Sleepers version 2.2.0

.github/workflows/sleeper.yml

@@ -22,25 +22,22 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [3.8]
+        python: [3.11]
         os: [ubuntu-22.04]
-        node: [10]
+        node: [16]
       fail-fast: false
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: setup python environment
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/requirements.txt"
+      - name: install uv
+        uses: yezz123/setup-uv@v1        
       - name: show versions
         run: ./ci/helpers/show_system_versions.bash
-      - uses: actions/cache@v2
-        name: getting cached data
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
       - name: set owner variable
         run: echo "OWNER=${GITHUB_REPOSITORY%/*}" >> $GITHUB_ENV
       - name: set docker image tag
@@ -74,13 +71,13 @@ jobs:
           make push-version
       - name: set up QEMU
         id: qemu
-        uses: docker/setup-qemu-action@v1
+        uses: docker/setup-qemu-action@v3
         with:
           image: tonistiigi/binfmt:latest
           platforms: all
       - name: setup docker buildx
         id: buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
         with:
           version: ${{ matrix.docker_buildx }}
           driver: docker-container # a must for multi-arch buildsplatform

services/sleeper/.cookiecutterrc

@@ -34,4 +34,4 @@ default_context:
     project_slug: "sleeper"
     project_type: "computational"
     release_date: "2020"
-    version: "2.1.6"
+    version: "2.2.0"

services/sleeper/Makefile

@@ -32,24 +32,22 @@ LOCAL_REGISTRY = ${LOCAL_REGISTRY_HOST}/${COMP_ITIS_PATH}
 # ENVIRON ----------------------------------
 .PHONY: devenv
 .venv:
-	python3 -m venv $@
+	uv venv $@
 	# upgrading package managers
-	$@/bin/pip3 install --upgrade \
+	uv pip install --upgrade \
 		pip \
 		wheel \
 		setuptools
-	# tooling
-	$@/bin/pip3 install pip-tools
 
 requirements.txt: .venv requirements.in
 	# freezes requirements
-	$</bin/pip-compile --upgrade --build-isolation --output-file $@ $(word2, $^)
+	uv pip compile --upgrade --build-isolation $(word 2, $^) --output-file $@ 
 
 devenv: .venv requirements.txt ## create a python virtual environment with tools to dev, run and tests cookie-cutter
 	# installing extra tools
-	@$</bin/pip3 install -r  $(word 2,$^)
+	uv pip install -r  $(word 2,$^)
 	# your dev environment contains
-	@$</bin/pip3 list
+	@$</bin/pip list
 	@echo "To activate the virtual environment, run 'source $</bin/activate'"
 
 

services/sleeper/VERSION

@@ -1 +1 @@
-2.1.6
+2.2.0

services/sleeper/docker-compose-build.yml

@@ -7,7 +7,7 @@ services:
       dockerfile: docker/custom/Dockerfile
       target: production
       args:
-        BASE_IMAGE: python:3.9-slim-buster
+        BASE_IMAGE: python:3.11-slim
 
   sleeper-gpu:
     image: local/${DOCKER_IMAGE_NAME}-gpu:${DOCKER_BUILD_TARGET}
@@ -16,12 +16,14 @@ services:
       dockerfile: docker/custom/Dockerfile
       target: production
       args:
-        BASE_IMAGE: nvidia/cuda:10.0-base-ubuntu18.04
+        INSTALL_EXTRAS: true
+        BASE_IMAGE: nvidia/cuda:12.3.1-base-ubuntu22.04
   sleeper-mpi:
     image: local/${DOCKER_IMAGE_NAME}-mpi:${DOCKER_BUILD_TARGET}
     build:
       context: ./
       dockerfile: docker/custom/Dockerfile
       target: production
       args:
-        BASE_IMAGE: nvidia/cuda:10.0-base-ubuntu18.04
+        INSTALL_EXTRAS: true
+        BASE_IMAGE: nvidia/cuda:12.3.1-base-ubuntu22.04

