Mention required tools in analysis/sims/ReadMe.md (#481)

* Mention required tools in analysis/sims/ReadMe.md

Add dev shell to analysis/sims/flake.nix which includes those tools.

* Add more tools to sims shell

Author: ch1bo

analysis/sims/ReadMe.md

@@ -8,36 +8,37 @@ These instructions are valid for the folders `2025w25/` and onwards.
 ### Running the simulation
 
 1. Navigate to the folder for the study, for example `2025w31c/`.
-2. Copy or link the Rust simulator `sim-cli` executable to that folder.
+2. Make sure to have the following tools installed: `yaml2json`, `jq` and `pigz`
+    - *Nix:* use the default dev shell of the `sims/` flake `nix develop ..`
+3. Copy or link the Rust simulator `sim-cli` executable to that folder.
     - If you want to reproduce the study, check out the git commit listed in the `sim-cli.hash` file.
-    - Otherwise, run `cargo build --release` in the [sim-rs](../../sim-rs/) folder.
-3. Copy of link the Haskell `leios-trace-processor` executable to that folder.
+    - Build with `cargo build --release` in the [sim-rs](../../sim-rs/) folder.
+    - Link with `ln -s ../../../sim-rs/target/release/sim-cli` from the study folder.
+4. Copy of link the Haskell `leios-trace-processor` executable to that folder.
     - *Cabal:* compile using `cabal build all`.
-    - *Nix:* compile using `nix build #leios-trace-processor`.
-4. You can execute individual scenarios by executing the `run.sh` script in the relevant folder.
+    - *Nix:* compile using `nix build ../..#leios-trace-processor && ln -s result/bin/leios-trace-processor`.
+5. You can execute individual scenarios by executing the `run.sh` script in the relevant folder.
     - *Nix:* run `./run.sh`, which will automatically fetch the package dependencies.
     - *Without Nix:* run `bash run.sh`, but make sure you have the dependent tools already installled, which are listed in the first lines of `run.sh`.
-5. The results folder will contain results:
+6. The results folder will contain results:
     - `sim.log.gz`: the simulation log file, but with a few of the minor message types discarded.
     - `lifecycle.csv.gz`: transaction lifecycle results.
     - `resoruces.csv.gz`: resource usage results.
     - `receipts.csv.gz`: message diffusion results.
     - `cpus.csv.gz`: CPU usage results.
     - `sizes.csv.gz`: BLock size results.
-6. You can also run several simulations at once using the `parallel` command-line tool.
-
+7. You can also run several simulations at once using the `parallel` command-line tool.
 
 ### Combining the results
 
-7. Execute the `combine-results.sh` script to bundle the results from multiple runs into the `results/` folder.
+8. Execute the `combine-results.sh` script to bundle the results from multiple runs into the `results/` folder.
     - *Nix:* run `./combine-results.sh`.
     - *Without nix:* run `bash combine-results.sh` after installing the required dependencies.
-
 
 ### Plot the results in Jupyter
 
-8. Start a Jupter notebook server using the command `nix run #../sims/`.
-9. In the web browser, navigate to the relevant experiment folder and open any `.ipynb` files of interest.
+9. Start a Jupter notebook server using the command `nix run #../sims/`.
+10. In the web browser, navigate to the relevant experiment folder and open any `.ipynb` files of interest.
 
 
 ## Data dictionary

analysis/sims/flake.nix

@@ -1,5 +1,5 @@
 {
-  description = "Your jupyenv project";
+  description = "Flake for simulations and analysis";
 
   nixConfig.extra-substituters = [
     "https://tweag-jupyter.cachix.org"
@@ -14,30 +14,45 @@
   inputs.nixpkgs.url = "github:nixos/nixpkgs/nixos-25.05";
   inputs.jupyenv.url = "github:tweag/jupyenv";
 
-  outputs = {
-    self,
-    flake-compat,
-    flake-utils,
-    nixpkgs,
-    jupyenv,
-    ...
-  } @ inputs:
-    flake-utils.lib.eachSystem
-    [
+  outputs =
+    { self
+    , flake-compat
+    , flake-utils
+    , nixpkgs
+    , jupyenv
+    , ...
+    } @ inputs:
+    flake-utils.lib.eachSystem [
       flake-utils.lib.system.x86_64-linux
     ]
-    (
-      system: let
+      (system:
+      let
         inherit (jupyenv.lib.${system}) mkJupyterlabNew;
-        jupyterlab = mkJupyterlabNew ({...}: {
+        jupyterlab = mkJupyterlabNew ({ ... }: {
           nixpkgs = inputs.nixpkgs;
-          imports = [(import ./kernels.nix {pkgs = nixpkgs;})];
+          imports = [ (import ./kernels.nix { pkgs = nixpkgs; }) ];
         });
-      in rec {
-        packages = {inherit jupyterlab;};
+        pkgs = import nixpkgs { inherit system; };
+      in
+      rec {
+        packages = { inherit jupyterlab; };
         packages.default = jupyterlab;
+
         apps.default.program = "${jupyterlab}/bin/jupyter-lab";
         apps.default.type = "app";
-      }
-    );
+
+        devShells.sims = pkgs.mkShell {
+          buildInputs = [
+            pkgs.remarshal # yaml2json
+            pkgs.jq
+            pkgs.ansifilter
+            pkgs.gnugrep
+            pkgs.gnused
+            pkgs.gzip
+            pkgs.pigz
+            pkgs.bc
+          ];
+        };
+        devShells.default = devShells.sims;
+      });
 }