Merge pull request #200024 from fabaff/docker-bump

python310Packages.docker: 6.0.0 -> 6.0.1

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

@@ -1,33 +1,51 @@
 { 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

@@ -1,40 +1,45 @@
 { lib
-, fetchFromGitHub
-, buildPythonPackage
-, numpy
-, tabulate
-, six
-, dm-tree
 , absl-py
-, wrapt
+, buildPythonPackage
+, dm-tree
 , 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
-    tensorflow
-  ];
+  passthru.optional-dependencies = {
+    tensorflow = [
+      tensorflow
+    ];
+  };
 
   checkInputs = [
     docutils

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

@@ -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

@@ -0,0 +1,32 @@
+{ 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

@@ -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

pkgs/top-level/python-packages.nix

@@ -10724,6 +10724,8 @@ self: super: with self; {
 
   structlog = callPackage ../development/python-modules/structlog { };
 
+  stubserver = callPackage ../development/python-modules/stubserver { };
+
   stumpy = callPackage ../development/python-modules/stumpy { };
 
   stups-cli-support = callPackage ../development/python-modules/stups-cli-support { };