services/sleeper/docker-compose-meta.yml

@@ -5,23 +5,27 @@ services:
         io.simcore.authors: '{"authors": [{"name": "Manuel Guidon", "email": "[email protected]",
           "affiliation": "IT''IS Foundation"}, {"name": "Odei Maiz", "email": "[email protected]",
           "affiliation": "IT''IS Foundation"}, {"name": "Andrei Neagu", "email": "[email protected]",
-          "affiliation": "IT''IS Foundation"}]}'
+          "affiliation": "IT''IS Foundation"}, {"name": "Sylvain Anderegg", "email":
+          "[email protected]", "affiliation": "IT''IS Foundation"}]}'
         io.simcore.contact: '{"contact": "[email protected]"}'
         io.simcore.description: '{"description": "A service which awaits for time
           to pass, two times."}'
         io.simcore.inputs: '{"inputs": {"input_1": {"displayOrder": 1, "label": "File
           with int number", "description": "Pick a file containing only one integer",
           "type": "data:text/plain", "fileToKeyMap": {"single_number.txt": "input_1"}},
           "input_2": {"displayOrder": 2, "label": "Sleep interval", "description":
-          "Choose an amount of time to sleep in range [0-65]", "defaultValue": 2,
+          "Choose an amount of time to sleep in range [0-900]", "defaultValue": 2,
           "type": "ref_contentSchema", "contentSchema": {"title": "Sleep interval",
-          "type": "integer", "x_unit": "second", "minimum": 0, "maximum": 65}}, "input_3":
+          "type": "integer", "x_unit": "second", "minimum": 0, "maximum": 900}}, "input_3":
           {"displayOrder": 3, "label": "Fail after sleep", "description": "If set
           to true will cause service to fail after it sleeps", "type": "boolean",
           "defaultValue": false}, "input_4": {"displayOrder": 4, "label": "Distance
           to bed", "description": "It will first walk the distance to bed", "defaultValue":
           0, "type": "ref_contentSchema", "contentSchema": {"title": "Distance to
-          bed", "type": "integer", "x_unit": "meter"}}}}'
+          bed", "type": "integer", "x_unit": "meter"}}, "input_5": {"displayOrder":
+          5, "label": "Dream of the night", "description": "It will dream a big dream",
+          "defaultValue": 0, "type": "ref_contentSchema", "contentSchema": {"title":
+          "Dream of the night", "type": "integer", "x_unit": "bytes"}}}}'
         io.simcore.integration-version: '{"integration-version": "1.0.0"}'
         io.simcore.key: '{"key": "simcore/services/comp/itis/sleeper"}'
         io.simcore.name: '{"name": "sleeper"}'
@@ -31,9 +35,11 @@ services:
           "output_1"}}, "output_2": {"displayOrder": 2, "label": "Random sleep interval",
           "description": "Interval is generated in range [1-9]", "type": "ref_contentSchema",
           "contentSchema": {"title": "Random sleep interval", "type": "integer", "x_unit":
-          "second"}}}}'
+          "second"}}, "output_3": {"displayOrder": 3, "label": "Dream output", "description":
+          "Contains some random data representing a dream", "type": "data:text/plain",
+          "fileToKeyMap": {"dream.txt": "output_3"}}}}'
         io.simcore.type: '{"type": "computational"}'
-        io.simcore.version: '{"version": "2.1.6"}'
+        io.simcore.version: '{"version": "2.2.0"}'
         org.label-schema.build-date: ${BUILD_DATE}
         org.label-schema.schema-version: '1.0'
         org.label-schema.vcs-ref: ${VCS_REF}
@@ -47,31 +53,41 @@ services:
         io.simcore.authors: '{"authors": [{"name": "Manuel Guidon", "email": "[email protected]",
           "affiliation": "IT''IS Foundation"}, {"name": "Odei Maiz", "email": "[email protected]",
           "affiliation": "IT''IS Foundation"}, {"name": "Andrei Neagu", "email": "[email protected]",
-          "affiliation": "IT''IS Foundation"}]}'
-        io.simcore.contact: '{"contact": "[email protected]"}'
