NixOS · mweinelt · Jun 24, 2024 · Jun 19, 2024 · Jun 19, 2024 · Jun 19, 2024
diff --git a/pkgs/applications/networking/mailreaders/alot/default.nix b/pkgs/applications/networking/mailreaders/alot/default.nix
@@ -1,5 +1,5 @@
 { lib
-, python3
+, python311
 , fetchFromGitHub
 , file
 , gnupg
@@ -9,7 +9,7 @@
 , withManpage ? false
 }:
 
-with python3.pkgs; buildPythonApplication rec {
+with python311.pkgs; buildPythonApplication rec {
   pname = "alot";
   version = "0.10";
 

diff --git a/pkgs/applications/office/libreoffice/default.nix b/pkgs/applications/office/libreoffice/default.nix
@@ -1,8 +1,9 @@
 { stdenv
 , fetchurl
+, fetchpatch2
 , lib
 , pam
-, python3
+, python311
 , libxslt
 , perl
 , perlPackages
@@ -244,6 +245,11 @@ in stdenv.mkDerivation (finalAttrs: {
     # - the remaining tests have notes in the patch
     # FIXME: get rid of this ASAP
     ./skip-broken-tests.patch
+    (fetchpatch2 {
+      name = "icu74-compat.patch";
+      url = "https://gitlab.archlinux.org/archlinux/packaging/packages/libreoffice-fresh/-/raw/main/libreoffice-7.5.8.2-icu-74-compatibility.patch?ref_type=heads.patch";
+      hash = "sha256-OGBPIVQj8JTYlkKywt4QpH7ULAzKmet5jTLztGpIS0Y=";
+    })
   ] ++ lib.optionals (variant == "still") [
     # Remove build config to reduce the amount of `-dev` outputs in the
     # runtime closure. This behavior was introduced by upstream in commit
@@ -372,7 +378,7 @@ in stdenv.mkDerivation (finalAttrs: {
     perl
     poppler
     postgresql
-    python3
+    python311
     sane-backends
     unixODBC
     unzip

diff --git a/pkgs/applications/science/biology/macs2/default.nix b/pkgs/applications/science/biology/macs2/default.nix
@@ -1,9 +1,11 @@
-{ lib, python3, fetchpatch, fetchPypi }:
+{ lib, python311, fetchpatch, fetchPypi }:
 
-python3.pkgs.buildPythonPackage rec {
+# pin python311 because macs2 does not support python 3.12
+# https://github.com/macs3-project/MACS/issues/598#issuecomment-1812622572
+python311.pkgs.buildPythonPackage rec {
   pname = "macs2";
   version = "2.2.9.1";
-  format = "pyproject";
+  pyproject = true;
 
   src = fetchPypi {
     pname = lib.toUpper pname;
@@ -20,20 +22,19 @@ python3.pkgs.buildPythonPackage rec {
     })
   ];
 
-  nativeBuildInputs = with python3.pkgs; [
+  build-system = with python311.pkgs; [
     cython_0
     numpy
     setuptools
-    wheel
   ];
 
-  propagatedBuildInputs = with python3.pkgs; [
+  dependencies = with python311.pkgs; [
     numpy
   ];
 
   __darwinAllowLocalNetworking = true;
 
-  nativeCheckInputs = with python3.pkgs; [
+  nativeCheckInputs = with python311.pkgs; [
     unittestCheckHook
   ];
 

diff --git a/pkgs/applications/version-management/commitizen/default.nix b/pkgs/applications/version-management/commitizen/default.nix
@@ -24,6 +24,7 @@ python3.pkgs.buildPythonApplication rec {
   };
 
   pythonRelaxDeps = [
+    "argcomplete"
     "decli"
   ];
 

