## changelog
- _semi\_avid_, _kzg_ and _aplonk_ examples have been added
- the `fs` module has been hidden behind an `fs` feature
- the `conversions` module has been properly hidden behind the `test` config feature
- the documentation has been completed
- some error messages have been improved

> **Note**
>
> the documentation of aPlonK has been left as-is for now

## changelog
- `src/main.rs` has been moved to a new crate: `bins/saclin` which stands for **S**emi-**A**VID **CLI** in **N**ushell
- dependencies of `komodo` have been fixed
- Nushell and Rust tests have been split in the Makefile: by default, only Rust tests will run locally and Nushell tests and examples can be run manually if desired. The CI will still run everything.
- the README has been updated
- test images have been moved to `assets/`
- the majority of the old `./nu-utils/` module have been moved to internals of `./benchmarks/` and imports have been fixed
- `cargo.nu` has been moved to `./bins/` and a new `./bins/README.md` mentions it
- `./bins/saclin/` has been created and should be a self-contained Rust crate + Nushell module

this MR is two-fold
- it restructures the two main Nushell modules so that they are easier to read and use
- it improves the "run" and "plot" modules for the benchmarks

## changelog
- `.nushell/` is now renamed to `nu-utils/`
- `benchmarks/` is now a valid Nushell module which exports a bunch of modules
  - `benchmarks linalg`: measure and plot linear algebra operations
  - `benchmarks setup`: measure and plot trusted setup building
  - `benchmarks commit`: measure and plot crafting commitments
  - `benchmarks recoding`: measure and plot the recoding of shards
  - `benchmarks fec`: measure and plot FEC operations, such as encoding and recoding, and allow combining these results with the pure recoding ones
- the submodules of `benchmarks` typically have a `run` and a `plot` command, whith the exception of `benchmarks fec` which has a `run` module and multiple "plot" commands in `benchmarks fec plot`
- the "run" commands will create a random temp file by default and ask for confirmation otherwise if the output file already exists, unless `--force` is used
- snippetds in `benchmarks/README.md` have been updated

see the changelogs of
- [Nushell `0.94.0`](https://www.nushell.sh/blog/2024-05-28-nushell_0_94_0.html)
- [Nushell `0.94.1`](https://www.nushell.sh/blog/2024-05-30-nushell_0_94_1.html)
- [Nushell `0.94.2`](https://www.nushell.sh/blog/2024-06-03-nushell_0_94_2.html)

i also removed the `bytes encode` and `bytes decode` commands from `.nushell/binary.nu` because... well they did not work anymore and they were not used anywhere 

this MR turns `./.nushell/` into a directory module by
- adding `mod.nu`
- exporting all the modules

all uses of `.nushell/` have been fixed to not mention `.nu` internal modules anymore.

>  **Note**  
> the `.nushell venv` module has been removed because, when the `$venv.VENV` activation script is not there, Nushell can't parse the whole `.nushell` module, which is very annoying to have to rely of the state of the external filesystem to be able to simply parse a module...

this also bumps Nushell to 0.93.0 to include the "extra" command `fmt`, see [Nushell 0.92.0](https://www.nushell.sh/blog/2024-04-02-nushell_0_92_0.html#incorporating-the-extra-feature-by-default-toc)

## new structure for the repository
- benchmarks are in `./benchmarks/` and can be run with either `cargo run --package benchmarks --bin <bench>` or the commands in `./benchmarks/README.md`
```
├── Cargo.toml
├── README.md
└── src
    └── bin
        ├── commit.rs
        ├── fec.rs
        ├── linalg.rs
        ├── operations
        │   ├── curve_group.rs
        │   └── field.rs
        ├── recoding.rs
        ├── setup.rs
        └── setup_size.rs
```

- examples are now in `./bins/` as standalone binaries and can be run either with `cargo run --package <pkg>` or with the help of the `cargo bin` command from `.nushell/cargo.nu`
```
├── curves
│   ├── Cargo.toml
│   ├── README.md
│   └── src
│       └── main.rs
├── inbreeding
│   ├── build.nu
│   ├── Cargo.toml
│   ├── consts.nu
│   ├── mod.nu
│   ├── plot.nu
│   ├── README.md
│   ├── run.nu
│   └── src
│       ├── environment.rs
│       ├── main.rs
│       └── strategy.rs
├── rank
│   ├── Cargo.toml
│   └── src
│       └── main.rs
└── rng
    ├── Cargo.toml
    └── src
        └── main.rs
```

- Nushell modules are now located in `./.nushell/`

## changelog
apart from the changes to the general structure of the repo:
- `binary.nu` -> `.nushell/binary.nu`
- new `cargo bin` command from `.nushell/cargo.nu`
- `error throw` is now defined in `.nushell/error.nu`
- main TOML has been greatly simplified because the dependencies of "examples" have been moved to the associated crates
- the rest is basically the same but in the new structure

this MR
- moves the last "recoding" benchmark to `examples/benches/`
- moves the README, which is now all alone, to `examples/benches/`
- adds a mention to `examples/benches/README.md` in `README.md`
- some minor improvements to the bench README

## TODO
- [x] find a way to plot the "recoding" results (thanks to !90)

related to
- dragoon/komodo!13

## description
in dragoon/komodo!13, i noticed that decoding can be pretty sensitive to the order of the shards...
this is why i thought testing all possible permutations of the shards could be beneficial 

see the [run attached to this MR](https://gitlab.isae-supaero.fr/dragoon/komodo/-/jobs/11281#L1120) to see all the combinations of shards used in the tests, e.g. `[0, 2, 3]` means that shards `0`, `2` and `3` have been used and shards `1` and `4` have been "_lost_" 

## changelog
this MR
- adds an inline `math` module to `tests/cli.nu` which defines
  - `choose` which computes all the sets of $k$ choose $n$ in $[|0, ..., n - 1|]$
  - `perm` which computes all the permutations on $[|0, ..., n - 1|]$
  - see the inline `_test_choose` and `_test_perm` commands for concrete examples of their behaviours
- compute all the permutation of $k'$ choose $n$ shards, where $k'$ ranges from $k$ to $n$
- run the reconstruction test on all these cases
- moves the CLI example from `README.md` to `examples/cli.nu`

> **Note**  
> also removes the newline added to the stdout of `komodo` commands, so that the output is prettier, without spurious empty lines

this is to make the passing of bytes easier as `cargo run` wants strings.