diff --git a/pkgs/development/lisp-modules/patches/nyxt-remove-build-operation.patch b/pkgs/development/lisp-modules/patches/nyxt-remove-build-operation.patch
deleted file mode 100644
index e050ce10b487..000000000000
--- a/pkgs/development/lisp-modules/patches/nyxt-remove-build-operation.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/nyxt.asd b/nyxt.asd
-index ea2630ce..fdf837e4 100644
---- a/nyxt.asd
-+++ b/nyxt.asd
-@@ -480,7 +480,6 @@ The renderer is configured from NYXT_RENDERER or `*nyxt-renderer*'."))
-   :defsystem-depends-on ("nasdf")
-   :class :nasdf-system
-   :depends-on (nyxt/gi-gtk)
--  :build-operation "program-op"
-   :build-pathname "nyxt"
-   :entry-point "nyxt:entry-point")
- 
diff --git a/pkgs/development/python-modules/onnx/1.15.0-CVE-2024-27318.patch b/pkgs/development/python-modules/onnx/1.15.0-CVE-2024-27318.patch
deleted file mode 100644
index 3b95d1fc588c..000000000000
--- a/pkgs/development/python-modules/onnx/1.15.0-CVE-2024-27318.patch
+++ /dev/null
@@ -1,360 +0,0 @@
-Based on upstream 66b7fb630903fdcf3e83b6b6d56d82e904264a20, adjusted to
-apply to 1.15.0 & avoid implicit inclusion of changes from other
-intermediate commits
-
-diff --git a/onnx/checker.cc b/onnx/checker.cc
-index fac56f56..c9fda9b2 100644
---- a/onnx/checker.cc
-+++ b/onnx/checker.cc
-@@ -13,7 +13,6 @@
- #include <vector>
- 
- #include "onnx/common/file_utils.h"
--#include "onnx/common/path.h"
- #include "onnx/defs/schema.h"
- #include "onnx/defs/tensor_proto_util.h"
- #include "onnx/proto_utils.h"
-@@ -135,85 +134,7 @@ void check_tensor(const TensorProto& tensor, const CheckerContext& ctx) {
-     for (const StringStringEntryProto& entry : tensor.external_data()) {
-       if (entry.has_key() && entry.has_value() && entry.key() == "location") {
-         has_location = true;
--#ifdef _WIN32
--        auto file_path = std::filesystem::path(utf8str_to_wstring(entry.value()));
--        if (file_path.is_absolute()) {
--          fail_check(
--              "Location of external TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be a relative path, but it is an absolute path: ",
--              entry.value());
--        }
--        auto relative_path = file_path.lexically_normal().make_preferred().wstring();
--        // Check that normalized relative path contains ".." on Windows.
--        if (relative_path.find(L"..", 0) != std::string::npos) {
--          fail_check(
--              "Data of TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be file inside the ",
--              ctx.get_model_dir(),
--              ", but the '",
--              entry.value(),
--              "' points outside the directory");
--        }
--        std::wstring data_path = path_join(utf8str_to_wstring(ctx.get_model_dir()), relative_path);
--        struct _stat64 buff;
--        if (_wstat64(data_path.c_str(), &buff) != 0) {
--          fail_check(
--              "Data of TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be stored in ",
--              entry.value(),
--              ", but it doesn't exist or is not accessible.");
--        }
--#else // POSIX
--        if (entry.value().empty()) {
--          fail_check("Location of external TensorProto ( tensor name: ", tensor.name(), ") should not be empty.");
--        } else if (entry.value()[0] == '/') {
--          fail_check(
--              "Location of external TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be a relative path, but it is an absolute path: ",
--              entry.value());
--        }
--        std::string relative_path = clean_relative_path(entry.value());
--        // Check that normalized relative path contains ".." on POSIX
--        if (relative_path.find("..", 0) != std::string::npos) {
--          fail_check(
--              "Data of TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be file inside the ",
--              ctx.get_model_dir(),
--              ", but the '",
--              entry.value(),
--              "' points outside the directory");
--        }
--        std::string data_path = path_join(ctx.get_model_dir(), relative_path);
--        // use stat64 to check whether the file exists
--#if defined(__APPLE__) || defined(__wasm__) || !defined(__GLIBC__)
--        struct stat buffer; // APPLE, wasm and non-glic stdlibs do not have stat64
--        if (stat((data_path).c_str(), &buffer) != 0) {
--#else
--        struct stat64 buffer; // All POSIX under glibc except APPLE and wasm have stat64
--        if (stat64((data_path).c_str(), &buffer) != 0) {
--#endif
--          fail_check(
--              "Data of TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be stored in ",
--              data_path,
--              ", but it doesn't exist or is not accessible.");
--        }
--        // Do not allow symlinks or directories.
