From 19b95bf2c32f3a21beb079e5839b0304400e745c Mon Sep 17 00:00:00 2001
From: SkohTV <contact@skoh.dev>
Date: Wed, 6 May 2026 18:21:36 -0400
Subject: [PATCH] python3Packages.cnvkit: 0.9.12 -> 0.9.13

---
 .../python-modules/cnvkit/default.nix         | 23 +++++++++----------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/pkgs/development/python-modules/cnvkit/default.nix b/pkgs/development/python-modules/cnvkit/default.nix
index eb6375367297..7007cbcabd7d 100644
--- a/pkgs/development/python-modules/cnvkit/default.nix
+++ b/pkgs/development/python-modules/cnvkit/default.nix
@@ -12,6 +12,7 @@
   pandas,
   pomegranate,
   pyfaidx,
+  pyparsing,
   pysam,
   reportlab,
   rPackages,
@@ -24,27 +25,29 @@
 }:
 buildPythonPackage rec {
   pname = "cnvkit";
-  version = "0.9.12";
+  version = "0.9.13";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "etal";
     repo = "cnvkit";
     tag = "v${version}";
-    hash = "sha256-ZdE3EUNZpEXRHTRKwVhuj3BWQWczpdFbg4pVr0+AHiQ=";
+    hash = "sha256-6W0rJUeHO7m3zacgkL3WzyFVmdet1zJAGyafsQv1AXE=";
   };
 
   patches = [
+    # test: update a call to --smooth-bootstrap[=int, now]
     (fetchpatch {
-      name = "fix-numpy2-compat";
-      url = "https://github.com/etal/cnvkit/commit/5cb6aeaf40ea5572063cf9914c456c307b7ddf7a.patch";
-      hash = "sha256-VwGAMGKuX2Kx9xL9GX/PB94/7LkT0dSLbWIfVO8F9NI=";
+      url = "https://github.com/etal/cnvkit/commit/c5c7c06b7fb873ed7ae44593c11a91d45f433e54.patch";
+      hash = "sha256-H9Nr4JL7bc9CQ/BmXkOAwjbr/ykvbnjyyWrVSrVH9kg=";
     })
   ];
 
   pythonRelaxDeps = [
     # https://github.com/etal/cnvkit/issues/815
     "pomegranate"
+    # https://github.com/etal/cnvkit/pull/1048
+    "pyparsing"
   ];
 
   nativeBuildInputs = [
@@ -59,13 +62,8 @@ buildPythonPackage rec {
     let
       rscript = lib.getExe' R "Rscript";
     in
-    # Numpy 2 compatibility
-    ''
-      substituteInPlace skgenome/intersect.py \
-        --replace-fail "np.string_" "np.bytes_"
-    ''
     # Patch shebang lines in R scripts
-    + ''
+    ''
       substituteInPlace cnvlib/segmentation/flasso.py \
         --replace-fail "#!/usr/bin/env Rscript" "#!${rscript}"
 
@@ -73,7 +71,7 @@ buildPythonPackage rec {
         --replace-fail "#!/usr/bin/env Rscript" "#!${rscript}"
 
       substituteInPlace cnvlib/segmentation/__init__.py \
-        --replace-fail 'rscript_path="Rscript"' 'rscript_path="${rscript}"'
+        --replace-fail 'rscript_path: str = "Rscript"' 'rscript_path="${rscript}"'
 
       substituteInPlace cnvlib/commands.py \
         --replace-fail 'default="Rscript"' 'default="${rscript}"'
@@ -87,6 +85,7 @@ buildPythonPackage rec {
     pandas
     pomegranate
     pyfaidx
+    pyparsing
     pysam
     reportlab
     rPackages.DNAcopy