Adding logo

[lizliz]

Description

Made a logo for the repo and updated the documentation

Motivation and Context

How has this been tested?

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have incremented the version number in the pyproject.toml file.
• I have added tests to cover my changes.
• All new and existing tests passed.

[Copilot]

Pull request overview

Adds repository branding assets and updates the Sphinx docs configuration to display the new logo and apply minor theme styling.

Changes:

• Added a make_logo.py script to generate doc_source/images/logo.png and logo_with_text.png from an example Reeb graph.
• Updated Sphinx configuration to use the new logo, add custom CSS, and adjust notebook highlighting.
• Added a BibTeX database file and a custom CSS override for the RTD theme sidebar header.

Reviewed changes

Copilot reviewed 4 out of 7 changed files in this pull request and generated 2 comments.

File	Description
make_logo.py	Adds a script to generate logo images used by the documentation.
doc_source/conf.py	Configures Sphinx to show the logo and load custom CSS; adds lexer override for notebook code blocks.
doc_source/cereeberus.bib	Adds bibliography entries for documentation.
doc_source/_static/custom.css	Adds minor RTD theme sidebar styling to match the new logo presentation.

Comments suppressed due to low confidence (3)

make_logo.py:59

• Image.open(...) is used without a context manager and then written back to the same path. On some platforms this can leave the file handle open and interfere with overwriting; using a with block ensures the input file is closed before saving the cropped output.

from PIL import Image
img1 = Image.open(out1)
img1 = img1.crop(img1.getbbox())
img1.save(out1)

make_logo.py:128

• The second output image repeats from PIL import Image and also opens/saves the same file without closing the input handle first. This can be simplified by reusing the earlier import and using a context manager here as well.

from PIL import Image
img = Image.open(out2)
img = img.crop(img.getbbox())
img.save(out2)

make_logo.py:19

• make_logo.py executes file-writing code at import time (module top-level). Adding a main() function and an if __name__ == "__main__": guard would prevent accidental imports (e.g., by tooling) from overwriting tracked image assets.

# ── Build the Reeb graph ──────────────────────────────────────────────────────
R = ex_rg.dancing_man(seed=5)

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