Merge 4a3faa5e86f524d955186f05a762b6bcec01cb94 into haskell-updates

14 files changed, 309 insertions, 52 deletions

diff --git a/pkgs/development/python-modules/bindep/default.nix b/pkgs/development/python-modules/bindep/default.nix
index 7feb91d8d971..99eca088b2ab 100644
--- a/pkgs/development/python-modules/bindep/default.nix
+++ b/pkgs/development/python-modules/bindep/default.nix
@@ -11,18 +11,17 @@
 
 buildPythonPackage rec {
   pname = "bindep";
-  version = "2.11.0";
+  version = "2.12.0";
   pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-rLLyWbzh/RUIhzR5YJu95bmq5Qg3hHamjWtqGQAufi8=";
+    hash = "sha256-wGtR5tC6OWWq2PPCXwpXS+D4AboHyxp4SV2olUZ952A=";
   };
 
   env.PBR_VERSION = version;
 
   build-system = [
-    distro
     pbr
     setuptools
   ];
@@ -41,7 +40,7 @@ buildPythonPackage rec {
 
   meta = with lib; {
     description = "Bindep is a tool for checking the presence of binary packages needed to use an application / library";
-    homepage = "https://docs.opendev.org/opendev/bindep/latest/";
+    homepage = "https://opendev.org/opendev/bindep";
     license = licenses.asl20;
     mainProgram = "bindep";
     maintainers = teams.openstack.members;
diff --git a/pkgs/development/python-modules/compliance-trestle/default.nix b/pkgs/development/python-modules/compliance-trestle/default.nix
new file mode 100755
index 000000000000..b67b80f02c01
--- /dev/null
+++ b/pkgs/development/python-modules/compliance-trestle/default.nix
@@ -0,0 +1,108 @@
+{
+  attrs,
+  buildPythonPackage,
+  cmarkgfm,
+  cryptography,
+  defusedxml,
+  datamodel-code-generator,
+  email-validator,
+  fetchFromGitHub,
+  furl,
+  ilcli,
+  importlib-resources,
+  jinja2,
+  lib,
+  mypy,
+  openpyxl,
+  orjson,
+  paramiko,
+  pytestCheckHook,
+  pydantic,
+  python-dotenv,
+  python-frontmatter,
+  requests,
+  ruamel-yaml,
+  setuptools,
+  setuptools-scm,
+}:
+
+buildPythonPackage rec {
+  pname = "compliance-trestle";
+  version = "3.7.0";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "oscal-compass";
+    repo = "compliance-trestle";
+    tag = "v${version}";
+    hash = "sha256-MEPleUM5gSCJjVaVbNtNzRl+Vvvk97h6Q/mOWIxFd2Q=";
+    fetchSubmodules = true;
+  };
+
+  pythonRelaxDeps = true;
+
+  postPatch = ''
+    substituteInPlace tests/trestle/misc/mypy_test.py \
+      --replace-fail "trestle'," "${placeholder "out"}/bin/trestle'," \
+  '';
+
+  build-system = [
+    setuptools
+    setuptools-scm
+  ];
+
+  dependencies = [
+    attrs
+    cmarkgfm
+    cryptography
+    defusedxml
+    datamodel-code-generator
+    email-validator
+    furl
+    ilcli
+    importlib-resources
+    jinja2
+    openpyxl
+    orjson
+    paramiko
+    pydantic
+    python-dotenv
+    python-frontmatter
+    requests
+    ruamel-yaml
+  ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+    mypy
+  ];
+
+  disabledTests = [
+    # Requires network access
+    "test_import_from_url"
+    "test_import_from_nist"
+    "test_remote_profile_relative_cat"
+
+    # AssertionError
+    "test_profile_generate_assemble_rev_5"
+    "test_ssp_assemble_fedramp_profile"
+    "test_ssp_generate_aggregates_no_cds"
+    "test_ssp_generate_aggregates_no_param_value_orig"
+  ];
+
+  disabledTestPaths = [
+    # Requires network access
+    "tests/trestle/core/remote"
+  ];
+
+  pythonImportsCheck = [ "trestle" ];
+
+  meta = {
+    description = "An opinionated tooling platform for managing compliance as code, using continuous integration and NIST's OSCAL standard";
+    homepage = "https://github.com/oscal-compass/compliance-trestle";
+    changelog = "https://github.com/oscal-compass/compliance-trestle/blob/${src.rev}/CHANGELOG.md";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ tochiaha ];
+    mainProgram = "trestle";
+  };
+}
diff --git a/pkgs/development/python-modules/elevenlabs/default.nix b/pkgs/development/python-modules/elevenlabs/default.nix
index 14e72f843c0b..9a359369cb12 100644
--- a/pkgs/development/python-modules/elevenlabs/default.nix
+++ b/pkgs/development/python-modules/elevenlabs/default.nix
@@ -12,7 +12,7 @@
 }:
 