--        if (!S_ISREG(buffer.st_mode)) {
--          fail_check(
--              "Data of TensorProto ( tensor name: ",
--              tensor.name(),
--              ") should be stored in ",
--              data_path,
--              ", but it is not regular file.");
--        }
--#endif
-+        resolve_external_data_location(ctx.get_model_dir(), entry.value(), tensor.name());
-       }
-     }
-     if (!has_location) {
-@@ -1054,6 +975,93 @@ void check_model(const ModelProto& model, bool full_check, bool skip_opset_compa
-   }
- }
- 
-+std::string resolve_external_data_location(
-+    const std::string& base_dir,
-+    const std::string& location,
-+    const std::string& tensor_name) {
-+#ifdef _WIN32
-+  auto file_path = std::filesystem::path(utf8str_to_wstring(location));
-+  if (file_path.is_absolute()) {
-+    fail_check(
-+        "Location of external TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be a relative path, but it is an absolute path: ",
-+        location);
-+  }
-+  auto relative_path = file_path.lexically_normal().make_preferred().wstring();
-+  // Check that normalized relative path contains ".." on Windows.
-+  if (relative_path.find(L"..", 0) != std::string::npos) {
-+    fail_check(
-+        "Data of TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be file inside the ",
-+        base_dir,
-+        ", but the '",
-+        location,
-+        "' points outside the directory");
-+  }
-+  std::wstring data_path = path_join(utf8str_to_wstring(base_dir), relative_path);
-+  struct _stat64 buff;
-+  if (_wstat64(data_path.c_str(), &buff) != 0) {
-+    fail_check(
-+        "Data of TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be stored in ",
-+        location,
-+        ", but it doesn't exist or is not accessible.");
-+  }
-+  return wstring_to_utf8str(data_path);
-+#else // POSIX
-+  if (location.empty()) {
-+    fail_check("Location of external TensorProto ( tensor name: ", tensor_name, ") should not be empty.");
-+  } else if (location[0] == '/') {
-+    fail_check(
-+        "Location of external TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be a relative path, but it is an absolute path: ",
-+        location);
-+  }
-+  std::string relative_path = clean_relative_path(location);
-+  // Check that normalized relative path contains ".." on POSIX
-+  if (relative_path.find("..", 0) != std::string::npos) {
-+    fail_check(
-+        "Data of TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be file inside the ",
-+        base_dir,
-+        ", but the '",
-+        location,
-+        "' points outside the directory");
-+  }
-+  std::string data_path = path_join(base_dir, relative_path);
-+  // use stat64 to check whether the file exists
-+#if defined(__APPLE__) || defined(__wasm__) || !defined(__GLIBC__)
-+  struct stat buffer; // APPLE, wasm and non-glic stdlibs do not have stat64
-+  if (stat((data_path).c_str(), &buffer) != 0) {
-+#else
-+  struct stat64 buffer; // All POSIX under glibc except APPLE and wasm have stat64
-+  if (stat64((data_path).c_str(), &buffer) != 0) {
-+#endif
-+    fail_check(
-+        "Data of TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be stored in ",
-+        data_path,
-+        ", but it doesn't exist or is not accessible.");
-+  }
-+  // Do not allow symlinks or directories.
