Sphinx gallery execution and performance profiling

Skill HolobiomicsLab/asb-skill-collections/collections/metabolomics/v2/skills/sphinx-gallery-execution-and-performance-profiling

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Install

npx -y skills add HolobiomicsLab/asb-skill-collections --skill sphinx-gallery-execution-and-performance-profiling

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Use when you have a Sphinx-based documentation project with multiple gallery scripts (e.

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sphinx-gallery-execution-and-performance-profiling

Summary

Measure and verify the aggregate execution time and memory footprint of a multi-backend Sphinx gallery by running all gallery scripts and comparing reported metrics against expected benchmarks. This skill ensures reproducibility and performance compliance across static and interactive visualization backends.

When to use

Apply this skill when you have a Sphinx-based documentation project with multiple gallery scripts (e.g., organized by plotting backend: matplotlib, bokeh, plotly) and need to validate that the total gallery execution time matches a known reference metric or baseline, or when establishing performance budgets for documentation builds.

When NOT to use

When gallery scripts are not organized within a Sphinx project or do not use sphinx_gallery extension; use ad-hoc profiling (e.g., timeit, cProfile) instead.
When only a single backend or a subset of gallery examples needs profiling; simpler profiling tools suffice for isolated script timing.
When the reference benchmark is unknown or intentionally being established for the first time; this skill assumes a known target metric for validation.

Inputs

Sphinx gallery script directory tree (gallery_scripts/ with backend subdirectories)
conf.py and gallery configuration (sphinx_gallery_conf)
19 example gallery scripts (Python files with docstrings and executable code blocks)
Python 3.12 conda environment with matplotlib, bokeh, plotly, and pyOpenMS-viz installed

Outputs

Aggregate execution time (e.g., 00:06.221 in HH:MM.SSS format)
Per-script execution time and memory usage metrics (from Sphinx timer)
Exit code and build log indicating success or failure of all 19 gallery scripts
HTML gallery documentation with rendered plots (static and interactive)

How to apply

Clone the repository and install dependencies in a Python 3.12 conda environment. Run sphinx-build to execute all gallery scripts via Sphinx autosummary and autodoc, collecting execution time and memory usage metrics reported by Sphinx's built-in execution timer. Sum the per-script execution times and compare the aggregate total against the reference benchmark (e.g., 00:06.221). Verify that all 19 example files (across ms_bokeh/, ms_matplotlib/, ms_plotly/ subdirectories) complete without error. Use this workflow to detect performance regressions, memory leaks, or backend-specific bottlenecks across visualizations of mass spectrometry data types (chromatograms, spectra, peakmaps).

Related tools

Sphinx (Documentation build system and gallery executor; runs sphinx-build to invoke autosummary and autodoc, measuring per-script execution time)
pyOpenMS-viz (Source library providing mass spectrometry visualization API (spectrum, chromatogram, peakmap plots) executed by gallery scripts across matplotlib, bokeh, plotly backends) — https://github.com/OpenMS/pyopenms_viz
matplotlib (Static plotting backend; one of three backends tested in the gallery example suite)
bokeh (Interactive plotting backend; one of three backends tested in the gallery example suite)
plotly (Interactive plotting backend; one of three backends tested in the gallery example suite)
pandas (Data manipulation and DataFrame interface for mass spectrometry data input to pyOpenMS-viz plot methods)
Python (Runtime environment (version 3.12) for executing gallery scripts and Sphinx build system)

Examples

conda create --name=pyopenms-viz python=3.12 && conda activate pyopenms-viz && git clone https://github.com/OpenMS/pyopenms_viz.git && cd pyopenms_viz && pip install -e . && sphinx-build -b html docs/ docs/_build/

Evaluation signals

Aggregate execution time reported by Sphinx matches the reference metric (00:06.221) within a tolerance (e.g., ±5%)
All 19 gallery scripts (across ms_bokeh/, ms_matplotlib/, ms_plotly/ directories) complete without error; sphinx-build exit code is 0
Per-script execution times are logged and individually plausible (no outliers >2× interquartile range suggesting hangs or failures)
Memory usage metrics are captured for each script; peak memory does not exceed system limits or documented budget
HTML gallery documentation builds successfully with all plots rendered (static matplotlib images, interactive bokeh/plotly widgets)

Limitations

Execution time is system-dependent (CPU, I/O, available memory); reproducibility across different hardware may vary; consider running on a standardized CI/CD environment.
Sphinx execution timer precision may be coarse (millisecond or second granularity); for fine-grained profiling use Python's timeit or cProfile.
Memory usage reported by Sphinx may not capture peak heap usage for all backends (e.g., bokeh/plotly may defer rendering to browser/client); consider supplementary tools (memory_profiler, tracemalloc).
Gallery script execution order and caching behavior (e.g., Sphinx gallery's image cache) can affect total time; clear caches or use --fresh-env flag for consistent baselines.

Evidence

[other] Verify that the aggregate total execution time matches the reported 00:06.221 metric and that all 19 example files complete successfully.: "Verify that the aggregate total execution time matches the reported 00:06.221 metric and that all 19 example files complete successfully"
[other] Run sphinx-build to execute all 19 gallery scripts located in gallery_scripts/ (ms_bokeh/, ms_matplotlib/, ms_plotly/) using Sphinx autosummary and autodoc.: "Run sphinx-build to execute all 19 gallery scripts located in gallery_scripts/ (ms_bokeh/, ms_matplotlib/, ms_plotly/) using Sphinx autosummary and autodoc"
[other] Collect execution time and memory usage metrics for each gallery script as reported by the Sphinx execution timer.: "Collect execution time and memory usage metrics for each gallery script as reported by the Sphinx execution timer"
[other] Clone the pyOpenMS-viz repository from GitHub and install dependencies via pip in a conda environment with Python 3.12.: "Clone the pyOpenMS-viz repository from GitHub and install dependencies via pip in a conda environment with Python 3.12"
[readme] integrates seamlessly with various plotting library backends (matpotlib, bokeh and plotly): "integrates seamlessly with various plotting library backends (matpotlib, bokeh and plotly)"