From bd9bff7ec0a080324812073be394daa00b7f7626 Mon Sep 17 00:00:00 2001
From: Dmitri Smirnov <dmixsmi@gmail.com>
Date: Wed, 29 May 2024 15:11:45 -0400
Subject: [PATCH 1/5] fix: use single command to execute container commands

---
 esi-shell | 24 ++----------------------
 1 file changed, 2 insertions(+), 22 deletions(-)

diff --git a/esi-shell b/esi-shell
index b2807ae..638b365 100755
--- a/esi-shell
+++ b/esi-shell
@@ -256,28 +256,8 @@ ohai "Using esi-shell image: ${IMG}"
 
 if [[ -n "${USABLE_DOCKER-}" ]]
 then
-  cmd="docker run --rm -dit ${DOCKER_GPU-} ${DOCKER_PLATFORM-} ${DOCKER_BIND_VOLUME-} -e OPTICKS_OPTIX_PREFIX=$OPTIX_DIR $IMG"
-  CONTAINER_ID=$(exec $cmd)
-
-  if [ $? -ne 0 ]
-  then
-    abort "Failed to start esi-shell"
-  fi
-
-  CONTAINER_ID=$(echo $CONTAINER_ID | cut -c -12)
-  ohai "Running docker container $CONTAINER_ID"
-
-  ohai "Setting up opticks environment. Please wait..."
-  if [[ -d $WORKDIR/.opticks ]]
-  then
-    ohai "Found existing $WORKDIR/.opticks. Will use it"
-  else
-    ohai "Creating new $WORKDIR/.opticks required by opticks"
-    docker exec -it $CONTAINER_ID sh -c 'cp -r $ESI_DIR/.opticks $HOME/'
-  fi
-
-  docker exec -it $CONTAINER_ID /opt/nvidia/nvidia_entrypoint.sh
-  confirm "Stop and remove container? [Y/n]" yes && docker rm -f $CONTAINER_ID || ohai "Remove container manually: docker rm -f $CONTAINER_ID"
+  cmd="docker run --rm -it ${DOCKER_GPU-} ${DOCKER_PLATFORM-} ${DOCKER_BIND_VOLUME-} -e OPTICKS_OPTIX_PREFIX=$OPTIX_DIR $IMG"
+  exec $cmd
 
 else
   abort "Docker client (>= $REQUIRED_DOCKER_VERSION) must be installed to proceed."

From 5b0ff881bf71c27c5f99442798452335af55ac12 Mon Sep 17 00:00:00 2001
From: Dmitri Smirnov <dmixsmi@gmail.com>
Date: Fri, 10 May 2024 10:05:16 -0400
Subject: [PATCH 2/5] feat(esi-shell): exec user command, pass through
 container options

---
 esi-shell | 41 +++++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/esi-shell b/esi-shell
index 638b365..71cc2a8 100755
--- a/esi-shell
+++ b/esi-shell
@@ -29,21 +29,34 @@ REQUIRED_DOCKER_VERSION=23.0.0
 IMAGE_NAME="ghcr.io/bnlnpps/esi-shell"
 DEFAULT_VERSION="latest"
 VERSION=$DEFAULT_VERSION
+CONTAINER_COMMAND=
+CONTAINER_OPTIONS=
 