 let
-  version = "1.9.0";
+  version = "1.50.5";
   tag = version;
 in
 buildPythonPackage {
@@ -24,7 +24,7 @@ buildPythonPackage {
     owner = "elevenlabs";
     repo = "elevenlabs-python";
     inherit tag;
-    hash = "sha256-0fkt2Z05l95b2S+xoyyy9VGAUZDI1SM8kdcP1PCrUg8=";
+    hash = "sha256-Cew8+L7NoQlvR2pILVmwNIa3WUfZzmEkf1+U2nglsnM=";
   };
 
   build-system = [ poetry-core ];
diff --git a/pkgs/development/python-modules/imap-tools/default.nix b/pkgs/development/python-modules/imap-tools/default.nix
index bc4b2ae8e79a..a7a0736d60db 100644
--- a/pkgs/development/python-modules/imap-tools/default.nix
+++ b/pkgs/development/python-modules/imap-tools/default.nix
@@ -8,14 +8,14 @@
 
 buildPythonPackage rec {
   pname = "imap-tools";
-  version = "1.9.0";
+  version = "1.9.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "ikvk";
     repo = "imap_tools";
     tag = "v${version}";
-    hash = "sha256-2frJqHKIOuERC8G6fJwJOdxcWHRQRRy1BxfZDrVhXEU=";
+    hash = "sha256-tlShiI90PAbWztrL5PgmE1D+/h6bUoSxAHxwGlQHvus=";
   };
 
   build-system = [ setuptools ];
diff --git a/pkgs/development/python-modules/jaxtyping/default.nix b/pkgs/development/python-modules/jaxtyping/default.nix
index 01d06d31eb12..f29fa882b578 100644
--- a/pkgs/development/python-modules/jaxtyping/default.nix
+++ b/pkgs/development/python-modules/jaxtyping/default.nix
@@ -6,6 +6,9 @@
   # build-system
   hatchling,
 
+  # dependencies
+  wadler-lindig,
+
   # tests
   cloudpickle,
   equinox,
@@ -20,18 +23,22 @@
 let
   self = buildPythonPackage rec {
     pname = "jaxtyping";
-    version = "0.2.36";
+    version = "0.2.37";
     pyproject = true;
 
     src = fetchFromGitHub {
       owner = "google";
       repo = "jaxtyping";
       tag = "v${version}";
-      hash = "sha256-TXhHh6Nka9TOnfFPaNyHmLdTkhzyFEY0mLSfoDf9KQc=";
+      hash = "sha256-0a/9TSQW/k5kuucHoSUhLtRk9k+5ycbI/g6V1id3v28=";
     };
 
     build-system = [ hatchling ];
 
