Remove clabe dependencies and adopt standard Bonsai environment directory

.github/workflows/dynamic-foraging-cicd.yml

@@ -51,7 +51,7 @@ jobs:
         run: dotnet tool restore
 
       - name: Setup Bonsai environment
-        working-directory: ./bonsai
+        working-directory: ./.bonsai
         run: ./setup.ps1
 
       - name: Run python unit tests

.gitignore

@@ -4,7 +4,7 @@ bin
 obj
 Packages
 Bonsai.exe.WebView2
-Bonsai/Settings/
+.bonsai/Settings/
 *.bin
 *.avi
 *.dll

README.md

@@ -45,7 +45,7 @@ Examples on how to generate these files can be found in the `./Examples` directo
 The workflow can thus be executed using the [Bonsai CLI](https://bonsai-rx.org/docs/articles/cli.html):
 
 ```powershell
-"./bonsai/bonsai.exe" "./src/main.bonsai" -p SessionPath=<path-to-session.json> -p RigPath=<path-to-rig.json> -p TaskLogicPath=<path-to-task_logic.json>
+"./.bonsai/bonsai.exe" "./src/main.bonsai" -p SessionPath=<path-to-session.json> -p RigPath=<path-to-rig.json> -p TaskLogicPath=<path-to-task_logic.json>
 ```
 
 However, for a better experiment management user experience, it is recommended to use the provided experiment launcher below.
@@ -166,24 +166,6 @@ Define the following modules within a curriculum:
 
 ---
 
-## 🎮 Experiment launcher (temporarily CLABE)
-
-To manage experiments and input files, this repository contains a launcher script that can be used to run the Dynamic Foraging task. A default script is located at `./scripts/aind-launcher.py`. It can be run from the command line as follows:
-
-```powershell
-uv run clabe run ./scripts/aind-launcher.py
-# or uv run ./scripts/main.py
-```
-
-Additional arguments can be passed to the script as needed. For instance to allow the script to run with uncommitted changes in the repository, the `--allow-dirty` flag can be used:
-
-```powershell
-uv run clabe run ./scripts/aind-launcher.py --allow-dirty
-```
-
-or via a `./local/clabe.yml` file. Additional custom launcher scripts can be created and used as needed. See documentation in the [`clabe` repository](https://allenneuraldynamics.github.io/clabe/) for more details.
-
-
 ## 🔍 Primary data quality-control
 
 Once an experiment is collected, the primary data quality-control script can be run to check the data for issues. This script can be launcher using:

pyproject.toml

@@ -43,7 +43,6 @@ dev = [
     "ruff",
     "codespell",
     "aind-behavior-dynamic-foraging[data]",
-    "aind-clabe[aind-services]>=0.10"
 ]
 
 docs = [

scripts/deploy.ps1

@@ -2,9 +2,6 @@ $scriptPath = $MyInvocation.MyCommand.Path
 $scriptDirectory = Split-Path -Parent $scriptPath
 Set-Location (Split-Path -Parent $scriptDirectory)
 
-Write-Output "Initializing and updating submodules..."
-&git submodule update --init --recursive
-
 Write-Output "Creating a Python  environment..."
 
 if (-not (Get-Command uv -ErrorAction SilentlyContinue)) {
@@ -17,7 +14,7 @@ if (Test-Path -Path ./.venv) {
 &uv venv
 .\.venv\Scripts\Activate.ps1
 Write-Output "Synchronizing environment..."
-&uv sync --extra launcher
+&uv sync
 Write-Output "Creating a Bonsai environment and installing packages..."
 if (Test-Path -Path "bonsai") {
     Set-Location "bonsai"

tests/test_bonsai.py

@@ -45,6 +45,7 @@ def test_deserialization(self):
             is_editor_mode=False,
             layout=None,
             additional_properties=workflow_props,
+            bonsai_exe=Path("./.bonsai/bonsai.exe").resolve(),
         )
         stdout = completed_proc.stdout.decode().split("\n")
         stdout = [line for line in stdout if (line or line != "")]