diff --git a/pkgs/by-name/fl/flye/aarch64-fix.patch b/pkgs/by-name/fl/flye/aarch64-fix.patch
diff --git a/pkgs/by-name/fl/flye/package.nix b/pkgs/by-name/fl/flye/package.nix
@@ -1,5 +1,6 @@
 { lib
 , fetchFromGitHub
+, fetchpatch
 , python3Packages
 , zlib
 , curl
@@ -11,6 +12,7 @@
 python3Packages.buildPythonApplication rec {
   pname = "flye";
   version = "2.9.4";
+  pyproject = true;
 
   src = fetchFromGitHub {
     owner = "fenderglass";
@@ -19,7 +21,33 @@ python3Packages.buildPythonApplication rec {
     hash = "sha256-lwiY0VTEsLMMXt1VowsS3jj44v30Z766xNRwQtQKr10=";
   };
 
-  nativeCheckInputs = [ python3Packages.pytestCheckHook ];
+  patches = [
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/691
+      name = "aarch64-fix.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/e4dcc3fdf0fa1430a974fcd7da31b03ea642df9b.patch";
+      hash = "sha256-Ny2daPt8eYOKnwZ6bdBoCcFWhe9eiIHF4vJU/occwU0=";
+    })
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/711
+      name = "remove-distutils.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/fb34f1ccfdf569d186a4ce822ee18eced736636b.patch";
+      hash = "sha256-52bnZ8XyP0HsY2OpNYMU3xJgotNVdQc/O2w3XIReUdQ=";
+    })
+    (fetchpatch {
+      # https://github.com/mikolmogorov/Flye/pull/670
+      name = "remove-find_module.patch";
+      url = "https://github.com/mikolmogorov/Flye/commit/441b1c6eb0f60b7c4fb1a40d659c7dabb7ad41b6.patch";
+      hash = "sha256-RytFIN1STK33/nvXpck6woQcwV/e1fmA8AgmptiIiDU=";
+    })
+  ];
+
+  postPatch = ''
+    substituteInPlace flye/polishing/alignment.py \
+      --replace-fail "/bin/bash" "${lib.getExe bash}"
+  '';
+
+  build-system = [ python3Packages.setuptools ];
 
   propagatedBuildInputs = [ coreutils ];
 
@@ -29,22 +57,18 @@ python3Packages.buildPythonApplication rec {
     libdeflate
   ];
 
-  patches = [ ./aarch64-fix.patch ];
+  pythonImportsCheck = [ "flye" ];
 
-  postPatch = ''
-    substituteInPlace flye/polishing/alignment.py \
-      --replace-fail "/bin/bash" "${lib.getExe bash}"
+  nativeCheckInputs = [ python3Packages.pytestCheckHook ];
 
-    substituteInPlace flye/tests/test_toy.py \
-      --replace-fail "find_executable(\"flye" "find_executable(\"$out/bin/flye" \
-      --replace-fail "[\"flye" "[\"$out/bin/flye"
+  preCheck = ''
+    export PATH=$out/bin:$PATH
   '';
 
   meta = with lib; {
     description = "De novo assembler for single molecule sequencing reads using repeat graphs";
     homepage = "https://github.com/fenderglass/Flye";
     license = licenses.bsd3;
-    platforms = platforms.unix;
     mainProgram = "flye";
     maintainers = with maintainers; [ assistant ];
   };

diff --git a/pkgs/by-name/fr/fritz-exporter/package.nix b/pkgs/by-name/fr/fritz-exporter/package.nix
@@ -20,6 +20,10 @@ python3.pkgs.buildPythonApplication rec {
     sed -i "/^addopts/d" pyproject.toml
   '';
 
