adjust versions in Dockerfile, clean args, add minor comments, dlc 2.3.5

DeepLabCut · MMathisLab · Sep 17, 2023 · Aug 4, 2022 · Aug 4, 2022 · Aug 5, 2022
commit dd252b9e601144d2cf4548ff055d29722a80ea80
diff --git a/docker/Dockerfile.base b/docker/Dockerfile.base
@@ -1,25 +1,29 @@
-ARG CUDA_VERSION=11.4.0-cudnn8-runtime-ubuntu20.04
+ARG CUDA_VERSION
 FROM nvidia/cuda:${CUDA_VERSION}
 
-ARG DEEPLABCUT_VERSION=2.2.1.1
+ARG DEEPLABCUT_VERSION
 ENV DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update -yy \ 
-    && apt-get install -yy --no-install-recommends python3 python3-pip python3-dev ffmpeg libsm6 libxext6 \
+    && apt-get install -yy --no-install-recommends python3.8 python3-pip python3-dev ffmpeg libsm6 libxext6 \
     && apt-get install -yy --no-install-recommends build-essential make cmake gcc g++ \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-RUN pip3 install --no-cache-dir --upgrade pip \
- && pip3 install --no-cache-dir --upgrade deeplabcut==${DEEPLABCUT_VERSION} numpy==1.19.5 decorator==4.4.2 tensorflow==2.5.0 \
- && pip3 list
+RUN pip3 install --upgrade \
+		deeplabcut==${DEEPLABCUT_VERSION} \
+		decorator==4.4.2 \ 
+		tensorflow==2.5.0 \
+		torch==1.12 \
+		numpy==1.21 \
+	&& pip3 list
 
 # The installed tensorflow version will not work with the latest protocol buffer version,
 # hence we are fixing the version to 3.20.
 #
 # See https://developers.google.com/protocol-buffers/docs/news/2022-05-06#python-updates
 # for details on why this is needed.
-RUN pip3 install --no-cache-dir protobuf==3.20.1
+RUN pip3 install protobuf==3.20.1
 
 # TODO required to fix permission errors when running the container with limited permission.
 RUN chmod a+rwx -R /usr/local/lib/python3.8/dist-packages/deeplabcut/pose_estimation_tensorflow/models/pretrained

diff --git a/docker/Dockerfile.core b/docker/Dockerfile.core
@@ -1,5 +1,5 @@
-ARG CUDA_VERSION=11.4.0-cudnn8-runtime-ubuntu20.04
-ARG DEEPLABCUT_VERSION=2.2.1.1
+ARG CUDA_VERSION
+ARG DEEPLABCUT_VERSION
 FROM deeplabcut/deeplabcut:${DEEPLABCUT_VERSION}-base-cuda${CUDA_VERSION}
 
 ENV DLClight True

diff --git a/docker/Dockerfile.gui b/docker/Dockerfile.gui
@@ -1,21 +1,17 @@
-ARG CUDA_VERSION=11.4.0-cudnn8-runtime-ubuntu20.04
-ARG DEEPLABCUT_VERSION=2.2.1.1
+ARG CUDA_VERSION
+ARG DEEPLABCUT_VERSION
+
 FROM deeplabcut/deeplabcut:${DEEPLABCUT_VERSION}-base-cuda${CUDA_VERSION}
 
 RUN DEBIAN_FRONTEND=noninteractive apt-get update -yy \ 
-    && DEBIAN_FRONTEND=noninteractive \
-         apt-get install -yy --no-install-recommends \
-         libgtk-3-dev python3-wxgtk4.0 locales \
+    && apt-get install -yy --no-install-recommends libgtk-3-dev python3-wxgtk4.0 locales \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* \
     && locale-gen en_US.UTF-8 en_GB.UTF-8
 
-ARG DEEPLABCUT_VERSION=2.2.1.1
-RUN pip3 install --no-cache-dir --upgrade pip \
- && pip3 install --no-cache-dir --upgrade deeplabcut[gui]==${DEEPLABCUT_VERSION} numpy==1.19.5 decorator==4.4.2 tensorflow==2.5.0 protobuf==3.20.1 \
+ARG DEEPLABCUT_VERSION
+RUN pip3 install --no-cache-dir --upgrade deeplabcut[gui]==${DEEPLABCUT_VERSION} \
  && pip3 list
 