 usage() {
   echo "Start esi-shell, the ESI containerized software environment."
   echo ""
   echo "USAGE:"
-  echo "  ./esi-shell [OPTIONS] [ -- COMMAND ]"
+  echo "  ./esi-shell [OPTIONS] [COMMAND] [-- CONTAINER_OPTIONS]"
   echo ""
-  echo "OPTIONAL ARGUMENTS:"
-  echo "  -v, --version    Version to install (Default: $DEFAULT_VERSION)"
+  echo "OPTIONS:"
+  echo "  -v, --version    Specific esi-shell version to use (Default: $DEFAULT_VERSION)"
   echo "  -h, --help       Print this message"
   echo ""
+  echo "COMMAND is a command to execute in the container, leave it empty for interactive shell. For example:"
+  echo "  pwd"
+  echo "  ls -la"
+  echo "  echo '\$HOME'"
+  echo "  tests/test_opticks.sh"
+  echo ""
+  echo "CONTAINER_OPTIONS will be passed to the underlying container command. For example:"
+  echo "  -- --volume \$PWD/mytests:/tmp/mytests"
+  echo "  -- -v \$HOME/optix:/usr/local/optix -e OPTICKS_OPTIX_PREFIX=/usr/local/optix"
+  echo ""
   echo "EXAMPLES:"
   echo "  - Start an interactive shell: ./esi-shell" 
-  echo "  - Use different version:      ./esi-shell -v 0.1.0"
-  echo "  - Execute a single command:   ./esi-shell -- <COMMAND>"
+  echo "  - Use specific version:       ./esi-shell -v 0.1.0"
+  echo "  - Execute a single command:   ./esi-shell echo \$OPTIX_DIR"
+  echo "  - Configure remote image:     ./esi-shell -- --pull=always -e HOME=\$HOME"
   echo ""
   exit "${1:-0}"
 }
@@ -86,7 +99,7 @@ warn() {
 }
 
 
-while [ $# -gt 0 ]
+while [[ $# -gt 0 ]]
 do
   case $1 in
     -v | --version)
@@ -95,15 +108,24 @@ do
       shift
       ;;
     -h | --help)
-      usage
+      usage 0
       ;;
     --)
       shift
+      CONTAINER_OPTIONS="$@"
       break
       ;;
-    *)
+    -*)
       warn "Unrecognized option: '$1'"
       usage 1
+      break
+      ;;
+    *)
+      _ALL_OTHER_ARGS="$@"
+      CONTAINER_COMMAND=${_ALL_OTHER_ARGS%% -- *}
+      CONTAINER_OPTIONS=${_ALL_OTHER_ARGS#* -- }
+      CONTAINER_OPTIONS=$([[ $CONTAINER_OPTIONS == $CONTAINER_COMMAND ]] && echo "" || echo $CONTAINER_OPTIONS)
+      break
       ;;
   esac
 done
@@ -256,9 +278,8 @@ ohai "Using esi-shell image: ${IMG}"
 
 if [[ -n "${USABLE_DOCKER-}" ]]
 then
-  cmd="docker run --rm -it ${DOCKER_GPU-} ${DOCKER_PLATFORM-} ${DOCKER_BIND_VOLUME-} -e OPTICKS_OPTIX_PREFIX=$OPTIX_DIR $IMG"
+  cmd="docker run --rm -it ${DOCKER_GPU-} ${DOCKER_PLATFORM-} ${DOCKER_BIND_VOLUME-} -e OPTICKS_OPTIX_PREFIX=${OPTIX_DIR} ${CONTAINER_OPTIONS} ${IMG} ${CONTAINER_COMMAND}"
   exec $cmd
-
 else
   abort "Docker client (>= $REQUIRED_DOCKER_VERSION) must be installed to proceed."
 fi

From 558f4bcc6f9486a717569769a5c57b209a498a7d Mon Sep 17 00:00:00 2001
From: Dmitri Smirnov <dmixsmi@gmail.com>
Date: Fri, 31 May 2024 10:38:42 -0400
Subject: [PATCH 3/5] ci: run test command in esi-shell

---
 .github/workflows/build-pull-request.yml | 6 +++++-
 .github/workflows/release.yml            | 4 ++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-pull-request.yml b/.github/workflows/build-pull-request.yml
index 17872a0..230b711 100644
--- a/.github/workflows/build-pull-request.yml
+++ b/.github/workflows/build-pull-request.yml
@@ -50,6 +50,10 @@ jobs:
           rm -rf /home/runner/.buildx-cache
           mv /home/runner/.buildx-cache-new /home/runner/.buildx-cache
 
-      - name: Run tests
+      - name: Test image
         run: |
           docker run --rm ${{ env.IMAGE_NAME }}:${{ env.TAG }} tests/test_opticks.sh
+
+      - name: Test esi-shell
+        run: |
+          ./esi-shell -v ${{ env.TAG }} "opticks-full-prepare && opticks-t"
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 4b80c0b..684cc6a 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -42,8 +42,8 @@ jobs:
           cache-from: ${{ env.IMAGE_NAME }}:latest
           cache-to: type=inline
 
