Repository navigation
Spec 015: BioPAX's exporter work ticked; the website's BioPAX planned (3) - #752
Closed
adamjohnwright wants to merge 3 commits into
Closed
adamjohnwright wants to merge 3 commits into
adamjohnwright wants to merge 3 commits into
Conversation
BioPAX3Exporter's own spec 001 has done T045-T048 and T051, and the species half of T049 and T050; each is ticked with its pull requests, and T031 is withdrawn for its ci/compare.py, as T030 was for SBML. T049 and T050 keep the website's part: the library's per-event files against the legacy service's. T052 becomes T069-T072, on SBML's terms: the operation in the library service, node's endpoint, the route, and the check on beta. Research R10 is amended: BioPAX joins the service here, with node as its client. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…easured T069's pom sets kotlin.version to the library's (Boot 2.7 would bring Kotlin's standard library down to 1.6.21), and its jar check covers the BioPAX library, kotlin-stdlib and paxtools-core. Its memory is measured at the worst case the shares allow, two BioPAX and two SBML conversions at once, and the largest's cold time against node's 290 s. T072 checks R6's headers rather than the legacy service's; T049 compares with T004's answers at the graph's release and sends what is left to BioPAX3Exporter. T020 merged as BioPAX3Exporter#79, not #78. T035 is withdrawn, the citations of T047 and T048 corrected, and the dependencies, strategy, spec, plan and checks no longer say SBML alone or T052 alone. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…ne release The legacy service reads the relational database at release 97 while beta's graph is at 98, so T049 runs the library on a private graph copy at the legacy database's release, and T072 checks beta's bodies by containment in the graph's release's species file instead. The plan's order of work, the data model's ontology comment, spec.md's citation and T035's releases follow. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Contributor
Author
|
Replaced by the next PR, which carries this one's commits and the fixes from its review. |
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.
Spec 015 (specs/015-graph-exports). This replaces #751 (and #750), carrying their commits. What they change is described in #751.
From #751's review:
ci/contained.py.🤖 Generated with Claude Code