Add support for running PennAI on Raspberry Pi

.coveragerc

@@ -1,5 +1,6 @@
 [run]
-; source = 
+relative_files = True
+; source =
 ; 	ai
 ; 	machine
 ; 	lab/pyutils
@@ -12,5 +13,5 @@ parallel = True
 ; the first path is the path on the local (travis) filesystem
 ; the second path is the path as it appears within the Docker container
 source =
-  $TRAVIS_BUILD_DIR
+  $GITHUB_WORKSPACE
   /appsrc/

.env

@@ -1,3 +1,3 @@
 #!/bin/sh
 # Docker production build environment
-TAG=0.18a0
+TAG=0.18

.gitattributes

@@ -1,6 +1,6 @@
 # Declare files that will always have LF line endings on checkout.
 release/*.sh text eol=lf
-tests/*.sh text eol=lf
+tests/**/*.sh text eol=lf
 .env text eol=lf
 
 data/recommenders/scikitlearn/KNNDatasetRecommender_classifier_accuracy_pmlb.pkl.gz filter=lfs diff=lfs merge=lfs -text

.github/workflows/pennai_tests.yml → .github/workflows/aliro_tests.yml

@@ -1,19 +1,15 @@
-name: Tests of PennAI
+name: Aliro CI/CD
 # Controls when the action will run.
 on:
-  # Triggers the workflow on push or pull request events
   push:
-  pull_request:
-    branches: [ master ]
-
+
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
   build_int_test:
-    name: Integration Tests of PennAI
+    name: Integration Tests
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
 
@@ -29,9 +25,9 @@ jobs:
       # Runs a set of commands using the runners shell
       - name: Run Integration Tests
         run: |
-          docker-compose  -f ./docker-compose-int-test.yml run tester bash -c "sh /root/wait_pennai.sh && npm test"
+          docker-compose -f ./docker-compose-int-test.yml run tester bash -c "sh /root/wait_pennai.sh && npm test"
           docker-compose -f ./docker-compose-int-test.yml down
-  # This workflow contains a single job called "build"
+
   build_web_app:
     name: Unit Tests for Webapp
     # The type of runner that the job will run on
@@ -44,30 +40,22 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: '3.7'
-
-
+
       # Runs a single command using the runners shell
       - name: Build Docker Images
         run: |
-          pip install coveralls
           docker-compose -f ./docker-compose-unit-test.yml build -m 8g
 
       # Runs a set of commands using the runners shell
       - name: Run Unit Tests
-        env:
-          COVERALLS_REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           git lfs fetch --all
-          docker run -v $(pwd):/appsrc -w /appsrc pennai_unit_tester mocha machine/test/test.js
-          docker run -v $(pwd):/appsrc -v /appsrc/lab/webapp/node_modules -w /appsrc/lab/webapp/ pennai_unit_tester npm run test
-          docker run -v $(pwd):/appsrc -w /appsrc pennai_unit_tester \
-              coverage run -m nose -s -v \
-              machine/test/learn_tests.py \
-              lab/pyutils/tests/*.py \
-              ai/tests/test_a*.py \
-              ai/tests/lab_*.py \
-              ai/tests/test_re*.py \
-              ai/tests/test_k*utils.py
+          docker-compose -f ./docker-compose-unit-test.yml up --abort-on-container-exit -V
+      - name: Coveralls
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+          flag-name: Unit Test for webapp
 
