diff options
author | Fabian Affolter <fabian@affolter-engineering.ch> | 2024-01-21 23:46:45 +0100 |
---|---|---|
committer | GitHub <noreply@github.com> | 2024-01-21 23:46:45 +0100 |
commit | 863909560429e42723c82d51f9818e4bce5d5600 (patch) | |
tree | 71a6c5da4b9400a820b6b3dd49fd6f8d022d764e /pkgs | |
parent | d675dfc2ed25de19789314b0cb9e2fa44d25bd89 (diff) | |
parent | 48433b4d361f5ee28dd8b0ce06769e2c94a17b6a (diff) |
Merge pull request #282534 from fabaff/cwltool-fix
cwltool: 3.1.20230213100550 -> 3.1.20240112164112
Diffstat (limited to 'pkgs')
-rw-r--r-- | pkgs/applications/science/misc/cwltool/default.nix | 26 | ||||
-rw-r--r-- | pkgs/development/python-modules/spython/default.nix | 59 | ||||
-rw-r--r-- | pkgs/top-level/python-packages.nix | 2 |
3 files changed, 80 insertions, 7 deletions
diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index 7c28f65f3bf7b..fb3b26a12edf1 100644 --- a/pkgs/applications/science/misc/cwltool/default.nix +++ b/pkgs/applications/science/misc/cwltool/default.nix @@ -7,32 +7,40 @@ python3.pkgs.buildPythonApplication rec { pname = "cwltool"; - version = "3.1.20230213100550"; - format = "setuptools"; + version = "3.1.20240112164112"; + pyproject = true; src = fetchFromGitHub { owner = "common-workflow-language"; - repo = pname; + repo = "cwltool"; rev = "refs/tags/${version}"; - hash = "sha256-BtHkIVadcccnYYX8lRqiCzO+/qFeBaZfdUuu6qrjysk="; + hash = "sha256-Y0DORypXlTDv04qh796oXPSTxCXGb7rLQ8Su+/As7Lo="; }; postPatch = '' substituteInPlace setup.py \ - --replace "ruamel.yaml >= 0.15, < 0.17.22" "ruamel.yaml" \ + --replace "ruamel.yaml >= 0.16, < 0.19" "ruamel.yaml" \ --replace "prov == 1.5.1" "prov" \ - --replace "setup_requires=PYTEST_RUNNER," "" + --replace '"schema-salad >= 8.4.20230426093816, < 9",' "" \ + --replace "PYTEST_RUNNER + " "" + substituteInPlace pyproject.toml \ + --replace "mypy==1.8.0" "mypy" \ + --replace "ruamel.yaml>=0.16.0,<0.18" "ruamel.yaml" ''; nativeBuildInputs = [ git - ]; + ] ++ (with python3.pkgs; [ + setuptools + setuptools-scm + ]); propagatedBuildInputs = with python3.pkgs; [ argcomplete bagit coloredlogs cwl-utils + mypy mypy-extensions prov psutil @@ -42,6 +50,10 @@ python3.pkgs.buildPythonApplication rec { ruamel-yaml schema-salad shellescape + spython + toml + types-psutil + types-requests typing-extensions ]; diff --git a/pkgs/development/python-modules/spython/default.nix b/pkgs/development/python-modules/spython/default.nix new file mode 100644 index 0000000000000..e5a2fdf161c89 --- /dev/null +++ b/pkgs/development/python-modules/spython/default.nix @@ -0,0 +1,59 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, setuptools +, pytestCheckHook +, pythonOlder +}: + +buildPythonPackage rec { + pname = "spython"; + version = "0.3.12"; + pyproject = true; + + disabled = pythonOlder "3.9"; + + src = fetchFromGitHub { + owner = "singularityhub"; + repo = "singularity-cli"; + rev = "refs/tags/${version}"; + hash = "sha256-fRtqOpDgVMYlVDwbPkrnpd7PT4fV+2WS6RmpJoxaKdQ="; + }; + + postPatch = '' + substituteInPlace setup.py \ + --replace '"pytest-runner"' "" + ''; + + nativeBuildInputs = [ + setuptools + ]; + + nativeCheckInputs = [ + pytestCheckHook + ]; + + pythonImportsCheck = [ + "spython" + ]; + + disabledTests = [ + # Assertion errors + "test_has_no_instances" + "test_check_install" + "test_check_get_singularity_version" + ]; + + disabledTestPaths = [ + # Tests are looking for something that doesn't exist + "spython/tests/test_client.py" + ]; + + meta = with lib; { + description = "Streamlined singularity python client (spython) for singularity"; + homepage = "https://github.com/singularityhub/singularity-cli"; + changelog = "https://github.com/singularityhub/singularity-cli/blob/${version}/CHANGELOG.md"; + license = licenses.mpl20; + maintainers = with maintainers; [ fab ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 6375fac04d610..6b518dc1a70ba 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -13706,6 +13706,8 @@ self: super: with self; { spyse-python = callPackage ../development/python-modules/spyse-python { }; + spython = callPackage ../development/python-modules/spython { }; + sqids = callPackage ../development/python-modules/sqids { }; sqlalchemy = callPackage ../development/python-modules/sqlalchemy { }; |