+  pythonRelaxDeps = [
+    "defusedxml"
+  ];
+
   nativeBuildInputs = with python3.pkgs; [
     poetry-core
   ];

diff --git a/pkgs/by-name/ha/hatch/package.nix b/pkgs/by-name/ha/hatch/package.nix
@@ -4,26 +4,23 @@
 , python3
 , cargo
 , git
+, uv
 }:
 
 python3.pkgs.buildPythonApplication rec {
   pname = "hatch";
-  version = "1.9.7";
+  version = "1.12.0";
   format = "pyproject";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-Gae4IXn5Tyrd2612qn5lq5DK1VqxA9U4J2N5NcnmYkw=";
+    hash = "sha256-roBHjRAxLfK0TWWck7wu1NM67N3OS3Y3gjG9+ByL9q0=";
   };
 
-  postPatch = ''
-    # Loosen hatchling runtime version dependency
-    sed -i 's/hatchling<1.22/hatchling/' pyproject.toml
-  '';
-
   nativeBuildInputs = with python3.pkgs; [
     hatchling
     hatch-vcs
+    uv
   ];
 
   propagatedBuildInputs = with python3.pkgs; [
@@ -62,25 +59,15 @@ python3.pkgs.buildPythonApplication rec {
   disabledTests = [
     # AssertionError: assert (1980, 1, 2, 0, 0, 0) == (2020, 2, 2, 0, 0, 0)
     "test_default"
-    "test_explicit_path"
-    "test_default_auto_detection"
-    "test_editable_default"
-    "test_editable_default_extra_dependencies"
-    "test_editable_default_force_include"
-    "test_editable_default_force_include_option"
-    "test_editable_exact"
-    "test_editable_exact_extra_dependencies"
-    "test_editable_exact_force_include"
-    "test_editable_exact_force_include_option"
-    "test_editable_exact_force_include_build_data_precedence"
-    "test_editable_pth"
-    # expects sh, finds bash
-    "test_all"
-    "test_already_installed_update_flag"
-    "test_already_installed_update_prompt"
     # Loosen hatchling runtime version dependency
     "test_core"
-    "test_correct"
+    # New failing
+    "test_guess_variant"
+    "test_open"
+    "test_no_open"
+    "test_uv_env"
+    "test_pyenv"
+    "test_pypirc"
   ] ++ lib.optionals stdenv.isDarwin [
     # https://github.com/NixOS/nixpkgs/issues/209358
     "test_scripts_no_environment"

diff --git a/pkgs/by-name/se/selenium-manager/package.nix b/pkgs/by-name/se/selenium-manager/package.nix
@@ -7,18 +7,18 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "selenium-manager";
-  version = "4.18.1";
+  version = "4.22.0";
 
   src = fetchFromGitHub {
     owner = "SeleniumHQ";
     repo = "selenium";
     rev = "selenium-${version}";
-    hash = "sha256-1C9Epsk9rFlShxHGGzbWl6smrMzPn2h3yCWlzUIMpY8=";
+    hash = "sha256-qBuZgI5SSBwxbSBrAT0W/HzzV2JmPL00hPJ6s57QTeg=";
   };
 
   sourceRoot = "${src.name}/rust";
 
-  cargoHash = "sha256-BystESOFIitw3ER2K1TPOf5luOBvKXFuqc/unL93yRY=";
+  cargoHash = "sha256-1CPUOAfBfUeZt5S8t5SM3oyrNwXKHplhHG5idVy4YrE=";
 
   buildInputs = lib.optionals stdenv.isDarwin [
     darwin.apple_sdk.frameworks.SystemConfiguration

diff --git a/pkgs/development/embedded/platformio/core.nix b/pkgs/development/embedded/platformio/core.nix
@@ -46,6 +46,9 @@ with python3Packages; buildPythonApplication rec {
   postPatch = ''
     # Disable update checks at runtime
     substituteInPlace platformio/maintenance.py --replace-fail '    check_platformio_upgrade()' ""
+
+    # Remove filterwarnings which fails on new deprecations in Python 3.12 for 3.14
+    rm tox.ini
   '';
 
   nativeBuildInputs = [

diff --git a/pkgs/development/interpreters/python/default.nix b/pkgs/development/interpreters/python/default.nix
@@ -16,14 +16,14 @@
   passthruFun = import ./passthrufun.nix args;
 
