feat: add tmux, argcomplete, and bump quarto to v1.6 (#36)

Resolves #35, #31, #26
FacsimiLab · Dec 18, 2024 · 3095cb7 · 3095cb7
2 parents 01d4b8c + a07d956
commit 3095cb7
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diff --git a/docker/base/Dockerfile b/docker/base/Dockerfile
@@ -4,43 +4,31 @@
 
 FROM mambaorg/micromamba:1.5 AS micromamba
 
+############################
+ARG IMAGE_VERSION="dev"
+ARG BASE_IMAGE_NAME
 ARG BASE_IMAGE_SHA
+ARG BASE_IMAGE_EXACT
+############################
+
+ENV BASE_IMAGE_NAME=${BASE_IMAGE_NAME}
 ENV BASE_IMAGE_SHA=${BASE_IMAGE_SHA}
 
-FROM docker.io/pranavmishra90/cuda:12.4.1-base-ubuntu22.04@sha256:50b0f0658af6b419a0a8110eff0569617d75413ebf27abd1f99a85b49d4d466f
+FROM docker.io/pranavmishra90/cuda:12.6.1-base-ubuntu22.04@sha256:0a8dc3a198e14e527a0e469d10f6cea8200c6cb8b87afada742da4d794797336
 
 # This base image was created with
 # ./build.sh -d --image-name pranavmishra90/cuda --cuda-version 12.4 --os ubuntu --os-version 22.04 --arch x86_64
 # taken from https://gitlab.com/nvidia/container-images/cuda || alternative: FROM nvidia/cuda:12.1.0-base-ubuntu22.04
 
-############################
-ARG IMAGE_VERSION="dev"
-############################
-
-ARG IMAGE_VERSION="dev"
-ARG ISO_DATETIME
-ARG BASE_IMAGE_SHA
-
-
-LABEL org.opencontainers.image.title="FacsimiLab-Base"
-LABEL version=${IMAGE_VERSION}
-LABEL org.opencontainers.image.version=${IMAGE_VERSION}
-LABEL org.opencontainers.image.authors='Pranav Kumar Mishra'
-LABEL org.opencontainers.image.description="Base image || FacsimiLab - A docker image for reproducible science, leveraging Python, Nvidia CUDA, Datalad, Quarto, and more."
-LABEL org.opencontainers.image.source="https://github.com/FacsimiLab/FacsimiLab-platform"
-LABEL org.opencontainers.image.licenses="MIT"
-LABEL org.opencontainers.image.created=${ISO_DATETIME}
-LABEL org.opencontainers.image.base.name="docker.io/pranavmishra90/cuda:12.4.1-base-ubuntu22.04"
-LABEL org.opencontainers.image.base.digest=${BASE_IMAGE_SHA}
+USER root
 
 ENV DEBIAN_FRONTEND="noninteractive"
 ENV TZ="America/Chicago"
 ENV LC_ALL=C.UTF-8
 ENV LANG=C.UTF-8
 
-ARG CACHE_BUST="1"
-
-RUN --mount=type=cache,target=/var/cache/apt \
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
+    chmod 777 /tmp /opt && \
     apt-get update -y \
     && apt-get install -y tzdata git ninja-build gnupg2 wget yadm && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
@@ -54,7 +42,7 @@ RUN mkdir -p /etc/apt/keyrings && \
     wget -O- http://neuro.debian.net/lists/jammy.us-tn.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
     apt-key adv --recv-keys --keyserver hkps://keyserver.ubuntu.com 0xA5D32F012649A5A9
 
-RUN --mount=type=cache,target=/var/cache/apt \
+RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     apt-get update && \
     apt-get --no-install-recommends install -y \
     # Additional dependences
@@ -75,6 +63,7 @@ RUN --mount=type=cache,target=/var/cache/apt \
     pipx \
     sudo \
     tini \
+    tmux \
     tree \
     unzip \
     yadm \
@@ -124,3 +113,19 @@ ENTRYPOINT ["/usr/local/bin/_entrypoint.sh"]
 
 CMD ["/bin/bash"]
 
+ARG IMAGE_VERSION="dev"
+ARG ISO_DATETIME
+ARG BASE_IMAGE_NAME
+ARG BASE_IMAGE_SHA
+
+
+LABEL org.opencontainers.image.title="FacsimiLab-Base"
+LABEL version=${IMAGE_VERSION}
+LABEL org.opencontainers.image.version=${IMAGE_VERSION}
+LABEL org.opencontainers.image.authors='Pranav Kumar Mishra'
+LABEL org.opencontainers.image.description="Base image || FacsimiLab - A docker image for reproducible science, leveraging Python, Nvidia CUDA, Datalad, Quarto, and more."
+LABEL org.opencontainers.image.source="https://github.com/FacsimiLab/FacsimiLab-platform"
+LABEL org.opencontainers.image.licenses="MIT"
+LABEL org.opencontainers.image.created=${ISO_DATETIME}
+LABEL org.opencontainers.image.base.name=${BASE_IMAGE_NAME}
+LABEL org.opencontainers.image.base.digest=${BASE_IMAGE_SHA}
diff --git a/docker/base/build.sh b/docker/base/build.sh
@@ -5,6 +5,8 @@ if [ -z ${facsimilab_version_num+x} ]; then facsimilab_version_num="dev"; else e
 # Adjust this according to the container name desired
 CONTAINER_NAME=facsimilab-base:$facsimilab_version_num
 
+if [ -z ${base_image_name+x} ]; then base_image_name="dev"; else echo "base_image_name is set to '$base_image_name'"; fi
+
 ##################################################################
 
