Merge pull request #130897 from veprbl/pr/toil

6 files changed, 136 insertions, 0 deletions

diff --git a/pkgs/applications/science/misc/toil/default.nix b/pkgs/applications/science/misc/toil/default.nix
new file mode 100644
index 000000000000..a25fbe7565ce
--- /dev/null
+++ b/pkgs/applications/science/misc/toil/default.nix
@@ -0,0 +1,39 @@
+{ lib, fetchFromGitHub, python3Packages }:
+
+python3Packages.buildPythonApplication rec {
+  pname = "toil";
+  version = "5.4.0";
+
+  src = python3Packages.fetchPypi {
+    inherit pname version;
+    sha256 = "73c0648828bd3610c07b7648dd06d6ec27efefdb09473bf01d05d91eb899c9fd";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "docker = " "docker = 'docker' #" \
+      --replace "addict = " "addict = 'addict' #"
+  '';
+
+  propagatedBuildInputs = with python3Packages; [
+    addict
+    docker
+    pytz
+    pyyaml
+    enlighten
+    psutil
+    python-dateutil
+    dill
+  ];
+  checkInputs = with python3Packages; [ pytestCheckHook ];
+
+  pytestFlagsArray = [ "src/toil/test" ];
+  pythonImportsCheck = [ "toil" ];
+
+  meta = with lib; {
+    homepage = "https://toil.ucsc-cgl.org/";
+    license = with licenses; [ asl20 ];
+    description = "Workflow engine written in pure Python";
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/development/python-modules/addict/default.nix b/pkgs/development/python-modules/addict/default.nix
new file mode 100644
index 000000000000..2bb531cff908
--- /dev/null
+++ b/pkgs/development/python-modules/addict/default.nix
@@ -0,0 +1,26 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "addict";
+  version = "2.4.0";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "b3b2210e0e067a281f5646c8c5db92e99b7231ea8b0eb5f74dbdf9e259d4e494";
+  };
+
+  checkInputs = [ pytestCheckHook ];
+
+  pythonImportsCheck = [ "addict" ];
+
+  meta = with lib; {
+    description = "Module that exposes a dictionary subclass that allows items to be set like attributes";
+    homepage = "https://github.com/mewwts/addict";
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/development/python-modules/enlighten/default.nix b/pkgs/development/python-modules/enlighten/default.nix
new file mode 100644
index 000000000000..8f58720bd264
--- /dev/null
+++ b/pkgs/development/python-modules/enlighten/default.nix
@@ -0,0 +1,37 @@
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+, blessed
+, prefixed
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "enlighten";
+  version = "1.10.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "3391916586364aedced5d6926482b48745e4948f822de096d32258ba238ea984";
+  };
+
+  propagatedBuildInputs = [
+    blessed
+    prefixed
+  ];
+  checkInputs = [ pytestCheckHook ];
+
+  pythonImportsCheck = [ "enlighten" ];
+  disabledTests =
+    # https://github.com/Rockhopper-Technologies/enlighten/issues/44
+    lib.optional stdenv.isDarwin "test_autorefresh"
+    ;
+
+  meta = with lib; {
+    description = "Enlighten Progress Bar for Python Console Apps";
+    homepage = "https://github.com/Rockhopper-Technologies/enlighten";
+    license = with licenses; [ mpl20 ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/development/python-modules/prefixed/default.nix b/pkgs/development/python-modules/prefixed/default.nix
new file mode 100644
index 000000000000..d5837fd90a1c
--- /dev/null
+++ b/pkgs/development/python-modules/prefixed/default.nix
@@ -0,0 +1,26 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, pytestCheckHook
+}:
+
+buildPythonPackage rec {
+  pname = "prefixed";
+  version = "0.3.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "ca48277ba5fa8346dd4b760847da930c7b84416387c39e93affef086add2c029";
+  };
+
+  checkInputs = [ pytestCheckHook ];
+
+  pythonImportsCheck = [ "prefixed" ];
+
+  meta = with lib; {
+    description = "Prefixed alternative numeric library";
+    homepage = "https://github.com/Rockhopper-Technologies/prefixed";
+    license = with licenses; [ mpl20 ];
+    maintainers = with maintainers; [ veprbl ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b64a5bb748ec..d8738ed9bf2e 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -14351,6 +14351,8 @@ in
 
   todoist-electron = callPackage ../applications/misc/todoist-electron { };
 
+  toil = callPackage ../applications/science/misc/toil { };
+
   travis = callPackage ../development/tools/misc/travis { };
 
   tree-sitter = callPackage ../development/tools/parsing/tree-sitter {
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index c4654534e6c9..0c5a7115e98b 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -199,6 +199,8 @@ in {
     inherit (pkgs.darwin.apple_sdk.frameworks) CoreFoundation Security;
   };
 
+  addict = callPackage ../development/python-modules/addict { };
+
   addic7ed-cli = callPackage ../development/python-modules/addic7ed-cli { };
 
   adext = callPackage ../development/python-modules/adext { };
@@ -2297,6 +2299,8 @@ in {
 
   enamlx = callPackage ../development/python-modules/enamlx { };
 
+  enlighten = callPackage ../development/python-modules/enlighten { };
+
   enocean = callPackage ../development/python-modules/enocean { };
 
   enrich = callPackage ../development/python-modules/enrich { };
@@ -5544,6 +5548,8 @@ in {
 
   precis-i18n = callPackage ../development/python-modules/precis-i18n { };
 
+  prefixed = callPackage ../development/python-modules/prefixed { };
+
   pre-commit = callPackage ../development/python-modules/pre-commit { };
 
   pre-commit-hooks = callPackage ../development/python-modules/pre-commit-hooks { };