Merge pull request #497 from EpistasisLab/docker_updates

Docker updates

.env

@@ -1,3 +1,6 @@
 #!/bin/sh
 # Docker production build environment
+# ARCH refers to the architecture of the development machine.
+#   If you are on arm64, set this to arm64, otherwise use x64
 TAG=0.20.a0
+ARCH=x64

.gitignore

@@ -62,3 +62,4 @@ MANIFEST
 
 .xz
 .exe
+run*Test.sh

docker-compose-int-test.yml

@@ -22,6 +22,8 @@ services:
     build:
       context: .
       dockerfile: docker/lab/Dockerfile
+      args:
+        - ARCH=${ARCH}
     tty: true
     stdin_open: true
     volumes:

docker-compose-multiarch.yml

@@ -0,0 +1,57 @@
+version: '3'
+
+services:
+  lab:
+    build:
+      context: .
+      dockerfile: docker/lab/Dockerfile
+      x-bake:
+        platforms:
+          - linux/arm64
+    tty: true
+    stdin_open: true
+    volumes:
+      - "./:/appsrc"
+      - "/appsrc/lab/webapp/node_modules"
+      - "/appsrc/lab/node_modules"
+    ports:
+      - "5080:5080"
+    env_file:
+      - ./config/common.env
+      - ./config/ai.env
+    depends_on:
+      - dbmongo
+
+  machine:
+    build:
+      context: .
+      dockerfile: docker/machine/Dockerfile
+      x-bake:
+        platforms:
+          - linux/arm64
+    tty: true
+    stdin_open: true
+    volumes:
+      - "./:/appsrc"
+      - "/appsrc/machine/node_modules"
+    ports:
+      - "5081:5081"
+    env_file: ./config/common.env
+    environment:
+      - MACHINE_PORT=5081
+    depends_on:
+      - lab
+      - dbmongo
+
+  dbmongo:
+    build:
+      context: .
+      dockerfile: docker/dbmongo/Dockerfile
+      x-bake:
+        platforms:
+          - linux/arm64
+    tty: true
+    stdin_open: true
+    ports:
+      - "27017:27017"
+    env_file: ./config/common.env

docker-compose-unit-test.yml

@@ -5,6 +5,8 @@ services:
     build:
       context: .
       dockerfile: tests/unit/Dockerfile
+      args:
+        - ARCH=${ARCH}
     working_dir: /appsrc
     command: bash -c "dos2unix tests/unit/unit_test_runner.sh && export PENNAI_UNIT_TESTS_JS_ONLY=$PENNAI_UNIT_TESTS_JS_ONLY && export PENNAI_UNIT_TESTS_PY_ONLY=$PENNAI_UNIT_TESTS_PY_ONLY && sh tests/unit/unit_test_runner.sh"
     tty: true

docker-compose.yml

@@ -5,9 +5,8 @@ services:
     build:
       context: .
       dockerfile: docker/lab/Dockerfile
-      x-bake:
-        platforms:
-          - linux/arm64
+      args:
+        - ARCH=${ARCH}
     tty: true
     stdin_open: true
     volumes:
@@ -26,9 +25,6 @@ services:
     build:
       context: .
       dockerfile: docker/machine/Dockerfile
-      x-bake:
-        platforms:
-          - linux/arm64
     tty: true
     stdin_open: true
     volumes:
@@ -47,9 +43,6 @@ services:
     build:
       context: .
       dockerfile: docker/dbmongo/Dockerfile
-      x-bake:
-        platforms:
-          - linux/arm64
     tty: true
     stdin_open: true
     ports:

docker/lab/Dockerfile

@@ -1,11 +1,7 @@
-# FROM python:3.7.11-stretch
 FROM python:3.7.16-slim-buster
 
-#nodejs
-# RUN wget --quiet https://nodejs.org/dist/v12.22.9/node-v12.22.9-linux-x64.tar.xz -O ~/node.tar.xz && \
-#     tar -xvf ~/node.tar.xz -C /opt/ && \
-#     rm ~/node.tar.xz
-# ENV PATH /opt/node-v12.22.9-linux-x64/bin:$PATH
+ARG ARCH
+ARG wheel_directory=docker/pywheels
 
 RUN apt-get update --fix-missing && \
     apt-get install -y wget xz-utils git \
@@ -48,8 +44,13 @@ ARG docker_filepath=docker/lab/files
 #     rm -rf /var/lib/apt/lists/*
 
 # setup python environment
+RUN mkdir /root/wheel
+COPY ${wheel_directory}/*.whl /root/wheel/
 COPY ${docker_filepath}/requirements.txt /root/
-RUN pip install --no-cache-dir -r /root/requirements.txt
+COPY ${docker_filepath}/requirements-surprise-${ARCH}.txt /root/
+RUN pip install --no-cache-dir --find-links=/root/wheel -r /root/requirements.txt
+RUN pip install --no-cache-dir --find-links=/root/wheel -r /root/requirements-surprise-${ARCH}.txt
+RUN rm -rf /root/wheel
 
