circt VS Automa.jl

MLIR (https://mlir.llvm.org/) is a quickly growing compiler toolkit which attempts to synthesize the learnings of LLVM and currently powers compilers for programming languages, machine learning and circuit design (https://github.com/llvm/circt). and there are a ton of companies with real employees working on it (including Microsoft) and MLIR is at the core of Chris Lattner’s new company, ModularAI. I’d recommend taking a look at it, there are a large number of ways to get involved and a number of paths from contributor to employee.

Might be good to target the CIRCT infrastructure at some point.

Even small optimizations like removing unused pins from internal modules are often times opposed.

Chris Lattner and others are currently working on an "industry" version of firrtl as part of the CIRCT hardware compiler framework: https://github.com/llvm/circt

Did you see the work being done on CIRCT? https://github.com/llvm/circt

I remember one of the reasons you did not want to use firrtl was that its compiler is implemented in Scala and thus hard to integrate into other projexts. CIRCT will solve that problem by providing a firrtl compiler implemented in C++. Other languages like Verilog/VHDL and new high level languages for HLS-like designs are also on the todo list.

Relevant: https://github.com/llvm/circt

You don't need to have any particular skills except familiarity with Julia, but it's obviously an advantage to have a bio background - depending on what you're going to do.

Usually, the best packages come about when people are motivated to creating something specific, for example if they think the status quo in some domain is not good enough.

I'm sure we can dig up a handful of old, badly maintained projects that could use some love. Off the top of my head, it would be nice to have

* Micro-optimized our smith-waterman algorithm. That's probably fairly easy to get started with if you're not a bio person

* A number of our parsers have not been properly maintained. We use finite state automata https://github.com/BioJulia/Automa.jl to create parsers. That's for more advanced users

Feel free to get in touch on the Julia Slack, or send me an email :)

I'm not in bioinformatics and don't do string processing, so I can't really help too much here.

I'd really urge you to come ask this on the julia Discourse Forum or Zulip and I promise you'll get high quality useful responses from people who understand your needs better than I.

> How do I find substrings & replace them efficiently? How do you split a string with delimiters? Regular Expressions?

This is something that the BioJulia people have put a lot of work into. Yes, you can use regular expressions, but they've managed to squeeze a lot of performance out of more specialized approaches, e.g.

https://github.com/BioJulia/Automa.jl

https://github.com/jakobnissen/ScanByte.jl

But for more straightforward usage, julia has the `findfirst` function which can search for occurrences of a substring, `replace` which can do replacements either with a literal pattern or a regex, and `split` which can split a string with delimiters.