Merge pull request #62 from ecmwf/consolidated

merge version 0.9.0

.dockerignore

@@ -1,3 +1,11 @@
 .git*
+.dockerignore
+.env
+.s3env
+.travis.yml
+.vscode
 hooks*
 Makefile
+docker-compose.yml
+venv*
+

.env

@@ -0,0 +1,28 @@
+#
+# local development server configuration
+#
+
+# the path inside the docker container that stores the GRIB and NetCDF data
+SKINNYWMS_DATA_PATH=/data/
+
+# the host ip the server should listen on
+# set to 0.0.0.0 to listen on all ips
+SKINNYWMS_HOST=0.0.0.0
+
+# the http port the flask server listens on
+SKINNYWMS_PORT=5000
+
+# enable/disable layer dimension grouping (by elevation)
+SKINNYWMS_ENABLE_DIMENSION_GROUPING=0
+
+# flask env to enable auto reload on code changes
+FLASK_ENV=development
+
+# # Configure Magics
+#MAGPLUS_HOME=/usr/local/lib/python3.6/site-packages/ecmwflibs
+#MAGICS_STYLE_PATH=/usr/local/lib/python3.6/site-packages/ecmwflibs/share/magics/styles/ecmwf
+MAGICS_STYLES_DEBUG=on
+
+MAGPLUS_DEBUG=on
+MAGPLUS_DEV=on
+MAGICS_QUIET=

.github/workflows/docker-latest.yml

@@ -0,0 +1,49 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Publish Latest Docker
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the develop branch
+  push:
+    branches: [ develop ]
+#   pull_request:
+#     branches: [ develop ]
+
+  # 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:
+    # 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
+      - name: Checkout Repo
+        uses: actions/checkout@v2
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: ./
+          file: ./Dockerfile
+          push: true
+          tags: ecmwf/skinnywms:latest
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/docker-release.yml

@@ -0,0 +1,54 @@
+# This is a basic workflow to help you get started with Actions
+
+name: Publish Tagged Images to DockerHub
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the develop branch
+  push:
+    tags: 
+      - '*'
+#   pull_request:
+#     branches: [ develop ]
+
+  # 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:
+    # 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 $GITHUB_WORKSPACE, so your job can access it
+      - name: Checkout Repo
+        uses: actions/checkout@v2
+
+      - name: Set tag
+        id: vars
+        run: echo ::set-output name=tag::${GITHUB_REF#refs/*/}
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: ./
+          file: ./Dockerfile
+          push: true
+          tags: ecmwf/skinnywms:${{ steps.vars.outputs.tag }}
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.gitignore

@@ -6,3 +6,6 @@ __pycache__/
 meta.xml
 *.pyc
 *&*
+venv/
+.venv/
+skinnywms/testdata/*/*

Dockerfile

@@ -1,26 +1,52 @@
 # Build image
-# Use slim python 3 + Magics image as base
-ARG MAGICS_IMAGE=ecmwf/magics:4.2.4
-FROM ${MAGICS_IMAGE}
+# Use slim python 3 image as base
+ARG PYTHON_IMAGE=python:3.8-slim-buster
+FROM ${PYTHON_IMAGE}
 
+# Install UWSGI
+RUN set -ex \
+    && apt-get update \
+    && apt-get install -y --no-install-recommends \
+        gcc \
+        build-essential \
+        libglib2.0 \
+    && rm -rf /var/lib/apt/lists/* \
+    && pip install uwsgi \
+    && apt-get purge -y --auto-remove \
+        gcc \
+        build-essential
+
+# Install skinnywms
 RUN set -eux \
     && mkdir -p /app/
 
 COPY . /app/skinnywms
-RUN pip install /app/skinnywms --no-dependencies
+RUN pip install /app/skinnywms
 
-# Install Python run-time dependencies.
-COPY requirements.txt /root/
-RUN set -ex \
-    && pip install -r /root/requirements.txt
+ENV SKINNYWMS_HOST=0.0.0.0
+ENV SKINNYWMS_PORT=5000
+ENV SKINNYWMS_MOUNT=/
+ENV SKINNYWMS_DATA_PATH=
+ENV SKINNYWMS_UWSGI_WORKERS=4
+
+#USER nobody
+
+# UWSGI entrypoint
+CMD uwsgi \
+        --http ${SKINNYWMS_HOST}:${SKINNYWMS_PORT} \
+        --master \
+        --process ${SKINNYWMS_UWSGI_WORKERS} \
+        --mount ${SKINNYWMS_MOUNT}=skinnywms.wmssvr:application \
+        --manage-script-name \
+        --uid nobody
 