+          "affiliation": "IT''IS Foundation"}, {"name": "Sylvain Anderegg", "email":
+          "[email protected]", "affiliation": "IT''IS Foundation"}]}'
+        io.simcore.contact: '{"contact": "[email protected]"}'
         io.simcore.description: '{"description": "A service which awaits for time
-          to pass."}'
+          to pass, two times."}'
         io.simcore.inputs: '{"inputs": {"input_1": {"displayOrder": 1, "label": "File
           with int number", "description": "Pick a file containing only one integer",
           "type": "data:text/plain", "fileToKeyMap": {"single_number.txt": "input_1"}},
           "input_2": {"displayOrder": 2, "label": "Sleep interval", "description":
-          "Choose an amount of time to sleep", "type": "integer", "unit": "second",
-          "defaultValue": 2}, "input_3": {"displayOrder": 3, "label": "Fail after
-          sleep", "description": "If set to true will cause service to fail after
-          it sleeps", "type": "boolean", "defaultValue": false}, "input_4": {"displayOrder":
-          4, "label": "Distance to bed", "description": "It will first walk the distance
-          to bed", "type": "integer", "unit": "meter", "defaultValue": 0}}}'
+          "Choose an amount of time to sleep in range [0-900]", "defaultValue": 2,
+          "type": "ref_contentSchema", "contentSchema": {"title": "Sleep interval",
+          "type": "integer", "x_unit": "second", "minimum": 0, "maximum": 900}}, "input_3":
+          {"displayOrder": 3, "label": "Fail after sleep", "description": "If set
+          to true will cause service to fail after it sleeps", "type": "boolean",
+          "defaultValue": false}, "input_4": {"displayOrder": 4, "label": "Distance
+          to bed", "description": "It will first walk the distance to bed", "defaultValue":
+          0, "type": "ref_contentSchema", "contentSchema": {"title": "Distance to
+          bed", "type": "integer", "x_unit": "meter"}}, "input_5": {"displayOrder":
+          5, "label": "Dream of the night", "description": "It will dream a big dream",
+          "defaultValue": 0, "type": "ref_contentSchema", "contentSchema": {"title":
+          "Dream of the night", "type": "integer", "x_unit": "bytes"}}}}'
         io.simcore.integration-version: '{"integration-version": "1.0.0"}'
         io.simcore.key: '{"key": "simcore/services/comp/itis/sleeper-gpu"}'
         io.simcore.name: '{"name": "sleeper-gpu"}'
         io.simcore.outputs: '{"outputs": {"output_1": {"displayOrder": 1, "label":
           "File containing one random integer", "description": "Integer is generated
           in range [1-9]", "type": "data:text/plain", "fileToKeyMap": {"single_number.txt":
           "output_1"}}, "output_2": {"displayOrder": 2, "label": "Random sleep interval",
-          "description": "Interval is generated in range [1-9]", "type": "integer",
-          "unit": "second"}}}'
+          "description": "Interval is generated in range [1-9]", "type": "ref_contentSchema",
+          "contentSchema": {"title": "Random sleep interval", "type": "integer", "x_unit":
+          "second"}}, "output_3": {"displayOrder": 3, "label": "Dream output", "description":
+          "Contains some random data representing a dream", "type": "data:text/plain",
+          "fileToKeyMap": {"dream.txt": "output_3"}}}}'
         io.simcore.type: '{"type": "computational"}'
-        io.simcore.version: '{"version": "2.1.4"}'
+        io.simcore.version: '{"version": "2.2.0"}'
         org.label-schema.build-date: ${BUILD_DATE}
         org.label-schema.schema-version: '1.0'
         org.label-schema.vcs-ref: ${VCS_REF}
@@ -87,31 +103,41 @@ services:
         io.simcore.authors: '{"authors": [{"name": "Manuel Guidon", "email": "[email protected]",
           "affiliation": "IT''IS Foundation"}, {"name": "Odei Maiz", "email": "[email protected]",
