Merge pull request #1 from jennydaman/master

Use Github Actions

.github/workflows/ci.yml

@@ -0,0 +1,156 @@
+# Automatically build multi-architectural tagged container images and push them to DockerHub
+# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds
+#
+# - targeted platforms: x86_64, PowerPC64, ARM64
+# - master is built as fnndsc/pl-lungct:latest
+# - tagged commits are built as fnndsc/pl-lungct:<tag>
+# - tagged commits are also uploaded to chrisstore.co
+#
+# In order to use this workflow, see
+# https://github.com/FNNDSC/cookiecutter-chrisapp/wiki/Automatic-Builds#steps-to-enable
+
+name: ci
+
+on:
+  push:
+    # we have to guess what the name of the default branch is
+    branches: [ master, main, trunk ]
+    tags: [ '**' ]
+  pull_request:
+    branches: [ master, main, trunk ]
+  release:
+    types: [ created ]
+
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v2
+      - name: build
+        run: docker build -t "${GITHUB_REPOSITORY,,}" .
+      - name: nose tests
+        run: docker run "${GITHUB_REPOSITORY,,}" nosetests
+
+  publish:
+    if: github.event_name == 'push' || github.event_name == 'release'
+    runs-on: ubuntu-20.04
+
+    # we want to both push the build to DockerHub, but also
+    # keep a local copy so that we can run
+    #
+    #     docker run fnndsc/pl-lungct lungct --json > App.json
+    #
+    # buildx currently does not support multiple output locations,
+    # neither can multi-architectural builds be loaded into docker.
+    # Here we use a local registry to cache the build.
+    services:
+      registry:
+        image: registry:2
+        ports:
+          - 5000:5000
+
+    steps:
+      - name: Get git tag
+        id: git_info
+        if: startsWith(github.ref, 'refs/tags/')
+        run: echo "::set-output name=tag::${GITHUB_REF##*/}"
+      - name: Decide image tag name
+        id: determine
+        env:
+          git_tag: ${{ steps.git_info.outputs.tag }}
+        run: |
+          repo="${GITHUB_REPOSITORY,,}"  # to lower case
+          # if build triggered by tag, use tag name
+          tag="${git_tag:-latest}"
+          dock_image=$repo:$tag
+          echo $dock_image
+          echo "::set-output name=dock_image::$dock_image"
+          echo "::set-output name=repo::$repo"
+
+      - uses: actions/checkout@v2
+
+      # QEMU is for emulating non-x86_64 platforms
+      - uses: docker/setup-qemu-action@v1
+      # buildx is the next-generation docker image builder
+      - uses: docker/setup-buildx-action@v1
+        with:
+          driver-opts: network=host
+      # save some time during rebuilds
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Login to DockerHub
+        id: dockerhub_login
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v2
+        id: docker_build
+        with:
+          context: .
+          file: ./Dockerfile
+          tags: |
+            ${{ steps.determine.outputs.dock_image }}
+            localhost:5000/${{ steps.determine.outputs.dock_image }}
+          platforms: linux/amd64,linux/ppc64le,linux/arm64
+          push: true
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+
+      - name: Get plugin meta
+        id: pluginmeta
+        run: |
+          repo=${{ steps.determine.outputs.repo }}
+          dock_image=${{ steps.determine.outputs.dock_image }}
+          docker pull localhost:5000/$dock_image
+          docker tag localhost:5000/$dock_image $dock_image
+          script=$(docker inspect --format '{{ (index .Config.Cmd 0) }}' $dock_image)
+          json="$(docker run --rm $dock_image $script --json)"
+          jq <<< "$json"  # pretty print in log
+
+          echo "::set-output name=json::$json"
+          echo "::set-output name=title::$(jq -r '.title' <<< "$json")"
+
+      - name: Update DockerHub description
+        uses: peter-evans/dockerhub-description@v2
+        continue-on-error: true  # it is not crucial that this works
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          short-description: ${{ steps.pluginmeta.outputs.title }}
+          readme-filepath: ./README.rst
+          repository: ${{ steps.determine.outputs.repo }}
+
+      - name: Upload to ChRIS Store
+        if: "!endsWith(steps.determine.outputs.dock_image, ':latest')"
+        run: |
+          repo=${{ steps.determine.outputs.repo }}
+          dock_image=${{ steps.determine.outputs.dock_image }}
+          descriptor_file=$(mktemp --suffix .json)
+          cat > $descriptor_file <<< "${{ steps.pluginmeta.outputs.json }}"
+          res=$(
+            curl -s -u "${{ secrets.CHRIS_STORE_USER }}" "https://chrisstore.co/api/v1/plugins/" \
+              -F "name=$(sed 's/^.*\///' <<< $repo)" \
+              -F "dock_image=$dock_image"  \
+              -F "descriptor_file=@$descriptor_file" \
+              -F "public_repo=https://github.com/${{ github.repository }}"
+          )
+          success=$?
+          if [ "$success" = "0" ]; then
+            href="$(jq -r '.collection.items[0].href' <<< "$res")"
+            echo $href
+            echo "::set-output name=pluginurl::$href"
+          else
+            echo "::error ::Failed upload to ChRIS Store"
+            echo "$res"
+            exit $success
+          fi
+

