Cleanup actions #81
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Cleanup actions #81
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… deploy tests on a PR, cleand up the makefile, and added stuff to contributing on the documentation.
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Pull Request Overview
This PR applies automated code formatting across the ceREEBerus codebase using Black, a Python auto-formatter. The changes standardize code style including quote consistency (single to double quotes), spacing around operators and parameters, line breaks, and indentation.
Key Changes
- Converted all string quotes from single to double quotes throughout the codebase
- Standardized spacing around operators, function parameters, and assignments
- Reformatted long lines and function calls for better readability
- Added trailing commas in multi-line structures
- Removed extraneous blank lines and standardized comment formatting
Reviewed Changes
Copilot reviewed 36 out of 37 changed files in this pull request and generated 40 comments.
Show a summary per file
| File | Description |
|---|---|
| requirements.txt | New file listing project dependencies |
| doc_source/contributing.rst | Expanded contributing guide with formatting, testing, and PR guidelines |
| cereeberus/cereeberus/reeb/reebgraph.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/reeb/merge.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/reeb/mapper.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/reeb/lowerstar.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/reeb/embeddedgraph.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/reeb/init.py | Reformatted with double quotes |
| cereeberus/cereeberus/distance/labeled_blocks.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/distance/interleave.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/distance/ilp.py | Reformatted with consistent spacing and quote style |
| cereeberus/cereeberus/distance/init.py | Reformatted with double quotes |
| cereeberus/cereeberus/data/*.py | Multiple data module files reformatted with consistent style |
| cereeberus/cereeberus/compute/*.py | Compute module files reformatted with consistent style |
Comments suppressed due to low confidence (2)
cereeberus/cereeberus/distance/interleave.py:4
- Import of 'block_diag' is not used.
from scipy.linalg import block_diag
cereeberus/cereeberus/distance/interleave.py:6
- Import of 'UnionFind' is not used.
from ..compute.unionfind import UnionFind
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| viridis = mpl.colormaps["viridis"].resampled(16) | ||
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There was a problem hiding this comment.
Variable viridis is not used.
Suggested change
| viridis = mpl.colormaps["viridis"].resampled(16) |
| search_data = {} | ||
| search_data = {} | ||
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| # -- Set the initial value of the distance bound to be infinity | ||
| distance_bound = np.inf |
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Variable distance_bound is not used.
Suggested change
| distance_bound = np.inf |
| titles[3] = f"$D_{{{end_graph}^{{n}}}}^{{V}} \\cdot ({titles[2][1:-1]})$" | ||
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| fig, axs = self._draw_matrix_mult(Top, Bottom, Result, Result_Dist, titles = titles) | ||
| fig, axs = self._draw_matrix_mult( |
There was a problem hiding this comment.
Variable fig is not used.
Suggested change
| fig, axs = self._draw_matrix_mult( | |
| self._draw_matrix_mult( |
| titles[3] = f"$D_{{{end_graph}^{{n}}}}^{{V}} \\cdot ({titles[2][1:-1]})$" | ||
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| fig, axs = self._draw_matrix_mult(Top, Bottom, Result, Result_Dist, titles = titles) | ||
| fig, axs = self._draw_matrix_mult( |
There was a problem hiding this comment.
Variable axs is not used.
Suggested change
| fig, axs = self._draw_matrix_mult( | |
| fig = self._draw_matrix_mult( |
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| fig, axs = self._draw_matrix_mult(Top, Bottom, Result, Result_Dist, titles = titles) | ||
| fig, axs = self._draw_matrix_mult( |
There was a problem hiding this comment.
Variable fig is not used.
Suggested change
| fig, axs = self._draw_matrix_mult( | |
| self._draw_matrix_mult( |
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| except: | ||
| print("Error") | ||
| print(f"c: {c}") | ||
| print(f"map_dict: {map_dict}") | ||
| print(f"cols_: {cols_}") | ||
| print(f"rows_: {rows_}") | ||
| print(f"blocks[i]: {self.blocks[i]}") | ||
| ValueError("Column object {c} not in map_dict") |
There was a problem hiding this comment.
Except block directly handles BaseException.
Suggested change
| except: | |
| print("Error") | |
| print(f"c: {c}") | |
| print(f"map_dict: {map_dict}") | |
| print(f"cols_: {cols_}") | |
| print(f"rows_: {rows_}") | |
| print(f"blocks[i]: {self.blocks[i]}") | |
| ValueError("Column object {c} not in map_dict") | |
| except KeyError: | |
| print("Error") | |
| print(f"c: {c}") | |
| print(f"map_dict: {map_dict}") | |
| print(f"cols_: {cols_}") | |
| print(f"rows_: {rows_}") | |
| print(f"blocks[i]: {self.blocks[i]}") | |
| raise ValueError(f"Column object {c} not in map_dict") |
| try: | ||
| nx.shortest_path(S.to_undirected(), u, v) | ||
| return n | ||
| except: |
There was a problem hiding this comment.
Except block directly handles BaseException.
| comp_to_new_vert = {} | ||
| # comp_to_new_vert is a dictionary with keys as indices of connected components in the list C and values as the name of the vertex in R_eps | ||
| for i,c in enumerate(C): | ||
| for i, c in enumerate(C): |
There was a problem hiding this comment.
Nested for statement uses loop variable 'i' of enclosing for statement.
| for i,c in enumerate(C_edge): | ||
| V_inv, E_inv = self.inv_image(cv - delta) | ||
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| for i, c in enumerate(C_edge): |
There was a problem hiding this comment.
Nested for statement uses loop variable 'i' of enclosing for statement.
| print(f"cols_: {cols_}") | ||
| print(f"rows_: {rows_}") | ||
| print(f"blocks[i]: {self.blocks[i]}") | ||
| ValueError("Column object {c} not in map_dict") |
There was a problem hiding this comment.
Instantiating an exception, but not raising it, has no effect.
Suggested change
| ValueError("Column object {c} not in map_dict") | |
| raise ValueError(f"Column object {c} not in map_dict") |
yemeen
reviewed
Nov 4, 2025
| branches: [ "main" ] | ||
| pull_request: | ||
| branches: [ "main" ] | ||
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yemeen
approved these changes
Nov 4, 2025
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Description
Lots of folder cleanup, no changes to the code.
Motivation and Context
Neurotic cleanup. Plus we want a nice version for anonymizing later.
How has this been tested?
Types of changes
Checklist
pyproject.tomlfile if a new version needs to be pushed to pypi (note that not incrementing the number won't push to pypi and throw an error, but it will update the documentation).