-+  if (!S_ISREG(buffer.st_mode)) {
-+    fail_check(
-+        "Data of TensorProto ( tensor name: ",
-+        tensor_name,
-+        ") should be stored in ",
-+        data_path,
-+        ", but it is not regular file.");
-+  }
-+  return data_path;
-+#endif
-+}
-+
- std::set<std::string> experimental_ops = {
-     "ATen",
-     "Affine",
-diff --git a/onnx/checker.h b/onnx/checker.h
-index 6796acab..83012213 100644
---- a/onnx/checker.h
-+++ b/onnx/checker.h
-@@ -160,7 +160,10 @@ void check_model_local_functions(
- 
- void check_model(const ModelProto& model, bool full_check = false, bool skip_opset_compatibility_check = false);
- void check_model(const std::string& model_path, bool full_check = false, bool skip_opset_compatibility_check = false);
--
-+std::string resolve_external_data_location(
-+    const std::string& base_dir,
-+    const std::string& location,
-+    const std::string& tensor_name);
- bool check_is_experimental_op(const NodeProto& node);
- 
- } // namespace checker
-diff --git a/onnx/common/path.h b/onnx/common/path.h
-index 6eaf5e67..09212747 100644
---- a/onnx/common/path.h
-+++ b/onnx/common/path.h
-@@ -31,11 +31,22 @@ inline std::wstring utf8str_to_wstring(const std::string& utf8str) {
-   if (utf8str.size() > INT_MAX) {
-     fail_check("utf8str_to_wstring: string is too long for converting to wstring.");
-   }
--  int size_required = MultiByteToWideChar(CP_UTF8, 0, utf8str.c_str(), (int)utf8str.size(), NULL, 0);
-+  int size_required = MultiByteToWideChar(CP_UTF8, 0, utf8str.c_str(), static_cast<int>(utf8str.size()), NULL, 0);
-   std::wstring ws_str(size_required, 0);
--  MultiByteToWideChar(CP_UTF8, 0, utf8str.c_str(), (int)utf8str.size(), &ws_str[0], size_required);
-+  MultiByteToWideChar(CP_UTF8, 0, utf8str.c_str(), static_cast<int>(utf8str.size()), &ws_str[0], size_required);
-   return ws_str;
- }
-+inline std::string wstring_to_utf8str(const std::wstring& ws_str) {
-+  if (ws_str.size() > INT_MAX) {
-+    fail_check("wstring_to_utf8str: string is too long for converting to UTF-8.");
-+  }
-+  int size_required =
-+      WideCharToMultiByte(CP_UTF8, 0, ws_str.c_str(), static_cast<int>(ws_str.size()), NULL, 0, NULL, NULL);
-+  std::string utf8str(size_required, 0);
-+  WideCharToMultiByte(
-+      CP_UTF8, 0, ws_str.c_str(), static_cast<int>(ws_str.size()), &utf8str[0], size_required, NULL, NULL);
-+  return utf8str;
-+}
- 
- #else
- std::string path_join(const std::string& origin, const std::string& append);
-diff --git a/onnx/cpp2py_export.cc b/onnx/cpp2py_export.cc
-index bc2594db..83cea68f 100644
---- a/onnx/cpp2py_export.cc
-+++ b/onnx/cpp2py_export.cc
-@@ -545,6 +545,8 @@ PYBIND11_MODULE(onnx_cpp2py_export, onnx_cpp2py_export) {
-       "full_check"_a = false,
-       "skip_opset_compatibility_check"_a = false);
- 
-+  checker.def("_resolve_external_data_location", &checker::resolve_external_data_location);
-+
-   // Submodule `version_converter`
-   auto version_converter = onnx_cpp2py_export.def_submodule("version_converter");
-   version_converter.doc() = "VersionConverter submodule";
-diff --git a/onnx/external_data_helper.py b/onnx/external_data_helper.py
-index bbc2717f..05c486c6 100644
---- a/onnx/external_data_helper.py
-+++ b/onnx/external_data_helper.py
-@@ -8,6 +8,7 @@ import uuid
- from itertools import chain
- from typing import Callable, Iterable, Optional
- 
-+import onnx.onnx_cpp2py_export.checker as c_checker
- from onnx.onnx_pb import AttributeProto, GraphProto, ModelProto, TensorProto
- 
- 
-@@ -39,9 +40,9 @@ def load_external_data_for_tensor(tensor: TensorProto, base_dir: str) -> None:
-         base_dir: directory that contains the external data.
