tskit-dev / tsbrowse

Utilities for evaluating inferred tree sequences
MIT License
3 stars 8 forks source link

Add metadata to tables, fix slow start #221

Closed benjeffery closed 3 weeks ago

benjeffery commented 3 weeks ago

Whilst working on other things and testing with a large TS I noticed that we are objectifying all the mutations several times. This means for a large TS start up can take way too long. I've reworked the loading code to not use the tskit row objects. Hopefully this is a good compromise. I've also added metadata to the table views.

github-actions[bot] commented 3 weeks ago

Automated Screenshots

These screenshots are automatically updated as the PR changes.

Click to view screenshots ### edges.png ![edges.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/edges.png) ### mutations-popup.png ![mutations-popup.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/mutations-popup.png) ### mutations.png ![mutations.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/mutations.png) ### nodes.png ![nodes.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/nodes.png) ### out_edges.png ![out_edges.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/out_edges.png) ### out_mutations.png ![out_mutations.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/out_mutations.png) ### out_nodes.png ![out_nodes.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/out_nodes.png) ### overview.png ![overview.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/overview.png) ### tables.png ![tables.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/tables.png) ### trees.png ![trees.png](https://raw.githubusercontent.com/tskit-dev/tsbrowse/pr-screenshots/pr_221/trees.png)
coveralls commented 3 weeks ago

Pull Request Test Coverage Report for Build 11704859490

Details


Totals Coverage Status
Change from base Build 11702423404: 0.1%
Covered Lines: 790
Relevant Lines: 866

💛 - Coveralls
benjeffery commented 3 weeks ago

Lgtm. What's the time difference roughly?

120s before, about 4s now for a 40k sample TS with 4M mutations.

jeromekelleher commented 3 weeks ago

Boom, nice job!