increase useability of the repo

[ScSteffen]

Summary

This PR addresses the CharmKiT-side accessibility and usability gaps from kitrt_accessibility_usability_plan.md after checking that they still existed locally.

Verified Gaps And Changes

• README onboarding drift existed: the README used the old ScSteffen/charm_kit clone URL and referenced install_KiT-RT.sh / update_KiT-RT.sh. Updated the README to use KiT-RT/CharmKiT, install_kitrt.sh, and update_kitrt.sh, and added a short decision guide for when to use CharmKiT versus kitrt_code.
• CharmKiT was not installable as a package CLI: pyproject.toml had package-mode = false and no console script. Added package metadata, src/__init__.py, and a charm-kit entry point backed by src/cli.py.
• Users had to know root-level runner scripts: added charm-kit run <case> and charm-kit submit <case> dispatch for lattice and hohlraum while keeping the existing scripts working.
• Container install was sudo-oriented: updated install_kitrt.sh to detect Apptainer/Singularity, reuse existing SIFs, optionally pull CPU/CUDA images, support KITRT_CONTAINER_BUILD=skip|fakeroot|sudo|auto, and reuse an existing kitrt_code checkout.
• The update workflow was documented but absent from git: added update_kitrt.sh and unignored it in .gitignore so it appears in the PR.
• --slurm --cuda was blocked: removed that blocker and added SLURM CUDA script generation using the CUDA SIF, --nv, and KITRT_CUDA_MPI_RANKS / SLURM_GPUS_ON_NODE rank selection.
• Runtime selection was Singularity-only: added KITRT_CONTAINER_RUNTIME support for local and generated SLURM container commands.
• SLURM template needed GPU guidance: added commented GPU directives and a stable command marker.
• Tests did not cover the new CLI and GPU SLURM path: added/updated tests for charm-kit, SLURM CUDA generation, and runner/model CUDA propagation.

Primary Files

• README.md
• .gitignore
• pyproject.toml
• src/__init__.py
• src/cli.py
• install_kitrt.sh
• update_kitrt.sh
• slurm_template.sh
• src/config_utils.py
• src/simulation_utils.py
• src/models/lattice.py
• src/models/hohlraum.py
• run_lattice.py
• run_hohlraum.py
• tests/test_charm_kit_cli.py
• tests/test_config_utils.py
• tests/test_cli_and_runner_flags.py
• tests/test_model_operations.py

Verification

• python3 -m py_compile run_lattice.py run_hohlraum.py src/cli.py src/config_utils.py src/simulation_utils.py src/models/lattice.py src/models/hohlraum.py tests/test_charm_kit_cli.py tests/test_config_utils.py tests/test_simulation_utils.py
• python3 -m pytest -q -> 32 passed
• poetry check -> exit 0 with deprecation warnings for legacy Poetry metadata and [tool.poetry.scripts]
• python3 -c "from src.cli import main; raise SystemExit(main(['--help']))"
• poetry run charm-kit --help -> exit 0; Poetry warns the script is not installed until poetry install is rerun
• git diff --check

Not Included

• Publishing releases, GHCR images, checksums, or official SIF artifacts. Those require repository/registry credentials.
• Site-specific SLURM account, partition, and GPU directives. The template documents where users should add them.
• The existing untracked kitrt_code/, out_cpu.txt, out_cuda.txt, and timings.txt files were left untouched.