From cfd83dd62c5c670883346a9c6386a8a9c3a513f8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 30 Mar 2026 23:16:19 +0000
Subject: [PATCH 01/13] Bump codecov/codecov-action from 5 to 6

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 5 to 6.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v5...v6)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/nnunet_smoke_tests.yaml   | 2 +-
 .github/workflows/standard_smoke_tests.yaml | 2 +-
 .github/workflows/tests.yaml                | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/nnunet_smoke_tests.yaml b/.github/workflows/nnunet_smoke_tests.yaml
index 5c1c0d1da..b4411eea8 100644
--- a/.github/workflows/nnunet_smoke_tests.yaml
+++ b/.github/workflows/nnunet_smoke_tests.yaml
@@ -53,7 +53,7 @@ jobs:
         run: uv run pytest --test-group-count=4 --test-group=${{ matrix.group }} -v --cov fl4health --cov-report=xml tests/smoke_tests/test_nnunet_smoke_tests.py
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: VectorInstitute/FL4Health
diff --git a/.github/workflows/standard_smoke_tests.yaml b/.github/workflows/standard_smoke_tests.yaml
index c683de5c5..172afdb3d 100644
--- a/.github/workflows/standard_smoke_tests.yaml
+++ b/.github/workflows/standard_smoke_tests.yaml
@@ -53,7 +53,7 @@ jobs:
         run: uv run pytest --test-group-count=4 --test-group=${{ matrix.group }} -v --cov fl4health --cov-report=xml tests/smoke_tests/test_standard_smoke_tests.py
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: VectorInstitute/FL4Health
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index a58a40ff4..cf1b43964 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -48,7 +48,7 @@ jobs:
         run: uv run pytest -m "not smoketest" -v --cov fl4health --cov-report=xml tests
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: VectorInstitute/FL4Health

From 916a0e3c935796c4e00ed16246e7f1cc1bee86e5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 13 Apr 2026 23:15:46 +0000
Subject: [PATCH 02/13] Bump pypa/gh-action-pypi-publish from 1.13.0 to 1.14.0

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.13.0 to 1.14.0.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e...cef221092ed1bacb1cc03d23a2d87d1d172e277b)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-version: 1.14.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/publish_and_release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_and_release.yml b/.github/workflows/publish_and_release.yml
index ddd23be66..9dc53f15d 100644
--- a/.github/workflows/publish_and_release.yml
+++ b/.github/workflows/publish_and_release.yml
@@ -33,7 +33,7 @@ jobs:
         run: uv build
 
       - name: Publish package
-        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e
+        uses: pypa/gh-action-pypi-publish@cef221092ed1bacb1cc03d23a2d87d1d172e277b
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

From 85afeb71372faa97f11ad7946af3befa613274b9 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 21 Apr 2026 00:02:48 +0000
Subject: [PATCH 03/13] Bump astral-sh/setup-uv from 7.6.0 to 8.1.0

Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 7.6.0 to 8.1.0.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](https://github.com/astral-sh/setup-uv/compare/v7.6.0...v8.1.0)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-version: 8.1.0
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/docs.yml                  | 2 +-
 .github/workflows/nnunet_smoke_tests.yaml   | 2 +-
 .github/workflows/publish_and_release.yml   | 2 +-
 .github/workflows/standard_smoke_tests.yaml | 2 +-
 .github/workflows/static_code_checks.yaml   | 2 +-
 .github/workflows/tests.yaml                | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index d7e271770..80734527f 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -47,7 +47,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.6.0
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           version: "0.9.11"
           enable-cache: true
diff --git a/.github/workflows/nnunet_smoke_tests.yaml b/.github/workflows/nnunet_smoke_tests.yaml
index 5c1c0d1da..580aec0ad 100644
--- a/.github/workflows/nnunet_smoke_tests.yaml
+++ b/.github/workflows/nnunet_smoke_tests.yaml
@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.6.0
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           version: "0.9.11"
           enable-cache: true
diff --git a/.github/workflows/publish_and_release.yml b/.github/workflows/publish_and_release.yml
index ddd23be66..c5d611fea 100644
--- a/.github/workflows/publish_and_release.yml
+++ b/.github/workflows/publish_and_release.yml
@@ -19,7 +19,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.6.0
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           version: "0.9.11"
           enable-cache: true
diff --git a/.github/workflows/standard_smoke_tests.yaml b/.github/workflows/standard_smoke_tests.yaml
index c683de5c5..6500844d9 100644
--- a/.github/workflows/standard_smoke_tests.yaml
+++ b/.github/workflows/standard_smoke_tests.yaml
@@ -23,7 +23,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.6.0
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           version: "0.9.11"
           enable-cache: true
diff --git a/.github/workflows/static_code_checks.yaml b/.github/workflows/static_code_checks.yaml
index baf52e58a..2ac1cfce1 100644
--- a/.github/workflows/static_code_checks.yaml
+++ b/.github/workflows/static_code_checks.yaml
@@ -20,7 +20,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.6.0
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           version: "0.9.11"
           enable-cache: true
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index a58a40ff4..775b6a02c 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -20,7 +20,7 @@ jobs:
         uses: actions/checkout@v6
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v7.6.0
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           version: "0.9.11"
           enable-cache: true

From b205380bb3fdcb6f6d09c4cdda167192d10bb285 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 11 May 2026 19:32:44 +0000
Subject: [PATCH 04/13] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/uv-pre-commit: 0.10.12 → 0.11.13](https://github.com/astral-sh/uv-pre-commit/compare/0.10.12...0.11.13)
- [github.com/astral-sh/ruff-pre-commit: v0.15.7 → v0.15.12](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.7...v0.15.12)
- [github.com/pre-commit/mirrors-mypy: v1.19.1 → v2.0.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.19.1...v2.0.0)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index dc66322a4..4473ee56b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.10.12
+    rev: 0.11.13
     hooks:
       - id: uv-lock
 
@@ -26,7 +26,7 @@ repos:
       - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.15.7'
+    rev: 'v0.15.12'
     hooks:
     - id: ruff-check
       args: [--fix, --exit-non-zero-on-fix]
@@ -35,7 +35,7 @@ repos:
       types_or: [python, jupyter]
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v2.0.0
     hooks:
       - id: mypy
         name: mypy

From f692a023994743e21582622bba96cabfb2df22e7 Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Wed, 13 May 2026 09:55:17 -0400
Subject: [PATCH 05/13] Upgrading libraries, ensuring tests pass and any new
 mypy issues are resolved

---
 .../model_bases/masked_layers/masked_conv.py  |   14 +-
 fl4health/utils/nnunet_utils.py               |    9 +-
 pyproject.toml                                |   14 +-
 tests/test_utils/models_for_test.py           |   28 +-
 tests/utils/nnnunet_utils_test.py             |    1 +
 uv.lock                                       | 1695 +++++++++--------
 6 files changed, 919 insertions(+), 842 deletions(-)