   build_pypkg:
     name: Unit Tests for scikit-learn API
@@ -80,18 +68,46 @@ jobs:
       - uses: actions/setup-python@v2
         with:
           python-version: '3.7'
-
       - name: Build Docker Images
         run: |
+          pip install coveralls
           docker-compose -f ./docker-compose-unit-test.yml build -m 8g
-
       # Runs a set of commands using the runners shell
       - name: Run Unit Tests
         run: |
           git lfs fetch --all
           git lfs pull
-          docker run -v $(pwd):/appsrc -w /appsrc pennai_unit_tester nosetests -s -v ai/tests/test_sklearn_api.py
-      # Run deployment steps if pervious steps are success
+          docker run -v $(pwd):/appsrc -w /appsrc aliro_unit_tester coverage run -m nose -s -v ai/tests/test_sklearn_api.py
+          coverage combine
+      - name: Coveralls
+        uses: AndreMiras/coveralls-python-action@develop
+        with:
+          parallel: true
+          flag-name: Unit Test for scikit-learn api
+
+  coveralls_finish:
+    name: Publish Coveralls
+    needs: [build_web_app, build_pypkg]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Coveralls Finished
+      uses: AndreMiras/coveralls-python-action@develop
+      with:
+        parallel-finished: true
+
+  deploy_pypkg:
+    if: ${{ github.event_name == 'release' && github.event.action == 'published' }}
+    name: Deploy python package
+    needs: build_pypkg
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.7'
       - name: Install dependencies
         if: ${{ github.event_name == 'release' && github.event.action == 'published' }}
         run: |
@@ -107,8 +123,10 @@ jobs:
           twine upload dist/*
 
   build_docs:
-    name: Doc Builder
-    needs: [build_int_test, build_web_app] 
+    # Only publish docs on master branch
+    if: github.ref == 'refs/heads/master'
+    name: Publish Docs
+    needs: [build_int_test, build_web_app, build_pypkg]
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
     # Steps represent a sequence of tasks that will be executed as part of the job

.gitignore

@@ -58,3 +58,4 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+.vscode

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "docker/pennai-arm64-deps"]
+	path = docker/pennai-arm64-deps
+	url = https://github.com/EpistasisLab/pennai-arm64-deps

.travis.yml

@@ -37,9 +37,9 @@ jobs:
             ai/tests/lab_*.py
             ai/tests/test_re*.py
             ai/tests/test_k*utils.py"
-        - coverage combine
+        #- coverage combine
         #- docker cp pennai_unit_tester:/.coverage ./
-        - coveralls
+        #- coveralls
     - stage: Test
       name: "Unit Tests for scikit-learn API"
       install:

Jenkinsfile

@@ -2,14 +2,16 @@
 pipeline {
     agent any
     parameters {
-        //string(name: 'STATUS_EMAIL', defaultValue: 'hwilli@pennmedicine.upenn.edu', description: 'Comma sep list of email addresses that should recieve test status notifications.')
-        string(name: 'STATUS_EMAIL', defaultValue: 'hwilli@pennmedicine.upenn.edu, weixuanf@upenn.edu, lacava@upenn.edu, mgstauff@gmail.com', description: 'Comma sep list of email addresses that should recieve test status notifications.')
+        string(
+            name: 'STATUS_EMAIL', 
+            defaultValue: '${DEFAULT_RECIPIENTS}', 
+            description: 'Comma sep list of email addresses that should recieve test status notifications.')
     }
     options {
         timeout(time: 1, unit: 'HOURS')
     }
     environment {
-        LOCAL_PENNAI_DEPLOY_DIR = '/data/git/pennai'
+        LOCAL_PENNAI_DEPLOY_DIR = '/data/git/Aliro'
         LOCAL_PENNAI_DEPLOY_FILE = "${LOCAL_PENNAI_DEPLOY_DIR}/docker-compose.yml"
     }
     stages {
@@ -63,14 +65,14 @@ pipeline {
             }
 
         }
-        stage('Stop PennAI Locally') {
+        stage('Stop Aliro Locally') {
             steps {
                 sh "docker-compose -f ${LOCAL_PENNAI_DEPLOY_FILE} stop"
             }
         }
         stage('Integration Tests') {
             steps {
-                // stop any running pennai test or dev instances
+                // stop any running Aliro test or dev instances
                 sh 'docker-compose -f ./docker-compose-int-test.yml stop'
 
                 // run the integration test instance
@@ -83,7 +85,7 @@ pipeline {
                 }
             }
         }
-        stage('Start PennAI Locally') {
+        stage('Start Aliro Locally') {
             steps {
                 sh "docker-compose -f ${LOCAL_PENNAI_DEPLOY_FILE} up --detach --force-recreate"
             }