+    dependencies = [
+      wadler-lindig
+    ];
+
     pythonImportsCheck = [ "jaxtyping" ];
 
     nativeCheckInputs = [
diff --git a/pkgs/development/python-modules/jupyter-server/default.nix b/pkgs/development/python-modules/jupyter-server/default.nix
index 071b3707225b..8eeffccb26a5 100644
--- a/pkgs/development/python-modules/jupyter-server/default.nix
+++ b/pkgs/development/python-modules/jupyter-server/default.nix
@@ -3,7 +3,6 @@
   stdenv,
   buildPythonPackage,
   fetchPypi,
-  pythonOlder,
   hatch-jupyter-builder,
   hatchling,
   pytestCheckHook,
@@ -37,7 +36,6 @@ buildPythonPackage rec {
   pname = "jupyter-server";
   version = "2.14.2";
   pyproject = true;
-  disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     pname = "jupyter_server";
@@ -45,12 +43,12 @@ buildPythonPackage rec {
     hash = "sha256-ZglQIaqWOM7SdsJIsdgYYuTFDyktV1kgu+lg3hxWsSs=";
   };
 
-  nativeBuildInputs = [
+  build-system = [
     hatch-jupyter-builder
     hatchling
   ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     argon2-cffi
     jinja2
     tornado
@@ -87,6 +85,11 @@ buildPythonPackage rec {
   pytestFlagsArray = [
     "-W"
     "ignore::DeprecationWarning"
+    # 19 failures on python 3.13:
+    # ResourceWarning: unclosed database in <sqlite3.Connection object at 0x7ffff2a0cc70>
+    # TODO: Can probably be removed at the next update
+    "-W"
+    "ignore::pytest.PytestUnraisableExceptionWarning"
   ];
 
   preCheck = ''
@@ -111,6 +114,10 @@ buildPythonPackage rec {
     ++ lib.optionals stdenv.hostPlatform.isLinux [
       # Failed: DID NOT RAISE <class 'tornado.web.HTTPError'>
       "test_copy_big_dir"
+    ]
+    ++ lib.optionals (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isx86_64) [
+      # TypeError: the JSON object must be str, bytes or bytearray, not NoneType
+      "test_terminal_create_with_cwd"
     ];
 
   disabledTestPaths = [
@@ -123,12 +130,12 @@ buildPythonPackage rec {
 
   __darwinAllowLocalNetworking = true;
 
-  meta = with lib; {
+  meta = {
     changelog = "https://github.com/jupyter-server/jupyter_server/blob/v${version}/CHANGELOG.md";
     description = "Backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications";
     mainProgram = "jupyter-server";
     homepage = "https://github.com/jupyter-server/jupyter_server";
-    license = licenses.bsdOriginal;
+    license = lib.licenses.bsdOriginal;
     maintainers = lib.teams.jupyter.members;
   };
 }
diff --git a/pkgs/development/python-modules/llama-cpp-python/default.nix b/pkgs/development/python-modules/llama-cpp-python/default.nix
index ec69378235e6..6c07005d4ddf 100644
--- a/pkgs/development/python-modules/llama-cpp-python/default.nix
+++ b/pkgs/development/python-modules/llama-cpp-python/default.nix
@@ -1,8 +1,10 @@
 {
   lib,
   stdenv,
+  gcc13Stdenv,
   buildPythonPackage,
   fetchFromGitHub,
+  fetchpatch2,
 
   # nativeBuildInputs
   cmake,
@@ -33,6 +35,9 @@
   cudaPackages ? { },
 
 }:
+let
+  stdenvTarget = if cudaSupport then gcc13Stdenv else stdenv;
+in
 buildPythonPackage rec {
   pname = "llama-cpp-python";
   version = "0.3.6";
@@ -47,6 +52,16 @@ buildPythonPackage rec {
   };
   # src = /home/gaetan/llama-cpp-python;
 
