diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix index a25fbe7565ce..b13ad0ad10ca 100644 --- a/pkgs/applications/science/misc/toil/default.nix +++ b/pkgs/applications/science/misc/toil/default.nix @@ -1,39 +1,46 @@ -{ lib, fetchFromGitHub, python3Packages }: +{ lib +, fetchFromGitHub +, python3 +}: -python3Packages.buildPythonApplication rec { +python3.pkgs.buildPythonApplication rec { pname = "toil"; - version = "5.4.0"; + version = "5.6.0"; + format = "setuptools"; - src = python3Packages.fetchPypi { + src = python3.pkgs.fetchPypi { inherit pname version; - sha256 = "73c0648828bd3610c07b7648dd06d6ec27efefdb09473bf01d05d91eb899c9fd"; + sha256 = "sha256-m6tzrRCCLULO+wB8htUlt0KESLm/vdIeTzBrihnAo/I="; }; - postPatch = '' - substituteInPlace setup.py \ - --replace "docker = " "docker = 'docker' #" \ - --replace "addict = " "addict = 'addict' #" - ''; - - propagatedBuildInputs = with python3Packages; [ + propagatedBuildInputs = with python3.pkgs; [ addict docker pytz pyyaml enlighten psutil + py-tes python-dateutil dill ]; - checkInputs = with python3Packages; [ pytestCheckHook ]; - pytestFlagsArray = [ "src/toil/test" ]; - pythonImportsCheck = [ "toil" ]; + checkInputs = with python3.pkgs; [ + pytestCheckHook + ]; + + pytestFlagsArray = [ + "src/toil/test" + ]; + + pythonImportsCheck = [ + "toil" + ]; meta = with lib; { + description = "Workflow engine written in pure Python"; homepage = "https://toil.ucsc-cgl.org/"; license = with licenses; [ asl20 ]; - description = "Workflow engine written in pure Python"; maintainers = with maintainers; [ veprbl ]; }; } diff --git a/pkgs/development/python-modules/py-tes/default.nix b/pkgs/development/python-modules/py-tes/default.nix new file mode 100644 index 000000000000..633dc6fa5f4a --- /dev/null +++ b/pkgs/development/python-modules/py-tes/default.nix @@ -0,0 +1,49 @@ +{ lib +, attrs +, buildPythonPackage +, fetchFromGitHub +, future +, python-dateutil +, pytestCheckHook +, pythonOlder +, requests +, requests-mock +}: + +buildPythonPackage rec { + pname = "py-tes"; + version = "0.4.2"; + format = "setuptools"; + + disabled = pythonOlder "3.7"; + + src = fetchFromGitHub { + owner = "ohsu-comp-bio"; + repo = pname; + rev = version; + hash = "sha256-HZeyCQHiqfdquWQD5axS73JDjDMUieONwm5VyA+vTFk="; + }; + + propagatedBuildInputs = [ + attrs + future + python-dateutil + requests + ]; + + checkInputs = [ + pytestCheckHook + requests-mock + ]; + + pythonImportsCheck = [ + "tes" + ]; + + meta = with lib; { + description = "Python SDK for the GA4GH Task Execution API"; + homepage = "https://github.com/ohsu-comp-bio/py-tes"; + license = with licenses; [ mit ]; + maintainers = with maintainers; [ fab ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 5b77053944a6..757c91f30b84 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -6408,6 +6408,8 @@ in { py-synologydsm-api = callPackage ../development/python-modules/py-synologydsm-api { }; + py-tes = callPackage ../development/python-modules/py-tes { }; + py-ubjson = callPackage ../development/python-modules/py-ubjson { }; py-zabbix = callPackage ../development/python-modules/py-zabbix { };