From ce752bc694f87fb3967967536c076099e95e13c3 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 7 Nov 2022 14:27:49 +0100 Subject: [PATCH 1/5] python310Packages.docker: 6.0.0 -> 6.0.1 --- pkgs/development/python-modules/docker/default.nix | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/pkgs/development/python-modules/docker/default.nix b/pkgs/development/python-modules/docker/default.nix index 0a01d5e4792e..46103311700d 100644 --- a/pkgs/development/python-modules/docker/default.nix +++ b/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"; From d284ffaa15bde72742ea78b01f88496ce6e56500 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 7 Nov 2022 14:36:58 +0100 Subject: [PATCH 2/5] trueseeing: relax docker contraint --- pkgs/tools/security/trueseeing/default.nix | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/tools/security/trueseeing/default.nix b/pkgs/tools/security/trueseeing/default.nix index 49b12c3c9d2f..d1014bd36772 100644 --- a/pkgs/tools/security/trueseeing/default.nix +++ b/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 From 41b1a58f40664a4422144d505cc5bc774758696b Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 7 Nov 2022 17:55:36 +0100 Subject: [PATCH 3/5] python310Packages.stubserver: init at 1.1 --- .../python-modules/stubserver/default.nix | 32 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 ++ 2 files changed, 34 insertions(+) create mode 100644 pkgs/development/python-modules/stubserver/default.nix diff --git a/pkgs/development/python-modules/stubserver/default.nix b/pkgs/development/python-modules/stubserver/default.nix new file mode 100644 index 000000000000..87b9cd988cce --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 6e5648173dd1..9ac101804a0c 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -10720,6 +10720,8 @@ 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 { }; From cad704eb95f5d4b7a283cd8d7498fa05672d4f20 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Tue, 8 Nov 2022 12:17:40 +0100 Subject: [PATCH 4/5] toil: 5.6.0 -> 5.7.1 --- .../science/misc/toil/default.nix | 64 ++++++++++++++++--- 1 file changed, 55 insertions(+), 9 deletions(-) diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix index b13ad0ad10ca..43cb6bbbc7ee 100644 --- a/pkgs/applications/science/misc/toil/default.nix +++ b/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/"; From e702dff003c9ec4dd63aa8db2c827900facb8cd9 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Tue, 8 Nov 2022 14:42:02 +0100 Subject: [PATCH 5/5] python310Packages.dm-sonnet: add missing input --- .../python-modules/dm-sonnet/default.nix | 39 +++++++++++-------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/pkgs/development/python-modules/dm-sonnet/default.nix b/pkgs/development/python-modules/dm-sonnet/default.nix index f857eac8503b..e089b91eb0f8 100644 --- a/pkgs/development/python-modules/dm-sonnet/default.nix +++ b/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