README.md

@@ -1,19 +1,18 @@
 [![Logo](./docs/source/_static/logo_blank_small.png)]()
 
-[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://github.com/EpistasisLab/pennai/blob/master/LICENSE) [![Master Build Status - Mac/Linux](https://travis-ci.org/EpistasisLab/pennai.svg?branch=master)](https://travis-ci.org/EpistasisLab/pennai) [![Coverage Status](https://coveralls.io/repos/github/EpistasisLab/pennai/badge.svg)](https://coveralls.io/github/EpistasisLab/pennai)
+[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://github.com/EpistasisLab/Aliro/blob/master/LICENSE) [![Aliro CI/CD](https://github.com/EpistasisLab/Aliro/actions/workflows/aliro_tests.yml/badge.svg)](https://github.com/EpistasisLab/Aliro/actions/workflows/aliro_tests.yml) [![Coverage Status](https://coveralls.io/repos/github/EpistasisLab/pennai/badge.svg)](https://coveralls.io/github/EpistasisLab/pennai)
 
-
-PennAI: AI-Driven Data Science
+Aliro: AI-Driven Data Science
 ==================================
 
-**PennAI** is an easy-to-use data science assistant.
+**Aliro** is an easy-to-use data science assistant.
 It allows researchers without machine learning or coding expertise to run supervised machine learning analysis through a clean web interface. 
 It provides results visualization and reproducible scripts so that the analysis can be taken anywhere. 
-And, it has an *AI* assistant that can choose the analysis to run for you.   Dataset profiles are generated and added to a knowledgebase as experiments are run, and the AI assistant learns from this to give more informed recommendations as it is used.   PennAI comes with an initial knowledgebase generated from the [PMLB benchmark suite](https://github.com/EpistasisLab/penn-ml-benchmarks).
+And, it has an *AI* assistant that can choose the analysis to run for you.   Dataset profiles are generated and added to a knowledgebase as experiments are run, and the AI assistant learns from this to give more informed recommendations as it is used.   Aliro comes with an initial knowledgebase generated from the [PMLB benchmark suite](https://github.com/EpistasisLab/penn-ml-benchmarks).
 
-[**Documentation**](https://epistasislab.github.io/pennai/) 
+[**Documentation**](https://epistasislab.github.io/Aliro/) 
 
-[**Latest Production Release**](https://github.com/EpistasisLab/pennai/releases/latest)
+[**Latest Production Release**](https://github.com/EpistasisLab/Aliro/releases/latest)
 
 Browse the repo:
  - [User Guide](./docs/guides/userGuide.md)
@@ -22,7 +21,7 @@ Browse the repo:
 About the Project
 =================
 
-PennAI is actively developed by the [Institute for Biomedical Informatics](http://upibi.org) at the University of Pennsylvania.
+Aliro is actively developed by the [Institute for Biomedical Informatics](http://upibi.org) at the University of Pennsylvania.
 Contributors include Heather Williams, Weixuan Fu, William La Cava, Josh Cohen,
 Steve Vitale, Sharon Tartarone, Randal Olson, Patryk Orzechowski, and Jason Moore. 
 

ai/__init__.py

@@ -1,8 +1,8 @@
-"""~This file is part of the PennAI library~
+"""~This file is part of the Aliro library~
 
 Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
 
-PennAI is maintained by:
+Aliro is maintained by:
     - Heather Williams (hwilli@upenn.edu)
     - Weixuan Fu (weixuanf@upenn.edu)
     - William La Cava (lacava@upenn.edu)

ai/ai.py

@@ -1,8 +1,8 @@
-"""~This file is part of the PennAI library~
+"""~This file is part of the Aliro library~
 
 Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
 
-PennAI is maintained by:
+Aliro is maintained by:
     - Heather Williams (hwilli@upenn.edu)
     - Weixuan Fu (weixuanf@upenn.edu)
     - William La Cava (lacava@upenn.edu)
@@ -63,7 +63,7 @@
 
 
 class AI():
-    """AI managing agent for Penn AI.
+    """AI managing agent for Aliro.
 
