snakemake: 8.23.0 -> 8.29.0 (#385979)

Co-authored-by: emaryn <[email protected]>

Author: emaryn

pkgs/by-name/sn/snakemake/package.nix

@@ -1,21 +1,23 @@
 {
   lib,
   stdenv,
-  fetchPypi,
+  fetchFromGitHub,
   python3Packages,
   stress,
   versionCheckHook,
+  writableTmpDirAsHomeHook,
 }:
 
 python3Packages.buildPythonApplication rec {
   pname = "snakemake";
-  version = "8.23.0";
-
+  version = "8.29.0";
   pyproject = true;
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-XENI9VJW62KyrxDGSwQiygggYZOu9yW2QSNyp4BO9Us=";
+  src = fetchFromGitHub {
+    owner = "snakemake";
+    repo = "snakemake";
+    tag = "v${version}";
+    hash = "sha256-vGa0N5jbm+b4FH1rkvZI5yI005K0D5AP29JGK2wscps=";
   };
 
   postPatch = ''
@@ -25,11 +27,11 @@ python3Packages.buildPythonApplication rec {
       --replace-fail 'del os.environ["PYTHONPATH"]' "pass"
     substituteInPlace snakemake/unit_tests/__init__.py \
       --replace-fail '"unit_tests/templates"' '"'"$PWD"'/snakemake/unit_tests/templates"'
+    substituteInPlace snakemake/assets/__init__.py \
+      --replace-fail "raise err" "return bytes('err','ascii')"
   '';
 
-  build-system = with python3Packages; [
-    setuptools
-  ];
+  build-system = with python3Packages; [ setuptools ];
 
   dependencies = with python3Packages; [
     appdirs
@@ -68,17 +70,21 @@ python3Packages.buildPythonApplication rec {
   # for the current basic test suite. Slurm, Tibanna and Tes require extra
   # setup.
 
-  nativeCheckInputs = with python3Packages; [
-    numpy
-    pandas
-    pytestCheckHook
-    pytest-mock
-    requests-mock
-    snakemake-executor-plugin-cluster-generic
-    snakemake-storage-plugin-fs
-    stress
-    versionCheckHook
-  ];
+  nativeCheckInputs =
+    (with python3Packages; [
+      numpy
+      pandas
+      pytestCheckHook
+      pytest-mock
+      requests-mock
+      snakemake-executor-plugin-cluster-generic
+      snakemake-storage-plugin-fs
+      stress
+      versionCheckHook
+      polars
+    ])
+    ++ [ writableTmpDirAsHomeHook ];
+
   versionCheckProgramArg = [ "--version" ];
 
   pytestFlagsArray = [
@@ -140,13 +146,7 @@ python3Packages.buildPythonApplication rec {
       "test_scopes_submitted_to_cluster"
     ];
 
-  pythonImportsCheck = [
-    "snakemake"
-  ];
-
-  preCheck = ''
-    export HOME="$(mktemp -d)"
-  '';
+  pythonImportsCheck = [ "snakemake" ];
 
   meta = {
     homepage = "https://snakemake.github.io";