Merge release-23.11 into staging-next-23.11

7 files changed, 143 insertions, 58 deletions

diff --git a/pkgs/development/python-modules/augeas/default.nix b/pkgs/development/python-modules/augeas/default.nix
index 6b70f3675268f..4872a4ac18d98 100644
--- a/pkgs/development/python-modules/augeas/default.nix
+++ b/pkgs/development/python-modules/augeas/default.nix
@@ -1,30 +1,36 @@
-{ stdenv, lib, buildPythonPackage, fetchFromGitHub, augeas, cffi }:
+{ lib
+, stdenv
+, fetchFromGitHub
+, buildPythonPackage
+, unittestCheckHook
+, pkg-config
+, augeas
+, cffi
+, pkgs # for libxml2
+}:
 buildPythonPackage rec {
     pname = "augeas";
-    version = "1.1.0";
+    version = "1.2.0";
 
     src = fetchFromGitHub {
       owner = "hercules-team";
       repo = "python-augeas";
       rev = "v${version}";
-      sha256 = "12q52ilcx059rn544x3712xq6myn99niz131l0fs3xx67456pajh";
+      hash = "sha256-Lq8ckra3sqN38zo1d5JsEq6U5TtLKRmqysoWNwR9J9A=";
     };
 
-    # TODO: not very nice!
-    postPatch =
-      let libname = "libaugeas${stdenv.hostPlatform.extensions.sharedLibrary}";
-      in
-      ''
-        substituteInPlace augeas/ffi.py \
-          --replace 'ffi.dlopen("augeas")' \
-                    'ffi.dlopen("${lib.makeLibraryPath [augeas]}/${libname}")'
-      '';
+    nativeBuildInputs = [ pkg-config ];
 
-    propagatedBuildInputs = [ cffi augeas ];
+    buildInputs = [ augeas pkgs.libxml2 ];
 
-    doCheck = false;
+    propagatedBuildInputs = [ cffi ];
+
+    nativeCheckInputs = [ unittestCheckHook ];
+
+    pythonImportsCheck = [ "augeas" ];
 
     meta = with lib; {
+      changelog = "https://github.com/hercules-team/python-augeas/releases/tag/v${version}";
       description = "Pure python bindings for augeas";
       homepage = "https://github.com/hercules-team/python-augeas";
       license = licenses.lgpl2Plus;
diff --git a/pkgs/development/python-modules/bitstring/default.nix b/pkgs/development/python-modules/bitstring/default.nix
index 55a6094c131bf..537905778ba3d 100644
--- a/pkgs/development/python-modules/bitstring/default.nix
+++ b/pkgs/development/python-modules/bitstring/default.nix
@@ -9,8 +9,8 @@
 
 buildPythonPackage rec {
   pname = "bitstring";
-  version = "4.1.2";
-  format = "pyproject";
+  version = "4.1.3";
+  pyproject = true;
 
   disabled = pythonOlder "3.7";
 
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "scott-griffiths";
     repo = pname;
     rev = "refs/tags/bitstring-${version}";
-    hash = "sha256-e4OnXwEuXz5m8d2PZOL5zDw8iGEzUg8LLk+xs/eGleA=";
+    hash = "sha256-RbHy36AnDlu/Ym5Ty2O9XfPj5xXd9hTgoClvISPoGBc=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/igraph/default.nix b/pkgs/development/python-modules/igraph/default.nix
index e85f78d4ca5a1..4aebfc1cecd1f 100644
--- a/pkgs/development/python-modules/igraph/default.nix
+++ b/pkgs/development/python-modules/igraph/default.nix
@@ -10,7 +10,7 @@
 
 buildPythonPackage rec {
   pname = "igraph";
-  version = "0.11.2";
+  version = "0.11.3";
 
   disabled = pythonOlder "3.8";
 
