Merge pull request #210904 from fabaff/cwltool-bump

cwltool: 3.1.20220224085855 -> 3.1.20221201130942

pkgs/applications/science/misc/cwltool/default.nix

@@ -7,19 +7,19 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "cwltool";
-  version = "3.1.20220224085855";
+  version = "3.1.20221201130942";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "common-workflow-language";
     repo = pname;
-    rev = version;
-    sha256 = "sha256-7+1xOV5Lodqtku0wX1urAEHsCcYKM3Vcd5RDg4DdVow=";
+    rev = "refs/tags/${version}";
+    hash = "sha256-PeddmHMJYtj/AAItmUVeyETizF7SKzkJ3bXYkeZU+xs=";
   };
 
   postPatch = ''
     substituteInPlace setup.py \
-      --replace "ruamel.yaml >= 0.15, < 0.17.18" "ruamel.yaml" \
+      --replace "ruamel.yaml >= 0.15, < 0.17.22" "ruamel.yaml" \
       --replace "prov == 1.5.1" "prov" \
       --replace "setup_requires=PYTEST_RUNNER," ""
   '';
@@ -32,6 +32,7 @@ python3.pkgs.buildPythonApplication rec {
     argcomplete
     bagit
     coloredlogs
+    cwl-utils
     mypy-extensions
     prov
     psutil
@@ -48,6 +49,7 @@ python3.pkgs.buildPythonApplication rec {
     mock
     nodejs
     pytest-mock
+    pytest-httpserver
     pytest-xdist
     pytestCheckHook
   ];
@@ -56,6 +58,7 @@ python3.pkgs.buildPythonApplication rec {
     "test_content_types"
     "test_env_filtering"
     "test_http_path_mapping"
+    "test_modification_date"
   ];
 
   disabledTestPaths = [
@@ -70,6 +73,7 @@ python3.pkgs.buildPythonApplication rec {
   meta = with lib; {
     description = "Common Workflow Language reference implementation";
     homepage = "https://www.commonwl.org";
+    changelog = "https://github.com/common-workflow-language/cwltool/releases/tag/${version}";
     license = with licenses; [ asl20 ];
     maintainers = with maintainers; [ veprbl ];
   };

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

@@ -0,0 +1,53 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytest-xdist
+, pytestCheckHook
+, pythonOlder
+, ruamel-yaml
+, schema-salad
+}:
+
+buildPythonPackage rec {
+  pname = "cwl-upgrader";
+  version = "1.2.4";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "common-workflow-language";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-3pKnkU8lks3w+N7w2qST9jr4/CS6YzgnBVLTlgq1gf0=";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "ruamel.yaml >= 0.15, < 0.17.22" "ruamel.yaml" \
+      --replace "setup_requires=PYTEST_RUNNER," ""
+    sed -i "/ruamel.yaml/d" setup.py
+  '';
+
+  propagatedBuildInputs = [
+    ruamel-yaml
+    schema-salad
+  ];
+
+  checkInputs = [
+    pytest-xdist
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "cwlupgrader"
+  ];
+
+  meta = with lib; {
+    description = "Library to interface with Yolink";
+    homepage = "https://github.com/common-workflow-language/cwl-utils";
+    changelog = "https://github.com/common-workflow-language/cwl-utils/releases/tag/v${version}";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fab ];
+  };
+}

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

@@ -0,0 +1,67 @@
+{ lib
+, buildPythonPackage
+, cachecontrol
+, cwl-upgrader
+, cwlformat
+, fetchFromGitHub
+, packaging
+, pytest-mock
+, pytest-xdist
+, pytestCheckHook
+, pythonOlder
+, rdflib
+, requests
+, schema-salad
+}:
+
+buildPythonPackage rec {
+  pname = "cwl-utils";
+  version = "0.21";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "common-workflow-language";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-y1zuYaxoE0XUk8UpCLsg4ty0sn+5Uu4ztRnUoJezO/o=";
+  };
+
+  propagatedBuildInputs = [
+    cachecontrol
+    cwl-upgrader
+    packaging
+    rdflib
+    requests
+    schema-salad
+  ];
+
+  checkInputs = [
+    cwlformat
+    pytest-mock
+    pytest-xdist
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "cwl_utils"
+  ];
+
+  disabledTests = [
+    # Don't run tests which require Node.js
+    "test_context_multiple_regex"
+    "test_value_from_two_concatenated_expressions"
+    "test_graph_split"
+    "test_caches_js_processes"
+    "test_load_document_with_remote_uri"
+  ];
+
+  meta = with lib; {
+    description = "Utilities for CWL";
+    homepage = "https://github.com/common-workflow-language/cwl-utils";
+    changelog = "https://github.com/common-workflow-language/cwl-utils/releases/tag/v${version}";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fab ];
+  };
+}

pkgs/development/python-modules/cwlformat/default.nix

@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, pythonOlder
+, ruamel-yaml
+}:
+
+buildPythonPackage rec {
+  pname = "cwlformat";
+  version = "2022.02.18";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.8";
+
+  src = fetchFromGitHub {
+    owner = "rabix";
+    repo = "cwl-format";
+    rev = "refs/tags/${version}";
+    hash = "sha256-FI8hUgb/KglTkubZ+StzptoSsYal71ITyyFNg7j48yk=";
+  };
+
+  propagatedBuildInputs = [
+    ruamel-yaml
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "cwlformat"
+  ];
+
+  meta = with lib; {
+    description = "Code formatter for CWL";
+    homepage = "https://github.com/rabix/cwl-format";
+    changelog = "https://github.com/rabix/cwl-format/releases/tag/${version}";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fab ];
+  };
+}

pkgs/top-level/python-packages.nix

@@ -2124,6 +2124,12 @@ self: super: with self; {
 
   cwcwidth = callPackage ../development/python-modules/cwcwidth { };
 
+  cwl-upgrader = callPackage ../development/python-modules/cwl-upgrader { };
+
+  cwl-utils = callPackage ../development/python-modules/cwl-utils { };
+
+  cwlformat = callPackage ../development/python-modules/cwlformat { };
+
   cx_Freeze = callPackage ../development/python-modules/cx_freeze { };
 
   cx_oracle = callPackage ../development/python-modules/cx_oracle { };