-     """
-     info = ExternalDataInfo(tensor)
--    file_location = _sanitize_path(info.location)
--    external_data_file_path = os.path.join(base_dir, file_location)
--
-+    external_data_file_path = c_checker._resolve_external_data_location(  # type: ignore[attr-defined]
-+        base_dir, info.location, tensor.name
-+    )
-     with open(external_data_file_path, "rb") as data_file:
-         if info.offset:
-             data_file.seek(info.offset)
-@@ -259,14 +260,6 @@ def _get_attribute_tensors(onnx_model_proto: ModelProto) -> Iterable[TensorProto
-     yield from _get_attribute_tensors_from_graph(onnx_model_proto.graph)
- 
- 
--def _sanitize_path(path: str) -> str:
--    """Remove path components which would allow traversing up a directory tree from a base path.
--
--    Note: This method is currently very basic and should be expanded.
--    """
--    return path.lstrip("/.")
--
--
- def _is_valid_filename(filename: str) -> bool:
-     """Utility to check whether the provided filename is valid."""
-     exp = re.compile('^[^<>:;,?"*|/]+$')
-diff --git a/onnx/test/test_external_data.py b/onnx/test/test_external_data.py
-index 63f6b4ef..bb14d279 100644
---- a/onnx/test/test_external_data.py
-+++ b/onnx/test/test_external_data.py
-@@ -3,6 +3,7 @@
- # SPDX-License-Identifier: Apache-2.0
- from __future__ import annotations
- 
-+import itertools
- import os
- import pathlib
- import tempfile
-@@ -204,6 +205,52 @@ class TestLoadExternalDataSingleFile(TestLoadExternalDataBase):
-         attribute_tensor = new_model.graph.node[0].attribute[0].t
-         np.testing.assert_allclose(to_array(attribute_tensor), self.attribute_value)
- 
-+    @parameterized.parameterized.expand(itertools.product((True, False), (True, False)))
-+    def test_save_external_invalid_single_file_data_and_check(
-+        self, use_absolute_path: bool, use_model_path: bool
-+    ) -> None:
-+        model = onnx.load_model(self.model_filename, self.serialization_format)
-+
-+        model_dir = os.path.join(self.temp_dir, "save_copy")
-+        os.mkdir(model_dir)
-+
-+        traversal_external_data_dir = os.path.join(
-+            self.temp_dir, "invlid_external_data"
-+        )
-+        os.mkdir(traversal_external_data_dir)
-+
-+        if use_absolute_path:
-+            traversal_external_data_location = os.path.join(
-+                traversal_external_data_dir, "tensors.bin"
-+            )
-+        else:
-+            traversal_external_data_location = "../invlid_external_data/tensors.bin"
-+
-+        external_data_dir = os.path.join(self.temp_dir, "external_data")
-+        os.mkdir(external_data_dir)
-+        new_model_filepath = os.path.join(model_dir, "model.onnx")
-+
-+        def convert_model_to_external_data_no_check(model: ModelProto, location: str):
-+            for tensor in model.graph.initializer:
-+                if tensor.HasField("raw_data"):
-+                    set_external_data(tensor, location)
-+
-+        convert_model_to_external_data_no_check(
-+            model,
-+            location=traversal_external_data_location,
-+        )
-+
-+        onnx.save_model(model, new_model_filepath, self.serialization_format)
-+        if use_model_path:
-+            with self.assertRaises(onnx.checker.ValidationError):
-+                _ = onnx.load_model(new_model_filepath, self.serialization_format)
-+        else:
-+            onnx_model = onnx.load_model(
-+                new_model_filepath, self.serialization_format, load_external_data=False
-+            )
