From 7063e1fcd021ced81fdb988a71f9166cf2ca7874 Mon Sep 17 00:00:00 2001
From: "R. Ryantm" <ryantm-bot@ryantm.com>
Date: Sat, 13 Jan 2024 16:24:08 +0000
Subject: python311Packages.biopython: 1.82 -> 1.83

---
 pkgs/development/python-modules/biopython/default.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'pkgs')

diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index cb27d3231d4f3..c56584be69d5c 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -7,12 +7,12 @@
 
 buildPythonPackage rec {
   pname = "biopython";
-  version = "1.82";
+  version = "1.83";
   format = "setuptools";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-qbENlZroipdEqRxs42AfTIbn7EFnm8k8KfZ5IY9hZ7s=";
+    hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=";
   };
 
   disabled = !isPy3k;
-- 
cgit 1.4.1


From 5b9de10b9e440b82a9a682a844e3d1abf93f76fb Mon Sep 17 00:00:00 2001
From: natsukium <tomoya.otabi@gmail.com>
Date: Sun, 14 Jan 2024 11:24:25 +0900
Subject: python311Packages.biopython: enable tests and refactor

---
 .../python-modules/biopython/default.nix           | 27 ++++++++++++++++++----
 1 file changed, 22 insertions(+), 5 deletions(-)

(limited to 'pkgs')

diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index c56584be69d5c..96470da22491e 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -1,25 +1,42 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, pythonOlder
+, setuptools
 , numpy
-, isPy3k
 }:
 
 buildPythonPackage rec {
   pname = "biopython";
   version = "1.83";
-  format = "setuptools";
+  pyproject = true;
+
+  disabled = pythonOlder "3.9";
 
   src = fetchPypi {
     inherit pname version;
     hash = "sha256-eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=";
   };
 
-  disabled = !isPy3k;
+  nativeBuildInputs = [
+    setuptools
+  ];
 
   propagatedBuildInputs = [ numpy ];
-  # Checks try to write to $HOME, which does not work with nix
-  doCheck = false;
+
+  pythonImportsCheck = [
+    "Bio"
+  ];
+
+  checkPhase = ''
+    runHook preCheck
+
+    cd Tests
+    python run_tests.py --offline
+
+    runHook postCheck
+  '';
+
   meta = {
     description = "Python library for bioinformatics";
     longDescription = ''
-- 
cgit 1.4.1


From 56f6323e3d2191ae61da9add1c4135f5a24ab702 Mon Sep 17 00:00:00 2001
From: Weijia Wang <9713184+wegank@users.noreply.github.com>
Date: Sat, 20 Jan 2024 21:55:44 +0100
Subject: python311Packages.biopython: create home before testing

---
 pkgs/development/python-modules/biopython/default.nix | 1 +
 1 file changed, 1 insertion(+)

(limited to 'pkgs')

diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index 96470da22491e..2ec814f56aef0 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -31,6 +31,7 @@ buildPythonPackage rec {
   checkPhase = ''
     runHook preCheck
 
+    export HOME=$(mktemp -d)
     cd Tests
     python run_tests.py --offline
 
-- 
cgit 1.4.1