From b44ebb5f50ff851a80a6c6d5208e77150aaf2d3d Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sat, 25 Nov 2023 09:19:55 +0100
Subject: [PATCH 1/2] python311Packages.uri-template: 1.2.0 -> 1.3.0

Diff: https://github.com/plinss/uri_template/compare/refs/tags/v1.2.0...v1.3.0
(cherry picked from commit 6011769ece3bd2b43bf9763a3bd2a54e2d930383)
---
 .../python-modules/uri-template/default.nix   | 33 ++++++++++++++-----
 1 file changed, 24 insertions(+), 9 deletions(-)

diff --git a/pkgs/development/python-modules/uri-template/default.nix b/pkgs/development/python-modules/uri-template/default.nix
index db7dc602aea0..7bebffce194a 100644
--- a/pkgs/development/python-modules/uri-template/default.nix
+++ b/pkgs/development/python-modules/uri-template/default.nix
@@ -1,30 +1,45 @@
-{ lib, buildPythonPackage, fetchFromGitHub, python }:
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, python
+, pythonOlder
+, setuptools
+, setuptools-scm
+}:
 
 buildPythonPackage rec {
   pname = "uri-template";
-  version = "1.2.0";
+  version = "1.3.0";
+  pyproject = true;
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "plinss";
     repo = "uri_template";
-    rev = "v${version}";
-    hash = "sha256-IAq6GpEwimq45FU0QugLZLSOhwAmC1KbpZKD0zyxsUs=";
+    rev = "refs/tags/v${version}";
+    hash = "sha256-38HFFqM6yfpsPrhIpE639ePy/NbLqKw7gbnE3y8sL3w=";
   };
 
-  postPatch = ''
-    sed -i -e 's/0.0.0/${version}/' setup.py
-  '';
+  env.SETUPTOOLS_SCM_PRETEND_VERSION = version;
+
+  nativeBuildInputs = [
+    setuptools
+    setuptools-scm
+  ];
 
   checkPhase = ''
     ${python.interpreter} test.py
   '';
 
-  pythonImportsCheck = [ "uri_template" ];
+  pythonImportsCheck = [
+    "uri_template"
+  ];
 
   meta = with lib; {
     description = "An implementation of RFC 6570 URI Templates";
     homepage = "https://github.com/plinss/uri_template/";
     license = licenses.mit;
-    maintainers = [];
+    maintainers = with maintainers; [ ];
   };
 }

From 937edb6590d2977a6f59eab7694ce33ea95c477b Mon Sep 17 00:00:00 2001
From: Fabian Affolter <mail@fabian-affolter.ch>
Date: Sat, 25 Nov 2023 12:17:31 +0100
Subject: [PATCH 2/2] python311Packages.phik: refactor, disable failing tests

(cherry picked from commit fc1c549b56d95855891e2ac3a64bf9468cd2f7e8)
---
 .../python-modules/phik/default.nix           | 70 ++++++++++++-------
 1 file changed, 45 insertions(+), 25 deletions(-)

diff --git a/pkgs/development/python-modules/phik/default.nix b/pkgs/development/python-modules/phik/default.nix
index adf507cb048b..bbc26de99cf7 100644
--- a/pkgs/development/python-modules/phik/default.nix
+++ b/pkgs/development/python-modules/phik/default.nix
@@ -2,27 +2,29 @@
 , buildPythonPackage
 , cmake
 , fetchFromGitHub
-, isPy3k
-, pytestCheckHook
-, nbconvert
 , joblib
 , jupyter
 , jupyter-client
-, numpy
-, scipy
-, pandas
 , matplotlib
+, nbconvert
 , ninja
 , numba
+, numpy
+, pandas
 , pybind11
+, pytestCheckHook
+, pythonOlder
 , scikit-build
+, scipy
+, setuptools
 }:
 
 buildPythonPackage rec {
   pname = "phik";
   version = "0.12.3";
-  disabled = !isPy3k;
-  format = "pyproject";
+  pyproject = true;
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "KaveIO";
@@ -31,11 +33,11 @@ buildPythonPackage rec {
     hash = "sha256-9o3EDhgmne2J1QfzjjNQc1mUcyCzoVrCnWXqjWkiZU0=";
   };
 
-  nativeCheckInputs = [
-    pytestCheckHook
-    nbconvert
-    jupyter
-    jupyter-client
+  nativeBuildInputs = [
+    cmake
+    ninja
+    scikit-build
+    setuptools
   ];
 
   propagatedBuildInputs = [
@@ -48,16 +50,19 @@ buildPythonPackage rec {
     pybind11
   ];
 
-  # uses setuptools to drive build process
-  dontUseCmakeConfigure = true;
-
-  nativeBuildInputs = [
-    cmake
-    ninja
-    scikit-build
+  nativeCheckInputs = [
+    pytestCheckHook
+    nbconvert
+    jupyter
+    jupyter-client
   ];
 
-  pythonImportsCheck = [ "phik" ];
+  # Uses setuptools to drive build process
+  dontUseCmakeConfigure = true;
+
+  pythonImportsCheck = [
+    "phik"
+  ];
 
   postInstall = ''
     rm -r $out/bin
@@ -68,12 +73,27 @@ buildPythonPackage rec {
     rm -r phik
   '';
 
+  disabledTests = [
+    # TypeError: 'numpy.float64' object cannot be interpreted as an integer
+    # https://github.com/KaveIO/PhiK/issues/73
+    "test_significance_matrix_hybrid"
+    "test_significance_matrix_mc"
+  ];
+
+  disabledTestPaths = [
+    # Don't test integrations
+    "tests/phik_python/integration/"
+  ];
+
   meta = with lib; {
     description = "Phi_K correlation analyzer library";
-    longDescription = "Phi_K is a new and practical correlation coefficient based on several refinements to Pearson’s hypothesis test of independence of two variables.";
-    homepage = "https://phik.readthedocs.io/en/latest/";
-    changelog = "https://github.com/KaveIO/PhiK/blob/${src.rev}/CHANGES.rst";
-    maintainers = with maintainers; [ melsigl ];
+    longDescription = ''
+      Phi_K is a new and practical correlation coefficient based on several refinements to
+      Pearson’s hypothesis test of independence of two variables.
+    '';
+    homepage = "https://phik.readthedocs.io/";
+    changelog = "https://github.com/KaveIO/PhiK/blob/${version}/CHANGES.rst";
     license = licenses.asl20;
+    maintainers = with maintainers; [ melsigl ];
   };
 }