Merge pull request #275882 from veprbl/pr/snakemake_8_0_1

snakemake: 7.32.4 -> 8.0.1

1 files changed, 22 insertions, 12 deletions

diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index 3acd66f790848..d279bd1e2cfd1 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -1,20 +1,28 @@
 { lib
 , fetchFromGitHub
 , python3
+, runtimeShell
 }:
 
 python3.pkgs.buildPythonApplication rec {
   pname = "snakemake";
-  version = "7.32.4";
+  version = "8.0.1";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-9KuMPqvM8ZCTuomc0R9MBxsK3KIpukDTrlwU6MHysK0=";
+    hash = "sha256-F4c/lgp7J6LLye+f3FpzaXz3zM7R+jXxTziPlVbxFxA=";
   };
 
+  postPatch = ''
+    patchShebangs --build tests/
+    patchShebangs --host snakemake/executors/jobscript.sh
+    substituteInPlace snakemake/shell.py \
+      --replace "/bin/sh" "${runtimeShell}"
+  '';
+
   propagatedBuildInputs = with python3.pkgs; [
     appdirs
     configargparse
@@ -23,6 +31,7 @@ python3.pkgs.buildPythonApplication rec {
     docutils
     gitpython
     humanfriendly
+    immutables
     jinja2
     jsonschema
     nbformat
@@ -32,6 +41,9 @@ python3.pkgs.buildPythonApplication rec {
     requests
     reretry
     smart-open
+    snakemake-interface-executor-plugins
+    snakemake-interface-common
+    snakemake-interface-storage-plugins
     stopit
     tabulate
     throttler
@@ -46,31 +58,29 @@ python3.pkgs.buildPythonApplication rec {
   # setup.
 
   nativeCheckInputs = with python3.pkgs; [
+    numpy
     pandas
     pytestCheckHook
     requests-mock
-    pillow
+    snakemake-executor-plugin-cluster-generic
   ];
 
   disabledTestPaths = [
-    "tests/test_slurm.py"
-    "tests/test_tes.py"
-    "tests/test_tibanna.py"
-    "tests/test_linting.py"
-    "tests/test_google_lifesciences.py"
-    "tests/test_conda_python_script/test_script.py"
+    "tests/test_conda_python_3_7_script/test_script.py"
   ];
 
   disabledTests = [
-    # Tests require network access
-    "test_github_issue1396"
-    "test_github_issue1460"
+    "test_deploy_sources"
   ];
 
   pythonImportsCheck = [
     "snakemake"
   ];
 
+  preCheck = ''
+    export HOME="$(mktemp -d)"
+  '';
+
   meta = with lib; {
     homepage = "https://snakemake.github.io";
     license = licenses.mit;