- add a timestamp to all the measurements of the _diversity_ from `inbreeding/mod.rs`
- allow to delay the measurement starts with `--measurement-schedule-start`, to help completing already existing measurements

> ❗ **Important**  
> existing measurement files will have to change shape from
> ```
> table<strategy: string, diversity: list<float>>
> ```
> to
> ```
> table<strategy: string, diversity: table<t: int, diversity: float>>
> ```

just a small QoL improvement

this MR is two-fold
- refactor `run.nu` and `plot.nu` from `scripts/inbreeding/` into Nushell modules with `--options` as argument instead of `options.nu` (a7cebb95, 6b72191f and 5f1c4963)
- introduce another level of depth to the measurements (a0e52e95)

> 💡 **Note**  
> in the table below
> - $s$ is the number of recoding scenarii averages together
> - $m$ is the number of measurements per point
> - two iterations of the same experiment are shown side by side for comparison

s   |    m | . | .
:--:|:----:|:-------------------------:|:-------------------------:
1   | 10   | ![inbreeding_1_10.1](/uploads/c593393edb3513c9d77b0fe134c27fd7/inbreeding_1_10.1.png) | ![inbreeding_1_10.2](/uploads/97c85b36833112de51a2b756ade53479/inbreeding_1_10.2.png)
1   | 100  | ![inbreeding_1_100.1](/uploads/af4da1d7cf76ef43fb39c2a3a529b7cd/inbreeding_1_100.1.png) | ![inbreeding_1_100.2](/uploads/e187298709d524437dea503be6ac555f/inbreeding_1_100.2.png)
1   | 1000 | ![inbreeding_1_1000.1](/uploads/394821777baeff9fec589440ba4c554c/inbreeding_1_1000.1.png) | ![inbreeding_1_1000.2](/uploads/1d592b791075f204f8a0ebdd739403dd/inbreeding_1_1000.2.png)
10  | 100  | ![inbreeding_10_100.1](/uploads/3c822e7669e9f0b4d97919e5a3bd4bca/inbreeding_10_100.1.png) | ![inbreeding_10_100.2](/uploads/aa6b54ec64f82ca386dae4e262dcd0b6/inbreeding_10_100.2.png)
100 | 10   | ![inbreeding_100_10.1](/uploads/7ef383143d981717b0ad01dee0359eb0/inbreeding_100_10.1.png) | ![inbreeding_100_10.2](/uploads/ce71a32a7f6e9ba3c4dae563aeefd856/inbreeding_100_10.2.png)
100 | 100  | ![inbreeding_100_100.1](/uploads/e2038273051f959d8be69fef9ba7a493/inbreeding_100_100.1.png) | ![inbreeding_100_100.2](/uploads/0ef30735597e1a6812484d1cac4d34ca/inbreeding_100_100.2.png)

we can see that
- the smaller the $s$, the more different the two figures are on each line -> this is likely due to the fact that, if only one recoding scenario is used, then repeating the same experiment will result in very different results and measurements. Running the same experiment $s$ times and averaging helps reducing the variance along this axis
- the smaller the $m$, the more noisy the measures of each points -> this is simply because, when $m$ is small, the variance of the empirical means measured for each point is higher

## final results
![inbreeding](/uploads/e561f4e4acad8eedbb3ccf1a4666c302/inbreeding.png)
![inbreeding_100_100_1](/uploads/37ab0eacb5159137595579dfbb20250c/inbreeding_100_100_1.png)

check for empty inputs in the `run.nu` scripts

up until now, elliptic curves have been hardcoded in the benchmarks, forcing to run them on all supported curves...

this MR makes it possible to use only a subset of curves.

