Refactor public API and add NVML installation fallback

[riccardoc95]

Changelog

Public API

The low-level nvml_* wrappers are no longer exported.
The public API has been split into files for easier maintenance. It is now focused on:

• cm_start()
• cm_timestamp()
• cm_stop()
• cm_parser()
• cm_vizdf()
• cm_plot_usage()
• CudaMonSession()

R CMD check notes

The cm_plot_usage() global variable notes were addressed by explicitly binding the ggplot variable:
tm <- value <- type <- label_y <- step <- NULL

NVML deprecation warning

The deprecated nvmlDeviceGetTemperature() call was replaced with the newer nvmlDeviceGetTemperatureV() NVML temperature API path.

Torch/reticulate dependency

The previous Python/torch-based GPU test path was removed from inst.

Process discovery

The monitoring code no longer parses ps command output directly. Process discovery was moved to the ps R package: a script with function process_pids is added.

Bioconductor GPU CI

Added .BBSoptions with GPU reliance configuration so Bioconductor can opt the package into GPU-capable builders.

Installation fallback

The configure logic now includes a fallback for systems where NVML is not available. This allows the package to install in non-NVIDIA or non-CUDA environments while still enabling NVML-backed monitoring when the library is available.

Documentation

Documentation was expanded and updated, including:

• clearer descriptions of GPU metrics
• updated examples
• labelled vignette chunks
• improved vignette formatting
• optional Rcollectl integration documented as an enhancement

Current MIG-related limitations

gpu_utilization_pct and memory_utilization_pct are not always available when running on MIG-enabled devices.

At the moment, these missing metrics are handled conservatively: when a metric is not reported, it is excluded from the plot.

The memory total field was also renamed from memory_total_bytes to memory_total_device_bytes to make its meaning explicit. This value refers to the total memory of the physical GPU device, not necessarily the memory limit of a specific MIG instance.