From 694e98f8a61f86fa723503e114b6fcb38d863595 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Thu, 13 Jan 2022 21:35:50 +0100
Subject: [PATCH 1/2] python3Packages.py-tes: init at 0.4.2

---
 .../python-modules/py-tes/default.nix         | 49 +++++++++++++++++++
 pkgs/top-level/python-packages.nix            |  2 +
 2 files changed, 51 insertions(+)
 create mode 100644 pkgs/development/python-modules/py-tes/default.nix

diff --git a/pkgs/development/python-modules/py-tes/default.nix b/pkgs/development/python-modules/py-tes/default.nix
new file mode 100644
index 000000000000..633dc6fa5f4a
--- /dev/null
+++ b/pkgs/development/python-modules/py-tes/default.nix
@@ -0,0 +1,49 @@
+{ lib
+, attrs
+, buildPythonPackage
+, fetchFromGitHub
+, future
+, python-dateutil
+, pytestCheckHook
+, pythonOlder
+, requests
+, requests-mock
+}:
+
+buildPythonPackage rec {
+  pname = "py-tes";
+  version = "0.4.2";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
+
+  src = fetchFromGitHub {
+    owner = "ohsu-comp-bio";
+    repo = pname;
+    rev = version;
+    hash = "sha256-HZeyCQHiqfdquWQD5axS73JDjDMUieONwm5VyA+vTFk=";
+  };
+
+  propagatedBuildInputs = [
+    attrs
+    future
+    python-dateutil
+    requests
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+    requests-mock
+  ];
+
+  pythonImportsCheck = [
+    "tes"
+  ];
+
+  meta = with lib; {
+    description = "Python SDK for the GA4GH Task Execution API";
+    homepage = "https://github.com/ohsu-comp-bio/py-tes";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ fab ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 7a82697055ab..004191d9382f 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -6398,6 +6398,8 @@ in {
 
   py-synologydsm-api = callPackage ../development/python-modules/py-synologydsm-api { };
 
+  py-tes = callPackage ../development/python-modules/py-tes { };
+
   py-ubjson = callPackage ../development/python-modules/py-ubjson { };
 
   py-zabbix = callPackage ../development/python-modules/py-zabbix { };

From 32003c3051f73892f5e465d0eb80f3d438e5dde2 Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Thu, 13 Jan 2022 21:37:08 +0100
Subject: [PATCH 2/2] toil: 5.4.0 -> 5.6.0

---
 .../science/misc/toil/default.nix             | 39 +++++++++++--------
 1 file changed, 23 insertions(+), 16 deletions(-)

diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix
index a25fbe7565ce..b13ad0ad10ca 100644
--- a/pkgs/applications/science/misc/toil/default.nix
+++ b/pkgs/applications/science/misc/toil/default.nix
@@ -1,39 +1,46 @@
-{ lib, fetchFromGitHub, python3Packages }:
+{ lib
+, fetchFromGitHub
+, python3
+}:
 
-python3Packages.buildPythonApplication rec {
+python3.pkgs.buildPythonApplication rec {
   pname = "toil";
-  version = "5.4.0";
+  version = "5.6.0";
+  format = "setuptools";
 
-  src = python3Packages.fetchPypi {
+  src = python3.pkgs.fetchPypi {
     inherit pname version;
-    sha256 = "73c0648828bd3610c07b7648dd06d6ec27efefdb09473bf01d05d91eb899c9fd";
+    sha256 = "sha256-m6tzrRCCLULO+wB8htUlt0KESLm/vdIeTzBrihnAo/I=";
   };
 
-  postPatch = ''
-    substituteInPlace setup.py \
-      --replace "docker = " "docker = 'docker' #" \
-      --replace "addict = " "addict = 'addict' #"
-  '';
-
-  propagatedBuildInputs = with python3Packages; [
+  propagatedBuildInputs = with python3.pkgs; [
     addict
     docker
     pytz
     pyyaml
     enlighten
     psutil
+    py-tes
     python-dateutil
     dill
   ];
-  checkInputs = with python3Packages; [ pytestCheckHook ];
 
-  pytestFlagsArray = [ "src/toil/test" ];
-  pythonImportsCheck = [ "toil" ];
+  checkInputs = with python3.pkgs; [
+    pytestCheckHook
+  ];
+
+  pytestFlagsArray = [
+    "src/toil/test"
+  ];
+
+  pythonImportsCheck = [
+    "toil"
+  ];
 
   meta = with lib; {
+    description = "Workflow engine written in pure Python";
     homepage = "https://toil.ucsc-cgl.org/";
     license = with licenses; [ asl20 ];
-    description = "Workflow engine written in pure Python";
     maintainers = with maintainers; [ veprbl ];
   };
 }