Add CLAUDE.md pointing at the specs rather than restating them - #76
Merged
Merged
Conversation
The repo had no CLAUDE.md, so an agent starting cold rediscovered the same traps each time: regenerating into a populated directory is a silent no-op because pre-fingerprint caches get adopted, PYTHONHASHSEED must be set before the interpreter starts, output/ is gitignored so those tests skip in CI, and more than one "the generator drops X" investigation has ended in the artifact being from a different Reactome release than the database. Now that spec-kit is in use the why belongs in specs/NNN-name/, so this file carries current state and pointers only. docs/DESIGN_DECISIONS.md and docs/UUID_DESIGN.md stay where they are: representational semantics are current state, not feature history. Also records the division of labour that keeps getting relitigated — the generator represents pathways as curators authored them, DeltaSignal decides how to process that — and the A/B protocol the benchmark needs, since non-converged solves return different values for a structurally identical network. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Independent of #74 and #75 — docs only.
The repo had no
CLAUDE.md, so an agent starting cold rediscovered the sametraps each time:
pre-fingerprint caches get adopted and the old networks are reproduced
while success is reported;
PYTHONHASHSEEDmust be set before the interpreter starts;output/is gitignored, so tests reading it skip in CI and a green CI runis not evidence they ran;
artifact being from a different Reactome release than the database.
Now that spec-kit is in use, the why belongs in
specs/NNN-name/, so thisfile carries current state and pointers only.
docs/DESIGN_DECISIONS.mdanddocs/UUID_DESIGN.mdstay where they are: representational semantics arecurrent state, not feature history.
Also records the division of labour that keeps getting relitigated — the
generator represents pathways as curators authored them, DeltaSignal decides
how to process that — and the A/B protocol the benchmark needs, since
non-converged solves return different values for a structurally identical
network.
🤖 Generated with Claude Code