Bacterial_branching example

[Armavica]

Hi, as part of the review that I am doing for JOSS (openjournals/joss-reviews#7723), I am trying to run the examples shared in the article.

I first went to cellular_raza-examples/bacterial_branching and ran cargo run --release. Then, I ran python src/plotting.py.
The video generated is the following, which does not look like Figure 3 of the article.

movie.mp4

I then tried to use the files listed on this page of the website. I used the following Cargo.toml file (copied from bacterial_branching example with just the name changed):

[package]
name = "cr_bacteria_branching"
version = "0.1.0"
edition = "2021"
authors = ["Jonas Pleyer <[email protected]>"]

[dependencies]
serde = { workspace = true, features=["rc"] }
rand = { workspace = true, features=["small_rng"] }
rand_chacha = { workspace = true }
nalgebra = { version="0.33" }
num = { workspace = true }
cellular_raza = { path="../../cellular_raza", features=["default"] }
plotters = { workspace = true }
rayon = "1.10.0"
ndarray = { version = "0.16.0", features = ["blas", "serde", "serde-1"] }

But upon running cargo run --release, I am getting the following error:

❯ cargo run --release                                                                           (cellular_raza) 
   Compiling cr_bact_branching v0.1.0 (/home/virgile/src/cellular_raza/cellular_raza-examples/bact_branching)
error[E0432]: unresolved import `cellular_raza::prelude::cpu_os_threads`
 --> cellular_raza-examples/bact_branching/src/main.rs:3:29
  |
3 | use cellular_raza::prelude::cpu_os_threads::*;
  |                             ^^^^^^^^^^^^^^ could not find `cpu_os_threads` in `prelude`

For more information about this error, try `rustc --explain E0432`.
error: could not compile `cr_bact_branching` (bin "cr_bact_branching") due to 1 previous error

Is there something that I am doing wrong?

Edit: Ok, I figured it out: I had to enable the cpu_os_threads feature. I obtained the following final state:

It looks a bit more like what is shown in the article. I saw that you state on this page that you lost the parameters that generated the illustration picture. While this might be fine for the documentation, I think that it ought to be possible to recreate the figures that you use in the article. Have you considered using for Figure 3 an illustration coming from a known set of parameters?

[jonaspleyer]

Edit: Ok, I figured it out: I had to enable the cpu_os_threads feature. I obtained the following final state:

I will include the Cargo.toml file on the website as well. You are right that without this file, the example is not complete.

Have you considered using for Figure 3 an illustration coming from a known set of parameters?

I had considered that. One reason why I did not recreate the plot was that the total Runtime was very large. I will re-asses this issue and decide if to show a (possibly smaller) example with known parameters.

TODO

• Add Cargo.toml file in website
• Parameters and Reproducability of the Bacterial Branching Example

[jonaspleyer]

For reference: I am actively working on this issue and will hopefully be able to resolve it in the coming week.