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)

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

@@ -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

@@ -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

@@ -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

@@ -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 ];
   };
 }