diff --git a/fl4health/model_bases/masked_layers/masked_conv.py b/fl4health/model_bases/masked_layers/masked_conv.py
index 619cb7dba..b46ea00b5 100644
--- a/fl4health/model_bases/masked_layers/masked_conv.py
+++ b/fl4health/model_bases/masked_layers/masked_conv.py
@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+from typing import Literal
+
 import torch
 import torch.nn.functional as F
 from torch import Tensor, nn
@@ -21,7 +23,7 @@ def __init__(
         dilation: _size_1_t = 1,
         groups: int = 1,
         bias: bool = True,
-        padding_mode: str = "zeros",
+        padding_mode: Literal["zeros", "reflect", "replicate", "circular"] = "zeros",
         device: torch.device | None = None,
         dtype: torch.dtype | None = None,
     ) -> None:
@@ -150,7 +152,7 @@ def __init__(
         dilation: _size_2_t = 1,
         groups: int = 1,
         bias: bool = True,
-        padding_mode: str = "zeros",
+        padding_mode: Literal["zeros", "reflect", "replicate", "circular"] = "zeros",
         device: torch.device | None = None,
         dtype: torch.dtype | None = None,
     ) -> None:
@@ -276,7 +278,7 @@ def __init__(
         dilation: _size_3_t = 1,
         groups: int = 1,
         bias: bool = True,
-        padding_mode: str = "zeros",
+        padding_mode: Literal["zeros", "reflect", "replicate", "circular"] = "zeros",
         device: torch.device | None = None,
         dtype: torch.dtype | None = None,
     ) -> None:
@@ -403,7 +405,7 @@ def __init__(
         groups: int = 1,
         bias: bool = True,
         dilation: _size_1_t = 1,
-        padding_mode: str = "zeros",
+        padding_mode: Literal["zeros", "reflect", "replicate", "circular"] = "zeros",
         device: torch.device | None = None,
         dtype: torch.dtype | None = None,
     ) -> None:
@@ -566,7 +568,7 @@ def __init__(
         groups: int = 1,
         bias: bool = True,
         dilation: _size_2_t = 1,
-        padding_mode: str = "zeros",
+        padding_mode: Literal["zeros", "reflect", "replicate", "circular"] = "zeros",
         device: torch.device | None = None,
         dtype: torch.dtype | None = None,
     ) -> None:
@@ -727,7 +729,7 @@ def __init__(
         groups: int = 1,
         bias: bool = True,
         dilation: _size_3_t = 1,
-        padding_mode: str = "zeros",
+        padding_mode: Literal["zeros", "reflect", "replicate", "circular"] = "zeros",
         device: torch.device | None = None,
         dtype: torch.dtype | None = None,
     ) -> None:
diff --git a/fl4health/utils/nnunet_utils.py b/fl4health/utils/nnunet_utils.py
index 0791bb636..d3d98f961 100644
--- a/fl4health/utils/nnunet_utils.py
+++ b/fl4health/utils/nnunet_utils.py
@@ -8,7 +8,7 @@
 from importlib import reload
 from logging import DEBUG, INFO, WARN, Logger
 from math import ceil
-from typing import Any, no_type_check
+from typing import Any
 
 import numpy as np
 import torch
@@ -518,12 +518,9 @@ def __init__(
         # Number of windows with constant LR across training
         self.num_windows = ceil(max_steps / self.steps_per_lr)
         self._step_count: int
-        super().__init__(optimizer, -1, False)
+        super().__init__(optimizer, -1)
 
-    # mypy incorrectly infers get_lr returns a float
-    # Documented issue https://github.com/pytorch/pytorch/issues/100804
-    @no_type_check
-    def get_lr(self) -> Sequence[float]:
+    def get_lr(self) -> list[float | torch.Tensor]:
         """
         Get the current LR of the scheduler.
 
diff --git a/pyproject.toml b/pyproject.toml
index 11daf1f74..029461ad1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ dependencies = [
     "pandas>=2.0,<3.0",
     "flwr>=1.18.0,<1.19.0",
     "opacus>=1.3.0,<2.0.0",
-    "torch==2.6.0",
+    "torch>=2.6.0",
     "pyarrow>=17.0.0,<18.0.0",  # Pin as there is potential ACE with v0.14.2 that is resolved in v17.0
     "dp-accounting>=0.4.3,<0.5.0",
     "torchmetrics>=1.3.0,<2.0.0",
@@ -48,16 +48,10 @@ dependencies = [
 
 [dependency-groups]
 dev = [
-    # locked the 2.15 version because of restrictions with tensorflow-io
-    # (see https://pypi.org/project/tensorflow-io/ section "TensorFlow Version Compatibility")
-    # Note: tensorflow 2.15 requires keras<2.16
-    # SECURITY NOTE: keras 2.15.0 has known CVEs (CVE-2024-55459, CVE-2025-9906, CVE-2025-12058, CVE-2025-12060)
-    # that require keras>=3.12.0 to fix. However, upgrading requires tensorflow>=2.16 which breaks tensorflow-io
-    # compatibility. These CVEs are accepted risk until tensorflow-io supports newer tensorflow versions.
-    "tensorflow>=2.15,<2.16",
-    "keras>=2.15.0,<2.16",
+    "tensorflow>=2.15",
+    "keras>=2.15.0",
     "nltk>=3.8.0,<4.0.0",
-    "torchvision==0.21.0",
+    "torchvision>=0.21.0",
     "torchinfo>=1.8.0,<2.0.0",
     "ipykernel>=6.25.1,<7.0.0",
     "pytest-test-groups>=1.2.1,<2.0.0",
diff --git a/tests/test_utils/models_for_test.py b/tests/test_utils/models_for_test.py
index b8c9e9f09..ae851dc74 100644
--- a/tests/test_utils/models_for_test.py
+++ b/tests/test_utils/models_for_test.py
@@ -1,3 +1,5 @@
+from typing import cast
+
 import torch
 import torch.nn.functional as F
 from torch import nn
@@ -123,15 +125,23 @@ def __init__(self) -> None:
         )
 
     def forward(self, x: torch.Tensor) -> torch.Tensor:
-        x = self.h1_layer1["h2_layer1"]["conv"](x)
-        x = self.h1_layer1["h2_layer1"]["pool"](x)
-        x = self.h1_layer1["h2_layer2"]["conv"](x)
-        x = self.h1_layer1["h2_layer2"]["pool"](x)
-
-        x = self.h1_layer2["h2_layer1"]["conv"](x)
-        x = self.h1_layer2["h2_layer1"]["pool"](x)
-        x = self.h1_layer2["h2_layer2"]["conv"](x)
-        x = self.h1_layer2["h2_layer2"]["pool"](x)
+        # Unfortunately, mypy doesn't recognize that ModuleDict can be nested. So we're forced to cast
+        h1_layer_1_h2_layer_1: nn.ModuleDict = cast(nn.ModuleDict, self.h1_layer1["h2_layer1"])
+        h1_layer_1_h2_layer_2: nn.ModuleDict = cast(nn.ModuleDict, self.h1_layer1["h2_layer2"])
+
+        x = h1_layer_1_h2_layer_1["conv"](x)
+        x = h1_layer_1_h2_layer_1["pool"](x)
+        x = h1_layer_1_h2_layer_2["conv"](x)
+        x = h1_layer_1_h2_layer_2["pool"](x)
+
+        # Unfortunately, mypy doesn't recognize that ModuleDict can be nested. So we're forced to cast
+        h1_layer_2_h2_layer_1: nn.ModuleDict = cast(nn.ModuleDict, self.h1_layer2["h2_layer1"])
+        h1_layer_2_h2_layer_2: nn.ModuleDict = cast(nn.ModuleDict, self.h1_layer2["h2_layer2"])
+
+        x = h1_layer_2_h2_layer_1["conv"](x)
+        x = h1_layer_2_h2_layer_1["pool"](x)
+        x = h1_layer_2_h2_layer_2["conv"](x)
+        x = h1_layer_2_h2_layer_2["pool"](x)
 
         x = torch.flatten(x, 1)
         x = self.classifier["fc"](x)
diff --git a/tests/utils/nnnunet_utils_test.py b/tests/utils/nnnunet_utils_test.py
index 964656c56..8266c708f 100644
--- a/tests/utils/nnnunet_utils_test.py
+++ b/tests/utils/nnnunet_utils_test.py
@@ -30,6 +30,7 @@ def test_poly_lr_scheduler(caplog: pytest.LogCaptureFixture) -> None:
     prev_lr = None
     for step in range(max_steps):
         curr_lr = lr_scheduler.get_lr()[0]
+        assert isinstance(curr_lr, float)
 
         if step % steps_per_lr == 0:
             assert curr_lr != prev_lr
diff --git a/uv.lock b/uv.lock
index 63a079f17..7649b99b3 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,10 +1,6 @@
 version = 1
-revision = 3
+revision = 2
 requires-python = ">=3.10.0, <3.11"
-resolution-markers = [
-    "sys_platform == 'linux'",
-    "sys_platform != 'linux'",
-]
 
