Merge pull request #130903 from veprbl/pr/cwltool

cwltool: init at 3.1.20210628163208

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

@@ -0,0 +1,41 @@
+{ lib
+, python3Packages
+}:
+
+python3Packages.buildPythonApplication rec {
+  pname = "cwltool";
+  version = "3.1.20210628163208";
+
+  src = python3Packages.fetchPypi {
+    inherit pname version;
+    sha256 = "21b885f725420413d2f87eadc5e81c08a9c91beceda89b35d1a702ec4df47e52";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace 'prov == 1.5.1' 'prov'
+  '';
+
+  propagatedBuildInputs = with python3Packages; [
+    argcomplete
+    bagit
+    coloredlogs
+    mypy-extensions
+    prov
+    psutil
+    pydot
+    schema-salad
+    shellescape
+    typing-extensions
+  ];
+
+  doCheck = false; # hard to setup
+  pythonImportsCheck = [ "cwltool" ];
+
+  meta = with lib; {
+    homepage = "https://www.commonwl.org";
+    license = with licenses; [ asl20 ];
+    description = "Common Workflow Language reference implementation";
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

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

@@ -0,0 +1,39 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, coverage
+, gettext
+, mock
+, pytestCheckHook
+, setuptools-scm
+}:
+
+buildPythonPackage rec {
+  pname = "bagit";
+  version = "1.8.1";
+
+  src = fetchFromGitHub {
+    owner = "LibraryOfCongress";
+    repo = "bagit-python";
+    rev = "v${version}";
+    hash = "sha256-t01P7MPWgOrktuW2zF0TIzt6u/jkLmrpD2OnqawhJaI=";
+  };
+
+  nativeBuildInputs = [ gettext setuptools-scm ];
+
+  SETUPTOOLS_SCM_PRETEND_VERSION = version;
+
+  checkInputs = [
+    mock
+    pytestCheckHook
+  ];
+  pytestFlagsArray = [ "test.py" ];
+  pythonImportsCheck = [ "bagit" ];
+
+  meta = with lib; {
+    description = "Python library and command line utility for working with BagIt style packages";
+    homepage = "https://libraryofcongress.github.io/bagit-python/";
+    license = with licenses; [ publicDomain ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

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

@@ -0,0 +1,45 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, cachecontrol
+, lockfile
+, mistune
+, rdflib
+, rdflib-jsonld
+, ruamel_yaml
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "schema-salad";
+  version = "8.1.20210716111910";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "3f851b385d044c58d359285ba471298b6199478a4978f892a83b15cbfb282f25";
+  };
+
+  propagatedBuildInputs = [
+    cachecontrol
+    lockfile
+    mistune
+    rdflib
+    rdflib-jsonld
+    ruamel_yaml
+  ];
+
+  checkInputs = [ pytestCheckHook ];
+  disabledTests = [
+    # setup for these tests requires network access
+    "test_secondaryFiles"
+    "test_outputBinding"
+  ];
+  pythonImportsCheck = [ "schema_salad" ];
+
+  meta = with lib; {
+    description = "Semantic Annotations for Linked Avro Data";
+    homepage = "https://github.com/common-workflow-language/schema_salad";
+    license = with licenses; [ asl20 ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

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

@@ -0,0 +1,27 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "shellescape";
+  version = "3.8.1";
+
+  src = fetchFromGitHub {
+    owner = "chrissimpkins";
+    repo = "shellescape";
+    rev = "v${version}";
+    hash = "sha256-HAe3Qf3lLeVWw/tVkW0J+CfoxSoOnCcWDR2nEWZn7HM=";
+  };
+
+  checkInputs = [ pytestCheckHook ];
+  pythonImportsCheck = [ "shellescape" ];
+
+  meta = with lib; {
+    description = "Shell escape a string to safely use it as a token in a shell command (backport of Python shlex.quote)";
+    homepage = "https://github.com/chrissimpkins/shellescape";
+    license = with licenses; [ mit psfl ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -13539,6 +13539,8 @@ with pkgs;
     inherit (llvmPackages_11) llvm libclang;
   };
 
+  cwltool = callPackage ../applications/science/misc/cwltool { };
+
   dprint = callPackage ../development/tools/dprint { };
 
   libcxx = llvmPackages.libcxx;

pkgs/top-level/python-packages.nix

@@ -995,6 +995,8 @@ in {
 
   bacpypes = callPackage ../development/python-modules/bacpypes { };
 
+  bagit = callPackage ../development/python-modules/bagit { };
+
   banal = callPackage ../development/python-modules/banal { };
 
   bandit = callPackage ../development/python-modules/bandit { };
@@ -7864,6 +7866,8 @@ in {
 
   schema = callPackage ../development/python-modules/schema { };
 
+  schema-salad = callPackage ../development/python-modules/schema-salad { };
+
   schiene = callPackage ../development/python-modules/schiene { };
 
   scikit-bio = callPackage ../development/python-modules/scikit-bio { };
@@ -8007,6 +8011,8 @@ in {
 
   sh = callPackage ../development/python-modules/sh { };
 
+  shellescape = callPackage ../development/python-modules/shellescape { };
+
   shellingham = callPackage ../development/python-modules/shellingham { };
 
   shiboken2 = toPythonModule (callPackage ../development/python-modules/shiboken2 {