Unverified Commit 68144159 authored by Fabian Affolter's avatar Fabian Affolter Committed by GitHub
Browse files

python3Packages.schema-salad: 8.9.20251102115403 -> 8.9.20260327095315,... 

python3Packages.schema-salad: 8.9.20251102115403 -> 8.9.20260327095315, python3Packages.cwl-upgrader: 1.2.14 -> 1.2.15, python3Packages.cwl-utils: 0.40 -> 0.41  (#507318)
parents 0c6312d5 a8ff54c2

pkgs/by-name/cw/cwltool/package.nix

+9 −8
Original line number Diff line number Diff line
@@ -7,23 +7,28 @@ 


python3Packages.buildPythonApplication (finalAttrs: {

  pname = "cwltool";

  version = "3.1.20251031082601";

  version = "3.1.20260315121657";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "common-workflow-language";

    repo = "cwltool";

    tag = finalAttrs.version;

    hash = "sha256-avRNOdL4Ig2cYQWh8SqX/KWfgXyVg0TVfVFrlqzUCLA=";

    hash = "sha256-0cd64fkaCMX+eaZ4maZW8sE+ZX7bTFy1DDY5leqf9B0=";

  };



  postPatch = ''

    substituteInPlace setup.py \

      --replace-fail "PYTEST_RUNNER + " ""

    substituteInPlace pyproject.toml \

      --replace-fail "mypy==1.18.2" "mypy"

      --replace-fail "mypy==1.19.1" "mypy"

  '';



  pythonRelaxDeps = [

    "prov"

    "rdflib"

  ];



  build-system = with python3Packages; [

    setuptools

    setuptools-scm
@@ -60,11 +65,6 @@ python3Packages.buildPythonApplication (finalAttrs: { 
    pytestCheckHook

  ];



  pythonRelaxDeps = [

    "prov"

    "rdflib"

  ];



  disabledTests = [

    "test_content_types"

    "test_env_filtering"
@@ -75,6 +75,7 @@ python3Packages.buildPythonApplication (finalAttrs: { 
  disabledTestPaths = [

    "tests/test_udocker.py"

    "tests/test_provenance.py"

    "tests/test_examples.py"

  ];



  pythonImportsCheck = [

pkgs/development/python-modules/cwl-upgrader/default.nix

+6 −6
Original line number Diff line number Diff line
@@ -10,16 +10,16 @@ 
  setuptools,

}:



buildPythonPackage rec {

buildPythonPackage (finalAttrs: {

  pname = "cwl-upgrader";

  version = "1.2.14";

  version = "1.2.15";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "common-workflow-language";

    repo = "cwl-upgrader";

    tag = "v${version}";

    hash = "sha256-bkICax7HIEo8ypttXgDmCl82JfVkV2T11fLRK1/0hz8=";

    tag = "v${finalAttrs.version}";

    hash = "sha256-7gmwz3a3IYky/Eof4fnSp3P5oSAko91drcX7i9CwZUY=";

  };



  postPatch = ''
@@ -46,9 +46,9 @@ buildPythonPackage rec { 
  meta = {

    description = "Library to upgrade CWL syntax to a newer version";

    homepage = "https://github.com/common-workflow-language/cwl-upgrader";

    changelog = "https://github.com/common-workflow-language/cwl-upgrader/releases/tag/${src.tag}";

    changelog = "https://github.com/common-workflow-language/cwl-upgrader/releases/tag/v${finalAttrs.src.tag}";

    license = lib.licenses.asl20;

    maintainers = with lib.maintainers; [ fab ];

    mainProgram = "cwl-upgrader";

  };

