From bf65de56c262c930c2eacd5d692c9cab13aaebc0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 3 Jun 2026 14:50:57 +0000
Subject: [PATCH 1/4] Bump astral-sh/setup-uv from 8.1.0 to 8.2.0

Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 8.1.0 to 8.2.0.
- [Release notes](https://github.com/astral-sh/setup-uv/releases)
- [Commits](https://github.com/astral-sh/setup-uv/compare/v8.1.0...v8.2.0)

---
updated-dependencies:
- dependency-name: astral-sh/setup-uv
  dependency-version: 8.2.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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 80734527f..62318c515 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@v8.1.0
+        uses: astral-sh/setup-uv@v8.2.0
         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 44eebed85..3bf90ea03 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@v8.1.0
+        uses: astral-sh/setup-uv@v8.2.0
         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 6ae499184..fe2427422 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@v8.1.0
+        uses: astral-sh/setup-uv@v8.2.0
         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 65c9fdd2d..ffd698012 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@v8.1.0
+        uses: astral-sh/setup-uv@v8.2.0
         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 70e776dcc..634dd44cc 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@v8.1.0
+        uses: astral-sh/setup-uv@v8.2.0
         with:
           version: "0.9.11"
           enable-cache: true
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 4ad024dea..9600c3694 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@v8.1.0
+        uses: astral-sh/setup-uv@v8.2.0
         with:
           version: "0.9.11"
           enable-cache: true

From 061fe879e2a13943653087a5e8bdcfcc394f6eed Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 8 Jun 2026 19:43:11 +0000
Subject: [PATCH 2/4] [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: 0.11.16 → 0.11.19](https://github.com/astral-sh/uv-pre-commit/compare/0.11.16...0.11.19)
- [github.com/astral-sh/ruff-pre-commit: v0.15.14 → v0.15.16](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.14...v0.15.16)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 736e86896..b81cb212b 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: 0.11.16
+    rev: 0.11.19
     hooks:
       - id: uv-lock
 
@@ -26,7 +26,7 @@ repos:
       - id: check-toml
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 'v0.15.14'
+    rev: 'v0.15.16'
     hooks:
     - id: ruff-check
       args: [--fix, --exit-non-zero-on-fix]

From 0779d16403c591502627f5f5fe6816e75a84c873 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 8 Jun 2026 23:03:40 +0000
Subject: [PATCH 3/4] Bump codecov/codecov-action from 6 to 7

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 6 to 7.
- [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/v6...v7)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-version: '7'
  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 44eebed85..f086e86c1 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@v6
+        uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: VectorInstitute/FL4Health
diff --git a/.github/workflows/standard_smoke_tests.yaml b/.github/workflows/standard_smoke_tests.yaml
index 65c9fdd2d..d8637b73c 100644
--- a/.github/workflows/standard_smoke_tests.yaml
+++ b/.github/workflows/standard_smoke_tests.yaml
@@ -53,7 +53,7 @@ jobs:
         run: uv run pytest --test-group-count=4 --test-group=${{ 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@v6
+        uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: VectorInstitute/FL4Health
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index 4ad024dea..5b09b9642 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@v6
+        uses: codecov/codecov-action@v7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           slug: VectorInstitute/FL4Health

From 9a27ea17e1b9455b5a59bd6c2cc07335e39b3039 Mon Sep 17 00:00:00 2001
From: David Emerson <43939939+emersodb@users.noreply.github.com>
Date: Tue, 9 Jun 2026 10:08:57 -0400
Subject: [PATCH 4/4] Upgrading some libraries to address vulnerabilities

---
 uv.lock | 426 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 215 insertions(+), 211 deletions(-)

diff --git a/uv.lock b/uv.lock
index a4c87b31c..f67a19a20 100644
--- a/uv.lock
+++ b/uv.lock
@@ -54,7 +54,7 @@ wheels = [
 
 [[package]]
 name = "aiohttp"
-version = "3.13.5"
+version = "3.14.1"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "aiohappyeyeballs" },
@@ -64,27 +64,29 @@ dependencies = [
     { name = "frozenlist" },
     { name = "multidict" },
     { name = "propcache" },
+    { name = "typing-extensions" },
     { name = "yarl" },
 ]
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