Dockerfile

@@ -1,50 +1,12 @@
-# Docker file for lungct ChRIS plugin app
-#
-# Build with
-#
-#   docker build -t <name> .
-#
-# For example if building a local version, you could do:
-#
-#   docker build --build-arg UID=$UID -t local/pl-lungct .
-#
-# In the case of a proxy (located at 192.168.13.14:3128), do:
-#
-#    export PROXY=http://192.168.13.14:3128
-#    docker build --build-arg http_proxy=$PROXY --build-arg UID=$UID -t local/pl-lungct .
-#
-# To run an interactive shell inside this container, do:
-#
-#   docker run -ti --entrypoint /bin/bash local/pl-lungct
-#
-# To pass an env var HOST_IP to container, do:
-#
-#   docker run -ti -e HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}') --entrypoint /bin/bash local/pl-lungct
-#
-# To debug from within a container:
-#
-#   docker run -ti -v $(pwd)/lungct:/usr/local/lib/python3.8/dist-packages/lungct -v $(pwd)/out:/outgoing local/pl-lungct lungct /outgoing
-#
-
-FROM fnndsc/ubuntu-python3:latest
+FROM python:3.9.1-slim-buster
 LABEL MAINTAINER="dev@babymri.org"
 
-# Pass a UID on build command line (see above) to set internal UID
-ARG UID=1001
-ENV UID=$UID DEBIAN_FRONTEND=noninteractive
-
 WORKDIR /usr/local/src
-COPY . .
-RUN pip --disable-pip-version-check install .                   \
-    && useradd -u $UID -ms /bin/bash localuser                  \
-    && apt update                                               \
-    && apt-get install -y sudo                                  \
-    && echo "localuser:localuser" | chpasswd                    \
-    && addgroup localuser sudo                                  \
-    && echo "localuser ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 
-# Start as user localuser
-# USER localuser
+COPY requirements.txt .
+RUN ["pip", "install", "-r", "requirements.txt"]
+
+COPY . .
+RUN ["pip", "install", "."]
 
-WORKDIR /usr/local/bin
 CMD ["lungct", "--help"]

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2017-2020 FNNDSC / BCH
+Copyright (c) 2017-2021 FNNDSC / BCH
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -1,11 +1,15 @@
 pl-lungct
 ================================
 
-.. image:: https://travis-ci.org/FNNDSC/lungct.svg?branch=master
-    :target: https://travis-ci.org/FNNDSC/lungct
+.. image:: https://img.shields.io/docker/v/fnndsc/pl-lungct?sort=semver
+    :target: https://hub.docker.com/r/fnndsc/pl-lungct
+
+.. image:: https://img.shields.io/github/license/fnndsc/pl-lungct
+    :target: https://github.com/FNNDSC/pl-lungct/blob/master/LICENSE
+
+.. image:: https://github.com/FNNDSC/pl-lungct/workflows/ci/badge.svg
+    :target: https://github.com/FNNDSC/pl-lungct/actions
 
-.. image:: https://img.shields.io/badge/python-3.8%2B-blue.svg
-    :target: https://github.com/FNNDSC/pl-lungCT/blob/master/setup.py
 
 .. contents:: Table of Contents
 

lungct/lungct.py

@@ -16,7 +16,6 @@
 from    os.path                 import abspath, basename, isdir
 from    distutils.dir_util      import copy_tree
 import  shutil
-import  pudb
 import  sys
 import  time
 import  glob
@@ -175,13 +174,11 @@ def run(self, options):
         print(Gstr_title)
         print('Version: %s' % self.get_version())
 
-        if len(options.dir):
-            print("Copying tree %s..." % options.dir)
-            copy_tree(options.dir, options.outputdir)
-            sys.exit(0)
-        else:
-            print("No directory specified and no copy performed.")
-            sys.exit(1)
+        if not isdir(options.dir):
+            raise ValueError("No directory specified and no copy performed.")
+
+        print("Copying tree %s..." % options.dir)
+        copy_tree(options.dir, options.outputdir)
 
     def show_man_page(self):
         """

requirements.txt

@@ -0,0 +1,2 @@
+chrisapp~=3.0.0rc2
+nose~=1.3.7

setup.py

@@ -13,7 +13,7 @@
     author_email     = 'dev@babyMRI.org',
     url              = 'http://wiki',
     packages         = ['lungct', 'data'],
-    install_requires = ['chrisapp~=2.0.0', 'pudb'],
+    install_requires = ['chrisapp'],
     test_suite       = 'nose.collector',
     tests_require    = ['nose'],
     license          = 'MIT',