From fd230b25b24d5afdde61d7cfd1b944f7668076db Mon Sep 17 00:00:00 2001
From: Alexis Praga <alexis@praga.dev>
Date: Fri, 30 May 2025 17:57:23 +0200
Subject: [PATCH] multiqc: 1.28 -> 1.29

Polars is now a dependencies.
Running it with nix in some configuration fails to remove temporary
directories. Before skipping this step, it retries 10 times and doubles the waiting
time each time. We set max retries to 2.
---
 pkgs/by-name/mu/multiqc/package.nix | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/pkgs/by-name/mu/multiqc/package.nix b/pkgs/by-name/mu/multiqc/package.nix
index ca3c29e213ac..522870eca897 100644
--- a/pkgs/by-name/mu/multiqc/package.nix
+++ b/pkgs/by-name/mu/multiqc/package.nix
@@ -10,7 +10,7 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "multiqc";
-  version = "1.28";
+  version = "1.29";
 
   # Two data sources. One for the code, another for the test data
   srcs = [
@@ -19,7 +19,7 @@ python3Packages.buildPythonApplication rec {
       owner = "MultiQC";
       repo = "MultiQC";
       tag = "v${version}";
-      hash = "sha256-rYZaecoVAO1RE44XCw60aVwvWhKcZ/RrG3WpVRcLbuA=";
+      hash = "sha256-KKLdDNf889lEbCyNpJFZoE8rNO50CRzNP4hKpKHRAcE=";
     })
     (fetchFromGitHub {
       owner = "MultiQC";
@@ -30,6 +30,15 @@ python3Packages.buildPythonApplication rec {
     })
   ];
 
+  # Multiqc cannot remove temporary directories in some case.
+  # Default is 10 retries, lower it to 2
+  postPatch = ''
+    substituteInPlace multiqc/utils/util_functions.py \
+      --replace-fail \
+        "max_retries: int = 10," \
+        "max_retries: int = 2,"
+  '';
+
   sourceRoot = "multiqc";
 
   dependencies = with python3Packages; [
@@ -43,6 +52,7 @@ python3Packages.buildPythonApplication rec {
     numpy
     packaging
     requests
+    polars
     pillow
     plotly
     pyyaml