+  patches = [
+    # fix segfault when running tests due to missing default Metal devices
+    (fetchpatch2 {
+      url = "https://github.com/ggerganov/llama.cpp/commit/acd38efee316f3a5ed2e6afcbc5814807c347053.patch?full_index=1";
+      stripLen = 1;
+      extraPrefix = "vendor/llama.cpp/";
+      hash = "sha256-71+Lpg9z5KPlaQTX9D85KS2LXFWLQNJJ18TJyyq3/pU=";
+    })
+  ];
+
   dontUseCmakeConfigure = true;
   SKBUILD_CMAKE_ARGS = lib.strings.concatStringsSep ";" (
     lib.optionals cudaSupport [
@@ -76,6 +91,8 @@ buildPythonPackage rec {
     ]
   );
 
+  stdenv = stdenvTarget;
+
   dependencies = [
     diskcache
     jinja2
@@ -99,7 +116,11 @@ buildPythonPackage rec {
 
   passthru = {
     updateScript = gitUpdater { rev-prefix = "v"; };
-    tests.llama-cpp-python = llama-cpp-python.override { cudaSupport = true; };
+    tests = lib.optionalAttrs stdenvTarget.hostPlatform.isLinux {
+      withCuda = llama-cpp-python.override {
+        cudaSupport = true;
+      };
+    };
   };
 
   meta = {
@@ -109,12 +130,6 @@ buildPythonPackage rec {
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ kirillrdy ];
     badPlatforms = [
-      # Segfaults during tests:
-      # tests/test_llama.py .Fatal Python error: Segmentation fault
-      # Current thread 0x00000001f3decf40 (most recent call first):
-      #   File "/private/tmp/nix-build-python3.12-llama-cpp-python-0.3.2.drv-0/source/llama_cpp/_internals.py", line 51 in __init__
-      lib.systems.inspect.patterns.isDarwin
-
       # cc1: error: unknown value ‘native+nodotprod+noi8mm+nosve’ for ‘-mcpu’
       "aarch64-linux"
     ];
diff --git a/pkgs/development/python-modules/mallard-ducktype/default.nix b/pkgs/development/python-modules/mallard-ducktype/default.nix
new file mode 100644
index 000000000000..f13d66593ed5
--- /dev/null
+++ b/pkgs/development/python-modules/mallard-ducktype/default.nix
@@ -0,0 +1,38 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  setuptools,
+}:
+
+buildPythonPackage rec {
+  pname = "mallard-ducktype";
+  version = "1.0.2";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "projectmallard";
+    repo = "mallard-ducktype";
+    tag = version;
+    hash = "sha256-jHjzTBBRBh//bOrdnyCRmZRmpupgDaDRuZGAd75baco=";
+  };
+
+  build-system = [ setuptools ];
+
+  checkPhase = ''
+    runHook preCheck
+    pushd tests
+    ./runtests
+    popd
+    runHook postCheck
+  '';
+
+  pythonImportsCheck = [ "mallard" ];
+
+  meta = {
+    description = "Parser for the lightweight Ducktype syntax for Mallard";
+    homepage = "https://github.com/projectmallard/mallard-ducktype";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ ];
+  };
+}
diff --git a/pkgs/development/python-modules/pyiskra/default.nix b/pkgs/development/python-modules/pyiskra/default.nix
index 0c12f0612792..c52242f8ed5b 100644
--- a/pkgs/development/python-modules/pyiskra/default.nix
+++ b/pkgs/development/python-modules/pyiskra/default.nix
@@ -9,14 +9,14 @@
 
 buildPythonPackage rec {
   pname = "pyiskra";
-  version = "0.1.14";
+  version = "0.1.15";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "Iskramis";
     repo = "pyiskra";
     tag = "v${version}";
-    hash = "sha256-OLNUa11UULiW6E8nVy5rUyN7iAD7KdM+R76m2zaDOgc=";
+    hash = "sha256-LIrhd2gDqa1AehnG0WVQKUNbFTuFkLcHwqNAjFejYk0=";
   };
 