-
-
 ENV DLClight=False
 CMD ["python3", "-m", "deeplabcut"]
diff --git a/docker/Dockerfile.jupyter b/docker/Dockerfile.jupyter
@@ -1,10 +1,23 @@
-ARG CUDA_VERSION=11.4.0-cudnn8-runtime-ubuntu20.04
-ARG DEEPLABCUT_VERSION=2.2.1.1
-FROM deeplabcut/deeplabcut:${DEEPLABCUT_VERSION}-gui-cuda${CUDA_VERSION}
-
-RUN pip install --no-cache-dir jupyter
-COPY ./examples /app/examples
-CMD ["jupyter", "notebook", \
-     "--no-browser", \
-     "--NotebookApp.password", "sha3_224:019dc9326f7c:689d6c568f840f6126fb438ba0cdb8ce94ddd0769399e152caf79931", \
-     "--ip", "0.0.0.0" ]
+ARG CUDA_VERSION
+ARG DEEPLABCUT_VERSION
+FROM deeplabcut/deeplabcut:${DEEPLABCUT_VERSION}-core-cuda${CUDA_VERSION}
+
+RUN pip3 install --no-cache-dir \
+        notebook==6.4.12 \
+        && pip3 list
+
+ENV PYTHONPATH "${PYTHONPATH}:/usr/lib/python3"
+
+ARG USER=docker_user
+RUN useradd -m ${USER} \
+    && cp /root/.bashrc /home/${USER}/ \
+    && mkdir /app /data /codebase \
+    && chown -R --from=root ${USER} /home/${SUSER} \
+                                /app /data /codebase
+ENV HOME /home/${USER}
+WORKDIR ${HOME}
+USER ${USER}
+
+RUN jupyter notebook --generate-config
+EXPOSE 8888
+ENTRYPOINT ["jupyter", "notebook", "--no-browser",  "--ip", "0.0.0.0"]
diff --git a/docker/build.sh b/docker/build.sh
@@ -4,118 +4,128 @@
 
 set -e
 
+# Set default Docker binary
 export DOCKER=${DOCKER:-'docker'}
 export DOCKER_BUILD="$DOCKER build"
 export BASENAME=deeplabcut/deeplabcut
 export DOCKERDIR=docker
 
+# Check if script is being run from the correct directory
 if [[ ! -d ./${DOCKERDIR} ]]; then
-    >&2 echo Run from repository root. Current pwd is
-    >&2 pwd
-    exit 1
+	echo >&2 Run from repository root. Current pwd is
+	pwd >&2
+	exit 1
 fi
 
+# List Docker images related to DeepLabCut
 list_images() {
-    $DOCKER images \
-    | grep '^deeplabcut ' \
-    | sed -s 's/\s\s\+/\t/g' \
-    | cut -f1,2 -d$'\t' --output-delimiter ':' \
-    | grep core
+	$DOCKER images |
+		grep '^deeplabcut ' |
+		sed -s 's/\s\s\+/\t/g' |
+		cut -f1,2 -d$'\t' --output-delimiter ':' |
+		grep core
 }
 
+# Run tests inside Docker containers
 run_test() {
-    kwargs=(
-        -u $(id -u) --tmpfs /.local --tmpfs /.cache
-        --tmpfs /test/.pytest_cache
-        --env DLClight=True -t
-        $1
-    )
+	kwargs=(
+		-u $(id -u) --tmpfs /.local --tmpfs /.cache
+		--tmpfs /test/.pytest_cache
+		--env DLClight=True -t
+		$1
+	)
 
-    # Unit tests
-    $DOCKER run ${kwargs[@]} python3 -m pytest -v tests || return 255
+	# Unit tests
+	$DOCKER run ${kwargs[@]} python3 -m pytest -v tests || return 255
 
-    # Functional tests
-    $DOCKER run ${kwargs[@]} python3 testscript_cli.py || return 255
+	# Functional tests
+	$DOCKER run ${kwargs[@]} python3 testscript_cli.py || return 255
 