 # Initialize the build
@@ -20,29 +22,27 @@ echo "$CONTAINER_NAME"
 export DOCKER_BUILDKIT=1 # use docker buildx caching
 export BUILDX_METADATA_PROVENANCE=max
 
-docker pull pranavmishra90/cuda:12.4.1-base-ubuntu22.04
+docker pull ${base_image_name}
 
-ubuntu_cuda_base_sha=$(docker inspect pranavmishra90/cuda:12.4.1-base-ubuntu22.04 --format '{{index .RepoDigests 0}}' | cut -d '@' -f2)
+ubuntu_cuda_base_sha=$(docker inspect ${base_image_name} --format '{{index .RepoDigests 0}}' | cut -d '@' -f2)
 
 echo "SHA: $ubuntu_cuda_base_sha"
 
+if [ -n "$base_image_name" ] && [ -n "$ubuntu_cuda_base_sha" ]; then
+  exact_base="${base_image_name}@${ubuntu_cuda_base_sha}"
+	echo "Base image: $exact_base"
+else
+  echo "Error: base_image_name or ubuntu_cuda_base_sha is not defined or empty."
+  exit 1
+fi
 
-	# --build-arg CACHE_BUST=$(date) \
-	# -t gitea.mishracloud.com/pranav/$CONTAINER_NAME \
-docker buildx build --progress=auto \
-	--pull \
+docker build -t pranavmishra90/$CONTAINER_NAME \
 	--build-arg IMAGE_VERSION=$facsimilab_version_num \
 	--build-arg ISO_DATETIME=$iso_datetime \
+	--build-arg BASE_IMAGE_EXACT=$exact_base \
+	--build-arg BASE_IMAGE_NAME=$base_image_name \
 	--build-arg BASE_IMAGE_SHA=$ubuntu_cuda_base_sha \
-	--cache-from pranavmishra90/facsimilab-base:dev \
-	--cache-from type=registry,mode=max,oci-mediatypes=true,ref=docker.io/pranavmishra90/facsimilab-base:buildcache \
-	--cache-to type=registry,mode=max,oci-mediatypes=true,ref=docker.io/pranavmishra90/facsimilab-base:buildcache \
-	--output type=registry,push=true,name=pranavmishra90/$CONTAINER_NAME \
-	--output type=registry,push=true,name=pranavmishra90/facsimilab-base:dev \
-	--output type=docker,name=pranavmishra90/$CONTAINER_NAME \
-	--output type=docker,name=pranavmishra90/facsimilab-base:dev \
-	--metadata-file ../metadata/01-base_metadata.json \
-	. --file Dockerfile
+	. --file ./Dockerfile
 
 # Calculate the total time
 end_time=$(date +%s)

diff --git a/docker/build-all.sh b/docker/build-all.sh
@@ -87,21 +87,22 @@ start_time=$(date +%s)
 printf "\n\n\n\n\n"
 echo "-----------------------------------------"
 
-# CUDA container
-#----------------------
-cd cuda
+# # CUDA container
+# #----------------------
+# cd cuda
+
+export base_image_name="pranavmishra90/cuda:12.6.1-base-ubuntu22.04"
 
-./build.sh -d --image-name pranavmishra90/cuda --cuda-version 12.6.1 --os ubuntu --os-version 22.04 --arch x86_64 --push
+# ./build.sh -d --image-name pranavmishra90/cuda --cuda-version 12.6.1 --os ubuntu --os-version 22.04 --arch x86_64 --push
 
-cd ..
+# cd ..
 
 # # Base container
 # #----------------------
 cd base
 
 bash build.sh
 
-
 # Main container
 #----------------------
 cd ../main
@@ -111,13 +112,13 @@ bash build.sh
 
 # Full container
 #----------------------
-cd ../full
+# cd ../full
 
-# Generate the lock file from the conda environment.yml
-# bash generate-lock.sh
+# # Generate the lock file from the conda environment.yml
+# # bash generate-lock.sh
 
-# Build the docker container
-bash build.sh
+# # Build the docker container
+# bash build.sh
 
 # Finished
 #----------------------

diff --git a/docker/full/python-env/environment.yml b/docker/full/python-env/environment.yml
@@ -22,6 +22,7 @@ dependencies:
   - black=24
   - black-jupyter=24
   - click>8.1
+  - argcomplete=3.5
   - dask-core=2024
 
   # Version control
@@ -78,7 +79,7 @@ dependencies:
   - imbalanced-learn
   - dtreeviz
 
-  # Next-generation -omics
+  # Next-generation Multiomics
   - scanpy=1.10
   - scvi-tools=1.1
   - muon=0.1

diff --git a/docker/main/build.sh b/docker/main/build.sh
@@ -19,7 +19,7 @@ echo "$CONTAINER_NAME"
 
 # Download necessary files
 
-quarto_version="1.5.56"
+quarto_version="1.6.39"
 
 # wget -nc --no-verbose https://github.com/quarto-dev/quarto-cli/releases/download/v1.4.555/quarto-1.4.555-linux-amd64.deb -O quarto.deb
 wget -nc --no-verbose https://github.com/quarto-dev/quarto-cli/releases/download/v$quarto_version/quarto-$quarto_version-linux-arm64.deb -O quarto.deb
@@ -130,4 +130,4 @@ docker image ls | grep facsimilab-main | grep dev
 
 echo "#######################################################################"
 echo "                      End of Main image build                          "
-echo "#######################################################################"
+echo "#######################################################################"
diff --git a/docker/main/environment.yml b/docker/main/environment.yml
@@ -23,6 +23,7 @@ dependencies:
   - black=24
   - black-jupyter=24
   - click>8.1
+  - argcomplete=3.5
 
   # Version control
   - datalad=1.1