From e11e570888402846cc24c1053488f267f274198b Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sun, 15 Jan 2023 12:21:28 +0100 Subject: [PATCH 1/4] python310Packages.cwl-upgrader: init at 1.2.4 --- .../python-modules/cwl-upgrader/default.nix | 53 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 55 insertions(+) create mode 100644 pkgs/development/python-modules/cwl-upgrader/default.nix diff --git a/pkgs/development/python-modules/cwl-upgrader/default.nix b/pkgs/development/python-modules/cwl-upgrader/default.nix new file mode 100644 index 000000000000..1c63c6605da4 --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index b4b340a42ba5..72cc04a90b22 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -2124,6 +2124,8 @@ self: super: with self; { cwcwidth = callPackage ../development/python-modules/cwcwidth { }; + cwl-upgrader = callPackage ../development/python-modules/cwl-upgrader { }; + cx_Freeze = callPackage ../development/python-modules/cx_freeze { }; cx_oracle = callPackage ../development/python-modules/cx_oracle { }; From 768366b645d8e69abe69c185d5b0cb59a90a54e6 Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sun, 15 Jan 2023 12:37:29 +0100 Subject: [PATCH 2/4] python310Packages.cwlformat: init at 2022.02.18 --- .../python-modules/cwlformat/default.nix | 42 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 44 insertions(+) create mode 100644 pkgs/development/python-modules/cwlformat/default.nix diff --git a/pkgs/development/python-modules/cwlformat/default.nix b/pkgs/development/python-modules/cwlformat/default.nix new file mode 100644 index 000000000000..201155eac595 --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 72cc04a90b22..bb5e0310b26c 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -2126,6 +2126,8 @@ self: super: with self; { cwl-upgrader = callPackage ../development/python-modules/cwl-upgrader { }; + cwlformat = callPackage ../development/python-modules/cwlformat { }; + cx_Freeze = callPackage ../development/python-modules/cx_freeze { }; cx_oracle = callPackage ../development/python-modules/cx_oracle { }; From 6441fff9c167f0de005609ee1fcd8743659d188e Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sun, 15 Jan 2023 12:53:15 +0100 Subject: [PATCH 3/4] python310Packages.cwl-utils: init at 0.21 --- .../python-modules/cwl-utils/default.nix | 67 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 69 insertions(+) create mode 100644 pkgs/development/python-modules/cwl-utils/default.nix diff --git a/pkgs/development/python-modules/cwl-utils/default.nix b/pkgs/development/python-modules/cwl-utils/default.nix new file mode 100644 index 000000000000..b0459f3961ae --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index bb5e0310b26c..d2bce583e3f6 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -2126,6 +2126,8 @@ self: super: with self; { 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 { }; From 1493baebd900807f1260624a7e7b8e12920f7bcf Mon Sep 17 00:00:00 2001 From: Fabian Affolter Date: Sun, 15 Jan 2023 13:23:22 +0100 Subject: [PATCH 4/4] cwltool: 3.1.20220224085855 -> 3.1.20221201130942 Changelog: https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20221201130942 --- pkgs/applications/science/misc/cwltool/default.nix | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index 6a1bdc3de160..5693344e6364 100644 --- a/pkgs/applications/science/misc/cwltool/default.nix +++ b/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 ]; };