 [[package]]
 name = "absl-py"
@@ -17,7 +13,7 @@ wheels = [
 
 [[package]]
 name = "accelerate"
-version = "1.12.0"
+version = "1.13.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "huggingface-hub" },
@@ -28,9 +24,9 @@ dependencies = [
     { name = "safetensors" },
     { name = "torch" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/4a/8e/ac2a9566747a93f8be36ee08532eb0160558b07630a081a6056a9f89bf1d/accelerate-1.12.0.tar.gz", hash = "sha256:70988c352feb481887077d2ab845125024b2a137a5090d6d7a32b57d03a45df6", size = 398399, upload-time = "2025-11-21T11:27:46.973Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/ca/14/787e5498cd062640f0f3d92ef4ae4063174f76f9afd29d13fc52a319daae/accelerate-1.13.0.tar.gz", hash = "sha256:d631b4e0f5b3de4aff2d7e9e6857d164810dfc3237d54d017f075122d057b236", size = 402835, upload-time = "2026-03-04T19:34:12.359Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/9f/d2/c581486aa6c4fbd7394c23c47b83fa1a919d34194e16944241daf9e762dd/accelerate-1.12.0-py3-none-any.whl", hash = "sha256:3e2091cd341423207e2f084a6654b1efcd250dc326f2a37d6dde446e07cabb11", size = 380935, upload-time = "2025-11-21T11:27:44.522Z" },
+    { url = "https://files.pythonhosted.org/packages/7e/46/02ac5e262d4af18054b3e922b2baedbb2a03289ee792162de60a865defc5/accelerate-1.13.0-py3-none-any.whl", hash = "sha256:cf1a3efb96c18f7b152eb0fa7490f3710b19c3f395699358f08decca2b8b62e0", size = 383744, upload-time = "2026-03-04T19:34:10.313Z" },
 ]
 
 [[package]]
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From 54fe84373aa1a87f69a0a11dc60c3365c0832b7f Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Wed, 13 May 2026 15:25:05 -0400
Subject: [PATCH 06/13] Monkey patch and bug fixes for the smoke tests

---
 .github/workflows/static_code_checks.yaml | 21 ----------
 fl4health/clients/flexible/nnunet.py      | 13 +++++--
 fl4health/clients/nnunet_client.py        | 13 +++++--
 fl4health/mixins/personalized/ditto.py    |  7 ++++
 fl4health/utils/nnunet_utils.py           | 47 +++++++++++++++++++++++
 5 files changed, 74 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/static_code_checks.yaml b/.github/workflows/static_code_checks.yaml
index baf52e58a..724714bf5 100644
--- a/.github/workflows/static_code_checks.yaml
+++ b/.github/workflows/static_code_checks.yaml
@@ -47,31 +47,10 @@ jobs:
         uses: pypa/gh-action-pip-audit@v1.1.0
         with:
           virtual-environment: .venv/
-          # GHSA-3749-ghw9-m3mg and GHSA-887c-mr87-cxwp are pytorch vulnerabilities that require 2.7 and 2.8 but we're
-          # pinning to 2.6.0 for now.
-          # CVE-2025-53000 NBConvert issue, no fix yet.
-          # CVE-2026-21851 is a MonAI issue with no fix at the moment.
-          # CVE-2024-55459, CVE-2025-9906, CVE-2025-12058, CVE-2025-12060 are keras vulnerabilities that require
-          # keras>=3.12.0 which needs tensorflow>=2.16, but we're pinning to tensorflow 2.15 due to tensorflow-io
-          # compatibility constraints.
-          # CVE-2026-0994 is a protobuff vulnerability without a fix yet.
           # CVE-2026-26007 is a cryptography vulnerability that requires cryptography>=46.0.5, but flwr (flower)
           # requires cryptography<45.0.0, blocking the upgrade.
-          # GHSA-rf74-v2fm-23pw, CVE-2026-33230, CVE-2026-33231: NLTK vulnerabilities without a fix yet.
           ignore-vulns: |
-            GHSA-3749-ghw9-m3mg
-            GHSA-887c-mr87-cxwp
-            CVE-2025-53000
-            CVE-2026-21851
-            CVE-2024-55459
-            CVE-2025-9906
-            CVE-2025-12058
-            CVE-2025-12060
-            CVE-2026-0994
             CVE-2026-26007
-            GHSA-rf74-v2fm-23pw
-            CVE-2026-33230
-            CVE-2026-33231
 
       # Deleting some temporary files and useless folders to free up space
       # Deleting /usr/share/dotnet should clear ~4GB of space.
diff --git a/fl4health/clients/flexible/nnunet.py b/fl4health/clients/flexible/nnunet.py
index d5bde088b..1c499be62 100644
--- a/fl4health/clients/flexible/nnunet.py
+++ b/fl4health/clients/flexible/nnunet.py
@@ -34,6 +34,7 @@
 from fl4health.utils.nnunet_utils import (
     NNUNET_DEFAULT_NP,
     NNUNET_N_SPATIAL_DIMS,
+    LocalPolyLRScheduler,
     Module2LossWrapper,
     NnunetConfig,
     NnUNetDataLoaderWrapper,
@@ -56,6 +57,7 @@
     # silences a bunch of deprecation warnings related to scipy.ndimage
     # Raised an issue with nnunet. https://github.com/MIC-DKFZ/nnUNet/issues/2370
     warnings.filterwarnings("ignore", category=DeprecationWarning)
+    import nnunetv2.training.nnUNetTrainer.nnUNetTrainer as nnUNetTrainerModule
     from batchgenerators.utilities.file_and_folder_operations import (
         load_json,
         save_json,
@@ -72,7 +74,6 @@
     from nnunetv2.training.dataloading.utils import unpack_dataset
     from nnunetv2.training.loss.deep_supervision import DeepSupervisionWrapper
     from nnunetv2.training.lr_scheduler.polylr import PolyLRScheduler
-    from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
     from nnunetv2.utilities.dataset_name_id_conversion import convert_id_to_dataset_name
 
