Renovate: all non-major dependencies

.github/workflows/main.yml

@@ -59,7 +59,7 @@ jobs:
             - name: Install uv
               uses: astral-sh/setup-uv@v4
               with:
-                  version: "0.10.4"
+                  version: "0.11.6"
                   python-version: "3.11"
                   enable-cache: true
 
@@ -79,7 +79,7 @@ jobs:
                   AZURE_KEY_VAULT_SECRET_NAME: test
 
             - name: Upload coverage reports to Codecov
-              uses: codecov/codecov-action@671740ac38dd9b0130fbe1cec585b89eea48d3de # v5.5.2
+              uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # v5.5.4
               with:
                   directory: ${{ matrix.package_dir }}
               env:
@@ -96,7 +96,7 @@ jobs:
             - name: Install uv
               uses: astral-sh/setup-uv@v4
               with:
-                  version: "0.10.4"
+                  version: "0.11.6"
                   python-version: "3.11"
                   enable-cache: true
 
@@ -178,7 +178,7 @@ jobs:
 
 
             - name: Upload coverage reports to Codecov
-              uses: codecov/codecov-action@671740ac38dd9b0130fbe1cec585b89eea48d3de # v5.5.2
+              uses: codecov/codecov-action@75cd11691c0faa626561e295848008c8a7dddffe # v5.5.4
               with:
                 directory: test
               env:

.pre-commit-config.yaml

@@ -14,15 +14,15 @@
 ---
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.2
+    rev: v0.15.10
     hooks:
       - id: ruff-check # linter
         args:
           - --fix
       - id: ruff-format # formatter
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v1.20.0
     hooks:
       - id: mypy
         entry: mypy .
@@ -31,7 +31,7 @@ repos:
         additional_dependencies:
           ["types-PyYAML", "types-requests", "types-python-slugify", "types-psycopg2"]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.36.2
+    rev: 0.37.1
     hooks:
       # Schemas taken from https://www.schemastore.org/json/
       - id: check-jsonschema
@@ -50,6 +50,6 @@ repos:
 
   # avoid forgetting to update the lock file after pyproject.toml changes
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.10.4
+    rev: 0.11.6
     hooks:
       - id: uv-lock

cli/pyproject.toml

@@ -8,7 +8,7 @@ requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 dependencies = [
     "core==0.2.0rc0",
-    "click==8.3.1",
+    "click==8.3.2",
     "tqdm==4.67.3",
 ]
 

docker/orthanc/Dockerfile

@@ -22,7 +22,7 @@ RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get autoremove --yes && apt-get clean --yes && rm -rf /var/lib/apt/lists/*
 
 # install uv
-COPY --from=ghcr.io/astral-sh/uv:0.10.4@sha256:4cac394b6b72846f8a85a7a0e577c6d61d4e17fe2ccee65d9451a8b3c9efb4ac /uv /uvx /bin/
+COPY --from=ghcr.io/astral-sh/uv:0.11.6@sha256:b1e699368d24c57cda93c338a57a8c5a119009ba809305cc8e86986d4a006754 /uv /uvx /bin/
 ENV PYTHONPATH=/.venv/lib64/python3.11/site-packages/
 
 FROM pixl_orthanc_uv AS pixl_orthanc_with_spec

docker/pixl-python/Dockerfile

@@ -35,7 +35,7 @@ EOF
 HEALTHCHECK CMD /usr/bin/curl -f http://0.0.0.0:8000/heart-beat || exit 1
 
 # install uv
-COPY --from=ghcr.io/astral-sh/uv:0.10.4@sha256:4cac394b6b72846f8a85a7a0e577c6d61d4e17fe2ccee65d9451a8b3c9efb4ac /uv /uvx /bin/
+COPY --from=ghcr.io/astral-sh/uv:0.11.6@sha256:b1e699368d24c57cda93c338a57a8c5a119009ba809305cc8e86986d4a006754 /uv /uvx /bin/
 
