Fix id_neighbours serializing as np.int64 instead of plain int in CSV output#156
Draft
Fix id_neighbours serializing as np.int64 instead of plain int in CSV output#156
Conversation
Co-authored-by: Pablo1990 <[email protected]>
Copilot
AI
changed the title
[WIP] Fix id neighbours showing integer type in CSV
Fix id_neighbours serializing as np.int64 instead of plain int in CSV output
Mar 10, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
graph.neighbors()(scikit-image RAG / networkx) yieldsnp.int64values, which were stored directly intoid_neighbours. When serialized to CSV, this produced unreadable output like[np.int64(31), np.int64(552), ...]instead of[31, 552, ...].Changes
src/epitools/analysis/cell_statistics.py— In_calculate_graph_statistics(), convert each neighbour ID to a plain Pythonintat collection time; also simplifies the conditional append with a ternary:tests/test_cell_statistics.py— Addstest_id_neighbours_contains_plain_intsto asserttype(n) is intfor every value in everyid_neighbourslist, guarding against regressions from future scikit-image/networkx version changes.Original prompt
💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.