From 5d11149ba6e12a089172fa70c2cfb0f8be722a68 Mon Sep 17 00:00:00 2001
From: bipin kumar <kbipinkumar@users.noreply.github.com>
Date: Sun, 14 May 2023 11:32:58 +0530
Subject: [PATCH] python-ncls: Set cython language_level to 3

---
 BioArchLinux/python-ncls/PKGBUILD      | 13 ++++++++++---
 BioArchLinux/python-ncls/cython3.patch | 18 ++++++++++++++++++
 2 files changed, 28 insertions(+), 3 deletions(-)
 create mode 100644 BioArchLinux/python-ncls/cython3.patch

diff --git a/BioArchLinux/python-ncls/PKGBUILD b/BioArchLinux/python-ncls/PKGBUILD
index 8ad307a01a..4a8f28d2ea 100644
--- a/BioArchLinux/python-ncls/PKGBUILD
+++ b/BioArchLinux/python-ncls/PKGBUILD
@@ -3,7 +3,7 @@
 pkgname=python-ncls
 _module=${pkgname#python-}
 pkgver=0.0.67
-pkgrel=2
+pkgrel=3
 pkgdesc="A wrapper for the nested containment list data structure"
 arch=('x86_64')
 url="https://github.com/biocore-ntnu/ncls"
@@ -23,13 +23,20 @@ makedepends=(
 
 options=(!emptydirs)
 source=("https://files.pythonhosted.org/packages/source/${_module::1}/$_module/$_module-$pkgver.tar.gz"
-        "LICENSE")
+        "LICENSE"
+        "cython3.patch")
 sha256sums=('fa3e673d60e97bb021a516287d74bb959870cf9d910ec82403b99c443d8f447e'
-            '48186409eb1721726d28884f40346a8380a893e95a50bef75584e2e9c2d4fcd5')
+            '48186409eb1721726d28884f40346a8380a893e95a50bef75584e2e9c2d4fcd5'
+            '174a620d7dce0952e9e657ff40f25e73f0f5a9e38c96fffc91ccbc20805a7ee4')
 
 prepare() {
     cp LICENSE "$_module-$pkgver"
+    cp cython3.patch "$_module-$pkgver"
     rm "$_module-$pkgver"/ncls/src/{fncls.c,ncls.c,ncls32.c}
+    # Set cython language_level to 3
+    cd "$_module-$pkgver"
+    patch -p1 < cython3.patch
+    
 }
 
 build() {
diff --git a/BioArchLinux/python-ncls/cython3.patch b/BioArchLinux/python-ncls/cython3.patch
new file mode 100644
index 0000000000..cb3a00865f
--- /dev/null
+++ b/BioArchLinux/python-ncls/cython3.patch
@@ -0,0 +1,18 @@
+--- a/setup.py	2023-05-14 00:15:53.983680836 +0530
++++ b/setup.py	2023-05-14 00:17:57.185420794 +0530
+@@ -63,12 +63,14 @@
+         "ncls.src.fncls", ["ncls/src/fncls.pyx", "ncls/src/fintervaldb.c"],
+         # define_macros=macros,
+         include_dirs=include_dirs)]
++for e in extensions:
++    e.cython_directives = {'language_level': "3"}
+ 
+ # using setuptools to cythonize if cython not found
+ # not recommended by cython docs, but still
+ try:
+     from Cython.Build import cythonize
+-    ext_modules = cythonize(extensions, language_level=2)
++    ext_modules = cythonize(extensions, compiler_directives={'language_level' : "3"})
+ except ImportError:
+     print()
+     print("Warning: Cannot compile with Cython. Using legacy build.")