Weekly Todos

This page is is not maintained anymore but has been moved to a trello board https://trello.com/b/r9hqtYLq/weekly-todos

18.11.2019

Lydia

• Second approval for PR 'Apply vectorise and parallel configurations'
• Run and test Vaquita
• prepare talk for Thursday (and User Stories for the talk)

Jörg

• Review the Tutorial PR again (#1320).
• Develop concrete work packages from my User Stories for Motif Descriptor.
• Set up the LaRA paper.

11.11.2019

Rene

• split user stories wiki page
• Fix the KNIME trunk build bug
• add new policy to alignment algorithm for configuring the scoring scheme (vectorised version)
• Implement the vectorised interface for computing the score for equal sized sequences (global alignment) including tests.
• Make the "train the trainer workshop" to become a "carpentry instructor"

Enrico

• Email to Regensburg
• Parallelise the IBF app for the FPGA people
• Get accustomed to the EPR dictionary
• Review the EPR dictionary on the SDSL
• [New] First review of Recomb paper
• [New] Get review for FM-Index PR Get FM-Index PR merged
• [New] Set up TAC Meeting

Svenja:

• Meeting C++
• Get file IO PR merged
• Get enum PR ready

Marcel:

• Prepare JC talk
• Meeting C++

Lydia

• Level 3 PR first approval
• finish 'Pairwise Alignment' tutorial
• Read and understand the Vaquita paper
• Text the IT about my orders

Josh

• Get the scoring scheme PR merged

Hannes

• Reisekostenabrechnung
• Meeting C++
• Some stuff with Sara and lambda

Jörg

• Develop the User Stories for lncRNA and T-Coffee.
• Prepare the presentation.

05.11.2019

Enrico

• Revise paper
• Reflect about the sense of life
• Parallelise the IBF app for the FPGA people

Rene

• split user stories wiki page
• I want to have the first approval for each of my PRs
• Write to the IT that the windows intel licences must be renewed
• Fix the KNIME trunk build bug -> replaced by aligned allocator bug
• pair programming with Lydia
• book travel for Heidelberg
• made to_simd_view stop on largest sequence end and not on chunk boundary.
• Made PR for all range interface tasks for the alignment algorithm.

Svenja

• file IO refactoring PR approval h-2
• Find Score type bug

Marcel

• Prepare JC talk
• Get visibility bug PRs merged: Ranges.

Lydia

• If level 2 gets merged make level 3 PR
• Continue to work on user stories
• tutorials until 'Pairwise Alignment' (about half)
• pair programming with rene

Joerg is on vacation

28.10.2019

Enrico

• Finish paper

Rene

• Final clean up PR ready
• Read up a little on story gathering

Svenja

• Get value_list validator PR merged
• Get level 2 vectorisation PR of result score_type ready
• Get bug fix for alignment IO short cigar string merged

Marcel

• Get together with hannes about the bug
• Get visibility bug PRs merged: IO, Alignment, Alphabet, Ranges.
• Trial and error with the matrix issue.

Joerg

• Get first review from Sven
• Get Level 3 PR of new configuration object ready (-> Lydia)
• Review PR about tutorials
• Brainstorming about my project

Sven

• Get the level 1 pr merged
• Review of Joergs PR level 2
• Get level 2 PR ready

Lydia

• Tutorials bis Ranges, keep track of the time to adjust the timings in a PR.
• Pair programming with Joerg level 2
• Prepare user stories.

21.10.2019

Enrico:

• Finish benchmarks on the thresholding app.
• Prepare a presentation for the JC.
• Get the visibility bug argument parser PR reviewed.

Rene

• Prepare and hold a presentation at the MPI.
• Finish a prototype for the vectorisation kernel for affine gap costs and asses further work.

Hannes:

• Debug search algorithms in lambda (SeqAn2 vs SeqAn3).

Svenja

• Get first review approval for #1298.
• Get PR for #1299 ready.
• Get IO visibility bug PR merged.

Marcel

• Take a look at Hannes' PR for 1-2 hours.
• Get visibility bug PRs merged: Core, IO, Std, Argument parser.
• Trial and error with the matrix issue.

Joerg

• Get visibility bug PR std merged.
• Create a PR for the new configurations vectorise and parallel.
• Explain the output format of LaRA in the Readme file and how to run T-Coffee.

Sven

• Review visibility bug argument parser.
• Get PR ready to review for issue #1308 (CI passes).

Lydia

• Prepare and hold lecture on Friday.
• Be done with all tutorials up to 'Parsing command line arguments with SeqAn'. (reduced)
• Pair programming with Joerg.