Update dockerfile to PyMC v4 (#5881)

* rename and update build docker container
* add a script for running docker container from bash
* update running docker container from juppyter notebook
* simplify into one bash script
* remove root user from Dockerfile
* remove obsolete scripts
* update documents on running PyMC in Docker

Author: danhphan

CONTRIBUTING.md

@@ -9,34 +9,5 @@ Quick links
 * [Pull request (PR) checklist](https://docs.pymc.io/en/latest/contributing/pr_checklist.html)
 * [Python style guide with pre-commit](https://docs.pymc.io/en/latest/contributing/python_style.html)
 * [Running the test suite](https://docs.pymc.io/en/latest/contributing/running_the_test_suite.html)
+* [Running PyMC in Docker](https://docs.pymc.io/en/latest/contributing/docker_container.html)
 * [Submitting a bug report or feature request](https://github.com/pymc-devs/pymc/issues)
-
-<!-- Commented out because our Docker image is outdated/broken.
-## Developing in Docker
-
-We have provided a Dockerfile which helps for isolating build problems, and local development.
-Install [Docker](https://www.docker.com/) for your operating system, clone this repo, then
-run `./scripts/start_container.sh`. This should start a local docker container called `pymc`,
-as well as a [`jupyter`](http://jupyter.org/) notebook server running on port 8888. The
-notebook should be opened in your browser automatically (you can disable this by passing
-`--no-browser`). The repo will be running the code from your local copy of `pymc`,
-so it is good for development.
-
-You may also use it to run the test suite, with
-
-```bash
-$  docker exec -it pymc  bash # logon to the container
-$  cd ~/pymc/tests
-$  . ./../../scripts/test.sh # takes a while!
-```
-
-This should be quite close to how the tests run on TravisCI.
-
-If the container was started without opening the browser, you
-need the notebook instances token to work with the notebook. This token can be
-accessed with
-
-```
-docker exec -it pymc jupyter notebook list
-```
--->

docs/source/contributing/docker_container.md

@@ -0,0 +1,18 @@
+(docker_container)=
+# Running PyMC in Docker
+
+We have provided a Dockerfile which helps for isolating build problems, and local development.
+Install [Docker](https://www.docker.com/) for your operating system, clone this repo, then
+run the following commands to build a `pymc` docker image.
+
+```bash
+cd pymc
+bash scripts/docker_container.sh build
+```
+
+After successfully building the docker image, you can start a local docker container called `pymc` either from `bash` or from [`jupyter`](http://jupyter.org/) notebook server running on port 8888.
+
+```bash
+bash scripts/docker_container.sh bash # running the container with bash
+bash scripts/docker_container.sh jupyter # running the container with jupyter notebook
+```

scripts/Dockerfile

@@ -1,18 +1,30 @@
-FROM jupyter/minimal-notebook
+FROM jupyter/base-notebook:python-3.9.12
 
-ARG SRC_DIR=.
+LABEL name="pymc"
+LABEL description="Environment for PyMC version 4"
 
-MAINTAINER Austin Rochford <[email protected]>
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
 
-ADD $SRC_DIR /home/jovyan/
-RUN /bin/bash /home/jovyan/scripts/create_testenv.sh --global --no-setup
+# Switch to jovyan to avoid container runs as root
+USER $NB_UID
 
-#  matplotlib nonsense
-ENV XDG_CACHE_HOME /home/$NB_USER/.cache/
-ENV MPLBACKEND=Agg
-# for prettier default plot styling
-RUN pip install seaborn
-# Import matplotlib the first time to build the font cache.
-RUN python -c "import matplotlib.pyplot"
+COPY /conda-envs/environment-dev-py39.yml .
+RUN mamba env create -f environment-dev-py39.yml && \
+    /bin/bash -c ". activate pymc-dev-py39 && \
+    mamba install -c conda-forge -y pymc" && \
+    conda clean --all -f -y
 
-ENV PYTHONPATH $PYTHONPATH:"$HOME"
+# Fix PkgResourcesDeprecationWarning
+RUN pip install --upgrade --user setuptools==58.3.0
+
+#Setup working folder
+WORKDIR /home/jovyan/work
+
+# For running from bash
+SHELL ["/bin/bash","-c"]
+RUN echo "conda activate pymc-dev-py39" >> ~/.bashrc && \
+    source ~/.bashrc
+
+# For running from jupyter notebook
+EXPOSE 8888
+CMD ["conda", "run", "--no-capture-output", "-n", "pymc-dev-py39", "jupyter","notebook","--ip=0.0.0.0","--port=8888","--no-browser"]

scripts/create_testenv.sh

@@ -0,0 +1,24 @@
+#! /bin/bash
+
+COMMAND="${1:-jupyter}"
+SRC_DIR=${SRC_DIR:-`pwd`}
+CONTAINER_NAME=${CONTAINER_NAME:-pymc}
+PORT=${PORT:-8888}
+
+# stop and remove previous instances of the pymc container to avoid naming conflicts
+if [[ $(docker ps -aq -f name=${CONTAINER_NAME}) ]]; then
+   echo "Shutting down and removing previous instance of ${CONTAINER_NAME} container..."
+   docker rm -f ${CONTAINER_NAME}
+fi
+
+# $COMMAND can be either `build` or `bash` or `jupyter`
+if [[ $COMMAND = 'build' ]]; then
+   docker build \
+      -t ${CONTAINER_NAME} \
+      -f $SRC_DIR/scripts/Dockerfile $SRC_DIR
+
+elif [[ $COMMAND = 'bash' ]]; then
+   docker run -it -v $SRC_DIR:/home/jovyan/work --rm  --name ${CONTAINER_NAME} ${CONTAINER_NAME} bash
+else
+   docker run -it -p $PORT:8888 -v $SRC_DIR:/home/jovyan/work --rm  --name ${CONTAINER_NAME} ${CONTAINER_NAME}
+fi