   build-system = [ setuptools ];
diff --git a/pkgs/development/python-modules/scrap-engine/default.nix b/pkgs/development/python-modules/scrap-engine/default.nix
index 0a8c9fed90e8..2583c637f7a8 100644
--- a/pkgs/development/python-modules/scrap-engine/default.nix
+++ b/pkgs/development/python-modules/scrap-engine/default.nix
@@ -8,13 +8,13 @@
 
 buildPythonPackage rec {
   pname = "scrap-engine";
-  version = "1.4.1";
+  version = "1.4.2";
   pyproject = true;
 
   src = fetchPypi {
     pname = "scrap_engine";
     inherit version;
-    hash = "sha256-qxzbVYFcSKcL2HtMlH9epO/sCx9HckWAt/NyVD8QJBQ=";
+    hash = "sha256-9jiStwFD5vhPSxWsEVmHOvfRgNgVOUvlzAa1Rmf+faE=";
   };
 
   build-system = [
diff --git a/pkgs/development/python-modules/stable-baselines3/default.nix b/pkgs/development/python-modules/stable-baselines3/default.nix
index a9d784707886..0cca87dd9857 100644
--- a/pkgs/development/python-modules/stable-baselines3/default.nix
+++ b/pkgs/development/python-modules/stable-baselines3/default.nix
@@ -22,16 +22,14 @@
 }:
 buildPythonPackage rec {
   pname = "stable-baselines3";
-  # TODO: To this date, the latest release (2.4.1) is not compatible with numpy 2 and does not build
-  # successfully on nixpkgs
-  version = "2.4.1-unstable-2025-01-07";
+  version = "2.5.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "DLR-RM";
     repo = "stable-baselines3";
-    rev = "b7c64a1aa4dd2fd3efed96e7a9ddb4d1f5c96112";
-    hash = "sha256-oyTOBRZsKkhhGKwwBN9HCV0t8+MkJYpWsTRdS+upMeI=";
+    tag = "v${version}";
+    hash = "sha256-4KOF/3/PxHHSo95zaqtPy5+h53VcUsMhSx85tGvXV2o=";
   };
 
   build-system = [ setuptools ];
diff --git a/pkgs/development/python-modules/wadler-lindig/default.nix b/pkgs/development/python-modules/wadler-lindig/default.nix
new file mode 100644
index 000000000000..7011c0a9ef16
--- /dev/null
+++ b/pkgs/development/python-modules/wadler-lindig/default.nix
@@ -0,0 +1,46 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+
+  # build-system
+  hatchling,
+
+  # tests
+  numpy,
+  pytestCheckHook,
+}:
+
+buildPythonPackage rec {
+  pname = "wadler-lindig";
+  version = "0.1.3";
+  pyproject = true;
+
+  src = fetchFromGitHub {
+    owner = "patrick-kidger";
+    repo = "wadler_lindig";
+    rev = "v${version}";
+    hash = "sha256-akb1x9UYbfEwnVS6ahpb42XnEl3y7kk3WkhwD8p7AA4=";
+  };
+
+  build-system = [
+    hatchling
+  ];
+
+  pythonImportsCheck = [
+    "wadler_lindig"
+  ];
+
+  nativeCheckInputs = [
+    numpy
+    pytestCheckHook
+  ];
+
+  meta = {
+    description = "A Wadler--Lindig pretty printer for Python";
+    homepage = "https://github.com/patrick-kidger/wadler_lindig";
+    changelog = "https://github.com/patrick-kidger/wadler_lindig/releases/tag/v${version}";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+}
diff --git a/pkgs/development/python-modules/whey-pth/default.nix b/pkgs/development/python-modules/whey-pth/default.nix
index c40292ede641..a389860d1e2d 100644
--- a/pkgs/development/python-modules/whey-pth/default.nix
+++ b/pkgs/development/python-modules/whey-pth/default.nix
@@ -1,21 +1,30 @@
 {
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGitHub,
   lib,
   setuptools,
   dom-toml,
   whey,
+  pytestCheckHook,
 }:
+
 buildPythonPackage rec {
   pname = "whey-pth";
   version = "0.0.6";
   pyproject = true;
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-CIpgqzNXW3VpS+k6BCpc2DNyqwgt/Af3ms59AH/V5KM=";
+  src = fetchFromGitHub {
+    owner = "repo-helper";
+    repo = "whey-pth";
+    tag = "v${version}";
+    hash = "sha256-A+bXB9F8FD+A1iRuETIxP12bkH/5NKcx01ERXJZAj+Q=";
   };
 