   sources = {
-    python311 = {
+    python312 = {
       sourceVersion = {
         major = "3";
-        minor = "11";
-        patch = "9";
+        minor = "12";
+        patch = "4";
         suffix = "";
       };
-      hash = "sha256-mx6JZSP8UQaREmyGRAbZNgo9Hphqy9pZzaV7Wr2kW4c=";
+      hash = "sha256-9tQZpth0OrJnAIAbSQjSbZfouYbhT5XeMbMt4rDnlVQ=";
     };
   };
 
@@ -68,25 +68,25 @@ in {
     inherit passthruFun;
   };
 
-  python311 = callPackage ./cpython ({
+  python311 = callPackage ./cpython {
     self = __splicedPackages.python311;
-    inherit (darwin) configd;
-    inherit passthruFun;
-  } // sources.python311);
-
-  python312 = callPackage ./cpython {
-    self = __splicedPackages.python312;
     sourceVersion = {
       major = "3";
-      minor = "12";
-      patch = "4";
+      minor = "11";
+      patch = "9";
       suffix = "";
     };
-    hash = "sha256-9tQZpth0OrJnAIAbSQjSbZfouYbhT5XeMbMt4rDnlVQ=";
+    hash = "sha256-mx6JZSP8UQaREmyGRAbZNgo9Hphqy9pZzaV7Wr2kW4c=";
     inherit (darwin) configd;
     inherit passthruFun;
   };
 
+  python312 = callPackage ./cpython ({
+    self = __splicedPackages.python312;
+    inherit (darwin) configd;
+    inherit passthruFun;
+  } // sources.python312);
+
   python313 = callPackage ./cpython {
     self = __splicedPackages.python313;
     sourceVersion = {
@@ -123,7 +123,7 @@ in {
     enableOptimizations = false;
     enableLTO = false;
     mimetypesSupport = false;
-  } // sources.python311)).overrideAttrs(old: {
+  } // sources.python312)).overrideAttrs(old: {
     # TODO(@Artturin): Add this to the main cpython expr
     strictDeps = true;
     pname = "python3-minimal";

diff --git a/pkgs/development/interpreters/python/update-python-libraries/update-python-libraries.py b/pkgs/development/interpreters/python/update-python-libraries/update-python-libraries.py
@@ -319,14 +319,17 @@ def get_prefix(string):
             tag_url = str(release["tarball_url"]).replace(
                 "tarball", "tarball/refs/tags"
             )
-            hash = (
-                subprocess.check_output(
-                    ["nix-prefetch-url", "--type", "sha256", "--unpack", tag_url],
-                    stderr=subprocess.DEVNULL,
+            try:
+                hash = (
+                    subprocess.check_output(
+                        ["nix-prefetch-url", "--type", "sha256", "--unpack", tag_url],
+                        stderr=subprocess.DEVNULL,
+                    )
+                    .decode("utf-8")
+                    .strip()
                 )
-                .decode("utf-8")
-                .strip()
-            )
+            except subprocess.CalledProcessError:
+                raise ValueError("nix-prefetch-url failed")
 
     return version, hash, prefix
 

diff --git a/pkgs/development/libraries/gobject-introspection/default.nix b/pkgs/development/libraries/gobject-introspection/default.nix
@@ -33,6 +33,7 @@ let
   pythonModules = pp: [
     pp.mako
     pp.markdown
+    pp.setuptools
   ];
 
   # https://discourse.gnome.org/t/dealing-with-glib-and-gobject-introspection-circular-dependency/18701
-Original file line number
+Diff line change
@@ Expand Up / @@ -24,6 +24,7 @@ python3.pkgs.buildPythonApplication rec { @@
       };
       pythonRelaxDeps = [
+        "argcomplete"
         "decli"
       ];
@@ Expand Down @@