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Archive 2021-10 Old Wiki

Organization

• Weekly Todos -- let's track our weekly progress
• Agile Project Execution -- Be an agile samurai ⚔️!
• Group Organization -- Never miss a meeting!
• Retrospectives -- How we conquer the world!
• Core Meeting notes -- Summary of strategy meetings for design decisions.
• Initial requirements (Seqan3 dependencies, compilers, platforms)

General Reading

On Modern C++ and design patterns used in SeqAn:

• Modern Cpp -- A list of recommended readings of modern C++
• CppSessions -- Slides to former cpp sessions about modern C++
• Concepts TS -- a small guide to C++ Concepts
• Dynamic and Static Polymorphism
• Ranges -- a small guide to C++ Ranges
• Strong Types -- a small guide to use strong types for expressive coding
• CRTP 🔗 -- the Curiously Recurring Template Pattern

Library Coding Guide

• Library structure -- filesystem, module and namespace hierarchies
• File structure and naming -- where to find/put what inside a file
• General formatting -- Spacing, Indention, Alignment and Naming
• Functions -- functions, arguments, return types...
• Metafunctions -- "functions" always evaluated at compile time
• Exceptions -- exception safety guarantees, noexcept specifier

from old_home:

• Classes and Structs --
• General Design Changes
• Style-Guide
• Namespaces
• Function parameters
• Thread Safety

TODO: rework or remove these:

• General Design Decisions
• Design Patterns

Infrastructure

Hosting / version control / contributing:

• The Git Repository Structure -- what to find where
• The Git workflow -- how to create commits and pull requests
• The Contributor License Agreement -- you need to sign this
• Good Code Reviews🔗 -- worth reading
• The Software Management

Documentation

• Setup
• Guidelines for Writing
• Document Concepts

Testing

• Unit tests -- Maintaining correctness
• Benchmarks -- Maintaining performance
• Continuous Integration

Deployment:

• ?

Miscellaneous

• SSH -- ssh in connection with the fu-berlin servers

HowTos

• Write a View

Migrating from SeqAn2

TODO

Modules

Documents on high-level design decisions in certain modules:

• Argument Parser seqan3/argument_parser
• Alphabet seqan3/alphabet
• ranges
  • Containers seqan3/containers
• Alignment seqan3/alignment
  • core
  • pairwise
  • pairwise (Myers)
  • multiple
  • score
• find
• graph
• search
• Indexes seqan3/index
• Input/Output seqan3/io
  • stream tokenisation, virtual_stream
  • Sequence (Fasta, Fastq...)
  • Alignment (SAM/BAM/CRAM, Blast)
  • Structure (vienna)
  • annotation (GTF, GFF...)

Drafts for new modules:

• Align module

External Submodules

• SDSL

Specifications

• I/O
  • Tokenization -- Specification of Tokenization
  • Stream -- Streams in SeqAn3