Migrated from miniconda to official python bullseye docker image (#3901)

* migrated to python bullseye

* added pybamm user to sudoers

* updated docker image to python:3.12-slim-bullseye

* Apply suggestions from code review

Co-authored-by: Eric G. Kratz <[email protected]>

* Update .github/workflows/docker.yml

Co-authored-by: Arjun Verma <[email protected]>

* reverted the docker workflow

* using uv to generate venv and edited docs

---------

Co-authored-by: Eric G. Kratz <[email protected]>
Co-authored-by: Arjun Verma <[email protected]>

docs/source/user_guide/installation/install-from-docker.rst

@@ -90,11 +90,11 @@ If you want to build the PyBaMM Docker image locally from the PyBaMM source code
 
       docker run -it pybamm
 
-5. Activate PyBaMM development environment inside docker container using:
+5. Activate PyBaMM development virtual environment inside docker container using:
 
 .. code-block:: bash
 
-      conda activate pybamm
+      source /home/pybamm/venv/bin/activate
 
 .. note::
 

scripts/Dockerfile

@@ -1,4 +1,5 @@
-FROM continuumio/miniconda3:latest
+FROM python:3.12-slim-bullseye
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
 
 WORKDIR /
 
@@ -21,17 +22,17 @@ ENV CMAKE_CXX_COMPILER=/usr/bin/g++
 ENV CMAKE_MAKE_PROGRAM=/usr/bin/make
 ENV LD_LIBRARY_PATH=/home/pybamm/.local/lib
 
-RUN conda create -n pybamm python=3.11
-RUN conda init --all
-SHELL ["conda", "run", "-n", "pybamm", "/bin/bash", "-c"]
-RUN conda install -y pip
+# Create a virtual environment
+ENV VIRTUAL_ENV=/home/pybamm/venv
+RUN uv venv $VIRTUAL_ENV
+RUN #!/bin/bash && source /home/pybamm/venv/bin/activate;
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
-RUN pip install --upgrade --user pip setuptools wheel wget
-RUN pip install cmake
+RUN uv pip install --upgrade setuptools wheel wget cmake
 
 RUN python scripts/install_KLU_Sundials.py && \
-    rm -rf pybind11 && \
-    git clone https://github.com/pybind/pybind11.git && \
-    pip install --user -e ".[all,dev,docs,jax]";
+rm -rf pybind11 && \
+git clone https://github.com/pybind/pybind11.git && \
+uv pip install -e ".[all,dev,docs,jax]";
 
 ENTRYPOINT ["/bin/bash"]