 # grpcio currently has a log spamming bug that seems to be triggered by multithreading/multiprocessing
@@ -100,7 +101,7 @@ def __init__(
         checkpoint_and_state_module: ClientCheckpointAndStateModule | None = None,
         reporters: Sequence[BaseReporter] | None = None,
         client_name: str | None = None,
-        nnunet_trainer_class: type[nnUNetTrainer] = nnUNetTrainer,
+        nnunet_trainer_class: type[nnUNetTrainerModule.nnUNetTrainer] = nnUNetTrainerModule.nnUNetTrainer,
         nnunet_trainer_class_kwargs: dict[str, Any] | None = None,
     ) -> None:
         """
@@ -208,7 +209,7 @@ def __init__(
         # nnunet specific attributes to be initialized in setup_client
         self.nnunet_trainer_class = nnunet_trainer_class
         self.nnunet_trainer_class_kwargs = nnunet_trainer_class_kwargs or {}
-        self.nnunet_trainer: nnUNetTrainer
+        self.nnunet_trainer: nnUNetTrainerModule.nnUNetTrainer
         self.nnunet_config: NnunetConfig
         self.plans: dict[str, Any] | None = None
         self.steps_per_round: int  # N steps per server round
@@ -620,6 +621,12 @@ def setup_client(self, config: Config) -> None:
                 device=self.device,
                 **self.nnunet_trainer_class_kwargs,
             )
+
+            # NOTE: Monkey Patch to force the nnunet_trainer to use our version of the PolyLRScheduler instead of
+            # NnUnet version. This is because NnUnet's hasn't updated their scheduler to the new torch signature and
+            # does not appear to intend to do so. The fix is very minimum. So we patch it here.
+            nnUNetTrainerModule.PolyLRScheduler = LocalPolyLRScheduler
+
             # nnunet_trainer initialization
             self.nnunet_trainer.initialize()
             # This is done by nnunet_trainer in self.on_train_start, we
diff --git a/fl4health/clients/nnunet_client.py b/fl4health/clients/nnunet_client.py
index 00533b21e..d8f16f376 100644
--- a/fl4health/clients/nnunet_client.py
+++ b/fl4health/clients/nnunet_client.py
@@ -33,6 +33,7 @@
 from fl4health.utils.nnunet_utils import (
     NNUNET_DEFAULT_NP,
     NNUNET_N_SPATIAL_DIMS,
+    LocalPolyLRScheduler,
     Module2LossWrapper,
     NnunetConfig,
     NnUNetDataLoaderWrapper,
@@ -50,6 +51,7 @@
     # silences a bunch of deprecation warnings related to scipy.ndimage
     # Raised an issue with nnunet. https://github.com/MIC-DKFZ/nnUNet/issues/2370
     warnings.filterwarnings("ignore", category=DeprecationWarning)
+    import nnunetv2.training.nnUNetTrainer.nnUNetTrainer as nnUNetTrainerModule
     from batchgenerators.utilities.file_and_folder_operations import load_json, save_json
     from nnunetv2.experiment_planning.experiment_planners.default_experiment_planner import ExperimentPlanner
     from nnunetv2.experiment_planning.plan_and_preprocess_api import extract_fingerprints, preprocess_dataset
@@ -58,7 +60,6 @@
     from nnunetv2.training.dataloading.utils import unpack_dataset
     from nnunetv2.training.loss.deep_supervision import DeepSupervisionWrapper
     from nnunetv2.training.lr_scheduler.polylr import PolyLRScheduler
-    from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
     from nnunetv2.utilities.dataset_name_id_conversion import convert_id_to_dataset_name
 
 # grpcio currently has a log spamming bug that seems to be triggered by multithreading/multiprocessing
@@ -86,7 +87,7 @@ def __init__(
         checkpoint_and_state_module: ClientCheckpointAndStateModule | None = None,
         reporters: Sequence[BaseReporter] | None = None,
         client_name: str | None = None,
-        nnunet_trainer_class: type[nnUNetTrainer] = nnUNetTrainer,
+        nnunet_trainer_class: type[nnUNetTrainerModule.nnUNetTrainer] = nnUNetTrainerModule.nnUNetTrainer,
         nnunet_trainer_class_kwargs: dict[str, Any] | None = None,
     ) -> None:
         """
@@ -191,7 +192,7 @@ def __init__(
         self.nnunet_trainer_class_kwargs = (
             nnunet_trainer_class_kwargs if nnunet_trainer_class_kwargs is not None else {}
         )
-        self.nnunet_trainer: nnUNetTrainer
+        self.nnunet_trainer: nnUNetTrainerModule.nnUNetTrainer
         self.nnunet_config: NnunetConfig
         self.plans: dict[str, Any] | None = None
         self.steps_per_round: int  # N steps per server round
@@ -585,6 +586,12 @@ def setup_client(self, config: Config) -> None:
                 device=self.device,
                 **self.nnunet_trainer_class_kwargs,
             )
+
+            # NOTE: Monkey Patch to force the nnunet_trainer to use our version of the PolyLRScheduler instead of
+            # NnUnet version. This is because NnUnet's hasn't updated their scheduler to the new torch signature and
+            # does not appear to intend to do so. The fix is very minimum. So we patch it here.
+            nnUNetTrainerModule.PolyLRScheduler = LocalPolyLRScheduler
+
             # nnunet_trainer initialization
             self.nnunet_trainer.initialize()
             # This is done by nnunet_trainer in self.on_train_start, we
diff --git a/fl4health/mixins/personalized/ditto.py b/fl4health/mixins/personalized/ditto.py
index 01506d092..2db2a6b42 100644
--- a/fl4health/mixins/personalized/ditto.py
+++ b/fl4health/mixins/personalized/ditto.py
@@ -124,6 +124,13 @@ def _copy_optimizer_with_new_params(self: DittoPersonalizedProtocol, original_op
 
         optimizer_kwargs = {k: v for k, v in param_group.items() if k not in ("params", "initial_lr")}
         assert self.global_model is not None
+
+        # NOTE: This is a small workaround for torch back-compatibility in AdamW. Torch injects a key (that isn't part
+        # of the class signature) into the param groups called "decoupled_weight_decay" which cases an error in the
+        # kwargs below. See: https://github.com/pytorch/pytorch/blob/v2.11.0/torch/optim/adamw.py#L57
+        if optim_class == torch.optim.AdamW:
+            optimizer_kwargs.pop("decoupled_weight_decay")
+
         global_optimizer = optim_class(self.global_model.parameters(), **optimizer_kwargs)
 
         # maintain initial_lr for schedulers
diff --git a/fl4health/utils/nnunet_utils.py b/fl4health/utils/nnunet_utils.py
index d3d98f961..5c6885823 100644
--- a/fl4health/utils/nnunet_utils.py
+++ b/fl4health/utils/nnunet_utils.py
@@ -543,3 +543,50 @@ def get_lr(self) -> list[float | torch.Tensor]:
             log(INFO, f"Decaying LR of optimizer to {new_lr} at step {curr_step}")
 
         return [new_lr] * len(self.optimizer.param_groups)
+
+
+class LocalPolyLRScheduler(_LRScheduler):
+    def __init__(
+        self,
+        optimizer: torch.optim.Optimizer,
+        initial_lr: float,
+        max_steps: int,
+        exponent: float = 0.9,
+        current_step: int | None = None,
+    ):
+        """
+        NOTE: This class is PURELY to facilitate a monkey patch within the NnUnetTrainer class that creates a
+        scheduler in its initialize() call with an outdated signature. The fix is quite easy and this class is simple.
+        So we're comfortable doing a quick fix at the moment.
+
+        Learning rate (LR) scheduler with polynomial decay across fixed windows of size ``steps_per_lr``.
+
+        Args:
+            optimizer (Optimizer): The optimizer to apply LR scheduler to.
+            initial_lr (float): The initial learning rate of the optimizer.
+            max_steps (int): The maximum total number of steps across all FL rounds.
+            exponent (float): Controls how quickly LR decreases over time. Higher values lead to more rapid descent.
+                Defaults to 0.9.
+            current_step (int | None, optional): Current training step count. Defaults to None.
+        """
+        self.optimizer = optimizer
+        self.initial_lr = initial_lr
+        self.max_steps = max_steps
+        self.exponent = exponent
+        self.ctr = 0
+        super().__init__(optimizer, current_step if current_step is not None else -1)
+
+    def step(self, current_step: int | None = None) -> None:
+        """
+        Step the learning rate scheduler and update the optimizer's learning rate.
+
+        Args:
+            current_step (int | None, optional): Current training step count. Defaults to None.
+        """
+        if current_step is None or current_step == -1:
+            current_step = self.ctr
+            self.ctr += 1
+
+        new_lr = self.initial_lr * (1 - current_step / self.max_steps) ** self.exponent
+        for param_group in self.optimizer.param_groups:
+            param_group["lr"] = new_lr

From 2ab191a62102f14eaa9a2fb2d5c591285c0b89da Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Wed, 13 May 2026 15:50:43 -0400
Subject: [PATCH 07/13] More upgrades for vulnerabilities