           "affiliation": "IT''IS Foundation"}, {"name": "Andrei Neagu", "email": "[email protected]",
-          "affiliation": "IT''IS Foundation"}]}'
-        io.simcore.contact: '{"contact": "[email protected]"}'
+          "affiliation": "IT''IS Foundation"}, {"name": "Sylvain Anderegg", "email":
+          "[email protected]", "affiliation": "IT''IS Foundation"}]}'
+        io.simcore.contact: '{"contact": "[email protected]"}'
         io.simcore.description: '{"description": "A service which awaits for time
-          to pass."}'
+          to pass, two times."}'
         io.simcore.inputs: '{"inputs": {"input_1": {"displayOrder": 1, "label": "File
           with int number", "description": "Pick a file containing only one integer",
           "type": "data:text/plain", "fileToKeyMap": {"single_number.txt": "input_1"}},
           "input_2": {"displayOrder": 2, "label": "Sleep interval", "description":
-          "Choose an amount of time to sleep", "type": "integer", "unit": "second",
-          "defaultValue": 2}, "input_3": {"displayOrder": 3, "label": "Fail after
-          sleep", "description": "If set to true will cause service to fail after
-          it sleeps", "type": "boolean", "defaultValue": false}, "input_4": {"displayOrder":
-          4, "label": "Distance to bed", "description": "It will first walk the distance
-          to bed", "type": "integer", "unit": "meter", "defaultValue": 0}}}'
+          "Choose an amount of time to sleep in range [0-900]", "defaultValue": 2,
+          "type": "ref_contentSchema", "contentSchema": {"title": "Sleep interval",
+          "type": "integer", "x_unit": "second", "minimum": 0, "maximum": 900}}, "input_3":
+          {"displayOrder": 3, "label": "Fail after sleep", "description": "If set
+          to true will cause service to fail after it sleeps", "type": "boolean",
+          "defaultValue": false}, "input_4": {"displayOrder": 4, "label": "Distance
+          to bed", "description": "It will first walk the distance to bed", "defaultValue":
+          0, "type": "ref_contentSchema", "contentSchema": {"title": "Distance to
+          bed", "type": "integer", "x_unit": "meter"}}, "input_5": {"displayOrder":
+          5, "label": "Dream of the night", "description": "It will dream a big dream",
+          "defaultValue": 0, "type": "ref_contentSchema", "contentSchema": {"title":
+          "Dream of the night", "type": "integer", "x_unit": "bytes"}}}}'
         io.simcore.integration-version: '{"integration-version": "1.0.0"}'
         io.simcore.key: '{"key": "simcore/services/comp/itis/sleeper-mpi"}'
         io.simcore.name: '{"name": "sleeper-mpi"}'
         io.simcore.outputs: '{"outputs": {"output_1": {"displayOrder": 1, "label":
           "File containing one random integer", "description": "Integer is generated
           in range [1-9]", "type": "data:text/plain", "fileToKeyMap": {"single_number.txt":
           "output_1"}}, "output_2": {"displayOrder": 2, "label": "Random sleep interval",
-          "description": "Interval is generated in range [1-9]", "type": "integer",
-          "unit": "second"}}}'
+          "description": "Interval is generated in range [1-9]", "type": "ref_contentSchema",
+          "contentSchema": {"title": "Random sleep interval", "type": "integer", "x_unit":
+          "second"}}, "output_3": {"displayOrder": 3, "label": "Dream output", "description":
+          "Contains some random data representing a dream", "type": "data:text/plain",
+          "fileToKeyMap": {"dream.txt": "output_3"}}}}'
         io.simcore.type: '{"type": "computational"}'
-        io.simcore.version: '{"version": "2.1.4"}'
+        io.simcore.version: '{"version": "2.2.0"}'
         org.label-schema.build-date: ${BUILD_DATE}
         org.label-schema.schema-version: '1.0'
         org.label-schema.vcs-ref: ${VCS_REF}

