Diego Javier Zea

REPL does not work as indicated in the README example

1

Hi, I've found the following error while trying to run the example in the README file: ``` julia> using LispSyntax julia> LispSyntax.init_repl() ERROR: UndefVarError: init_repl not defined ``` Cheers,

``` D:\>"C:\Users\Diego\AppData\Local\Julia-1.2.0\bin\julia.exe" C:\Users\Diego\.julia\packages\MIToS\Hha81\scripts\SplitStockholm.jl -h ERROR: LoadError: ArgumentError: Package ArgParse not found in current path: - Run `import Pkg; Pkg.add("ArgParse")` to install the ArgParse package. ```

```julia parse(""" # P D K Q L D E R E H T I E # P D A Q R I K A K R N A K...

- [ ] deprecate `@residue...` macros and use kw args instead - [ ] make `map...freq` simpler with kw args and default values

The updated `mitos-benchmarks/MIToS` benchmark shows small regression in `read`/`write` of MSA for Julia 1.0.2 and MIToS 2.3.1. Maybe, it's related to the use of `length(::String)`: https://discourse.julialang.org/t/performance-of-length-string/12672 Also, `@profile` shows that...

Actual test coverage is ~89%. That's great! However, would be great to increase that number to make this package more reliable and avoid future regressions ;) It's easy to see...

We've started to port MIToS benchmarks to this repository (in the *benchmark* folder) to use [PkgBenchmark](https://github.com/JuliaCI/PkgBenchmark.jl). Actually, old bechmarks for MIToS are in: - [ ] [mitos-benchmarks](https://github.com/diegozea/mitos-benchmarks) - [ ]...

MIToS should avoid `push!` calls

1

...when it's possible to gain performance: https://github.com/JuliaLang/julia/issues/5364

Plot: PDB structures

2

PV can be useful for this: https://github.com/biasmv/pv

Deal with redirect on download...

2

Maybe using [LibCurl.jl](https://github.com/JuliaWeb/LibCURL.jl) and setting [CURLOPT_FOLLOWLOCATION](https://curl.haxx.se/libcurl/c/CURLOPT_FOLLOWLOCATION.html) to false... Or maybe copy download from base but using `--max-redirect 0` for `wget` and `curl` without `-L`.