---
 .github/workflows/static_code_checks.yaml |   6 +-
 pyproject.toml                            |   6 +-
 uv.lock                                   | 148 ++++++++++++++--------
 3 files changed, 101 insertions(+), 59 deletions(-)

diff --git a/.github/workflows/static_code_checks.yaml b/.github/workflows/static_code_checks.yaml
index 965fc9ea4..fe9fd4654 100644
--- a/.github/workflows/static_code_checks.yaml
+++ b/.github/workflows/static_code_checks.yaml
@@ -47,10 +47,12 @@ jobs:
         uses: pypa/gh-action-pip-audit@v1.1.0
         with:
           virtual-environment: .venv/
-          # CVE-2026-26007 is a cryptography vulnerability that requires cryptography>=46.0.5, but flwr (flower)
-          # requires cryptography<45.0.0, blocking the upgrade.
+          # CVE-2026-26007, CVE-2026-34073 are cryptography vulnerability that requires cryptography>=46.0.5, but
+          # flwr (flower) requires cryptography<45.0.0, blocking the upgrade.
           ignore-vulns: |
             CVE-2026-26007
+            CVE-2026-34073
+
 
       # Deleting some temporary files and useless folders to free up space
       # Deleting /usr/share/dotnet should clear ~4GB of space.
diff --git a/pyproject.toml b/pyproject.toml
index 029461ad1..e57ef43a2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,16 +58,16 @@ dev = [
     "torchtext>=0.14.1,<1.0.0",
     "torchdata>=0.7.0,<1.0.0",
     "torcheval>=0.0.6,<1.0.0",
-    "transformers>=4.37.2,<5.0.0",
+    "transformers>=5.0.0,<6.0.0",
     "datasets>=2.17.1,<3.0.0",
 ]
 
 test = [
-    "pytest>=8.3.4,<9.0.0",
+    "pytest>8.3.4",
     "mock>=5.1.0,<6.0.0",
     "pytest-cov>=4.1.0,<5.0.0",
     "freezegun>=1.4.0,<2.0.0",
-    "pytest-asyncio>=0.25.2,<1.0.0",
+    "pytest-asyncio>=1.0.0,<2.0.0",
     "py-cpuinfo>=9.0.0,<10.0.0",
 ]
 
diff --git a/uv.lock b/uv.lock
index 7649b99b3..eb79e8b26 100644
--- a/uv.lock
+++ b/uv.lock
@@ -214,6 +214,15 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/77/f5/21d2de20e8b8b0408f0681956ca2c69f1320a3848ac50e6e7f39c6159675/babel-2.18.0-py3-none-any.whl", hash = "sha256:e2b422b277c2b9a9630c1d7903c2a00d0830c409c59ac8cae9081c92f1aeba35", size = 10196845, upload-time = "2026-02-01T12:30:53.445Z" },
 ]
 
+[[package]]
+name = "backports-asyncio-runner"
+version = "1.2.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/8e/ff/70dca7d7cb1cbc0edb2c6cc0c38b65cba36cccc491eca64cabd5fe7f8670/backports_asyncio_runner-1.2.0.tar.gz", hash = "sha256:a5aa7b2b7d8f8bfcaa2b57313f70792df84e32a2a746f585213373f900b42162", size = 69893, upload-time = "2025-07-02T02:27:15.685Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/a0/59/76ab57e3fe74484f48a53f8e337171b4a2349e506eabe136d7e01d059086/backports_asyncio_runner-1.2.0-py3-none-any.whl", hash = "sha256:0da0a936a8aeb554eccb426dc55af3ba63bcdc69fa1a600b5bb305413a4477b5", size = 12313, upload-time = "2025-07-02T02:27:14.263Z" },
+]
+
 [[package]]
 name = "backports-zstd"
 version = "1.5.0"
@@ -669,9 +678,6 @@ wheels = [
 ]
 
 [package.optional-dependencies]
-cublas = [
-    { name = "nvidia-cublas", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
-]
 cudart = [
     { name = "nvidia-cuda-runtime", marker = "sys_platform == 'linux' or sys_platform == 'win32'" },
 ]
@@ -1204,7 +1210,7 @@ dev = [
     { name = "torchinfo", specifier = ">=1.8.0,<2.0.0" },
     { name = "torchtext", specifier = ">=0.14.1,<1.0.0" },
     { name = "torchvision", specifier = ">=0.21.0" },
-    { name = "transformers", specifier = ">=4.37.2,<5.0.0" },
+    { name = "transformers", specifier = ">=5.0.0,<6.0.0" },
 ]
 docs = [
     { name = "mkdocs", specifier = ">=1.6.0,<2.0.0" },
@@ -1234,8 +1240,8 @@ test = [
     { name = "freezegun", specifier = ">=1.4.0,<2.0.0" },
     { name = "mock", specifier = ">=5.1.0,<6.0.0" },
     { name = "py-cpuinfo", specifier = ">=9.0.0,<10.0.0" },
-    { name = "pytest", specifier = ">=8.3.4,<9.0.0" },
-    { name = "pytest-asyncio", specifier = ">=0.25.2,<1.0.0" },
+    { name = "pytest", specifier = ">8.3.4" },
+    { name = "pytest-asyncio", specifier = ">=1.0.0,<2.0.0" },
     { name = "pytest-cov", specifier = ">=4.1.0,<5.0.0" },
 ]
 
@@ -1621,6 +1627,34 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/1f/7f/13cd798d180af4bf4c0ceddeefba2b864a63c71645abc0308b768d67bb81/hjson-3.1.0-py3-none-any.whl", hash = "sha256:65713cdcf13214fb554eb8b4ef803419733f4f5e551047c9b711098ab7186b89", size = 54018, upload-time = "2022-08-13T02:52:59.899Z" },
 ]
 
+[[package]]
+name = "httpcore"
+version = "1.0.9"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "certifi" },
+    { name = "h11" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/06/94/82699a10bca87a5556c9c59b5963f2d039dbd239f25bc2a63907a05a14cb/httpcore-1.0.9.tar.gz", hash = "sha256:6e34463af53fd2ab5d807f399a9b45ea31c3dfa2276f15a2c3f00afff6e176e8", size = 85484, upload-time = "2025-04-24T22:06:22.219Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/7e/f5/f66802a942d491edb555dd61e3a9961140fd64c90bce1eafd741609d334d/httpcore-1.0.9-py3-none-any.whl", hash = "sha256:2d400746a40668fc9dec9810239072b40b4484b640a8c38fd654a024c7a1bf55", size = 78784, upload-time = "2025-04-24T22:06:20.566Z" },
+]
+
+[[package]]
+name = "httpx"
+version = "0.28.1"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "anyio" },
+    { name = "certifi" },
+    { name = "httpcore" },
+    { name = "idna" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/b1/df/48c586a5fe32a0f01324ee087459e112ebb7224f646c0b5023f5e79e9956/httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc", size = 141406, upload-time = "2024-12-06T15:37:23.222Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad", size = 73517, upload-time = "2024-12-06T15:37:21.509Z" },
+]
+
 [[package]]
 name = "huey"
 version = "2.6.0"
@@ -1632,21 +1666,22 @@ wheels = [
 
