Rules Reference

SciTeX Linter enforces 47 rules across 8 categories. Rules use the STX- prefix.

Category S: Structure

Rule	Severity	Description
STX-S001	error	Missing @stx.session decorator on main function
STX-S002	error	Missing if __name__ == '__main__' guard
STX-S003	error	argparse detected — @stx.session auto-generates CLI from function signature
STX-S004	warning	@stx.session function should return an integer exit code
STX-S005	warning	Missing import scitex as stx
STX-S006	warning	@stx.session function missing explicit INJECTED parameters

Category I: Imports

Rule	Severity	Description
STX-I001	warning	Use stx.plt instead of importing matplotlib.pyplot directly
STX-I002	warning	Use stx.stats instead of importing scipy.stats directly
STX-I003	warning	Use stx.io instead of pickle for file I/O
STX-I004	warning	Use stx.io for CSV/DataFrame I/O instead of pandas I/O functions
STX-I005	warning	Use stx.io for array I/O instead of numpy save/load
STX-I006	info	Use rngg (injected by @stx.session) for reproducible randomness
STX-I007	warning	Use logger (injected by @stx.session) instead of logging module

Category IO: I/O Calls

Rule	Severity	Description
STX-IO001	warning	np.save() detected — use stx.io.save() for provenance tracking
STX-IO002	warning	np.load() detected — use stx.io.load() for provenance tracking
STX-IO003	warning	pd.read_csv() detected — use stx.io.load() for provenance tracking
STX-IO004	warning	.to_csv() detected — use stx.io.save() for provenance tracking
STX-IO005	warning	pickle.dump() detected — use stx.io.save() for provenance tracking
STX-IO006	warning	json.dump() detected — use stx.io.save() for provenance tracking
STX-IO007	warning	.savefig() detected — use stx.io.save(fig, path) for metadata embedding

Category P: Plotting

Rule	Severity	Description
STX-P001	info	ax.plot() — consider ax.stx_line() for automatic CSV data export
STX-P002	info	ax.scatter() — consider ax.stx_scatter() for automatic CSV data export
STX-P003	info	ax.bar() — consider ax.stx_bar() for automatic sample size annotation
STX-P004	info	plt.show() is non-reproducible in batch/CI environments
STX-P005	info	print() inside @stx.session — use logger for tracked logging

Category ST: Statistics

Rule	Severity	Description
STX-ST001	warning	scipy.stats.ttest_ind() — use stx.stats.ttest_ind() for auto effect size + CI
STX-ST002	warning	scipy.stats.mannwhitneyu() — use stx.stats.mannwhitneyu() for auto effect size
STX-ST003	warning	scipy.stats.pearsonr() — use stx.stats.pearsonr() for auto CI + power
STX-ST004	warning	scipy.stats.f_oneway() — use stx.stats.anova_oneway() for post-hoc + effect sizes
STX-ST005	warning	scipy.stats.wilcoxon() — use stx.stats.wilcoxon() for auto effect size
STX-ST006	warning	scipy.stats.kruskal() — use stx.stats.kruskal() for post-hoc + effect sizes

Category PA: Path Handling

Rule	Severity	Description
STX-PA001	warning	Absolute path in stx.io call — use relative paths for reproducibility
STX-PA002	warning	open() detected — use stx.io.save()/stx.io.load() which includes auto-logging
STX-PA003	info	os.makedirs()/mkdir() detected — stx.io.save() creates directories automatically
STX-PA004	warning	os.chdir() detected — scripts should be run from project root
STX-PA005	info	Path without ./ prefix in stx.io call — use ./ for explicit relative intent

Category FM: Figure/Millimeter (opt-in)

These rules detect inch-based matplotlib anti-patterns and suggest mm-based alternatives. FM rules require figrecipe or scitex[plt] to be installed, and must be explicitly enabled via enable = ["FM"] in config or SCITEX_LINTER_ENABLE=FM.

Rule	Severity	Description
STX-FM001	warning	figsize= detected — inch-based figure sizing is imprecise for publications
STX-FM002	warning	tight_layout() detected — layout is unpredictable across plot types
STX-FM003	warning	bbox_inches="tight" detected — can crop important elements unpredictably
STX-FM004	info	constrained_layout=True detected — conflicts with mm-based layout control
STX-FM005	info	subplots_adjust() with hardcoded fractions — fragile across figure sizes
STX-FM006	info	plt.savefig() detected — no provenance tracking
STX-FM007	info	rcParams direct modification detected — hard to maintain across figures
STX-FM008	warning	set_size_inches() detected — bypasses mm-based layout control
STX-FM009	warning	ax.set_position() detected — conflicts with mm-based layout control

Severity Summary

Severity	Count	Behavior
error	3	Must fix. Exit code 2. Blocks execution in --strict mode.
warning	25	Should fix. Exit code 1. Does not block execution.
info	17	Suggestions. Exit code 0.