Addressing missing fonts in Linux

[yaront]

Added an option to customize font family in volcano plots and bubble maps
Suppressed missing fonts messages if system's fallback is a valid font

Closes #54

[Copilot]

Pull request overview

This pull request addresses missing fonts in Linux by adding font family customization options to volcano plots and bubble maps, and suppressing matplotlib font manager warning messages for missing system fonts.

• Adds a font_family parameter to plotting functions allowing users to specify custom font families
• Suppresses matplotlib font_manager warnings by setting the logger level to ERROR when a valid system fallback font exists
• Removes trailing whitespace in several functions

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 8 comments.

File	Description
src/kinase_library/modules/enrichment.py	Adds logging configuration to suppress font warnings and implements font_family parameter in plot_volcano and plot_bubblemap functions
src/kinase_library/enrichment/mea.py	Adds font_family parameter to plot_volcano method and passes it through to the base plotting function; removes trailing whitespace
src/kinase_library/enrichment/differential_phosphorylation.py	Adds logging configuration to suppress font warnings and implements font_family parameter in volcano plotting methods; removes trailing whitespace
src/kinase_library/enrichment/binary_enrichment.py	Adds font_family parameter to plot_volcano method and passes it through to the base plotting function; removes trailing whitespace

Comments suppressed due to low confidence (5)

src/kinase_library/modules/enrichment.py:199

• combine_diff_phos_enrichment_results returns tuple of size 2 and tuple of size 3.

def combine_diff_phos_enrichment_results(enrichment_results_dict, enrichment_type='combined', data_type='kl_object',
                                        lff_col_name=None, pval_col_name=None, cont_kins_col_name=None):

src/kinase_library/modules/enrichment.py:507

• Except block directly handles BaseException.

    except:

src/kinase_library/enrichment/binary_enrichment.py:609

• Instantiating an exception, but not raising it, has no effect.

                ValueError(f'Warning: kins_label_dict has unexpected keys: {set(kins_label_dict) - set(kins_labels.values())}')

src/kinase_library/enrichment/differential_phosphorylation.py:707

• Instantiating an exception, but not raising it, has no effect.

                ValueError(f'Warning: kins_label_dict has unexpected keys: {set(kins_label_dict) - set(kins_labels.values())}')

src/kinase_library/enrichment/mea.py:573

• Instantiating an exception, but not raising it, has no effect.

                ValueError(f'Warning: kins_label_dict has unexpected keys: {set(kins_label_dict) - set(kins_labels.values())}')

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[Copilot]

Modifying global matplotlib rcParams within a function can have unintended side effects. The font_family change persists after the function returns and affects all subsequent matplotlib operations in the same Python session, not just this plot. Consider using a context manager approach to temporarily change the font family. For example, you could use with mpl.rc_context({'font.family': font_family}): to wrap the plotting code, which would restore the original font settings after the plot is complete.

[Copilot]

The parameter type should be 'str' instead of 'string' to maintain consistency with other parameter documentation in this file. All other string parameters in the codebase use 'str' (e.g., lines 390, 392, 421, 575, etc.).

[Copilot]

The parameter type should be 'str' instead of 'string' to maintain consistency with other parameter documentation in this file. All other string parameters in the codebase use 'str' (e.g., lines 752, 770, 772, etc.).

[Copilot]

The parameter type should be 'str' instead of 'string' to maintain consistency with other parameter documentation in this codebase. All other string parameters in the file use 'str' (e.g., lines 527, 531, 533, 538, etc.).

[Copilot]

The parameter type should be 'str' instead of 'string' to maintain consistency with other parameter documentation in this codebase. All other string parameters in the file use 'str' (e.g., lines 667, 671, 673, 678, etc.).

[Copilot]

The parameter type should be 'str' instead of 'string' to maintain consistency with other parameter documentation in this codebase. All other string parameters in the file use 'str' (e.g., lines 847, 849, 851, 856, etc.).

[Copilot]

The parameter type should be 'str' instead of 'string' to maintain consistency with other parameter documentation in this codebase. All other string parameters in the file use 'str' (e.g., lines 555, 559, 561, 566, etc.).

[Copilot]

Modifying global matplotlib rcParams within a function can have unintended side effects. The font_family change persists after the function returns and affects all subsequent matplotlib operations in the same Python session, not just this plot. Consider using a context manager approach to temporarily change the font family. For example, you could use with mpl.rc_context({'font.family': font_family}): to wrap the plotting code, which would restore the original font settings after the plot is complete.