-      - name: Run tests
-        run: docker run --rm ${{ env.IMAGE_NAME }}:latest tests/test_opticks.sh
+      - name: Test esi-shell
+        run: ./esi-shell "opticks-full-prepare && opticks-t"
 
       - name: Declare latest and push
         run: docker push ${{ env.IMAGE_NAME }}:latest

From 0cf2a438ffc1038c1fac0aed2e7bb43d5183cb31 Mon Sep 17 00:00:00 2001
From: Dmitri Smirnov <dmixsmi@gmail.com>
Date: Fri, 31 May 2024 18:03:10 -0400
Subject: [PATCH 4/5] fix(env): activate virtual environment via poetry

---
 Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 0d60d45..e4b4e84 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -67,6 +67,7 @@ ENV OPTICKS_COMPUTE_CAPABILITY=89
 ENV LD_LIBRARY_PATH=${OPTICKS_PREFIX}/lib:${LD_LIBRARY_PATH}
 ENV PATH=${OPTICKS_PREFIX}/lib:${PATH}
 ENV NVIDIA_DRIVER_CAPABILITIES=graphics,compute,utility
+ENV VIRTUAL_ENV_DISABLE_PROMPT=1
 
 WORKDIR $ESI_DIR
 
@@ -79,9 +80,11 @@ COPY README.md .
 COPY NVIDIA-OptiX-SDK-7.6.0-linux64-x86_64.sh .
 COPY pyproject.toml .
 
+RUN poetry install
 RUN patch -p1 opticks/sysrap/sevt.py patches/opticks-fix-update-array-dtype-for-numpy-1.26.patch
 
 COPY <<-"EOF" /etc/profile.d/z20_opticks.sh
+    source $(poetry env info --path)/bin/activate
     source $OPTICKS_HOME/opticks.bash
     opticks-
 EOF
@@ -89,5 +92,3 @@ EOF
 RUN mkdir -p $OPTIX_DIR && ./NVIDIA-OptiX-SDK-7.6.0-linux64-x86_64.sh --skip-license --prefix=$OPTIX_DIR
 RUN opticks-full
 RUN rm -fr $OPTIX_DIR/* $ESI_DIR/NVIDIA-OptiX-SDK-7.6.0-linux64-x86_64.sh
-
-RUN poetry install

From 4c600c5ea0367df1be1c4d33dd6ea353d1573a69 Mon Sep 17 00:00:00 2001
From: Dmitri Smirnov <dmixsmi@gmail.com>
Date: Fri, 31 May 2024 18:45:45 -0400
Subject: [PATCH 5/5] fix(esi-shell): run commands without TTY

---
 esi-shell | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/esi-shell b/esi-shell
index 71cc2a8..5ac4fd9 100755
--- a/esi-shell
+++ b/esi-shell
@@ -270,6 +270,11 @@ done
 #  DOCKER_PLATFORM="--platform linux/amd64"
 #fi
 
+if [[ -z ${CONTAINER_COMMAND-} ]]
+then
+  CONTAINER_OPTIONS+=" -i -t"
+fi
+
 USABLE_SINGULARITY="$(find_tool singularity)"
 USABLE_DOCKER="$(find_tool docker)"
 
@@ -278,7 +283,7 @@ ohai "Using esi-shell image: ${IMG}"
 
 if [[ -n "${USABLE_DOCKER-}" ]]
 then
-  cmd="docker run --rm -it ${DOCKER_GPU-} ${DOCKER_PLATFORM-} ${DOCKER_BIND_VOLUME-} -e OPTICKS_OPTIX_PREFIX=${OPTIX_DIR} ${CONTAINER_OPTIONS} ${IMG} ${CONTAINER_COMMAND}"
+  cmd="docker run --rm ${DOCKER_GPU-} ${DOCKER_PLATFORM-} ${DOCKER_BIND_VOLUME-} -e OPTICKS_OPTIX_PREFIX=${OPTIX_DIR} ${CONTAINER_OPTIONS} ${IMG} ${CONTAINER_COMMAND}"
   exec $cmd
 else
   abort "Docker client (>= $REQUIRED_DOCKER_VERSION) must be installed to proceed."