Major changes for v3.0.0 release

.devcontainer/devcontainer.json

@@ -1,7 +1,7 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-docker-compose
 {
-	"name": "Development",
+	"name": "bughog-devcontainer",
 
 	// Update the 'dockerComposeFile' list if you have more compose files or use different names.
 	// The .devcontainer/docker-compose.yml file contains any overrides you need/want to make.
@@ -14,12 +14,20 @@
 	"service": "core_dev",
 	"runServices": ["node_dev", "nginx_dev"],
 
+	"containerEnv": {
+		"UV_PROJECT_ENVIRONMENT": "/app/.venv"
+	},
+
 	// The optional 'workspaceFolder' property is the path VS Code should open by default when
 	// connected. This is typically a file mount in .devcontainer/docker-compose.yml
 	"workspaceFolder": "/app",
 	"customizations": {
 		"vscode": {
+			"settings": {
+				"python.defaultInterpreterPath": "/app/.venv/bin/python"
+			},
 			"extensions": [
+				"astral-sh.ty",
 				"charliermarsh.ruff",
 				"ms-python.debugpy",
 				"ms-python.python",
@@ -28,8 +36,7 @@
 		}
 	},
 
-	// Install pip requirements
-	"postCreateCommand": "pip install -r requirements.txt"
+	"postCreateCommand": "uv sync --dev --locked",
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -38,7 +45,7 @@
 	// "forwardPorts": [],
 
 	// Uncomment the next line if you want to keep your containers running after VS Code shuts down.
-	// "shutdownAction": "none",
+	"shutdownAction": "stopCompose",
 
 	// Configure tool-specific properties.
 	// "customizations": {},

.github/workflows/run-tests-and-linter.yml

@@ -3,68 +3,65 @@ on: [push]
 jobs:
   pytest:
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Cache Python dependencies
-        id: cache-pip
-        uses: actions/cache@v3
-        env:
-          cache-name: cache-python-dependencies
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('**/requirements_dev.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-build-${{ env.cache-name }}-
-            ${{ runner.os }}-build-
-            ${{ runner.os }}-
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.11"
+          enable-cache: true
+
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements_dev.txt
-          pip install genbadge[all]
-      - name: Test with pytest
-        run: |
-          pytest --ignore=test/availability
+        run: uv sync --dev --locked
+
+      - name: Run pytest
+        run: uv run pytest --ignore=test/availability
+
       - name: Generate badge
         run: |
-          genbadge tests -i junit.xml -o pytest.svg
-          genbadge coverage -i coverage.xml -o coverage.svg
-      - name: Upload tests badge as artifact
+          uv run genbadge tests -i junit.xml -o pytest.svg
+          uv run genbadge coverage -i coverage.xml -o coverage.svg
+
+      - name: Upload test badge
         uses: actions/upload-artifact@v4
         with:
           name: pytest
           path: pytest.svg
           overwrite: true
-      - name: Upload coverage badge as artifact
+
+      - name: Upload coverage badge
         uses: actions/upload-artifact@v4
         with:
           name: coverage
           path: coverage.svg
           overwrite: true
 
+
   flake8:
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.11"
+          enable-cache: true
+
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install flake8 genbadge[all]
+          uv sync --dev --locked
+
       - name: Lint with flake8
         run: |
-          flake8 --exit-zero --output-file flake8.txt
+          uv run flake8 --exit-zero --output-file flake8.txt
+
       - name: Generate badge
         run: |
-          genbadge flake8 -i flake8.txt -o flake8.svg
-      - name: Upload badge with GitHub pages
+          uv run genbadge flake8 -i flake8.txt -o flake8.svg
+
+      - name: Upload badge
         uses: actions/upload-artifact@v4
         with:
           name: flake8

.gitignore

@@ -1,8 +1,15 @@
-test/resources/repositories
-browser/binaries/
 database/data/
+
 nginx/ssl/certs/*
 nginx/ssl/keys/*
+
+subject/*/executables/*
+
+subject/*/experiments/*
+!subject/*/experiments/_default_files/
+!subject/*/experiments/_tests/
+!subject/*/experiments/examples/
+
 !**/.gitkeep
 **/node_modules
 **/junit.xml

.vscode/launch.json

@@ -8,12 +8,14 @@
             "name": "BugHog",
             "type": "debugpy",
             "request": "launch",
-            "program": "/app/bci/app.py",
+            "program": "${workspaceFolder}/bughog/app.py",
+            "python": "${workspaceFolder}/.venv/bin/python",
+            "cwd": "${workspaceFolder}",
             "purpose": [
                 "debug-test"
             ],
             "env": {
-                "PYTHONPATH": "/app",
+                "PYTHONPATH": "${workspaceFolder}",
                 "DISPLAY": ":1",
                 "MOZ_DISABLE_CONTENT_SANDBOX": "1",
                 "PATH":"${PATH}:$HOME/.local/bin"