-+            with self.assertRaises(onnx.checker.ValidationError):
-+                load_external_data_for_model(onnx_model, external_data_dir)
-+
- 
- @parameterized.parameterized_class(
-     [
diff --git a/pkgs/development/python-modules/scikit-posthocs/0001-increased-abs-tolerance-for-wilcoxon-test.patch b/pkgs/development/python-modules/scikit-posthocs/0001-increased-abs-tolerance-for-wilcoxon-test.patch
deleted file mode 100644
index e3fa524e5a4f..000000000000
--- a/pkgs/development/python-modules/scikit-posthocs/0001-increased-abs-tolerance-for-wilcoxon-test.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-From 02266a00ce0eb6a089e7efe07816da1aa5152fc9 Mon Sep 17 00:00:00 2001
-From: Maksim Terpilovskii <maximtrp@gmail.com>
-Date: Sun, 31 Jul 2022 12:25:14 +0300
-Subject: [PATCH] increased abs tolerance for wilcoxon test
-
----
- tests/test_posthocs.py | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/tests/test_posthocs.py b/tests/test_posthocs.py
-index 956d808..8cc65e4 100644
---- a/tests/test_posthocs.py
-+++ b/tests/test_posthocs.py
-@@ -471,7 +471,7 @@ class TestPosthocs(unittest.TestCase):
-                               [2.857818e-06, 1.230888e-05, 1]])
- 
-         results = sp.posthoc_wilcoxon(self.df.sort_index(), val_col = 'pulse', group_col = 'kind')
--        self.assertTrue(np.allclose(results, r_results))
-+        self.assertTrue(np.allclose(results, r_results, atol=1e-4))
- 
- 
-     def test_posthoc_scheffe(self):
--- 
-2.36.1
-
diff --git a/pkgs/development/python-modules/scikit-posthocs/0002-Update-test_posthocs.py.patch b/pkgs/development/python-modules/scikit-posthocs/0002-Update-test_posthocs.py.patch
deleted file mode 100644
index fa4d6d3ececf..000000000000
--- a/pkgs/development/python-modules/scikit-posthocs/0002-Update-test_posthocs.py.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-From 5416ffba3ab01aebab3909400b5a9e847022898e Mon Sep 17 00:00:00 2001
-From: Maksim Terpilovskii <maximtrp@gmail.com>
-Date: Thu, 16 Mar 2023 00:20:02 +0300
-Subject: [PATCH] Update test_posthocs.py
-
----
- tests/test_posthocs.py | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/tests/test_posthocs.py b/tests/test_posthocs.py
-index 8cc65e4..42ca5f3 100644
---- a/tests/test_posthocs.py
-+++ b/tests/test_posthocs.py
-@@ -71,7 +71,7 @@ class TestPosthocs(unittest.TestCase):
-         a = splt.sign_plot(x, flat=True, labels=False)
-         with self.assertRaises(ValueError):
-             splt.sign_plot(x.astype(float), flat=True, labels=False)
--        self.assertTrue(isinstance(a, ma._subplots.Axes))
-+        self.assertTrue(isinstance(a, ma._axes.Axes))
- 
-     def test_sign_plot_nonflat(self):
- 
-@@ -85,7 +85,7 @@ class TestPosthocs(unittest.TestCase):
-         with self.assertRaises(ValueError):
-             splt.sign_plot(x.astype(np.int64), labels=False)
- 
--        self.assertTrue(isinstance(a, ma._subplots.Axes) and isinstance(cbar, mpl.colorbar.ColorbarBase))
-+        self.assertTrue(isinstance(a, ma._axes.Axes) and isinstance(cbar, mpl.colorbar.ColorbarBase))
- 
-     # Outliers tests
-     def test_outliers_iqr(self):
--- 
-2.36.1
-
diff --git a/pkgs/development/python-modules/sopel/python311-support.patch b/pkgs/development/python-modules/sopel/python311-support.patch
deleted file mode 100644
index dfa0283409ac..000000000000
--- a/pkgs/development/python-modules/sopel/python311-support.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-diff --git a/sopel/plugins/handlers.py b/sopel/plugins/handlers.py