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-fail 'setuptools!=61.*,<=67.1.0,>=40.6.0' setuptools
+  '';
+
   build-system = [ setuptools ];
 
   dependencies = [
@@ -23,14 +32,18 @@ buildPythonPackage rec {
     whey
   ];
 
-  postPatch = ''
-    substituteInPlace pyproject.toml \
-      --replace-fail '"setuptools!=61.*,<=67.1.0,>=40.6.0"' '"setuptools"'
-  '';
+  pythonImportsCheck = [ "whey_pth" ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  # missing dependency coincidence
+  doCheck = false;
 
   meta = {
-    description = "Extension to whey to support .pth files.";
-    homepage = "https://pypi.org/project/whey-pth";
+    description = "Extension to whey to support .pth files";
+    homepage = "https://github.com/repo-helper/whey-pth";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ tyberius-prime ];
   };
diff --git a/pkgs/development/python-modules/whey/default.nix b/pkgs/development/python-modules/whey/default.nix
index 7c1aaec13e6c..61ef34e74ad6 100644
--- a/pkgs/development/python-modules/whey/default.nix
+++ b/pkgs/development/python-modules/whey/default.nix
@@ -1,30 +1,41 @@
 {
   buildPythonPackage,
-  fetchPypi,
+  fetchFromGitHub,
   lib,
   setuptools,
   attrs,
   click,
   consolekit,
   dist-meta,
+  docutils,
   dom-toml,
   domdf-python-tools,
+  editables,
   handy-archives,
   natsort,
   packaging,
   pyproject-parser,
+  pytestCheckHook,
   shippinglabel,
 }:
+
 buildPythonPackage rec {
   pname = "whey";
   version = "0.1.1";
   pyproject = true;
 
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-l72fjczuuDXg/cDiqJ7roNVm4X+au+1u4AA8Szs1bNo=";
+  src = fetchFromGitHub {
+    owner = "repo-helper";
+    repo = "whey";
+    tag = "v${version}";
+    hash = "sha256-s2jZmuFj0gTWVTcXWcBhcu5RBuaf/qMS/xzIpIoG1ZE=";
   };
 
+  postPatch = ''
+    substituteInPlace pyproject.toml \
+      --replace-fail 'setuptools!=61.*,<=67.1.0,>=40.6.0' setuptools
+  '';
+
   build-system = [ setuptools ];
 
   dependencies = [
@@ -41,14 +52,29 @@ buildPythonPackage rec {
     shippinglabel
   ];
 
-  postPatch = ''
-    substituteInPlace pyproject.toml \
-      --replace-fail '"setuptools!=61.*,<=67.1.0,>=40.6.0"' '"setuptools"'
-  '';
+  pythonImportsCheck = [ "whey" ];
+
+  optional-dependencies = {
+    all = lib.flatten (lib.attrValues (lib.filterAttrs (n: v: n != "all") optional-dependencies));
+    editable = [
+      editables
+    ];
+    readme = [
+      docutils
+      pyproject-parser
+    ] ++ pyproject-parser.optional-dependencies.readme;
+  };
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  # missing dependency pyproject-examples
+  doCheck = false;
 
   meta = {
-    description = "A simple Python wheel builder for simple projects.";
-    homepage = "https://pypi.org/project/whey";
+    description = "Simple Python wheel builder for simple projects";
+    homepage = "https://github.com/repo-helper/whey";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ tyberius-prime ];
   };