@@ -20,7 +20,7 @@ buildPythonPackage rec {
     owner = "igraph";
     repo = "python-igraph";
     rev = "refs/tags/${version}";
-    hash = "sha256-evYnUv2PWO+LbVBBQPa708dQb8Wq8SQ92bJ6clQNV/g=";
+    hash = "sha256-Pki0ygcQeuC5E4SwhzGX7oIe9LUSgoBKiXbtcpjL3ng=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/lpc-checksum/default.nix b/pkgs/development/python-modules/lpc-checksum/default.nix
new file mode 100644
index 0000000000000..2ebdba9fe095a
--- /dev/null
+++ b/pkgs/development/python-modules/lpc-checksum/default.nix
@@ -0,0 +1,38 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, poetry-core
+, pytestCheckHook
+, intelhex
+}:
+
+buildPythonPackage rec {
+  pname = "lpc-checksum";
+  version = "3.0.0";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "basilfx";
+    repo = "lpc_checksum";
+    rev = "v${version}";
+    hash = "sha256-POgV0BdkMLmdjBh/FToPPmJTAxsPASB7ZE32SqGGKHk=";
+  };
+
+  nativeBuildInputs = [
+    poetry-core
+    pytestCheckHook
+  ];
+
+  propagatedBuildInputs = [
+    intelhex
+  ];
+
+  pythonImportsCheck = [ "lpc_checksum" ];
+
+  meta = with lib; {
+    description = "Python script to calculate LPC firmware checksums";
+    homepage = "https://pypi.org/project/lpc-checksum/";
+    license = licenses.mit;
+    maintainers = with maintainers; [ otavio ];
+  };
+}
diff --git a/pkgs/development/python-modules/phik/default.nix b/pkgs/development/python-modules/phik/default.nix
index adf507cb048b3..bbc26de99cf74 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 = [
@@ -48,17 +50,20 @@ buildPythonPackage rec {
     pybind11
   ];
 
-  # uses setuptools to drive build process
+  nativeCheckInputs = [
+    pytestCheckHook
+    nbconvert
+    jupyter
+    jupyter-client
+  ];
+
+  # Uses setuptools to drive build process
   dontUseCmakeConfigure = true;
 
-  nativeBuildInputs = [
-    cmake
-    ninja
-    scikit-build
+  pythonImportsCheck = [
+    "phik"
   ];
 
-  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 ];
   };
 }
diff --git a/pkgs/development/python-modules/radios/default.nix b/pkgs/development/python-modules/radios/default.nix
index 047946b251759..73630f59fd3aa 100644
--- a/pkgs/development/python-modules/radios/default.nix
+++ b/pkgs/development/python-modules/radios/default.nix
@@ -8,26 +8,28 @@
 , awesomeversion
 , backoff
 , cachetools
+, mashumaro
+, orjson
 , pycountry
-, pydantic
 , yarl
+, aresponses
 , pytest-asyncio
 , pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "radios";
-  version = "0.1.1";
+  version = "0.3.0";
+  pyproject = true;
 
-  disabled = pythonOlder "3.9";
+  disabled = pythonOlder "3.11";
 
-  format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "frenck";
     repo = "python-radios";
     rev = "v${version}";
-    hash = "sha256-NCBch9MCWVD6ez0sIUph8rwOOzEMZtwC4atXJe53xZM=";
+    hash = "sha256-bzo+SA8kqc2GcxSV0TiIJyPVG+JshdsMoXSUhZYSphU=";
   };
 
   postPatch = ''
@@ -46,18 +48,22 @@ buildPythonPackage rec {
     awesomeversion
     backoff
     cachetools
+    mashumaro
+    orjson
     pycountry
-    pydantic
     yarl
   ];
 
   nativeCheckInputs = [
+    aresponses
     pytest-asyncio
     pytestCheckHook
   ];
 
   pythonImportsCheck = [ "radios" ];
 
+  __darwinAllowLocalNetworking = true;
+
   meta = with lib; {
     description = "Asynchronous Python client for the Radio Browser API";
     homepage = "https://github.com/frenck/python-radios";
diff --git a/pkgs/development/python-modules/uri-template/default.nix b/pkgs/development/python-modules/uri-template/default.nix
index db7dc602aea05..7bebffce194a3 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; [ ];
   };
 }