Merge pull request #1627 from henrykironde/dokr2

Setup Docker registry uploader

.github/workflows/docker-publish.yml

@@ -0,0 +1,140 @@
+name: Docker
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+on:
+  push:
+    # Publish semver tags as releases.
+    tags: [ 'v*.*.*' ]
+  pull_request:
+    branches: [ main ]
+
+env:
+  # Use docker.io for Docker Hub if empty
+  REGISTRY: docker.io
+  # github.repository as <account>/<repo>
+  IMAGE_NAME: ${{ github.repository }}
+
+
+jobs:
+
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    services:
+      mysqldb_retriever:
+        image: mysql:5.7
+        env:
+          MYSQL_USER: travis
+          MYSQL_PASSWORD: Password12!
+          MYSQL_ROOT_PASSWORD: Password12!
+          MYSQL_DATABASE: testdb_retriever
+        ports:
+          - 3306:3306
+        options: >-
+          --health-cmd="mysqladmin ping"
+          --health-interval=10s
+          --health-timeout=5s
+          --health-retries=3
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Postgresql with Postgis
+        uses: huaxk/postgis-action@v1
+        with:
+          postgresql version: '11'
+          postgresql user: 'postgres'
+          postgresql password: 'Password12!'
+          postgresql db: 'testdb_retriever'
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        env:
+          LC_ALL : en_US.UTF-8
+          ENV LANG : en_US.UTF-8
+          ENV LANGUAGE : en_US.UTF-8
+          TZ: America/New_York
+          DEBIAN_FRONTEND: noninteractive
+        run: |
+          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update && sudo apt-get install -y --no-install-recommends apt-utils
+          sudo apt-get install -y --force-yes tzdata
+          sudo apt-get install -y --force-yes build-essential wget git locales locales-all > /dev/null
+          sudo apt-get install -y --force-yes libpq-dev
+          sudo apt-get install libgdal-dev
+          sudo apt-get install gdal-bin
+          export CPLUS_INCLUDE_PATH=/usr/include/gdal
+          export C_INCLUDE_PATH=/usr/include/gdal
+          pip install GDAL==3.2.3 
+          sudo apt-get install -y --force-yes postgis
+          
+      - name: Setup paths and files
+        run : |
+          cd ..
+          chmod 0755 retriever/cli_tools/entrypoint.sh
+          sh retriever/cli_tools/entrypoint.sh
+          echo "export PATH="/usr/bin/python:$PATH"" >> ~/.profile
+          echo "export PYTHONPATH="/usr/bin/python:$PYTHONPATH"" >> ~/.profile
+          echo "export PGPASSFILE="~/.pgpass"" >> ~/.profile
+          chmod 0644 ~/.profile
+      
+      - name: PostGIS check version
+        run : |
+          export PGPASSWORD='Password12!'
+          psql -d testdb_retriever -U postgres -h localhost -p 5432 -c "SELECT PostGIS_version();"
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install flake8 pytest yapf codecov pytest-cov pytest-xdist -U
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      
+      - name: Install retriever
+        run: |
+          pip install -e .
+          export PGPASSFILE="~/.pgpass"
+          chmod 600 ~/.pgpass
+          chmod 600 ~/.my.cnf
+
+      # Login against a Docker registry except on PR
+      # https://github.com/docker/login-action
+      - name: Log into registry ${{ env.REGISTRY }}
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Extract metadata (tags, labels) for Docker
+      # https://github.com/docker/metadata-action
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tag-custom: latest
+
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          file: docker/Dockerfile
+
+

docker/Dockerfile

@@ -1,25 +1,21 @@
-# Download base image ubuntu 18.04
-FROM ubuntu:18.04
+# Download base image ubuntu .04
+FROM osgeo/gdal
 
 MAINTAINER Weecology "https://github.com/weecology/retriever"
 
 # Installing Gdal and configuring it
-RUN add-apt-repository ppa:ubuntugis/ppa &&\
+RUN export CPLUS_INCLUDE_PATH=/usr/include/gdal &&\
+    export C_INCLUDE_PATH=/usr/include/gdal &&\
     apt-get update && apt-get install -y --no-install-recommends apt-utils &&\
     # Manually install tzdata to allow for non-interactive install
     apt-get install -y --force-yes tzdata &&\
     apt-get install -y --force-yes build-essential wget git locales locales-all > /dev/null &&\
     apt-get install -y --force-yes postgresql-client mariadb-client > /dev/null &&\
     apt-get install -y --force-yes libpq-dev &&\
-    apt-get install gdal-bin &&\
-    apt-get install libgdal-dev &&\
-    export CPLUS_INCLUDE_PATH=/usr/include/gdal &&\
-    export C_INCLUDE_PATH=/usr/include/gdal &&\
-    pip install GDAL 
-
-# Installing GDAL
-RUN apt-add-repository ppa:ubuntugis/ubuntugis-unstable &&\
-    apt install -y gdal-bin python-gdal python3-gdal
+    apt-get install -y --force-yes libgdal-dev &&\
+    apt install -y --force-yes  gdal-bin &&\
+    # Installing postgis
+    apt-get install -y --force-yes postgis
 
 # Set encoding
 ENV LC_ALL en_US.UTF-8
@@ -51,10 +47,7 @@ RUN pip install pymysql &&\
     pip install Pillow &&\
     pip install kaggle &&\
     pip install inquirer
-
-# Install Postgis after Python is setup
-RUN apt-get install -y --force-yes postgis
-
+RUN pip install GDAL
 COPY . ./retriever
 RUN chmod 0755 /retriever/cli_tools/entrypoint.sh
 ENTRYPOINT ["/retriever/cli_tools/entrypoint.sh"]