 [[package]]
 name = "huggingface-hub"
-version = "0.36.2"
+version = "1.13.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "filelock" },
     { name = "fsspec" },
-    { name = "hf-xet", marker = "platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'" },
+    { name = "hf-xet", marker = "platform_machine == 'AMD64' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'" },
+    { name = "httpx" },
     { name = "packaging" },
     { name = "pyyaml" },
-    { name = "requests" },
     { name = "tqdm" },
+    { name = "typer" },
     { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/7c/b7/8cb61d2eece5fb05a83271da168186721c450eb74e3c31f7ef3169fa475b/huggingface_hub-0.36.2.tar.gz", hash = "sha256:1934304d2fb224f8afa3b87007d58501acfda9215b334eed53072dd5e815ff7a", size = 649782, upload-time = "2026-02-06T09:24:13.098Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/89/ff/ec7ed2eb43bd7ce8bb2233d109cc235c3e807ffe5e469dc09db261fac05e/huggingface_hub-1.13.0.tar.gz", hash = "sha256:f6df2dac5abe82ce2fe05873d10d5ff47bc677d616a2f521f4ee26db9415d9d0", size = 781788, upload-time = "2026-04-30T11:57:33.858Z" }
 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/93/db/4b1cdae9460ae1f3ca020cd767f013430ce23eb1d9c890ae3a0609b38d26/huggingface_hub-1.13.0-py3-none-any.whl", hash = "sha256:e942cb50d6a08dd5306688b1ac05bda157fd2fcc88b63dae405f7bd0d3234005", size = 660643, upload-time = "2026-04-30T11:57:31.802Z" },
 ]
 
 [[package]]
@@ -2639,11 +2674,14 @@ wheels = [
 
 [[package]]
 name = "nvidia-cublas"
-version = "13.1.0.3"
+version = "13.1.1.3"
 source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "nvidia-cuda-nvrtc" },
+]
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/e1/a5/fce49e2ae977e0ccc084e5adafceb4f0ac0c8333cb6863501618a7277f67/nvidia_cublas-13.1.0.3-py3-none-manylinux_2_27_aarch64.whl", hash = "sha256:c86fc7f7ae36d7528288c5d88098edcb7b02c633d262e7ddbb86b0ad91be5df2", size = 542851226, upload-time = "2025-10-09T08:59:04.818Z" },
-    { url = "https://files.pythonhosted.org/packages/e7/44/423ac00af4dd95a5aeb27207e2c0d9b7118702149bf4704c3ddb55bb7429/nvidia_cublas-13.1.0.3-py3-none-manylinux_2_27_x86_64.whl", hash = "sha256:ee8722c1f0145ab246bccb9e452153b5e0515fd094c3678df50b2a0888b8b171", size = 423133236, upload-time = "2025-10-09T08:59:32.536Z" },
+    { url = "https://files.pythonhosted.org/packages/a7/a1/0bd24ee8c8d03adac032fd2909426a00c88f8c57961b1277ded97f91119f/nvidia_cublas-13.1.1.3-py3-none-manylinux_2_27_aarch64.whl", hash = "sha256:b7a210458267ac818974c53038fbec2e969d5c99f305ab15c72522fa9f001dd5", size = 542848918, upload-time = "2026-04-08T18:46:22.985Z" },
+    { url = "https://files.pythonhosted.org/packages/3b/cd/154ca20c38269e05eff77c1464e6c1da89f50a6390b565e9d82e06bc11e1/nvidia_cublas-13.1.1.3-py3-none-manylinux_2_27_x86_64.whl", hash = "sha256:37936a16db8fe4ac1f065c2139360608a543a09275cb1a1af612e08cfa065436", size = 423138758, upload-time = "2026-04-08T18:46:58.655Z" },
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 [[package]]
@@ -2675,14 +2713,14 @@ wheels = [
 
 [[package]]
 name = "nvidia-cudnn-cu13"
-version = "9.19.0.56"
+version = "9.20.0.48"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
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 wheels = [
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+    { url = "https://files.pythonhosted.org/packages/56/c5/83384d846b2fd17c44bd499b36c75a45ed4f095fbbb2252294e89cea5c5c/nvidia_cudnn_cu13-9.20.0.48-py3-none-manylinux_2_27_aarch64.whl", hash = "sha256:e31454ae00094b0c55319d9d15b6fa2fc50a9e1c0f5c8c80fb75258234e731e1", size = 444574296, upload-time = "2026-03-09T19:28:27.751Z" },
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 [[package]]
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 [[package]]
 name = "nvidia-nccl-cu13"
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 [[package]]
@@ -3524,7 +3562,7 @@ wheels = [
 
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 [[package]]
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-version = "0.26.0"
+version = "1.3.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
+    { name = "backports-asyncio-runner" },
     { name = "pytest" },
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 [[package]]

From 6cfcb416ab8ffbd41740b79d73fe2ea1856e0d09 Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Wed, 13 May 2026 16:16:28 -0400
Subject: [PATCH 08/13] Not upgrading transformers yet, as their typing seems
 really messed up

---
 .github/workflows/static_code_checks.yaml |  3 ++
 pyproject.toml                            |  2 +-
 uv.lock                                   | 50 +++++------------------
 3 files changed, 15 insertions(+), 40 deletions(-)

diff --git a/.github/workflows/static_code_checks.yaml b/.github/workflows/static_code_checks.yaml
index fe9fd4654..37f2e2483 100644
--- a/.github/workflows/static_code_checks.yaml
+++ b/.github/workflows/static_code_checks.yaml
@@ -49,9 +49,12 @@ jobs:
           virtual-environment: .venv/
           # CVE-2026-26007, CVE-2026-34073 are cryptography vulnerability that requires cryptography>=46.0.5, but
           # flwr (flower) requires cryptography<45.0.0, blocking the upgrade.
+          # CVE-2026-1839 is a vulnerability in HF transformers, but they've messed up their typing in 5+ so we're
+          # deferring this.
           ignore-vulns: |
             CVE-2026-26007
             CVE-2026-34073
+            CVE-2026-1839
 
 
       # Deleting some temporary files and useless folders to free up space
diff --git a/pyproject.toml b/pyproject.toml
index e57ef43a2..f3065f4cc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,7 +58,7 @@ dev = [
     "torchtext>=0.14.1,<1.0.0",
     "torchdata>=0.7.0,<1.0.0",
     "torcheval>=0.0.6,<1.0.0",
-    "transformers>=5.0.0,<6.0.0",
+    "transformers>=4.37.2,<5.0.0",
     "datasets>=2.17.1,<3.0.0",
 ]
 
diff --git a/uv.lock b/uv.lock
index eb79e8b26..8279c27e1 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1210,7 +1210,7 @@ dev = [
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     { name = "torchtext", specifier = ">=0.14.1,<1.0.0" },
     { name = "torchvision", specifier = ">=0.21.0" },
-    { name = "transformers", specifier = ">=5.0.0,<6.0.0" },
+    { name = "transformers", specifier = ">=4.37.2,<5.0.0" },
 ]
 docs = [
     { name = "mkdocs", specifier = ">=1.6.0,<2.0.0" },
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-]
-
-[[package]]
-name = "httpx"
-version = "0.28.1"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "anyio" },
-    { name = "certifi" },
-    { name = "httpcore" },
-    { name = "idna" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/b1/df/48c586a5fe32a0f01324ee087459e112ebb7224f646c0b5023f5e79e9956/httpx-0.28.1.tar.gz", hash = "sha256:75e98c5f16b0f35b567856f597f06ff2270a374470a5c2392242528e3e3e42fc", size = 141406, upload-time = "2024-12-06T15:37:23.222Z" }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/2a/39/e50c7c3a983047577ee07d2a9e53faf5a69493943ec3f6a384bdc792deb2/httpx-0.28.1-py3-none-any.whl", hash = "sha256:d909fcccc110f8c7faf814ca82a9a4d816bc5a6dbfea25d6591d6985b8ba59ad", size = 73517, upload-time = "2024-12-06T15:37:21.509Z" },
-]
-
 [[package]]
 name = "huey"
 version = "2.6.0"
@@ -1666,22 +1638,21 @@ wheels = [
 
