Merge pull request #200024 from fabaff/docker-bump (9ac32534) · Commits · nix / nixpkgs

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

+55 −9

Original line number	Diff line number	Diff line
		{ lib
		, fetchFromGitHub
		, python3
		, rsync
		}:

		python3.pkgs.buildPythonApplication rec {
		pname = "toil";
		version = "5.6.0";
		version = "5.7.1";
		format = "setuptools";

		src = python3.pkgs.fetchPypi {
		inherit pname version;
		sha256 = "sha256-m6tzrRCCLULO+wB8htUlt0KESLm/vdIeTzBrihnAo/I=";
		src = fetchFromGitHub {
		owner = "DataBiosphere";
		repo = pname;
		rev = "refs/tags/releases/${version}";
		hash = "sha256-m+XvNyzd0ly2YqKhgxezgGaCXLs3CmupJMnp5RIZqNI=";
		};

		postPatch = ''
		substituteInPlace requirements.txt \
		--replace "docker>=3.7.2, <6" "docker"
		'';

		propagatedBuildInputs = with python3.pkgs; [
		addict
		dill
		docker
		pytz
		pyyaml
		enlighten
		psutil
		py-tes
		pypubsub
		python-dateutil
		dill
		pytz
		pyyaml
		requests
		typing-extensions
		];

		checkInputs = with python3.pkgs; [
		checkInputs = [
		rsync
		] ++ (with python3.pkgs; [
		boto
		botocore
		flask
		mypy-boto3-s3
		pytestCheckHook
		];
		stubserver
		]);

		pytestFlagsArray = [
		"src/toil/test"
		@@ -37,6 +55,34 @@ python3.pkgs.buildPythonApplication rec {
		"toil"
		];

		disabledTestPaths = [
		# Tests are reaching their timeout
		"src/toil/test/docs/scriptsTest.py"
		"src/toil/test/jobStores/jobStoreTest.py"
		"src/toil/test/provisioners/aws/awsProvisionerTest.py"
		"src/toil/test/src"
		"src/toil/test/wdl"
		"src/toil/test/utils/utilsTest.py"
		];

		disabledTests = [
		# Tests fail starting with 5.7.1
		"testServices"
		"testConcurrencyWithDisk"
		"testJobConcurrency"
		"testNestedResourcesDoNotBlock"
		"test_omp_threads"
		"testFileSingle"
		"testFileSingle10000"
		"testFileSingleCheckpoints"
		"testFileSingleNonCaching"
		"testFetchJobStoreFiles"
		"testFetchJobStoreFilesWSymlinks"
		"testJobStoreContents"
		"test_cwl_on_arm"
		"test_cwl_toil_kill"
		];

		meta = with lib; {
		description = "Workflow engine written in pure Python";
		homepage = "https://toil.ucsc-cgl.org/";

pkgs/development/python-modules/dm-sonnet/default.nix

+21 −16

Original line number	Diff line number	Diff line
		{ lib
		, fetchFromGitHub
		, absl-py
		, buildPythonPackage
		, numpy
		, tabulate
		, six
		, dm-tree
		, absl-py
		, wrapt
		, docutils
		, etils
		, fetchFromGitHub
		, numpy
		, pythonOlder
		, tabulate
		, tensorflow
		, tensorflow-datasets }:
		, tensorflow-datasets
		, wrapt
		}:

		buildPythonPackage rec {
		pname = "dm-sonnet";
		version = "2.0.0";
		format = "setuptools";

		disabled = pythonOlder "3.6";

		src = fetchFromGitHub {
		owner = "deepmind";
		repo = "sonnet";
		rev = "v${version}";
		sha256 = "sha256-YSMeH5ZTfP1OdLBepsxXAVczBG/ghSjCWjoz/I+TFl8=";
		hash = "sha256-YSMeH5ZTfP1OdLBepsxXAVczBG/ghSjCWjoz/I+TFl8=";
		};

		buildInputs = [
		absl-py
		propagatedBuildInputs = [
		dm-tree
		etils
		numpy
		six
		tabulate
		wrapt
		];
		] ++ etils.optional-dependencies.epath;

		propagatedBuildInputs = [
		tabulate
		passthru.optional-dependencies = {
		tensorflow = [
		tensorflow
		];
		};

		checkInputs = [
		docutils

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

+10 −3

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

		buildPythonPackage rec {
		pname = "docker";
		version = "6.0.0";
		version = "6.0.1";
		format = "pyproject";

		disabled = pythonOlder "3.7";

		src = fetchPypi {
		inherit pname version;
		sha256 = "sha256-GeMwRwr0AWfSk7A1JXjB+iLXSzTT7fXU/5DrwgO7svE=";
		hash = "sha256-iWxCguXHr1xF6LaDsLDDOTKXT+blD8aQagqDYWqz2pc=";
		};

		nativeBuildInputs = [
		@@ -47,10 +48,16 @@ buildPythonPackage rec {
		];

		# Deselect socket tests on Darwin because it hits the path length limit for a Unix domain socket
		disabledTests = lib.optionals stdenv.isDarwin [ "api_test" "stream_response" "socket_file" ];
		disabledTests = lib.optionals stdenv.isDarwin [
		"api_test" "stream_response" "socket_file"
		];

		dontUseSetuptoolsCheck = true;

		pythonImportsCheck = [
		"docker"
		];

		meta = with lib; {
		description = "An API client for docker written in Python";
		homepage = "https://github.com/docker/docker-py";

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

0 → 100644

+32 −0

Original line number	Diff line number	Diff line
		{ lib
		, buildPythonPackage
		, fetchPypi
		, pythonOlder
		}:

		buildPythonPackage rec {
		pname = "stubserver";
		version = "1.1";
		format = "setuptools";

		disabled = pythonOlder "3.7";

		src = fetchPypi {
		inherit pname version;
		hash = "sha256-j9R7wpvb07FuN5EhIpE7xTSf26AniQZN4iLpxMjNYKA=";
		};

		# Tests are not shipped and the source not tagged
		doCheck = false;

		pythonImportsCheck = [
		"stubserver"
		];

		meta = with lib; {
		description = "Web and FTP server for use in unit and7or acceptance tests";
		homepage = "https://github.com/tarttelin/Python-Stub-Server";
		license = licenses.bsd2;
		maintainers = with maintainers; [ fab ];
		};
		}

pkgs/tools/security/trueseeing/default.nix

+2 −1

Original line number	Diff line number	Diff line
		@@ -31,7 +31,8 @@ python3.pkgs.buildPythonApplication rec {

		postPatch = ''
		substituteInPlace pyproject.toml \
		--replace "attrs~=21.4" "attrs>=21.4"
		--replace "attrs~=21.4" "attrs>=21.4" \
		--replace "docker~=5.0.3" "docker"
		'';

		# Project has no tests