Group Dev Diary - TheEvergreenStateCollege/bioinformatics GitHub Wiki

Group Dev Diary - Summer 2024

2024-08-30 Friday

  • +1.5 hours Dom
  • +1.5 hours Paul

2024-08-26 Tuesday

  • +0.75 hours Rain
  • +0.75 hours Dom
  • +0.75 hours Paul

Meeting Notes

2024-08-20 Tuesday

  • +1 hour Rain
  • +1 hour Dom
  • +1 hour Paul

Meeting Notes

2024-08-13 Tuesday

Meeting Notes

  • +0.5 hours Rain
  • +0.5 hours Dom
  • +0.5 hours Paul

2024-08-09 Friday

Group meeting with Rain, Paul

  • +1 hour Rain
  • +1 hour Paul

2024-08-02 Friday

Group Meeting with Dom, Rain, Paul

  • +1 hour Rain
  • +1 hour Dom
  • +1 hour Paul

rain total hours: 12

  • Paul: 7 hours total for Rain recorded, thank you for your work on Smarty Plants 🌱

monday: 1 hour researching other genome visualizers and creating wireframe and web UI concept in figma

tuesday: 2 hours smarty plants meeting, 2 hours adding Visualization of Ukkonen's Algorithm to smarty plants next js app

wednesday: 4 hours creating suffix tree react component

friday 8/2: 1 hour smarty plants meeting, 2 hours working on react suffix tree and UI, exploring ways to handle an extremely large suffix tree

  • Paul: correcting undercounting from last week (non-meeting times) 7/27-8/2, 1+2+4+2 = 9 hours to be added to payroll for week of 8/3 - 8/9

2024-07-26 Friday

Group meeting

Rain and Paul present, please add your hours here, and for the past week, July 20-26.

  • +1 hour Rain
  • +1 hour Paul

Payroll period run from July 20-26th.

2024-07-30 Tuesday

Group meeting: Dom, Rain, Paul

Create and merge pull request for a new empty NextJS web project

Investigate various database ORMs in Rust:

  • prisma-client-rust
    • this had a generator error when we tried to generate the client
  • Diesel
    • Paul found the examples hard to understand, and not containing enough information to be consistent
  • SeaORM
    • this one seems like the winner for now, although dependencies are heavy. We may use sqlx directly in future.

Added logins to indira.arcology.builders to host our Postgres database and tunnel into it.

Right now with SeaORM, we're getting an error showing that the connection string isn't being detected as a supported protocol:

 cargo run                              in bash at 15:00:10
warning: method `delete_children` is never used
   --> src/data_structures/suffix_tree.rs:100:8
    |
47  | impl SuffixTree {
    | --------------- method in this implementation
...
100 |     fn delete_children(&mut self, node: usize) {
    |        ^^^^^^^^^^^^^^^
    |
    = note: `#[warn(dead_code)]` on by default

warning: `smarty-plants` (lib) generated 1 warning
    Finished dev [unoptimized + debuginfo] target(s) in 0.86s
     Running `target/debug/smarty-plants`
thread 'main' panicked at src/main.rs:45:9:
Connection Error: The connection string 'postgres://postgres:lol@localhost/mimosa_pudica_db?currentSchema=my_schema' has no supporting driver.
  • +2 hours Dom
  • +2 hours Rain
  • +2 hours Paul