resources_not_submitted_to_cluster"
		"test_group_job_resources_with_pipe"
		"test_group_jobs_resources"
		"test_group_jobs_resources_with_limited_resources"
		"test_group_jobs_resources_with_max_threads"
		"test_issue850"
		"test_issue860"
		"test_multicomp_group_jobs"
		"test_queue_input"
		"test_queue_input_dryrun"
		"test_queue_input_forceall"
		"test_resources_submitted_to_cluster"
		"test_scopes_submitted_to_cluster"
		];

		pythonImportsCheck = [
		@@ -121,10 +148,11 @@ python3.pkgs.buildPythonApplication rec {
		export HOME="$(mktemp -d)"
		'';

		meta = with lib; {
		meta = {
		homepage = "https://snakemake.github.io";
		license = licenses.mit;
		license = lib.licenses.mit;
		description = "Python-based execution environment for make-like workflows";
		changelog = "https://github.com/snakemake/snakemake/blob/v${version}/CHANGELOG.md";
		mainProgram = "snakemake";
		longDescription = ''
		Snakemake is a workflow management system that aims to reduce the complexity of
		@@ -133,6 +161,10 @@ python3.pkgs.buildPythonApplication rec {
		workflows are essentially Python scripts extended by declarative code to define
		rules. Rules describe how to create output files from input files.
		'';
		maintainers = with maintainers; [ helkafen renatoGarcia veprbl ];
		maintainers = with lib.maintainers; [
		helkafen
		renatoGarcia
		veprbl
		];
		};
		}

pkgs/development/python-modules/conda-inject/default.nix

0 → 100644

+47 −0

Original line number	Diff line number	Diff line
		{
		lib,
		buildPythonPackage,
		fetchFromGitHub,

		# build-system
		poetry-core,

		# dependencies
		pyyaml,
		}:

		buildPythonPackage rec {
		pname = "conda-inject";
		version = "1.3.2";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "koesterlab";
		repo = "conda-inject";
		rev = "refs/tags/v${version}";
		hash = "sha256-M4+bz7ZuHlcF8tF5kSCUjjkIHG75eCCW1IJxcwxNL6o=";
		};

		build-system = [
		poetry-core
		];

		dependencies = [
		pyyaml
		];

		pythonImportsCheck = [
		"conda_inject"
		];

		# no tests
		doCheck = false;

		meta = {
		description = "Helper functions for injecting a conda environment into the current python environment";
		homepage = "https://github.com/koesterlab/conda-inject";
		changelog = "https://github.com/koesterlab/conda-inject/blob/${src.rev}/CHANGELOG.md";
		license = lib.licenses.mit;
		maintainers = with lib.maintainers; [ GaetanLepage ];
		};
		}

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

+10 −9

Original line number	Diff line number	Diff line
		@@ -10,19 +10,19 @@

		buildPythonPackage rec {
		pname = "snakemake-interface-executor-plugins";
		version = "9.2.0";
		format = "pyproject";
		version = "9.3.2";
		pyproject = true;

		src = fetchFromGitHub {
		owner = "snakemake";
		repo = pname;
		repo = "snakemake-interface-executor-plugins";
		rev = "refs/tags/v${version}";
		hash = "sha256-WMbJP17YnDzFVcr6YepT5Ltw+Jo6PPn7ayIrjx2k+go=";
		hash = "sha256-3XdsEnL+kuYhNOeAxkAsjTJ2R6NOtq97zPhQg9kdFkI=";
		};

		nativeBuildInputs = [ poetry-core ];
		build-system = [ poetry-core ];

		propagatedBuildInputs = [
		dependencies = [
		argparse-dataclass
		throttler
		snakemake-interface-common
		@@ -30,10 +30,11 @@ buildPythonPackage rec {

		pythonImportsCheck = [ "snakemake_interface_executor_plugins" ];

		meta = with lib; {
		meta = {
		description = "This package provides a stable interface for interactions between Snakemake and its executor plugins";
		homepage = "https://github.com/snakemake/snakemake-interface-executor-plugins";
		license = licenses.mit;
		maintainers = with maintainers; [ veprbl ];
		changelog = "https://github.com/snakemake/snakemake-interface-executor-plugins/blob/${src.rev}/CHANGELOG.md";
		license = lib.licenses.mit;
		maintainers = with lib.maintainers; [ veprbl ];
		};
		}

pkgs/top-level/all-packages.nix

+0 −2

Original line number	Diff line number	Diff line
		@@ -18387,8 +18387,6 @@ with pkgs;

		smc = callPackage ../tools/misc/smc { };

		snakemake = callPackage ../applications/science/misc/snakemake { };

		snore = callPackage ../tools/misc/snore { };

		snzip = callPackage ../tools/archivers/snzip { };

pkgs/top-level/python-packages.nix

+3 −1

Original line number	Diff line number	Diff line
		@@ -2514,6 +2514,8 @@ self: super: with self; {

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

		conda-inject = callPackage ../development/python-modules/conda-inject { };

		conda-libmamba-solver = callPackage ../development/python-modules/conda-libmamba-solver { };

		conda-package-handling = callPackage ../development/python-modules/conda-package-handling { };
		@@ -14536,7 +14538,7 @@ self: super: with self; {
		});

		snakemake = toPythonModule (pkgs.snakemake.override {
		python3 = python;
		python3Packages = self;
		});

		snakemake-executor-plugin-cluster-generic = callPackage ../development/python-modules/snakemake-executor-plugin-cluster-generic { };