services/sleeper/docker/custom/Dockerfile

@@ -1,24 +1,63 @@
-
-ARG BASE_IMAGE="nvidia/cuda:10.0-base-ubuntu18.04"
+# syntax=docker/dockerfile:1
+ARG BASE_IMAGE="nvidia/cuda:12.0.0-base-ubuntu22.04"
 FROM ${BASE_IMAGE} as base
 #
 #  USAGE:
 #     cd services/sleeper
 #     docker build -f Dockerfile -t sleeper:prod --target production ../../
-#     docker run sleeper:prod
+#       docker run sleeper:prod
 #
 
-LABEL maintainer="Andrei Neagu <[email protected]>"
+LABEL maintainer=sanderegg
 
 # simcore-user uid=8004(${SC_USER_NAME}) gid=8004(${SC_USER_NAME}) groups=8004(${SC_USER_NAME})
-ENV SC_USER_ID 8004
-ENV SC_USER_NAME scu
-RUN adduser --uid ${SC_USER_ID} --disabled-password --gecos "" --shell /bin/sh --home /home/${SC_USER_NAME} ${SC_USER_NAME}
-
-RUN apt-get update --fix-missing && \
-    apt-get install -y wget bzip2 ca-certificates curl git python3 python3-pip jq && \
-    apt-get clean && \
-    rm -rf /var/lib/apt/lists/*
+ENV SC_USER_ID=8004 \
+    SC_USER_NAME=scu \
+    SC_BUILD_TARGET=base
+
+RUN adduser \
+    --uid ${SC_USER_ID} \
+    --disabled-password \
+    --gecos "" \
+    --shell /bin/sh \
+    --home /home/${SC_USER_NAME} ${SC_USER_NAME}
+
+# Sets utf-8 encoding for Python et al
+ENV LANG=C.UTF-8
+
+# Turns off writing .pyc files; superfluous on an ephemeral container.
+ENV PYTHONDONTWRITEBYTECODE=1 \
+    VIRTUAL_ENV=/home/scu/.venv
+
+# Ensures that the python and pip executables used in the image will be
+# those from our virtualenv.
+ENV PATH="${VIRTUAL_ENV}/bin:$PATH"
+
+RUN --mount=type=cache,target=/var/cache/apt,mode=0755,sharing=private \
+    --mount=type=cache,target=/var/lib/apt,mode=0755,sharing=private \
+    set -eux \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends \
+    jq \
+    gosu \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    # verify that the binary works
+    && gosu nobody true
+
+# Define an argument that dictates whether to run the installation commands
+ARG INSTALL_EXTRAS=false
+RUN --mount=type=cache,target=/var/cache/apt,mode=0755,sharing=private \
+    --mount=type=cache,target=/var/lib/apt,mode=0755,sharing=private \
+    if [ "$INSTALL_EXTRAS" = "true" ]; then \
+    set -eux \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends \
+    python3 \
+    python3-pip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*; \
+    fi
 
 # for ARM architecture this helps a lot VS building packages
 ENV PIP_EXTRA_INDEX_URL=https://www.piwheels.org/simple
@@ -33,10 +72,21 @@ ENV PIP_EXTRA_INDEX_URL=https://www.piwheels.org/simple
 
 FROM base as build
 
-ENV SC_BUILD_TARGET build
+ENV SC_BUILD_TARGET=build
+
+# NOTE: install https://github.com/astral-sh/uv ultra-fast rust-based pip replacement
+RUN --mount=type=cache,mode=0755,target=/root/.cache/pip \
+    pip install uv~=0.1
 
-# Instlling python
-RUN pip3 install --upgrade pip wheel setuptools
+# NOTE: python virtualenv is used here such that installed
+# packages may be moved to production image easily by copying the venv
+RUN uv venv "${VIRTUAL_ENV}"
+
+RUN --mount=type=cache,mode=0755,target=/root/.cache/pip \
+    uv pip install --upgrade  \
+    pip~=24.0  \
+    wheel \
+    setuptools
 
 # ------------------------------------------------------------------------------------
 
@@ -61,14 +111,20 @@ RUN cp -R src/sleeper/* /build/bin
 #
 FROM base as production
 
-ENV SC_BUILD_TARGET production
-ENV SC_BOOT_MODE production
+ENV SC_BUILD_TARGET=production \
+    SC_BOOT_MODE=production
+
+ENV PYTHONOPTIMIZE=TRUE
 
 
 ENV INPUT_FOLDER="/input" \
     OUTPUT_FOLDER="/output"
 
 WORKDIR /home/${SC_USER_NAME}
+# ensure home folder is read/writable for user scu
+RUN chown -R ${SC_USER_NAME} /home/${SC_USER_NAME}
+# Starting from clean base image, copies pre-installed virtualenv from prod-only-deps
+COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} --from=build  ${VIRTUAL_ENV} ${VIRTUAL_ENV}
 
 # copy docker bootup scripts
 COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} docker/custom/*.sh docker/