cleanup a little bit

build-local-docker.sh

@@ -9,13 +9,18 @@ image="pharmbio-notebook"
 echo "tensorflow_version=$tensorflow_version"
 echo "tag=$tag"
 echo "image=$image"
-#switched to buildx build
-# Build docker image for this container.
-# docker buildx build --no-cache -t ghcr.io/pharmbio/$image:$tag \
-#              --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-jupyter \
-#              -f ./docker/env.cpu.Dockerfile . || exit 1
+
+## CPU version
+#DOCKER_BUILDKIT=1 docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag} \
+#             --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-jupyter \
+#             -f docker/env.cuda.Dockerfile . || exit 1
+
+# GPU version
 DOCKER_BUILDKIT=1 docker buildx build --no-cache -t ghcr.io/pharmbio/$image:${tag}-gpu \
              --build-arg BASE_IMAGE=tensorflow/tensorflow:${tensorflow_version}-gpu-jupyter \
              -f docker/env.cuda.Dockerfile . || exit 1
 
+echo Push image with command:
+echo docker push "ghcr.io/pharmbio/$image:${tag}-gpu"
+
 #docker push "ghcr.io/pharmbio/$image:$tag-devel"

docker/env.cuda.Dockerfile

@@ -15,10 +15,7 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
 # Install base dependencies
 ENV DEBIAN_FRONTEND=noninteractive
-# >apt_installs.txt to save instead of executing
-RUN <<EOF
- apt-get update
- apt-get install -y --no-install-recommends \
+RUN apt-get update && apt-get install -y --no-install-recommends \
     apt-transport-https \
     ca-certificates \
     software-properties-common \
@@ -46,8 +43,7 @@ RUN <<EOF
     sqlite3 \
     libgl1-mesa-glx \
     python3-venv \
-    openjdk-17-jdk-headless \
-EOF
+    openjdk-17-jdk-headless
 
 # Install Rust (comment out if not needed)
 #RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
@@ -59,21 +55,12 @@ COPY requirements.txt .
 RUN python3 -m pip install --no-cache-dir --upgrade pip && \
     python3 -m pip install --no-cache-dir -r requirements.txt
 
-
-# Breakpoint - temporary shell for debugging
-RUN --mount=type=cache,target=/tmp \
-    echo "Entering breakpoint shell"; \
-    sleep infinity
-
-RUN echo "Step 2: Continuing after breakpoint"
-
-RUN <<EOF 
-        echo "Installing for CUDA framework" 
-        python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
+RUN echo "Installing for CUDA framework" 
+RUN python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
                 torch==2.4.1 \
                 torchvision \
-                torchaudio;
-EOF
+                torchaudio
+
 
 # RUN python3 -m pip install --no-cache-dir --index-url https://download.pytorch.org/whl/cu121 \ 
 #         torch==2.2.1 \
@@ -116,4 +103,4 @@ WORKDIR /home/jovyan
 # Then the entrypoint will start jupyter notebook server
 #
 COPY entrypoint.sh /
-CMD /entrypoint.sh
+CMD /entrypoint.sh

requirements.txt

@@ -10,7 +10,6 @@ matplotlib
 pandas
 polars
 pillow
-jupyterlab
 tifffile
 #chembl-webresource-client
 albumentations