Merge branch 'dev' into renovate/mcr.microsoft.com-devcontainers-miniconda

Author: mashehu

.devcontainer/build-devcontainer/Dockerfile

@@ -27,7 +27,7 @@ RUN rm -f /etc/apt/sources.list.d/yarn.list && \
     rm -rf /var/lib/apt/lists/*
 
 # Final stage to copy only the required files after installation
-FROM mcr.microsoft.com/devcontainers/base:2.1.7-debian12@sha256:4d49e42a3eda8a8fd8437ecd8830d50a9113dc0f3623226db5e5c10a2b156f1e AS final
+FROM mcr.microsoft.com/devcontainers/base:2.1.8-debian12@sha256:17e6cc517b483d1108b333d4c34352b0a21617f0117052e9b259d47113a9dc37 AS final
 
 # Copy only the conda environment and site-packages from build stage
 COPY --from=build /opt/conda /opt/conda

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.11
+    rev: v0.15.12
     hooks:
       - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -33,7 +33,7 @@ repos:
               tests/pipelines/__snapshots__/.*
           )$
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.20.0"
+    rev: "v1.20.2"
     hooks:
       - id: mypy
         additional_dependencies:
@@ -44,7 +44,7 @@ repos:
           - types-setuptools
           - pydantic
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.11.4
+    rev: 0.11.7
     hooks:
       - id: uv-lock
   - repo: local

CHANGELOG.md

@@ -68,8 +68,11 @@
 - nextflow source CI: set up uv ([#4208](https://github.com/nf-core/tools/pull/4208))
 - Include AI and LLM usage guidelines in CONTRIBUTING.md ([#4211](https://github.com/nf-core/tools/pull/4211))
 - Update conda-incubator/setup-miniconda action to v4 ([#4215](https://github.com/nf-core/tools/pull/4215))
+- Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.8 ([#4218](https://github.com/nf-core/tools/pull/4218))
+- Update pre-commit hooks ([#4219](https://github.com/nf-core/tools/pull/4219))
 - Update dependency textual to v8.2.4 ([#4217](https://github.com/nf-core/tools/pull/4217))
 - Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 1a85cf3 ([#4220](https://github.com/nf-core/tools/pull/4220))
+- Update python:3.14-slim Docker digest to 5b3879b ([#4221](https://github.com/nf-core/tools/pull/4221))
 
 ### Download
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.14-slim@sha256:bc389f7dfcb21413e72a28f491985326994795e34d2b86c8ae2f417b4e7818aa
+FROM python:3.14-slim@sha256:5b3879b6f3cb77e712644d50262d05a7c146b7312d784a18eff7ff5462e77033
 LABEL authors="phil.ewels@seqera.io,erik.danielsson@scilifelab.se" \
     description="Docker image containing requirements for nf-core/tools"