.vscode/settings.json

@@ -1,7 +1,5 @@
 {
-    "python.defaultInterpreterPath": "/usr/local/bin/python",
-    "python.linting.enabled": true,
-    "python.linting.flake8Enabled": true,
+    "python.defaultInterpreterPath": "/app/.venv/bin/python",
     "python.testing.pytestArgs": [
         "test"
     ],

Dockerfile

@@ -1,8 +1,8 @@
 FROM node:22.14-alpine AS ui-build-stage
 WORKDIR /app
-COPY /bci/web/vue/package*.json ./
+COPY /bughog/web/vue/package*.json ./
 RUN npm install
-COPY /bci/web/vue ./
+COPY /bughog/web/vue ./
 RUN npm run build
 
 
@@ -21,10 +21,11 @@ CMD ["start.sh"]
 
 
 FROM python:3.13-slim-bullseye AS base
+COPY --from=ghcr.io/astral-sh/uv:0.9.7 /uv /uvx /bin/
 WORKDIR /app
 
 RUN apt-get update
-RUN apt install -y curl gconf-service libasound2 libatk1.0-0 libc6 libcairo2 libcups2 libdbus-1-3 libexpat1 libfontconfig1 libgcc1 libgconf-2-4 libgdk-pixbuf2.0-0 libglib2.0-0 libnspr4 libstdc++6 libx11-6 libx11-xcb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxext6 libxfixes3 libxi6 libxrandr2 libxrender1 libxss1 libxtst6 ca-certificates fonts-liberation libappindicator1 libnss3 lsb-release xdg-utils libgbm-dev xvfb dbus-x11 libnss3-tools python3-pip python3-tk python3-xlib gnome-screenshot vim git procps &&\
+RUN apt install -y curl gconf-service libasound2 libatk1.0-0 libc6 libcairo2 libcups2 libdbus-1-3 libexpat1 libfontconfig1 libgcc1 libgconf-2-4 libgdk-pixbuf2.0-0 libglib2.0-0 libnspr4 libstdc++6 libx11-6 libx11-xcb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxext6 libxfixes3 libxi6 libxrandr2 libxrender1 libxss1 libxtst6 ca-certificates fonts-liberation libappindicator1 libnss3 lsb-release xdg-utils libgbm-dev xvfb dbus-x11 libnss3-tools python3-tk python3-xlib gnome-screenshot vim git procps &&\
     rm -rf /var/lib/apt/lists/*
 
 # Install Docker
@@ -53,37 +54,28 @@ RUN curl -sSLo multiarch-support.deb https://snapshot.debian.org/archive/debian-
     ln -s /usr/lib/x86_64-linux-gnu/libplc4.so /usr/lib/x86_64-linux-gnu/libplc4.so.0d  &&\
     ln -s /usr/lib/x86_64-linux-gnu/libnspr4.so /usr/lib/x86_64-linux-gnu/libnspr4.so.0d
 
-RUN mkdir -p /app/logs && \
-    mkdir -p /app/browser/binaries/chromium/downloaded && \
-    mkdir -p /app/browser/binaries/firefox/downloaded && \
-    mkdir -p /app/browser/binaries/chromium/artisanal && \
-    mkdir -p /app/browser/binaries/firefox/artisanal
-
-COPY browser/profiles /app/browser/profiles
+COPY subject/web_browser/profiles /app/subject/web_browser/profiles
 COPY --chmod=0755 scripts/ /app/scripts/
-RUN cp /app/scripts/daemon/xvfb /etc/init.d/xvfb
+RUN cp /app/scripts/daemon/xvfb /etc/init.d/xvfb &&\
+    mkdir -p /app/logs
 
 # Install python packages
-COPY requirements.txt /app/requirements.txt
-RUN pip install --user -r /app/requirements.txt
+COPY pyproject.toml uv.lock /app/
+RUN uv sync --no-dev --locked
+ENV PATH="/app/.venv/bin:$PATH"
 
 # Initiate PyAutoGUI
 RUN touch /root/.Xauthority && \
     xauth add ${HOST}:0 . $(xxd -l 16 -p /dev/urandom)
 
+
 FROM base AS core
 # Copy rest of source code
-COPY bci /app/bci
+COPY bughog /app/bughog
 ENTRYPOINT [ "/app/scripts/boot/core.sh" ]
 
 
 FROM base AS worker
 # Copy rest of source code
-COPY bci /app/bci
+COPY bughog /app/bughog
 ENTRYPOINT [ "/app/scripts/boot/worker.sh" ]
-
-
-FROM base AS dev
-COPY requirements_dev.txt /app/requirements_dev.txt
-RUN pip install --user -r requirements_dev.txt
-ENTRYPOINT [ "/app/scripts/boot/core.sh" ]