-index 76902aa0..05f0279d 100644
---- a/sopel/plugins/handlers.py
-+++ b/sopel/plugins/handlers.py
-@@ -46,20 +46,15 @@ from __future__ import absolute_import, division, print_function, unicode_litera
- 
- import imp
- import importlib
-+import importlib.util
- import inspect
- import itertools
- import os
-+import sys
- 
- from sopel import loader
- from . import exceptions
- 
--try:
--    reload = importlib.reload
--except AttributeError:
--    # py2: no reload function
--    # TODO: imp is deprecated, to be removed when py2 support is dropped
--    reload = imp.reload
--
- 
- class AbstractPluginHandler(object):
-     """Base class for plugin handlers.
-@@ -301,7 +296,7 @@ class PyModulePlugin(AbstractPluginHandler):
- 
-         This method assumes the plugin is already loaded.
-         """
--        self._module = reload(self._module)
-+        self._module = importlib.reload(self._module)
- 
-     def is_loaded(self):
-         return self._module is not None
-@@ -402,45 +397,31 @@ class PyFilePlugin(PyModulePlugin):
- 
-         if good_file:
-             name = os.path.basename(filename)[:-3]
--            module_type = imp.PY_SOURCE
-+            spec = importlib.util.spec_from_file_location(
-+                name,
-+                filename,
-+            )
-         elif good_dir:
-             name = os.path.basename(filename)
--            module_type = imp.PKG_DIRECTORY
-+            spec = importlib.util.spec_from_file_location(
-+                name,
-+                os.path.join(filename, '__init__.py'),
-+                submodule_search_locations=filename,
-+            )
-         else:
-             raise exceptions.PluginError('Invalid Sopel plugin: %s' % filename)
- 
-         self.filename = filename
-         self.path = filename
--        self.module_type = module_type
-+        self.module_spec = spec
- 
-         super(PyFilePlugin, self).__init__(name)
- 
-     def _load(self):
--        # The current implementation uses `imp.load_module` to perform the
--        # load action, which also reloads the module. However, `imp` is
--        # deprecated in Python 3, so that might need to be changed when the
--        # support for Python 2 is dropped.
--        #
--        # However, the solution for Python 3 is non-trivial, since the
--        # `importlib` built-in module does not have a similar function,
--        # therefore requires to dive into its public internals
--        # (``importlib.machinery`` and ``importlib.util``).
--        #
--        # All of that is doable, but represents a lot of work. As long as
--        # Python 2 is supported, we can keep it for now.
--        #
--        # TODO: switch to ``importlib`` when Python2 support is dropped.
--        if self.module_type == imp.PY_SOURCE:
--            with open(self.path) as mod:
--                description = ('.py', 'U', self.module_type)
--                mod = imp.load_module(self.name, mod, self.path, description)
--        elif self.module_type == imp.PKG_DIRECTORY:
--            description = ('', '', self.module_type)
--            mod = imp.load_module(self.name, None, self.path, description)
--        else:
--            raise TypeError('Unsupported module type')
--
--        return mod
-+        module = importlib.util.module_from_spec(self.module_spec)
-+        sys.modules[self.name] = module
-+        self.module_spec.loader.exec_module(module)
-+        return module
- 
-     def get_meta_description(self):
-         """Retrieve a meta description for the plugin.