From 088aee7bf0c0067ad927d4a8da66ba1aca60bbda Mon Sep 17 00:00:00 2001 From: Dmitry Kalinkin Date: Wed, 21 Jul 2021 00:47:26 -0400 Subject: [PATCH 1/4] pythonPackages.bagit: init at 1.8.1 --- .../python-modules/bagit/default.nix | 39 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 41 insertions(+) create mode 100644 pkgs/development/python-modules/bagit/default.nix diff --git a/pkgs/development/python-modules/bagit/default.nix b/pkgs/development/python-modules/bagit/default.nix new file mode 100644 index 000000000000..7663cf8cf1a9 --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 172fdc4b6681..26dba3485425 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -991,6 +991,8 @@ 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 { }; From ee63a081baa0b31e8a8f39ef07cb6cd86df5d82f Mon Sep 17 00:00:00 2001 From: Dmitry Kalinkin Date: Wed, 21 Jul 2021 00:51:09 -0400 Subject: [PATCH 2/4] pythonPackages.schema-salad: init at 8.1.20210716111910 --- .../python-modules/schema-salad/default.nix | 45 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 47 insertions(+) create mode 100644 pkgs/development/python-modules/schema-salad/default.nix diff --git a/pkgs/development/python-modules/schema-salad/default.nix b/pkgs/development/python-modules/schema-salad/default.nix new file mode 100644 index 000000000000..007cca251436 --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 26dba3485425..8c5d9ecb1e53 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -7793,6 +7793,8 @@ 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 { }; From 81e3df355a6ea9cf3af0565de9604eaee08ebafb Mon Sep 17 00:00:00 2001 From: Dmitry Kalinkin Date: Wed, 21 Jul 2021 00:51:37 -0400 Subject: [PATCH 3/4] pythonPackages.shellescape: init at 3.8.1 --- .../python-modules/shellescape/default.nix | 27 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 ++ 2 files changed, 29 insertions(+) create mode 100644 pkgs/development/python-modules/shellescape/default.nix diff --git a/pkgs/development/python-modules/shellescape/default.nix b/pkgs/development/python-modules/shellescape/default.nix new file mode 100644 index 000000000000..2d7309d88215 --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 8c5d9ecb1e53..52a2bbf83060 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -7938,6 +7938,8 @@ 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 { From 3f24366cdad97834f0662d5844996f9d439e82cc Mon Sep 17 00:00:00 2001 From: Dmitry Kalinkin Date: Wed, 21 Jul 2021 00:52:10 -0400 Subject: [PATCH 4/4] cwltool: init at 3.1.20210628163208 --- .../science/misc/cwltool/default.nix | 41 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 + 2 files changed, 43 insertions(+) create mode 100644 pkgs/applications/science/misc/cwltool/default.nix diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix new file mode 100644 index 000000000000..21e3c47b323d --- /dev/null +++ b/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 ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index ed1329180b20..ec1c177e2c5b 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -13403,6 +13403,8 @@ in inherit (llvmPackages_11) llvm libclang; }; + cwltool = callPackage ../applications/science/misc/cwltool { }; + dprint = callPackage ../development/tools/dprint { }; libcxx = llvmPackages.libcxx;