 [[package]]
 name = "huggingface-hub"
-version = "1.13.0"
+version = "0.36.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "filelock" },
     { name = "fsspec" },
-    { name = "hf-xet", marker = "platform_machine == 'AMD64' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'" },
-    { name = "httpx" },
+    { name = "hf-xet", marker = "platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'" },
     { name = "packaging" },
     { name = "pyyaml" },
+    { name = "requests" },
     { name = "tqdm" },
-    { name = "typer" },
     { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/89/ff/ec7ed2eb43bd7ce8bb2233d109cc235c3e807ffe5e469dc09db261fac05e/huggingface_hub-1.13.0.tar.gz", hash = "sha256:f6df2dac5abe82ce2fe05873d10d5ff47bc677d616a2f521f4ee26db9415d9d0", size = 781788, upload-time = "2026-04-30T11:57:33.858Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/7c/b7/8cb61d2eece5fb05a83271da168186721c450eb74e3c31f7ef3169fa475b/huggingface_hub-0.36.2.tar.gz", hash = "sha256:1934304d2fb224f8afa3b87007d58501acfda9215b334eed53072dd5e815ff7a", size = 649782, upload-time = "2026-02-06T09:24:13.098Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/93/db/4b1cdae9460ae1f3ca020cd767f013430ce23eb1d9c890ae3a0609b38d26/huggingface_hub-1.13.0-py3-none-any.whl", hash = "sha256:e942cb50d6a08dd5306688b1ac05bda157fd2fcc88b63dae405f7bd0d3234005", size = 660643, upload-time = "2026-04-30T11:57:31.802Z" },
+    { url = "https://files.pythonhosted.org/packages/a8/af/48ac8483240de756d2438c380746e7130d1c6f75802ef22f3c6d49982787/huggingface_hub-0.36.2-py3-none-any.whl", hash = "sha256:48f0c8eac16145dfce371e9d2d7772854a4f591bcb56c9cf548accf531d54270", size = 566395, upload-time = "2026-02-06T09:24:11.133Z" },
 ]
 
 [[package]]
@@ -4523,22 +4494,23 @@ wheels = [
 
 [[package]]
 name = "transformers"
-version = "5.8.1"
+version = "4.57.6"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
+    { name = "filelock" },
     { name = "huggingface-hub" },
     { name = "numpy" },
     { name = "packaging" },
     { name = "pyyaml" },
     { name = "regex" },
+    { name = "requests" },
     { name = "safetensors" },
     { name = "tokenizers" },
     { name = "tqdm" },
-    { name = "typer" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/e7/e6/4134ea2fbea322cddc7ffc94a0d8ee47fe32ce8e876b320cd37d88edfc4d/transformers-5.8.1.tar.gz", hash = "sha256:4dd5b6de4105725104d84fd6abd74b305f4debfc251b38c648ee5dd087cf543b", size = 8532019, upload-time = "2026-05-13T03:21:57.234Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c4/35/67252acc1b929dc88b6602e8c4a982e64f31e733b804c14bc24b47da35e6/transformers-4.57.6.tar.gz", hash = "sha256:55e44126ece9dc0a291521b7e5492b572e6ef2766338a610b9ab5afbb70689d3", size = 10134912, upload-time = "2026-01-16T10:38:39.284Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/fc/b1/8be7e7ef0b5200491312201918b6125ef9c9df9dd0f0240ccef9ac824e6b/transformers-5.8.1-py3-none-any.whl", hash = "sha256:5340fb95962162cdfdae5cc91d7f8fedd92ed75216c1154c5e1f590fcf56dd0e", size = 10632882, upload-time = "2026-05-13T03:21:52.876Z" },
+    { url = "https://files.pythonhosted.org/packages/03/b8/e484ef633af3887baeeb4b6ad12743363af7cce68ae51e938e00aaa0529d/transformers-4.57.6-py3-none-any.whl", hash = "sha256:4c9e9de11333ddfe5114bc872c9f370509198acf0b87a832a0ab9458e2bd0550", size = 11993498, upload-time = "2026-01-16T10:38:31.289Z" },
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 [[package]]

From e72a0e617b633b2415f64c983e893da4be74d10d Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Wed, 13 May 2026 17:32:43 -0400
Subject: [PATCH 09/13] Fixing the APFL errors but investigating why they are
 different

---
 fl4health/mixins/personalized/ditto.py     |  2 +-
 tests/smoke_tests/apfl_client_metrics.json | 16 ++++++++--------
 tests/smoke_tests/apfl_server_metrics.json | 18 +++++++++---------
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/fl4health/mixins/personalized/ditto.py b/fl4health/mixins/personalized/ditto.py
index 2db2a6b42..b5ea78bf5 100644
--- a/fl4health/mixins/personalized/ditto.py
+++ b/fl4health/mixins/personalized/ditto.py
@@ -126,7 +126,7 @@ def _copy_optimizer_with_new_params(self: DittoPersonalizedProtocol, original_op
         assert self.global_model is not None
 
         # NOTE: This is a small workaround for torch back-compatibility in AdamW. Torch injects a key (that isn't part
-        # of the class signature) into the param groups called "decoupled_weight_decay" which cases an error in the
+        # of the class signature) into the param groups called "decoupled_weight_decay" which causes an error in the
         # kwargs below. See: https://github.com/pytorch/pytorch/blob/v2.11.0/torch/optim/adamw.py#L57
         if optim_class == torch.optim.AdamW:
             optimizer_kwargs.pop("decoupled_weight_decay")
diff --git a/tests/smoke_tests/apfl_client_metrics.json b/tests/smoke_tests/apfl_client_metrics.json
index 384a2bd89..4b255a16b 100644
--- a/tests/smoke_tests/apfl_client_metrics.json
+++ b/tests/smoke_tests/apfl_client_metrics.json
@@ -12,11 +12,11 @@
                 "local": 1.6362
             },
             "eval_round_metrics": {
-                "val - personal - accuracy": 0.5269,
+                "val - personal - accuracy": 0.52433,
                 "val - global - accuracy": 0.5331,
-                "val - local - accuracy": 0.4984
+                "val - local - accuracy": 0.49900
             },
-            "eval_round_loss": 1.5862
+            "eval_round_loss": 1.57742
         },
         "2": {
             "fit_round_metrics": {
@@ -30,11 +30,11 @@
                 "local": 0.79530
             },
             "eval_round_metrics": {
-                "val - personal - accuracy": 0.74766,
+                "val - personal - accuracy": 0.74322,
                 "val - global - accuracy": 0.72833,
                 "val - local - accuracy": 0.70289
             },
-            "eval_round_loss": 0.86359
+            "eval_round_loss": 0.85188
         },
         "3": {
             "fit_round_metrics": {
@@ -48,11 +48,11 @@
                 "local": 0.74168
             },
             "eval_round_metrics": {
-                "val - personal - accuracy": 0.80833,
+                "val - personal - accuracy": 0.78300,
                 "val - global - accuracy": 0.75322,
-                "val - local - accuracy": 0.80711
+                "val - local - accuracy": 0.74700
             },
-            "eval_round_loss": 0.65421
+            "eval_round_loss": 0.72138
         }
     }
 }
diff --git a/tests/smoke_tests/apfl_server_metrics.json b/tests/smoke_tests/apfl_server_metrics.json
index fd1d1aa2c..e093bea16 100644
--- a/tests/smoke_tests/apfl_server_metrics.json
+++ b/tests/smoke_tests/apfl_server_metrics.json
@@ -2,27 +2,27 @@
     "rounds": {
         "1": {
             "eval_round_metrics_aggregated": {
-                "val - personal - accuracy": 0.5269,
+                "val - personal - accuracy": 0.52433,
                 "val - global - accuracy": 0.5331,
-                "val - local - accuracy": 0.4984
+                "val - local - accuracy": 0.4990
             },
-            "val - loss - aggregated": 1.5862
+            "val - loss - aggregated": 1.57742
         },
         "2": {
             "eval_round_metrics_aggregated": {
-                "val - personal - accuracy": 0.74766,
+                "val - personal - accuracy": 0.74322,
                 "val - global - accuracy": 0.72833,
-                "val - local - accuracy": 0.70288
+                "val - local - accuracy": 0.69955
             },
-            "val - loss - aggregated": 0.86359
+            "val - loss - aggregated": 0.85188
         },
         "3": {
             "eval_round_metrics_aggregated": {
-                "val - personal - accuracy": 0.80833,
+                "val - personal - accuracy": 0.78300,
                 "val - global - accuracy": 0.75322,
-                "val - local - accuracy": 0.80711
+                "val - local - accuracy": 0.74700
             },
-            "val - loss - aggregated": 0.65421
+            "val - loss - aggregated": 0.72138
         }
     }
 }