> 💡 **Note**  
> when running the same commands from !104, minus the "inbreeding" ones which are not affected by this MR, the time goes from 12min 33sec to 4min 28sec 🎉 


## TODO
- [x] setup
- [x] commit
- [x] recoding
- [x] fec
- [ ] linalg
- [ ] setup size
- [ ] field operations
- [ ] group operations

> 💡 **Note**  
> because all the unticked bullet points above are far from critical to the paper and do require to measure all curves, i won't change these for now

this MR moves run and plot commands from `examples/benches/README.md` to
- `scripts/setup/`: `run.nu` and `plot.nu`
- `scripts/commit/`: `run.nu` and `plot.nu`
- `scripts/recoding/`: `run.nu` and `plot.nu`
- `scripts/fec/`: `run.nu` and `plot.nu`
- `scripts/inbreeding/`: `build.nu`, `run.nu` and `plot.nu`

to generate all the figures at once
```bash
use scripts/setup/run.nu; seq 0 13 | each { 2 ** $in } | run --output data/setup.ndjson
use ./scripts/setup/plot.nu; plot data/setup.ndjson --save ~/setup.pdf

use scripts/commit/run.nu; seq 0 13 | each { 2 ** $in } | run --output data/commit.ndjson
use ./scripts/commit/plot.nu; plot data/commit.ndjson --save ~/commit.pdf

use scripts/recoding/run.nu; seq 0 18 | each { 512 * 2 ** $in } | run --ks [2, 4, 8, 16] --output data/recoding.ndjson
use ./scripts/recoding/plot.nu; plot data/recoding.ndjson --save ~/recoding.pdf

use scripts/fec/run.nu; seq 0 18 | each { 512 * 2 ** $in } | run --ks [2, 4, 8, 16] --output data/fec.ndjson
use ./scripts/fec/plot.nu; plot encoding data/fec.ndjson --save ~/encoding.pdf
use ./scripts/fec/plot.nu; plot decoding data/fec.ndjson --save ~/decoding.pdf
use ./scripts/fec/plot.nu; plot e2e data/fec.ndjson --save ~/e2e.pdf

use ./scripts/fec/plot.nu; plot combined data/fec.ndjson --recoding data/recoding.ndjson --save ~/comparison.pdf
use ./scripts/fec/plot.nu; plot ratio data/fec.ndjson --recoding data/recoding.ndjson --save ~/ratio.pdf

./scripts/inbreeding/build.nu
./scripts/inbreeding/run.nu --output data/inbreeding.nuon
./scripts/inbreeding/plot.nu data/inbreeding.nuon --save ~/inbreeding.pdf
```

> 💡 **Note**  
> this took around 27min 18sec in total on my machine with 14min 45sec for the inbreeding section only and 12min 33sec for the rest

- new `scripts/plot.nu` with common tools and options
- better sets of parameters
- better commands in `benches/README.md`

i've moved the plotting scripts to [GPLT](https://gitlab.isae-supaero.fr/a.stevan/gplt) which allows to install a single command, called `gplt`, with two subcommands
- `gplt plot` which is the same as old `python scripts/plot/plot.py`
- `gplt multi_bar` which is the same as old `python scripts/plot/multi_bar.py`

- fix the path to the "bench" readme and remove it from the plot scripts
- "BLS-12-381" to "BLS12-381" for consistency

this MR goes from
```rust
let xs = seq 0 5 | each { 2 ** $in } | wrap x
let twice = $xs | insert measurement { 2 * $in.x } | insert error { 0.1 + 0.5 * $in.x }
let square = $xs | insert measurement { $in.x ** 2 } | insert error { 1 + 1.5 * $in.x }

python scripts/plot/plot.py --title title --x-label x --y-label y --fullscreen ([
    { group: "x ^ 2", items: $square },
    { group: "2 * x", items: $twice }
] | to json)
```
to
```rust
let xs = seq 0 5 | each { 2 ** $in }
let twice = $xs | wrap x | insert y { 2 * $in.x } | insert e { 0.1 + 0.5 * $in.x }
let square = $xs | wrap x | insert y { $in.x ** 2 } | insert e { 1 + 1.5 * $in.x }

python scripts/plot/plot.py --title title --x-label x --y-label y --fullscreen ([
    { name: "x ^ 2", points: $square },
    { name: "2 * x", points: $twice }
] | to json)
```
updates the "bench" README and adds type annotations to the `plot.py` script.

