feat(docker): upgrade base images and dependencies to DHI trixie

[gafda]

This pull request updates the development and runtime environments for multiple languages and tools, focusing on improved consistency, newer base images and language versions, and refreshed package dependencies. It also introduces an .editorconfig for standardized formatting across the codebase. The most important changes are grouped below.

Environment and Base Image Updates

• Switched all language Dockerfiles (C/C++, D, Fortran, R) to use the trixie-debian13-dev base image, ensuring compilers and development libraries are available at runtime. (docker/c-cpp.Dockerfile, docker/d.Dockerfile, docker/fortran.Dockerfile, docker/r.Dockerfile) [1] [2] [3] [4] [5]
• Updated Go and Rust Dockerfiles to use newer language versions: Go 1.26 and Rust 1.93, including all build and runtime stages. (docker/go.Dockerfile, docker/rust.Dockerfile) [1] [2] [3] [4] [5]
• Bumped PHP version from 8.4.17 to 8.5.3 in its Dockerfile. (docker/php.Dockerfile)

Dependency and Package Refresh

• Refreshed Python requirements files for core, analysis, utilities, visualization, and document processing, updating to newer versions, adding missing packages, and improving grouping by functionality. (docker/requirements/python-core.txt, docker/requirements/python-analysis.txt, docker/requirements/python-utilities.txt, docker/requirements/python-visualization.txt, docker/requirements/python-documents.txt) [1] [2] [3] [4] [5]
• Updated Go module requirements to use Go 1.26 and added several new libraries for image processing, CSV, Office documents, and markdown. (docker/requirements/go.mod)
• Refreshed Node.js global package list for improved organization and coverage, including new utilities, web scraping, office formats, and UI libraries. (docker/requirements/nodejs.txt)
• Updated Rust dependencies for serialization, data formats, office documents, markdown, utilities, and plotting, with newer versions and added features. (docker/requirements/rust-Cargo.toml)

Python Runtime Optimization

• Refined the set of system libraries and runtime tools installed in the Python Dockerfile for better support of image processing, cryptography, fonts, and external utilities; removed some tools from the final image. (docker/python.Dockerfile) [1] [2]

Codebase Maintenance

• Added a new .editorconfig file to standardize code formatting and indentation rules for all supported languages and file types. (.editorconfig)

[gafda]

@aron-muon : First PR from original PR #33

[Copilot]

Pull request overview

This PR upgrades the project’s Docker-based execution environments to newer DHI “trixie/debian13” base images and refreshes language/package dependency sets, while adding a repo-wide .editorconfig for consistent formatting.

Changes:

• Upgraded multiple language Docker images (Go, Rust, PHP, R, C/C++, D, Fortran) to newer DHI base images / language versions.
• Refreshed dependency preload manifests for Python, Go, Rust, and Node.js.
• Introduced .editorconfig to standardize formatting rules across file types.

Reviewed changes

Copilot reviewed 17 out of 17 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
docker/rust.Dockerfile	Bumps Rust base image version used for build + runtime stages.
docker/requirements/rust-Cargo.toml	Updates/expands the Rust dependency preload set (data formats, office, markdown, etc.).
docker/requirements/python-visualization.txt	Refreshes visualization stack versions.
docker/requirements/python-utilities.txt	Reorganizes and updates utility/security/networking dependencies.
docker/requirements/python-documents.txt	Refreshes document-processing dependencies and reorganizes by category.
docker/requirements/python-core.txt	Updates core Python data stack versions and requirements.
docker/requirements/python-analysis.txt	Updates math/science/analysis dependency versions.
docker/requirements/nodejs.txt	Expands and reorganizes global Node.js tool/library list.
docker/requirements/go.mod	Updates Go version directive and expands module preload list.
docker/r.Dockerfile	Switches R image stages to trixie-debian13-dev base.
docker/python.Dockerfile	Adjusts runtime library/tool installation and reduces copied runtime executables.
docker/php.Dockerfile	Bumps PHP major/minor version args.
docker/go.Dockerfile	Bumps Go base images across all stages.
docker/fortran.Dockerfile	Switches Fortran base to trixie-debian13-dev and documents rationale.
docker/d.Dockerfile	Switches D base to trixie-debian13-dev and documents rationale.
docker/c-cpp.Dockerfile	Switches C/C++ base to trixie-debian13-dev and documents rationale.
.editorconfig	Adds formatting rules intended to standardize indentation/whitespace per file type.

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[aron-muon]

Thank you!

[github-actions]

🎉 This PR is included in version 2.2.0 🎉

The release is available on GitHub release

Your semantic-release bot 📦🚀