From a9b78d41d61d105c612697ee14fedf06ac2bb07b Mon Sep 17 00:00:00 2001
From: Gaetan Lepage <gaetan@glepage.com>
Date: Mon, 2 Mar 2026 00:03:49 +0000
Subject: [PATCH] python3Packages.biom-format: cleanup, fix build

---
 .../python-modules/biom-format/default.nix    | 32 +++++++++++++------
 1 file changed, 23 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/biom-format/default.nix b/pkgs/development/python-modules/biom-format/default.nix
index cb608eeb1d95..619917349882 100644
--- a/pkgs/development/python-modules/biom-format/default.nix
+++ b/pkgs/development/python-modules/biom-format/default.nix
@@ -2,13 +2,19 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  setuptools,
+
+  # build-system
   cython,
-  click,
   numpy,
-  scipy,
-  pandas,
+  setuptools,
+
+  # dependencies
+  click,
   h5py,
+  pandas,
+  scipy,
+
+  # tests
   pytestCheckHook,
 }:
 
@@ -24,18 +30,24 @@ buildPythonPackage (finalAttrs: {
     hash = "sha256-FjIC21LoqltixBstbbANByjTNxVm/3YCxdWaD9KbOQ0=";
   };
 
+  # https://numpy.org/doc/stable//release/2.4.0-notes.html#removed-numpy-in1d
+  postPatch = ''
+    substituteInPlace biom/table.py \
+      --replace-fail "np.in1d" "np.isin"
+  '';
+
   build-system = [
-    setuptools
     cython
     numpy
+    setuptools
   ];
 
   dependencies = [
     click
-    numpy
-    scipy
-    pandas
     h5py
+    numpy
+    pandas
+    scipy
   ];
 
   # make pytest resolve the package from $out
@@ -53,8 +65,10 @@ buildPythonPackage (finalAttrs: {
   pythonImportsCheck = [ "biom" ];
 
   meta = {
-    homepage = "http://biom-format.org/";
     description = "Biological Observation Matrix (BIOM) format";
+    homepage = "http://biom-format.org/";
+    downloadPage = "https://github.com/biocore/biom-format";
+    changelog = "https://github.com/biocore/biom-format/blob/${finalAttrs.src.tag}/ChangeLog.md";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ tomasajt ];
   };