Add HDF5 dependency to dev containers

[jbeirer]

This PR installs the HDF5 dependency in the docker containers, which is required in preparation for #84

Summary by CodeRabbit

• Chores
  • Docker images now include HDF5 library with C++ support enabled (version 1.14.6 by default), supporting HDF5-dependent workflows in containerized environments.

[coderabbitai]

📝 Walkthrough

Walkthrough

Both Dockerfile configurations now include a new build stage for HDF5 library compilation and installation. A versioned build argument HDF5_VERSION (default 1.14.6) is introduced, followed by source code retrieval, CMake configuration with C++ bindings enabled, compilation, installation to /usr/local, and temporary directory cleanup.

Changes

Cohort / File(s)	Summary
Docker HDF5 Build Stage docker/alma10/Dockerfile, docker/ubuntu24/Dockerfile	Added new build stage that fetches HDF5 source, configures via CMake with C++ bindings enabled, builds, and installs to /usr/local. Includes new build argument ARG HDF5_VERSION=1.14.6 with tools, examples, testing, and static library builds disabled.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 A hop, a skip, HDF5 we'll fetch,
From source code's garden, a perfect match,
CMAKE builds it bright, no tools to compile,
Into /usr/local goes our file,
Dockers now blessed with data delight! 📦

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title accurately describes the primary change: adding HDF5 as a dependency to development container configurations (both alma10 and ubuntu24 Dockerfiles).
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch main-addHDF5dep

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against the current code and only fix it if needed.

Inline comments:
In `@docker/alma10/Dockerfile`:
- Around line 106-120: The Dockerfile currently builds and installs HDF5 from
source (ARG HDF5_VERSION / RUN git clone ... && cmake ... --install to
/usr/local) while the Alma image also installs the distro hdf5-devel package,
causing duplicate headers/libraries; pick one approach and remove the other:
either delete this source-build RUN block (lines that clone hdf5_src, configure
and install to /usr/local) and rely on the distro hdf5-devel package, or remove
hdf5-devel from root_dependencies.txt and keep the source build (ensuring
CMAKE_INSTALL_PREFIX=/usr/local remains intentional); make the change so only
one HDF5 stack is installed and update any README or build comments to reflect
the chosen path.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 960882ef-38ec-487c-9a51-f836e1344850

📥 Commits

Reviewing files that changed from the base of the PR and between 71ed126 and 433f04f.

📒 Files selected for processing (2)

• docker/alma10/Dockerfile
• docker/ubuntu24/Dockerfile

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ All tests successful. No failed tests found.
see 125 files with indirect coverage changes

[jbeirer]

For some very strange reason, this PR was merged to main but the commit does not appear in the main branch... Re-trying again in #89