Adding plt.show()

[r-sayar]

PR Type

documentation

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Description

• Added plt.show() to the plotting sections of the user guide to ensure that plots are displayed when the code is executed.
• Improved the clarity and usability of the documentation by ensuring that visual outputs are shown.

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Changes walkthrough 📝

	Relevant files
Documentation	centroiding.rst Add `plt.show()` to display plots in documentation              docs/source/user_guide/centroiding.rst Added plt.show() to display plots in the user guide. Enhanced the documentation by ensuring plots are rendered. +4/-0

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[codiumai-pr-agent-pro]

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⏱️ Estimated effort to review: 1 🔵⚪⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Documentation Consistency The added plt.show() calls are not consistent with the rest of the documentation. It's unclear if these calls are necessary for the documentation or if they should be part of the code examples. Code Formatting There's an extra empty line after the plt.show() call in the second code block, which is inconsistent with the first code block.

[codiumai-pr-agent-pro]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
Enhancement	Add labels to the x and y axes for better interpretation of the plot Add labels to the x and y axes using plt.xlabel() and plt.ylabel() before plt.show(). This will provide more context about what the plot represents. docs/source/user_guide/centroiding.rst [56-61] plt.xlim(771.8, 774) # zoom into isotopic pattern plt.stem( centroided_spectra[0].get_peaks()[0], centroided_spectra[0].get_peaks()[1] ) # plot as vertical lines - +plt.xlabel("m/z") +plt.ylabel("Intensity") plt.show() Apply this suggestion Suggestion importance[1-10]: 8 Why: Adding axis labels significantly improves the plot's interpretability by clearly indicating what the axes represent. This enhancement is valuable for users to understand the data being presented in the documentation.	8
	Add a descriptive title to the plot for better context and readability Consider adding a title to the plot using plt.title() before plt.show(). This will make the plot more informative and easier to understand in the context of the documentation. docs/source/user_guide/centroiding.rst [32-37] plt.xlim(771.8, 774) # zoom into isotopic pattern plt.plot( profile_spectra[0].get_peaks()[0], profile_spectra[0].get_peaks()[1] ) # plot the first spectrum - +plt.title("Isotopic Pattern in Profile Mode") plt.show() Apply this suggestion Suggestion importance[1-10]: 7 Why: Adding a title to the plot enhances the documentation by providing context, making it easier for users to understand the plot's purpose. This suggestion is relevant and improves the clarity of the documentation.	7

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