     Responsible for:
     - checking for user requests for recommendations,
@@ -74,17 +74,13 @@ class AI():
 
     :param rec_class: ai.BaseRecommender - recommender to use
     :param api_path: string - path to the lab api server
-    :param extra_payload: dict - any additional payload that needs to be 
-    specified
+    :param extra_payload: dict - any additional payload that needs to be specified
     :param user: string - test user
-    :param rec_score_file: file - pickled score file to keep persistent scores
-    between sessions
+    :param rec_score_file: file - pickled score file to keep persistent scores between sessions
     :param verbose: Boolean
-    :param warm_start: Boolean - if true, attempt to load the ai state from the 
-    file provided by rec_score_file
+    :param warm_start: Boolean - if true, attempt to load the ai state from the file provided by rec_score_file
     :param n_recs: int - number of recommendations to make for each request
-    :param datasets: str or False - if not false, a comma seperated list of 
-    datasets to turn the ai on for at startup
+    :param datasets: str or False - if not false, a comma seperated list of datasets to turn the ai on for at startup
     :param use_pmlb_knowledgebase: Boolean
     """
 
@@ -137,7 +133,7 @@ def __init__(self,
 
         # api parameters, will be removed from self once the recommenders no 
         # longer call the api directly.
-        # See #98 <https://github.com/EpistasisLab/pennai/issues/98>
+        # See #98 <https://github.com/EpistasisLab/Aliro/issues/98>
         if api_path == None:
             api_path = ('http://' + os.environ['LAB_HOST'] + ':' +
                         os.environ['LAB_PORT'])
@@ -563,9 +559,9 @@ def load_state(self):
 import argparse
 
 def main():
-    """Handles command line arguments and runs Penn-AI."""
+    """Handles command line arguments and runs Aliro."""
     parser = argparse.ArgumentParser(
-            description='PennAI is a recommendation system for data science. ',
+            description='Aliro is a recommendation system for data science. ',
             add_help=False)
     parser.add_argument('-h','--help',action='help',
                         help="Show this help message and exit.")
@@ -621,7 +617,7 @@ def main():
             'slopeone': SlopeOneRecommender
             }
 
-    print('=======','Penn AI','=======')#,sep='\n')
+    print('=======','Aliro','=======')#,sep='\n')
 
     pennai = AI(rec_class=name_to_rec[args.REC],
             api_path=args.API_PATH, user=args.USER,

ai/api_utils.py

@@ -1,8 +1,8 @@
-"""~This file is part of the PennAI library~
+"""~This file is part of the Aliro library~
 
 Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
 
-PennAI is maintained by:
+Aliro is maintained by:
     - Heather Williams (hwilli@upenn.edu)
     - Weixuan Fu (weixuanf@upenn.edu)
     - William La Cava (lacava@upenn.edu)
@@ -26,7 +26,7 @@
 
 """
 """
-API utility functions for Penn-AI
+API utility functions for Aliro
 """
 
 import pandas as pd
@@ -62,7 +62,7 @@ class RECOMMENDER_STATUS(Enum):
     RUNNING = 'running'
 
 class LabApi:
-    """Class for communicating with the PennAI server
+    """Class for communicating with the Aliro server
     """
 
     def __init__(self, api_path, user, api_key, extra_payload, verbose):

ai/knowledgebase_utils.py

@@ -1,8 +1,8 @@
-"""~This file is part of the PennAI library~
+"""~This file is part of the Aliro library~
 
 Copyright (C) 2017 Epistasis Lab, University of Pennsylvania
 
-PennAI is maintained by:
+Aliro is maintained by:
     - Heather Williams (hwilli@upenn.edu)
     - Weixuan Fu (weixuanf@upenn.edu)
     - William La Cava (lacava@upenn.edu)