snakemake: 7.14.2 -> 7.25.3 (#230524)

4 files changed, 71 insertions, 8 deletions

diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index f162e2329a7..f3828176131 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -5,14 +5,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "snakemake";
-  version = "7.14.2";
+  version = "7.25.3";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-4XduybmDmlux3zvjbN1ouaJ1PkNO8h6vHuxgZ3YLBrw=";
+    hash = "sha256-KrstajTocVX5Tw7aiPoJ9vxJ0nKF+jqJcYJKrJvBt0Q=";
   };
 
   propagatedBuildInputs = with python3.pkgs; [
@@ -21,22 +21,20 @@ python3.pkgs.buildPythonApplication rec {
     connection-pool
     datrie
     docutils
-    filelock
     gitpython
+    humanfriendly
     jinja2
     jsonschema
     nbformat
-    networkx
     psutil
     pulp
-    pygraphviz
     pyyaml
-    ratelimiter
     requests
-    retry
+    reretry
     smart-open
     stopit
     tabulate
+    throttler
     toposort
     wrapt
     yte
@@ -44,7 +42,7 @@ python3.pkgs.buildPythonApplication rec {
 
   # See
   # https://github.com/snakemake/snakemake/blob/main/.github/workflows/main.yml#L99
-  # for the current basic test suite. Tibanna and Tes require extra
+  # for the current basic test suite. Slurm, Tibanna and Tes require extra
   # setup.
 
   nativeCheckInputs = with python3.pkgs; [
@@ -54,6 +52,7 @@ python3.pkgs.buildPythonApplication rec {
   ];
 
   disabledTestPaths = [
+    "tests/test_slurm.py"
     "tests/test_tes.py"
     "tests/test_tibanna.py"
     "tests/test_linting.py"
diff --git a/pkgs/development/python-modules/reretry/default.nix b/pkgs/development/python-modules/reretry/default.nix
new file mode 100644
index 00000000000..c4c6928af04
--- /dev/null
+++ b/pkgs/development/python-modules/reretry/default.nix
@@ -0,0 +1,18 @@
+{ lib, buildPythonPackage, fetchPypi }:
+
+buildPythonPackage rec {
+  pname = "reretry";
+  version = "0.11.8";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-8nkfzr5RLqLx0VOih0d4UjqAZIYLWRzZCvwhqL7UMuM=";
+  };
+
+  meta = with lib; {
+    description = "An easy to use retry decorator.";
+    homepage = "https://github.com/leshchenko1979/reretry";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ renatoGarcia ];
+  };
+}
diff --git a/pkgs/development/python-modules/throttler/default.nix b/pkgs/development/python-modules/throttler/default.nix
new file mode 100644
index 00000000000..2742cdaa293
--- /dev/null
+++ b/pkgs/development/python-modules/throttler/default.nix
@@ -0,0 +1,42 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pytestCheckHook
+, aiohttp
+, codecov
+, flake8
+, pytest
+, pytest-asyncio
+, pytest-cov
+}:
+
+buildPythonPackage rec {
+  pname = "throttler";
+  version = "1.2.2";
+
+  src = fetchFromGitHub {
+    owner = "uburuntu";
+    repo = pname;
+    rev = "refs/tags/v${version}";
+    hash = "sha256-fE35zPjBUn4e1VRkkIUMtYJ/+LbnUxnxyfnU+UEPwr4=";
+  };
+
+  checkInputs = [
+    aiohttp
+    codecov
+    flake8
+    pytest
+    pytest-asyncio
+    pytest-cov
+    pytestCheckHook
+  ];
+
+  pytestFlagsArray = [ "tests/" ];
+
+  meta = with lib; {
+    description = "Zero-dependency Python package for easy throttling with asyncio support.";
+    homepage = "https://github.com/uburuntu/throttler";
+    license = licenses.mit;
+    maintainers = with maintainers; [ renatoGarcia ];
+  };
+}
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 1df7f1a0dd0..1d848085781 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10366,6 +10366,8 @@ self: super: with self; {
 
   requirements-parser = callPackage ../development/python-modules/requirements-parser { };
 
+  reretry = callPackage ../development/python-modules/reretry { };
+
   resampy = callPackage ../development/python-modules/resampy { };
 
   resolvelib = callPackage ../development/python-modules/resolvelib { };
@@ -11881,6 +11883,8 @@ self: super: with self; {
 
   thriftpy2 = callPackage ../development/python-modules/thriftpy2 { };
 
+  throttler = callPackage ../development/python-modules/throttler { };
+
   thumborPexif = callPackage ../development/python-modules/thumborpexif { };
 
   tkinter = callPackage ../development/python-modules/tkinter {