Configured Dockerfile for aqc_venv and fixed Linux paths

Dockerfile

@@ -16,13 +16,9 @@ ENV DEBIAN_FRONTEND=noninteractive \
     VTK_SILENCE_GET_VOID_POINTER_WARNINGS=1
 
 # 3. Install System Dependencies
-# This is the most critical part for PyVista/VTK. We need the OS
-# graphics libraries (libosmesa, libgl1) and the X Virtual FrameBuffer (xvfb).
-#
-# *** UPDATED this section to use current package names (e.g., libgl1, libegl1) ***
-#
+# Added 'git' here because we need it to clone aqc-research
 RUN apt-get update && apt-get install -y --no-install-recommends \
-  build-essential cmake wget xvfb nginx \
+  build-essential cmake wget xvfb nginx git \
     libosmesa6 libosmesa6-dev \
     libgl1 libgl1-mesa-dev \
     libegl1 libegl1-mesa-dev \
@@ -49,9 +45,21 @@ RUN python3 -m pip install --upgrade pip setuptools wheel \
 COPY --chown=user:user . .
 COPY docker/nginx.conf /etc/nginx/nginx.conf
 
-# 7. Install the local adapt-aqc package
-# We do this after copying the files so the source code is available
-RUN python3 -m pip install ./utils/adapt-aqc
+# ---------------------------------------------------------------------------
+# [NEW] Create the 'aqc_venv' and install dependencies exactly as requested
+# ---------------------------------------------------------------------------
+RUN python3 -m venv utils/aqc_venv && \
+    # 1. Upgrade pip inside the new venv
+    utils/aqc_venv/bin/pip install --upgrade pip setuptools wheel && \
+    # 2. Clone aqc-research inside utils
+    cd utils && \
+    git clone https://github.com/bjader/aqc-research.git && \
+    # 3. Install aqc-research into the venv
+    ../utils/aqc_venv/bin/pip install ./aqc-research && \
+    # # 4. Remove the cloned folder
+    # rm -rf aqc-research && \
+    # 5. Install adapt-aqc (editable mode) into the venv
+    ../utils/aqc_venv/bin/pip install -e ./adapt-aqc
 
 # Prepare writable directories for nginx (running as non-root later)
 RUN mkdir -p /tmp/nginx/body /tmp/nginx/proxy /tmp/nginx/fastcgi /tmp/nginx/uwsgi /tmp/nginx/scgi \
@@ -61,6 +69,9 @@ RUN mkdir -p /tmp/nginx/body /tmp/nginx/proxy /tmp/nginx/fastcgi /tmp/nginx/uwsg
 # 7. Switch to the non-root user
 USER user
 
+# Note: We do NOT set PYTHONPATH for adapt-aqc here because it is installed 
+# inside the 'aqc_venv' which your code calls via subprocess.
+
 # Default runtime configuration for multiprocess layout
 ENV OMP_NUM_THREADS=1 \
   APP_HOST=127.0.0.1 \

utils/base_functions.py

@@ -1,3 +1,7 @@
+import sys
+import os
+from pathlib import Path
+
 import numpy as np
 import scipy.sparse as sp
 import math