-    return 0
+	return 0
 }
 export -f run_test
 
+# Iterate through build matrix and perform actions
 iterate_build_matrix() {
-    ## TODO(stes): Consider adding legacy versions for CUDA
-    ## if there is demand from users:
-    # 10.2-runtime-ubuntu18.04 \
-    # 11.1.1-runtime-ubuntu18.04 \
-    mode=${1:-build}
-    for cuda_version in \
-        11.4.0-cudnn8-runtime-ubuntu20.04 \
-        11.7.0-cudnn8-runtime-ubuntu20.04
-    do
-        for deeplabcut_version in \
-            2.2.0.6 \
-            2.2.1.1
-        do
-            for stage in base core test gui jupyter; do
-                tag=${deeplabcut_version}-${stage}-cuda${cuda_version}
-                case "$mode" in
-                    build)
-                        echo \
-                         --build-arg=CUDA_VERSION=${cuda_version} \
-                         --build-arg=DEEPLABCUT_VERSION=${deeplabcut_version} \
-                         "--tag=${BASENAME}:$tag" \
-                         -f "Dockerfile.${stage}" \.
-                    ;;
-                    clean|test|push)
-                        echo ${BASENAME}:${tag}
-                    ;;
-                esac
-            done
-        done
-    done
+	## TODO(stes): Consider adding legacy versions for CUDA
+	## if there is demand from users:
+
+	mode=${1:-build}
+	for cuda_version in \
+		11.4.3-cudnn8-runtime-ubuntu20.04; do
+		for deeplabcut_version in \
+			2.3.5; do #2.3.2 \
+			for stage in \
+				base core test gui jupyter; do
+				tag=${deeplabcut_version}-${stage}-cuda${cuda_version}-latest
+				case "$mode" in
+				build)
+					echo \
+						--build-arg=CUDA_VERSION=${cuda_version} \
+						--build-arg=DEEPLABCUT_VERSION=${deeplabcut_version} \
+						"--tag=${BASENAME}:$tag" \
+						-f "Dockerfile.${stage}" \.
+					;;
+				push | clean | test)
+					echo ${BASENAME}:${tag}
+					;;
+				esac
+			done
+		done
+	done
 }
 
+# Get Git hash
 githash() {
-    git log -1 --pretty=format:"%h"
+	git log -1 --pretty=format:"%h"
 }
 
+# Create logs directory and set log file name
 mkdir -p logs
 logfile=logs/$(date +%y%m%d-%H%M%S)-$(githash)
 echo "Logging to $logdir.*"
 
+# Iterate through command line arguments
 for arg in "$@"; do
-case $1 in
-    clean)
-          iterate_build_matrix clean \
-          | tr '\n' '\0' \
-          | xargs -I@ -0 bash -c "docker image rm @ |& grep -v 'No such image'"
-    ;;
-    build)
-        echo "DeepLabCut docker build:: $(git log -1 --oneline)"
-        cp -r examples ${DOCKERDIR}
-        (
-          cd ${DOCKERDIR}
-          iterate_build_matrix \
-          | tr '\n' '\0' \
-          | xargs -I@ -0 bash -c "echo Building @; $DOCKER build @ || exit 255"
-          echo Successful build.
-        ) |& tee ${logfile}.build
-    ;;
-    test)
-        (
-          echo "DeepLabCut docker build:: $(git log -1 --oneline)"
-          iterate_build_matrix test \
-          | grep '\-test\-' \
-          | tr '\n' '\0' \
-          | xargs -0 -I@ bash -c "run_test @ || exit 255"
-          echo Successful test.
-        ) |& tee ${logfile}.test
-    ;;
-    push)
-        iterate_build_matrix push \
-        | grep -v '\-test\-' \
-        | tr '\n' '\0' \
-        | xargs -I@ -0 echo ${DOCKER} push @
-    ;;
-esac
+	case $1 in
+	clean)
+		iterate_build_matrix clean |
+			tr '\n' '\0' |
+			xargs -I@ -0 bash -c "docker image rm @ |& grep -v 'No such image'"
+		;;
+	build)
+		echo "DeepLabCut docker build:: $(git log -1 --oneline)"
+		cp -r examples ${DOCKERDIR}
+		(
+			cd ${DOCKERDIR}
+			iterate_build_matrix |
+				tr '\n' '\0' |
+				xargs -I@ -0 bash -c "echo Building @; $DOCKER build @ || exit 255"
+			echo Successful build.
+		) |& tee ${logfile}.build
+		;;
+	test)
+		(
+			echo "DeepLabCut docker build:: $(git log -1 --oneline)"
+			iterate_build_matrix test |
+				grep '\-test\-' |
+				tr '\n' '\0' |
+				xargs -0 -I@ bash -c "run_test @ || exit 255"
+			echo Successful test.
+		) |& tee ${logfile}.test
+		;;
+	push)
+		iterate_build_matrix push |
+			grep -v '\-test\-' |
+			tr '\n' '\0' |
+			xargs -I@ -0 bash -c "echo docker push @-latest; \
+				docker tag @ @-latest; \
+				docker push @-latest; \
+				docker image rm @ |& grep -v 'No such image'"
+		;;
+	*)
+		echo "Usage: $0 [build|test|push]"
+		exit 1
+		;;
+	esac
 done
-