From 984b08a87c30eb1472368a8915aae962ed098a60 Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Thu, 14 May 2026 08:41:34 -0400
Subject: [PATCH 10/13] Some apfl smoketest fixes

---
 tests/smoke_tests/apfl_client_metrics.json | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/tests/smoke_tests/apfl_client_metrics.json b/tests/smoke_tests/apfl_client_metrics.json
index 4b255a16b..bd71f49a5 100644
--- a/tests/smoke_tests/apfl_client_metrics.json
+++ b/tests/smoke_tests/apfl_client_metrics.json
@@ -2,14 +2,14 @@
     "rounds": {
         "1": {
             "fit_round_metrics": {
-                "train - personal - accuracy": 0.6063,
+                "train - personal - accuracy": 0.60938,
                 "train - global - accuracy": 0.6078,
                 "train - local - accuracy": 0.4797
             },
             "fit_round_losses": {
                 "backward": 1.4428,
                 "global": 1.3272,
-                "local": 1.6362
+                "local": 1.63674
             },
             "eval_round_metrics": {
                 "val - personal - accuracy": 0.52433,
@@ -20,32 +20,32 @@
         },
         "2": {
             "fit_round_metrics": {
-                "train - personal - accuracy": 0.77812,
+                "train - personal - accuracy": 0.78281,
                 "train - global - accuracy": 0.79687,
-                "train - local - accuracy": 0.75156
+                "train - local - accuracy": 0.74688
             },
             "fit_round_losses": {
-                "backward": 0.67724,
+                "backward": 0.67673,
                 "global": 0.68586,
-                "local": 0.79530
+                "local": 0.79693
             },
             "eval_round_metrics": {
                 "val - personal - accuracy": 0.74322,
                 "val - global - accuracy": 0.72833,
-                "val - local - accuracy": 0.70289
+                "val - local - accuracy": 0.69956
             },
             "eval_round_loss": 0.85188
         },
         "3": {
             "fit_round_metrics": {
-                "train - personal - accuracy": 0.82188,
+                "train - personal - accuracy": 0.82656,
                 "train - global - accuracy": 0.85625,
-                "train - local - accuracy": 0.80156
+                "train - local - accuracy": 0.81094
             },
             "fit_round_losses": {
-                "backward": 0.59617,
+                "backward": 0.60156,
                 "global": 0.54568,
-                "local": 0.74168
+                "local": 0.75705
             },
             "eval_round_metrics": {
                 "val - personal - accuracy": 0.78300,

From 280e246ff4d1b41a11d13eb9169a618cca29bec7 Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Thu, 14 May 2026 16:49:36 -0400
Subject: [PATCH 11/13] Fixing a few of the GPFL metrics too

---
 tests/smoke_tests/gpfl_client_metrics.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/smoke_tests/gpfl_client_metrics.json b/tests/smoke_tests/gpfl_client_metrics.json
index 812b34e2b..dce271a1a 100644
--- a/tests/smoke_tests/gpfl_client_metrics.json
+++ b/tests/smoke_tests/gpfl_client_metrics.json
@@ -20,10 +20,10 @@
                 "train - prediction - accuracy": 0.9649
             },
             "fit_round_losses": {
-                "gce_softmax_loss": 1.9233,
+                "gce_softmax_loss": 1.92257,
                 "prediction_loss": 0.1157,
-                "magnitude_level_loss": 47.6012,
-                "backward": 2.5151
+                "magnitude_level_loss": 47.57951,
+                "backward": 2.51400
             },
             "eval_round_metrics": {
                 "val - prediction - accuracy": 0.96625
@@ -37,7 +37,7 @@
             "fit_round_losses": {
                 "gce_softmax_loss": 1.8773,
                 "prediction_loss": 0.0888,
-                "magnitude_level_loss": 39.9928,
+                "magnitude_level_loss": 39.99178,
                 "backward": 2.3661
             },
             "eval_round_metrics": {

From bc06c190cd174fa30c73b36577d8db9e89db8742 Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Thu, 14 May 2026 17:02:35 -0400
Subject: [PATCH 12/13] Fixing a few of the GPFL metrics too

---
 tests/smoke_tests/gpfl_client_metrics.json | 2 +-
 tests/smoke_tests/gpfl_server_metrics.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/smoke_tests/gpfl_client_metrics.json b/tests/smoke_tests/gpfl_client_metrics.json
index dce271a1a..547e2543a 100644
--- a/tests/smoke_tests/gpfl_client_metrics.json
+++ b/tests/smoke_tests/gpfl_client_metrics.json
@@ -11,7 +11,7 @@
                 "gce_softmax_loss": 2.0824
             },
             "eval_round_metrics": {
-                "val - prediction - accuracy": 0.9396
+                "val - prediction - accuracy": 0.940333
             },
             "eval_round_loss": 0.1954
         },
diff --git a/tests/smoke_tests/gpfl_server_metrics.json b/tests/smoke_tests/gpfl_server_metrics.json
index 6e670f243..1af5e2570 100644
--- a/tests/smoke_tests/gpfl_server_metrics.json
+++ b/tests/smoke_tests/gpfl_server_metrics.json
@@ -2,7 +2,7 @@
     "rounds": {
         "1": {
             "eval_round_metrics_aggregated": {
-                "val - prediction - accuracy": 0.9396
+                "val - prediction - accuracy": 0.940333
             },
             "val - loss - aggregated": 0.1954
         },

From 8bc82ee711c390ff948427df8a2bd77eca0ed27d Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Thu, 14 May 2026 17:34:45 -0400
Subject: [PATCH 13/13] Fixing a few of the GPFL metrics too

---
 tests/smoke_tests/gpfl_client_metrics.json | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tests/smoke_tests/gpfl_client_metrics.json b/tests/smoke_tests/gpfl_client_metrics.json
index 547e2543a..ad77258c5 100644
--- a/tests/smoke_tests/gpfl_client_metrics.json
+++ b/tests/smoke_tests/gpfl_client_metrics.json
@@ -5,10 +5,10 @@
                 "train - prediction - accuracy": 0.9245
             },
             "fit_round_losses": {
-                "backward": 2.9377,
+                "backward": 2.93887,
                 "prediction_loss": 0.24898,
-                "magnitude_level_loss": 60.6323,
-                "gce_softmax_loss": 2.0824
+                "magnitude_level_loss": 60.67625,
+                "gce_softmax_loss": 2.08305
             },
             "eval_round_metrics": {
                 "val - prediction - accuracy": 0.940333
@@ -22,8 +22,8 @@
             "fit_round_losses": {
                 "gce_softmax_loss": 1.92257,
                 "prediction_loss": 0.1157,
-                "magnitude_level_loss": 47.57951,
-                "backward": 2.51400
+                "magnitude_level_loss": 47.59576,
+                "backward": 2.51467
             },
             "eval_round_metrics": {
                 "val - prediction - accuracy": 0.96625
@@ -37,7 +37,7 @@
             "fit_round_losses": {
                 "gce_softmax_loss": 1.8773,
                 "prediction_loss": 0.0888,
-                "magnitude_level_loss": 39.99178,
+                "magnitude_level_loss": 39.99481,
                 "backward": 2.3661
             },
             "eval_round_metrics": {