From c7eea98549edddd9be63af731f5a0fcbd609c51d Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 6 Apr 2026 18:33:15 +0200 Subject: [PATCH 1/6] python3Packages.schema-salad: 8.9.20251102115403 -> 8.9.20260327095315 --- .../python-modules/schema-salad/default.nix | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/pkgs/development/python-modules/schema-salad/default.nix b/pkgs/development/python-modules/schema-salad/default.nix index 17de4fa288ea..214389029d5a 100644 --- a/pkgs/development/python-modules/schema-salad/default.nix +++ b/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/${src.tag}"; - license = with lib.licenses; [ asl20 ]; + license = lib.licenses.asl20; maintainers = with lib.maintainers; [ veprbl ]; }; } From a011771bb4fa755a18083839266d0baa4d8499ad Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 6 Apr 2026 18:36:16 +0200 Subject: [PATCH 2/6] python3Packages.cwl-upgrader: 1.2.14 -> 1.2.15 Diff: https://github.com/common-workflow-language/cwl-upgrader/compare/v1.2.14...v1.2.15 Changelog: https://github.com/common-workflow-language/cwl-upgrader/releases/tag/v1.2.15 --- pkgs/development/python-modules/cwl-upgrader/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/cwl-upgrader/default.nix b/pkgs/development/python-modules/cwl-upgrader/default.nix index 6dccb78314b6..e0dbc1e4df7e 100644 --- a/pkgs/development/python-modules/cwl-upgrader/default.nix +++ b/pkgs/development/python-modules/cwl-upgrader/default.nix @@ -12,14 +12,14 @@ buildPythonPackage rec { pname = "cwl-upgrader"; - version = "1.2.14"; + version = "1.2.15"; pyproject = true; src = fetchFromGitHub { owner = "common-workflow-language"; repo = "cwl-upgrader"; tag = "v${version}"; - hash = "sha256-bkICax7HIEo8ypttXgDmCl82JfVkV2T11fLRK1/0hz8="; + hash = "sha256-7gmwz3a3IYky/Eof4fnSp3P5oSAko91drcX7i9CwZUY="; }; postPatch = '' From 46f7e7ea2c0c88eaa53a137122ec304446e6c700 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 6 Apr 2026 18:37:50 +0200 Subject: [PATCH 3/6] python3Packages.cwl-upgrader: migrate to finalAttrs --- pkgs/development/python-modules/cwl-upgrader/default.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/development/python-modules/cwl-upgrader/default.nix b/pkgs/development/python-modules/cwl-upgrader/default.nix index e0dbc1e4df7e..bf378e69b529 100644 --- a/pkgs/development/python-modules/cwl-upgrader/default.nix +++ b/pkgs/development/python-modules/cwl-upgrader/default.nix @@ -10,7 +10,7 @@ setuptools, }: -buildPythonPackage rec { +buildPythonPackage (finalAttrs: { pname = "cwl-upgrader"; version = "1.2.15"; pyproject = true; @@ -18,7 +18,7 @@ buildPythonPackage rec { src = fetchFromGitHub { owner = "common-workflow-language"; repo = "cwl-upgrader"; - tag = "v${version}"; + tag = "v${finalAttrs.version}"; hash = "sha256-7gmwz3a3IYky/Eof4fnSp3P5oSAko91drcX7i9CwZUY="; }; @@ -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"; }; -} +}) From 99de7935b4906bbade28d18573c22e950ee3da0a Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 6 Apr 2026 18:40:57 +0200 Subject: [PATCH 4/6] python3Packages.cwl-utils: 0.40 -> 0.41 Changelog: https://github.com/common-workflow-language/cwl-utils/releases/tag/v0.41 --- .../python-modules/cwl-utils/default.nix | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/pkgs/development/python-modules/cwl-utils/default.nix b/pkgs/development/python-modules/cwl-utils/default.nix index 66334e24b503..37392acb299a 100644 --- a/pkgs/development/python-modules/cwl-utils/default.nix +++ b/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 { pname = "cwl-utils"; - version = "0.40"; + version = "0.41"; pyproject = true; src = fetchFromGitHub { owner = "common-workflow-language"; repo = "cwl-utils"; tag = "v${version}"; - hash = "sha256-A9+JvtSTPfXK/FGJ8pplT06kkuatZu1fgjjmg74oTvE="; + hash = "sha256-78Kx+LCEcPE7qsV6MFtfSY6tVj5KZhifFOib7beCU2c="; }; - build-system = [ setuptools ]; + build-system = [ hatchling ]; dependencies = [ cwl-upgrader @@ -62,15 +62,6 @@ buildPythonPackage rec { "test_cwl_inputs_to_jsonschema" ]; - disabledTestPaths = [ - # Tests require podman - "tests/test_docker_extract.py" - # Tests requires singularity - "tests/test_js_sandbox.py" - # Circular dependencies - "tests/test_graph_split.py" - ]; - meta = { description = "Utilities for CWL"; homepage = "https://github.com/common-workflow-language/cwl-utils"; From 2ea6fbd4104373cfcfbf53a5829d0a5d3be73089 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 6 Apr 2026 18:41:49 +0200 Subject: [PATCH 5/6] python3Packages.cwl-utils: migrate to finalAttrs --- pkgs/development/python-modules/cwl-utils/default.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/development/python-modules/cwl-utils/default.nix b/pkgs/development/python-modules/cwl-utils/default.nix index 37392acb299a..e91507d1815b 100644 --- a/pkgs/development/python-modules/cwl-utils/default.nix +++ b/pkgs/development/python-modules/cwl-utils/default.nix @@ -16,7 +16,7 @@ schema-salad, }: -buildPythonPackage rec { +buildPythonPackage (finalAttrs: { pname = "cwl-utils"; version = "0.41"; pyproject = true; @@ -24,7 +24,7 @@ buildPythonPackage rec { src = fetchFromGitHub { owner = "common-workflow-language"; repo = "cwl-utils"; - tag = "v${version}"; + tag = "v${finalAttrs.version}"; hash = "sha256-78Kx+LCEcPE7qsV6MFtfSY6tVj5KZhifFOib7beCU2c="; }; @@ -65,8 +65,8 @@ buildPythonPackage rec { meta = { description = "Utilities for CWL"; homepage = "https://github.com/common-workflow-language/cwl-utils"; - changelog = "https://github.com/common-workflow-language/cwl-utils/releases/tag/v${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 ]; }; -} +}) From a8ff54c2f63dad3ba378a2583f83c334938d82f6 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Mon, 6 Apr 2026 20:19:44 +0200 Subject: [PATCH 6/6] cwltool: 3.1.20251031082601 -> 3.1.20260315121657 Changelog: https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20260315121657 --- pkgs/by-name/cw/cwltool/package.nix | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/pkgs/by-name/cw/cwltool/package.nix b/pkgs/by-name/cw/cwltool/package.nix index 7fb80d9a0cb1..0c583225f398 100644 --- a/pkgs/by-name/cw/cwltool/package.nix +++ b/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 = [