}
 
})

pkgs/development/python-modules/cwl-utils/default.nix

+8 −17
Original line number Diff line number Diff line
@@ -4,6 +4,7 @@ 
  cwl-upgrader,

  cwlformat,

  fetchFromGitHub,

  hatchling,

  jsonschema,

  packaging,

  pytest-mock,
@@ -13,22 +14,21 @@ 
  requests,

  ruamel-yaml,

  schema-salad,

  setuptools,

}:



buildPythonPackage rec {

buildPythonPackage (finalAttrs: {

  pname = "cwl-utils";

  version = "0.40";

  version = "0.41";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "common-workflow-language";

    repo = "cwl-utils";

    tag = "v${version}";

    hash = "sha256-A9+JvtSTPfXK/FGJ8pplT06kkuatZu1fgjjmg74oTvE=";

    tag = "v${finalAttrs.version}";

    hash = "sha256-78Kx+LCEcPE7qsV6MFtfSY6tVj5KZhifFOib7beCU2c=";

  };



  build-system = [ setuptools ];

  build-system = [ hatchling ];



  dependencies = [

    cwl-upgrader
@@ -62,20 +62,11 @@ buildPythonPackage rec { 
    "test_cwl_inputs_to_jsonschema"

  ];



  disabledTestPaths = [

    # Tests require podman

    "tests/test_docker_extract.py"

    # Tests requires singularity

    "tests/test_js_sandbox.py"

    # Circular dependencies

    "tests/test_graph_split.py"

  ];



  meta = {

    description = "Utilities for CWL";

    homepage = "https://github.com/common-workflow-language/cwl-utils";

    changelog = "https://github.com/common-workflow-language/cwl-utils/releases/tag/v${version}";

    changelog = "https://github.com/common-workflow-language/cwl-utils/releases/tag/v${finalAttrs.src.tag}";

    license = lib.licenses.asl20;

    maintainers = with lib.maintainers; [ fab ];

  };

}
 
})

pkgs/development/python-modules/schema-salad/default.nix

+9 −7
Original line number Diff line number Diff line
@@ -5,11 +5,12 @@ 
  cachecontrol,

  fetchFromGitHub,

  mistune,

  mypy,

  mypy-extensions,

  mypy,

  pytestCheckHook,

  rdflib,

  requests,

  rich-argparse,

  ruamel-yaml,

  setuptools-scm,

  types-dataclasses,
@@ -19,24 +20,24 @@ 


buildPythonPackage rec {

  pname = "schema-salad";

  version = "8.9.20251102115403";

  version = "8.9.20260327095315";

  pyproject = true;



  src = fetchFromGitHub {

    owner = "common-workflow-language";

    repo = "schema_salad";

    tag = version;

    hash = "sha256-3axwM3fSxDIG1P0CvcqzqwpdDkhg/5pY7AmjUpU3mEk=";

    hash = "sha256-j3jevOMsNHT9+HI/8MD4MUwj+IHUisKMs/OA5wpweao=";

  };



  pythonRelaxDeps = [ "mistune" ];



  postPatch = ''

    substituteInPlace setup.py \

      --replace-fail 'pytest_runner + ["setuptools_scm>=8.0.4,<9"]' '["setuptools_scm"]'

      --replace-fail 'pytest_runner + ["setuptools_scm>=8.0.4,<11"]' '["setuptools_scm"]'

    substituteInPlace pyproject.toml \

      --replace-fail '"setuptools_scm[toml]>=8.0.4,<9"' '"setuptools_scm[toml]"' \

      --replace-fail "mypy[mypyc]==1.17.0" "mypy"

      --replace-fail '"setuptools_scm[toml]>=8.0.4,<11"' '"setuptools_scm[toml]"' \

      --replace-fail "mypy[mypyc]==1.19.1" "mypy"

    sed -i "/black>=/d" pyproject.toml

  '';
@@ -49,6 +50,7 @@ buildPythonPackage rec { 
    mypy-extensions

    rdflib

    requests

    rich-argparse

    ruamel-yaml

    types-dataclasses

    types-requests
@@ -83,7 +85,7 @@ buildPythonPackage rec { 
    description = "Semantic Annotations for Linked Avro Data";

    homepage = "https://github.com/common-workflow-language/schema_salad";

    changelog = "https://github.com/common-workflow-language/schema_salad/releases/tag/${src.tag}";

    license = with lib.licenses; [ asl20 ];

    license = lib.licenses.asl20;

    maintainers = with lib.maintainers; [ veprbl ];

  };

}