 WORKDIR /app
 # specify what we're installing using build time arg

hasher/pyproject.toml

@@ -8,12 +8,12 @@ requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 dependencies = [
     "core==0.2.0rc0",
-    "azure-identity==1.25.2",
+    "azure-identity==1.25.3",
     "azure-keyvault==4.2.0",
-    "fastapi==0.129.0",
-    "hypothesis==6.151.9",
+    "fastapi==0.135.3",
+    "hypothesis==6.151.12",
     "requests==2.32.5",
-    "uvicorn==0.41.0",
+    "uvicorn==0.44.0",
 ]
 
 [project.optional-dependencies]

pixl_core/pyproject.toml

@@ -7,10 +7,10 @@ readme = "README.md"
 requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 dependencies = [
-    "aio_pika==9.5.8",
-    "azure-identity==1.25.2",
+    "aio_pika==9.6.2",
+    "azure-identity==1.25.3",
     "azure-keyvault==4.2.0",
-    "fastapi==0.129.0",
+    "fastapi==0.135.3",
     "jsonpickle==4.1.1",
     "loguru==0.7.3",
     "pandas==2.3.3",
@@ -22,7 +22,7 @@ dependencies = [
     "python-slugify==8.0.4",
     "PyYAML==6.0.3",
     "requests==2.32.5",
-    "sqlalchemy==2.0.46",
+    "sqlalchemy==2.0.49",
     "token-bucket==0.3.0",
     "xnat==0.7.2",
 ]

pixl_dcmd/pyproject.toml

@@ -12,7 +12,7 @@ dependencies = [
     "dicom-anonymizer==1.0.13.post1",
     "dicom-validator==0.7.3",
     "logger==1.4",
-    "pydicom==2.4.4",
+    "pydicom==2.4.5",
     "pydicom-data",
     "python-decouple==3.8",
     "requests==2.32.5",

pixl_export/pyproject.toml

@@ -8,7 +8,7 @@ requires-python = ">=3.11"
 classifiers = ["Programming Language :: Python :: 3"]
 dependencies = [
     "core==0.2.0rc0",
-    "uvicorn==0.41.0",
+    "uvicorn==0.44.0",
     "azure-storage-blob==12.28.0",
 ]
 

pixl_imaging/pyproject.toml

@@ -10,8 +10,8 @@ dependencies = [
     "core==0.2.0rc0",
     "aiohttp==3.13.3",
     "alembic==1.18.4",
-    "pydicom==2.4.4",
-    "uvicorn==0.41.0",
+    "pydicom==2.4.5",
+    "uvicorn==0.44.0",
 ]
 
 [project.optional-dependencies]

pyproject.toml

@@ -52,19 +52,19 @@ build-backend = "hatchling.build"
 
 [dependency-groups]
 dev = [
-    "mypy==1.19.1",
+    "mypy==1.20.0",
     "pre-commit==4.5.1",
     "pytest==8.4.2",
     "ruff>=0.11",
     "pytest-mock==3.15.1",
     "httpx==0.28.*",
     "pytest-asyncio==0.26.0",
-    "pytest-check==2.6.2",
+    "pytest-check==2.8.0",
     "pytest-cov==6.3.0",
     "pytest-pixl==0.2.0rc0",
     "xnat4tests==0.4.1",
     "dcm2niix==1.0.20250506",
-    "nibabel==5.3.3",
+    "nibabel==5.4.2",
 ]
 
 [tool.coverage.report]

pytest-pixl/pyproject.toml

@@ -9,7 +9,7 @@ classifiers = [
     "Programming Language :: Python :: 3"
 ]
 dependencies = [
-    "pydicom==2.4.4",
+    "pydicom==2.4.5",
     "pyftpdlib==2.2.0",
     "pyOpenSSL==24.3.0",
     "python-decouple==3.8",