remove --break-system-packages from pip install commands

.github/workflows/docker_images.yml

@@ -840,9 +840,10 @@ jobs:
           docker cp docs/notebook_validation.py cuda-quantum:"/home/cudaq/notebook_validation.py"
           # In containers without GPU support, UCX does not work properly since it is configured to work with GPU-support.
           # Hence, don't enforce UCX when running these tests.
-          docker exec cuda-quantum bash -c "python3 -m pip install --break-system-packages pandas scipy seaborn h5py contfrac"
           docker exec cuda-quantum bash -c "sudo apt install -y python3-venv"
-          (docker exec cuda-quantum bash -c "unset OMPI_MCA_pml && set -o pipefail && bash validate_container.sh | tee /tmp/validation.out") && passed=true || passed=false
+          docker exec cuda-quantum bash -lc "python3 -m venv /opt/cudaq-venv"
+          docker exec cuda-quantum bash -lc "source /opt/cudaq-venv/bin/activate && pip install pandas scipy seaborn h5py contfrac"
+          (docker exec cuda-quantum bash -c "source /opt/cudaq-venv/bin/activate &&  nset OMPI_MCA_pml && set -o pipefail && bash validate_container.sh | tee /tmp/validation.out") && passed=true || passed=false
           docker cp cuda-quantum:"/tmp/validation.out" /tmp/validation.out
           docker stop cuda-quantum
 

docker/build/devdeps.Dockerfile

@@ -58,7 +58,7 @@ ENV PIP_BREAK_SYSTEM_PACKAGES=1
 RUN apt-get update && apt-get install -y --no-install-recommends \
         wget git unzip \
         python3-dev python3-pip && \
-    python3 -m pip install --no-cache-dir numpy --break-system-packages && \
+    python3 -m pip install --no-cache-dir numpy && \
     apt-get autoremove -y --purge && apt-get clean && rm -rf /var/lib/apt/lists/*
 ADD scripts/install_toolchain.sh /cuda-quantum/scripts/install_toolchain.sh
 RUN source /cuda-quantum/scripts/install_toolchain.sh \
@@ -156,7 +156,7 @@ ENV PATH="${PATH}:/usr/local/cmake-3.28/bin"
 RUN apt-get update && apt-get install -y --no-install-recommends \
         git gdb ninja-build file lldb \
         python3 python3-pip libpython3-dev \
-    && python3 -m pip install --no-cache-dir --break-system-packages \
+    && python3 -m pip install --no-cache-dir \
         lit==18.1.4 pytest==8.2.0 numpy==1.26.4 requests==2.31.0 \
         fastapi==0.111.0 uvicorn==0.29.0 pydantic==2.7.1 llvmlite==0.42.0 \
         pyspelling==2.10 pymdown-extensions==10.8.1 yapf \
@@ -167,7 +167,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 COPY --from=prereqs /usr/local/bin/doxygen /usr/local/bin/doxygen
 ENV PATH="${PATH}:/usr/local/bin"
 RUN apt-get update && apt-get install -y --no-install-recommends python3 python3-pip pandoc aspell aspell-en \
-    && python3 -m pip install --no-cache-dir --break-system-packages \
+    && python3 -m pip install --no-cache-dir \
         ipython==8.15.0 pandoc==2.3 sphinx==5.3.0 sphinx_rtd_theme==1.2.0 sphinx-reredirects==0.1.2 \
         sphinx-copybutton==0.5.2 sphinx_inline_tabs==2023.4.21 enum-tools[sphinx] breathe==4.34.0 \
         nbsphinx==0.9.2 sphinx_gallery==0.13.0 myst-parser==1.0.0 ipykernel==6.29.4 notebook==7.3.2 \

docker/build/devdeps.ext.Dockerfile

@@ -183,7 +183,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     else \
         cupy_version=13.4.1; \
     fi && \
-    python3 -m pip install --break-system-packages cupy-cuda$(echo $CUDA_VERSION | cut -d . -f1)x==${cupy_version} cuquantum-cu$(echo $CUDA_VERSION | cut -d . -f1)==25.09.1 && \
+    python3 -m pip install cupy-cuda$(echo $CUDA_VERSION | cut -d . -f1)x==${cupy_version} cuquantum-cu$(echo $CUDA_VERSION | cut -d . -f1)==25.09.1 && \
     if [ "$(python3 --version | grep -o [0-9\.]* | cut -d . -f -2)" != "3.12" ]; then \
         echo "expecting Python version 3.12"; \
     fi

docker/build/devdeps.ompi.Dockerfile

@@ -34,7 +34,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
         gcc g++ gfortran python3 python3-pip \
         libcurl4-openssl-dev libssl-dev liblapack-dev libpython3-dev \
         bzip2 make sudo vim curl git wget \
-    && pip install --no-cache-dir numpy --break-system-packages \
+    && pip install --no-cache-dir numpy \
     && apt-get autoremove -y --purge && apt-get clean && rm -rf /var/lib/apt/lists/* 
 
 # 2 - Install SLURM PMI2 version 21.08.8

docker/release/cudaq.Dockerfile

@@ -58,11 +58,11 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
 RUN apt-get update && apt-get install -y --no-install-recommends \
         libstdc++-13-dev python3 python3-pip adduser \
     && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* \
-    && python3 -m pip install --no-cache-dir --break-system-packages numpy scipy \
+    && python3 -m pip install --no-cache-dir numpy scipy \
     && ln -s /bin/python3 /bin/python
 RUN apt-get update && apt-get install -y --no-install-recommends gcc g++ python3-dev \
     # Ref: https://github.com/qutip/qutip/issues/2412
-    && python3 -m pip install --no-cache-dir --break-system-packages notebook==7.3.2 "qutip<5" matplotlib \
+    && python3 -m pip install --no-cache-dir notebook==7.3.2 "qutip<5" matplotlib \
     && apt-get remove -y gcc g++ python3-dev \
     && apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/*