 ## Webserver
 

docker/lab/files/requirements-surprise-arm64.txt

@@ -0,0 +1 @@
+scikit-surprise==1.0.8.2

docker/lab/files/requirements-surprise-x64.txt

@@ -0,0 +1 @@
+-e git+https://github.com/lacava/surprise.git@1.1.1.1#egg=scikit-surprise

docker/lab/files/requirements.txt

@@ -7,5 +7,4 @@ cython==0.29.32
 xgboost==1.6.2
 simplejson==3.17.2
 requests==2.25.1
-joblib==1.2.0
--e git+https://github.com/lacava/surprise.git@1.1.1.1#egg=scikit-surprise
+joblib==1.2.0

docker/machine/Dockerfile

@@ -1,12 +1,6 @@
-# FROM python:3.7.11-stretch
 FROM python:3.7.16-slim-buster
 
-#nodejs
-# RUN wget --quiet https://nodejs.org/dist/v12.22.9/node-v12.22.9-linux-x64.tar.xz -O ~/node.tar.xz && \
-#     tar -xvf ~/node.tar.xz -C /opt/ && \
-#     rm ~/node.tar.xz
-# ENV PATH /opt/node-v12.22.9-linux-x64/bin:$PATH
-
+ARG wheel_directory=docker/pywheels
 ARG docker_filepath=docker/machine/files
 
 RUN apt-get update --fix-missing && apt-get install -y \
@@ -36,11 +30,11 @@ RUN apt-get update --fix-missing && apt-get install -y \
     apt-get clean
 
 # setup python environment
+RUN mkdir /root/wheel
+COPY ${wheel_directory}/*.whl /root/wheel/
 COPY ${docker_filepath}/requirements.txt /root/
-RUN pip install --no-cache-dir -r /root/requirements.txt
-COPY ${docker_filepath}/requirements_shap.txt /root/
-RUN pip install --no-cache-dir -r /root/requirements_shap.txt
-
+RUN pip install --no-cache-dir --find-links=/root/wheel -r /root/requirements.txt
+RUN rm -rf /root/wheel
 
 # setup node environment
 RUN npm install -g pm2 --silent --progress=false

docker/machine/files/requirements.txt

@@ -8,4 +8,5 @@ mlxtend==0.16.0
 pydot==1.4.2
 requests==2.25.1
 xgboost==1.6.2
-joblib==1.2.0
+joblib==1.2.0
+shap==0.37.0

docs/guides/userGuide.md

@@ -34,12 +34,7 @@ We have built a custom Raspberry Pi OS Image containing Aliro (configured to be
 7. Insert the MicroSD Card into your Raspberry Pi 400 and start it up.
 8. When the Operating System has finished starting up, double-click the Aliro-Ed Icon on the Destop or launch the Web Browser.
 
-Now that Aliro is up and running, you are ready to run experiments, Aliro Ed comes preloaded with the following datasets:
-  - [BNGBreastTumor.tsv](https://github.com/EpistasisLab/pmlb/tree/master/datasets/1201_BNG_breastTumor)
-  - [ESL.tsv](https://github.com/EpistasisLab/pmlb/tree/master/datasets/1027_ESL)
-  - [Iris.tsv](https://github.com/EpistasisLab/pmlb/tree/master/datasets/iris)
-  - [Titanic.tsv](https://github.com/EpistasisLab/pmlb/tree/master/datasets/titanic)
-  - Other datasets can be downloaded from the [Penn Machine Learning Benchmarks](https://github.com/EpistasisLab/pmlb)
+Now that Aliro is up and running, you are ready to run experiments, Aliro Ed comes preloaded with some data sets for you to experiment with. Other datasets can be downloaded from the [Penn Machine Learning Benchmarks](https://github.com/EpistasisLab/pmlb)
 
 You may also load your own datasets, please see the following sections below for further instructions:
   - [Adding Data Sets](#adding-datasets)

runIntTest.sh

@@ -1,4 +1,4 @@
 #!/usr/bin/bash
 
 docker system prune -a -f --volumes
-docker-compose -f docker-compose-int-test.yml up --abort-on-container-exit -V
+docker compose -f docker-compose-int-test.yml up --abort-on-container-exit -V

runUnitTest.sh

@@ -1,4 +1,4 @@
 #!/usr/bin/bash
 
 docker system prune -a -f --volumes
-docker-compose -f docker-compose-unit-test.yml up --abort-on-container-exit -V
+docker compose -f docker-compose-unit-test.yml up --abort-on-container-exit -V

tests/unit/Dockerfile

@@ -1,5 +1,8 @@
 FROM python:3.7.16-buster
 
+ARG ARCH
+ARG wheel_directory=docker/pywheels
+
 #nodejs
 RUN ARCH= && dpkgArch="$(dpkg --print-architecture)" \
     && case "${dpkgArch##*-}" in \
@@ -36,13 +39,17 @@ COPY /tests/unit/requirements.txt /root/test_requirements.txt
 RUN pip install --no-cache-dir -r /root/test_requirements.txt
 
 ## machine and lab container
+COPY ${wheel_directory}/*.whl /root/wheel/
 COPY /docker/lab/files/requirements.txt /root/lab_requirements.txt
-RUN pip install --no-cache-dir -r /root/lab_requirements.txt
+RUN pip install --no-cache-dir --find-links=/root/wheel -r /root/lab_requirements.txt
+COPY /docker/lab/files/requirements-surprise-${ARCH}.txt /root/surprise_requirements.txt
+RUN pip install --no-cache-dir --find-links=/root/wheel -r /root/surprise_requirements.txt
 
 COPY /docker/machine/files/requirements.txt /root/mach_requirements.txt
-RUN pip install --no-cache-dir -r /root/mach_requirements.txt
-COPY /docker/machine/files/requirements_shap.txt /root/mach_requirements_shap.txt
-RUN pip install --no-cache-dir -r /root/mach_requirements_shap.txt
+RUN pip install --no-cache-dir --find-links=/root/wheel -r /root/mach_requirements.txt
+# COPY /docker/machine/files/requirements_shap.txt /root/mach_requirements_shap.txt
+# RUN pip install --no-cache-dir -r /root/mach_requirements_shap.txt
+RUN rm -rf /root/wheel
 
 # install lab/node_modules to an anon volume
 WORKDIR /appsrc/lab