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)

> 💡 **Note**  
> - in the following examples, any part of the `$.style` specification is optional and can either be ommitted or set to `null`
> - the default values for `$.style` are given in `plot.py --help`

```rust
let xs = seq 0 5 | each { 2 ** $in } | wrap x
let twice = $xs | insert measurement { 2 * $in.x } | insert error { 0.1 + 0.5 * $in.x }
let square = $xs | insert measurement { $in.x ** 2 } | insert error { 1 + 1.5 * $in.x }
```
and try
```rust
python scripts/plot/plot.py --title title --x-label x --y-label y --fullscreen ([
    { group: "x ^ 2", items: $square },
    { group: "2 * x", items: $twice }
] | to json)
```
vs
```rust
python scripts/plot/plot.py --title title --x-label x --y-label y --fullscreen ([
    {
        group: "x ^ 2",
        items: $square,
        style: {
            color: "red",
            alpha: 0.5,
            line: {
                marker: 's',
                width: 2,
                type: "dashed",
            },
        }
    },
    {
        group: "2 * x",
        items: $twice,
        style: {
            color: "purple",
            alpha: 0.1,
            line: {
                marker: 'o',
                width: 5,
                type: "dotted",
            },
        }
    }
] | to json)
```

## changelog
- use `out> *.ndjson` in the README to simplify running the benchmarks
- create a `scripts/math.nu` module with `ns-to-ms` and `compute-stats` to refactor some of the most common operations
- add `--fullscreen` to `plot.py` and `multi_bar.py`
- add `--x-scale` and `--y-scale` to `plot.py`

## changelog
- benchmarks
  - _commit_ has been removed in favor of `examples/benches/commit.rs`
  - _linalg_ has been migrated to `examples/benches/` as `bench_linalg`
  - _setup_ has been migrated to `examples/benches/` as `bench_setup`
- `read-atomic-ops` command has been moved to `scripts/parse.nu` module
- `scripts/plot/bench_commit.py` has been made more general and renamed to `scripts/plot/plot.py`
- `scripts/plot/benches.py` has been removed because it's not required anymore => `plot.py` and `multi_bar.py` are general enough

this MR
- bumps PLNK to 0.6.0
- update all existing code
- uses the PLNK lib in `examples/benches/commit.rs`
- fixes the y label of the plot in `scripts/plot/bench_commit.py`: was _ns_, should be _ms_

we see that the Arkworks / Komodo versions of the same curves are basically the same.
![Figure_1](/uploads/faa1523bbd3037390eb0c56f037995ea/Figure_1.png)

this MR adds two now benchmarks:
- `field_operations` in `benches/operations/field.rs`
- `curve_group_operations` in `benches/operations/curve_group.rs`

as well as `scripts/plot/multi_bar.py` to plot the results, see `benches/README.md` for the commands to run.

## results
![curve_group](/uploads/0a27dcdc7965090b0429867e1822a40c/curve_group.png)

![field](/uploads/461455568a0a637f78f9c2b6d1a68f59/field.png)

this MR
- adds an Arkworks bench oneshot function to the `bench_commit` example
- adapts the `measure!` macro to pass a _pairing-friendly_ curve
- give different linestyle to curves in the Python script

## example measurements
![Figure_1](/uploads/4b7f52eb3a8c894317cc34057652020f/Figure_1.png)

i ended up adding a bunch of changes to the benchmarks 😊 

## changelog
* 805a2454 reduce the number of loops and the warmup time
* f7ce05c3 don't serialize for real to save time
* 37a2a7e2 don't try to compress with validation
* 409f3e3c don't multiply degree by 1_024
* 610024a9 fix setup
* 3d5e7c58 fix setup
* 3d3167fb run benchmarks on BLS12-381, BN-254 and PALLAS
* da2a71a1 pass name of the curve as parameter
* 954fd6d3 plot commit for all curves
* f980b30f plot all curves in linalg
* 5e41df1d rename `labels` to `keys` in commit
* 8bb64f99 filter setup by curves
* 0163c8f9 plot all curves in setup
* 8c91c6d8 split the setup of Komodo and the serde benchmarks
* 0784f294 add a manual benchmark to measure the commit
* 608a3fd1 move the "example benches" to `examples/benches/`
* 10f9a37c add a script to plot results from `bench_commit`
* 6d512fa6 move plot script from `benches/` to `scripts/plot/`
* a4e6ffbc measure VESTA