 # demo application will listen at http://0.0.0.0:5000
 EXPOSE 5000/tcp
 
 # start demo
 # add option --path <directory with grib files>
 # to look for grib files in specific directory
-CMD python /app/skinnywms/demo.py --host='0.0.0.0' --port=5000
+###CMD python /app/skinnywms/demo.py --host='0.0.0.0' --port=5000
 
 # METADATA
 # Build-time metadata as defined at http://label-schema.org

README.md

@@ -6,6 +6,7 @@ The principle is simple: skinny will browse the directory, or the single file pa
 [![Docker Build Status](https://img.shields.io/docker/cloud/build/ecmwf/skinnywms.svg)](https://hub.docker.com/r/ecmwf/skinnywms)
 [![Docker Pulls](https://img.shields.io/docker/pulls/ecmwf/skinnywms)](https://hub.docker.com/r/ecmwf/skinnywms)[![PyPI version](https://badge.fury.io/py/skinnywms.svg)](https://badge.fury.io/py/skinnywms) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/skinnywms/badges/version.svg)](https://anaconda.org/conda-forge/skinnywms) [![Anaconda-Server Badge](https://anaconda.org/conda-forge/skinnywms/badges/downloads.svg)](https://anaconda.org/conda-forge/skinnywms)
 
+
 Features:
 ---------
 SkinnyWMS implements 3 of the WMS endpoints:
@@ -36,13 +37,41 @@ skinny-wms --path /path/to/mydata
 ```bash
 uwsgi --http localhost:5000 --master --process 20 --mount /=skinnywms.wmssvr:application --env SKINNYWMS_DATA_PATH=/path/to/mydata
 ```
+
+
 Run using Docker
 ----------------
 
+By default the docker image will start the application using uwsgi and will load and display some demo data.
+
+* Run the demo:
+```bash
+docker run --rm -p 5000:5000 -it ecmwf/skinnywms 
+```
+Now you can try the leaflet demo at http://localhost:5000/
+
+* Run using data on your machine:
+```bash
+docker run --rm -p 5000:5000 -it \
+    --volume=/path/to/my/data:/path/inside/the/container \
+    --env SKINNYWMS_DATA_PATH=/path/inside/the/container \
+      ecmwf/skinnywms
+```
+Now you can access the leaflet demo with your data at http://localhost:5000/
+
+* Configure different options by setting environment variables accordingly:
 ```bash
- docker run --rm -p 5000:5000 -i -t ecmwf/skinnywms 
- ```
- Now you can try the leaflet demo at http://localhost:5000/
+docker run --rm -p 5000:5000 -it \
+    --volume=/path/to/my/data:/path/inside/the/container \
+    --env SKINNYWMS_DATA_PATH=/path/inside/the/container \
+    --env SKINNYWMS_HOST=0.0.0.0 \
+    --env SKINNYWMS_PORT=5000 \
+    --env SKINNYWMS_MOUNT=/mymodel/ \
+    --env SKINNYWMS_UWSGI_WORKERS=4 \
+    --env SKINNYWMS_ENABLE_DIMENSION_GROUPING=1 \
+      ecmwf/skinnywms
+```
+Now you can access the ```GetCapabilities`` document for your data at http://localhost:5000/mymodel/wms?request=GetCapabilities
 
 
 Installation
@@ -67,6 +96,13 @@ Limitations:
 ------------
 - SkinnyWMS will perform better on well formatted and documented NetCDF and GRIB.
 
+- grib fields containing corresponding wind components u,v need to be placed together in a single grib file in order to be displayed as vectors/wind barbs in SkinnyWMS. You can combine multiple grib files into a single file using ecCodes ``grib_copy`` (included in the docker image), e.g.:
+```bash
+grib_copy input_wind_u_component.grb2 input_wind_v_component.grib2 output_wind_u_v_combined.grb2
+```
+
+- The time and elevation dimension implementations follow [OGC Met Ocean DWG WMS 1.3 Best Practice for using Web Map Services (WMS) with Time-Dependent or Elevation-Dependent Data](https://external.ogc.org/twiki_public/MetOceanDWG/MetOceanWMSBPOnGoingDrafts). To enable dimension grouping (disabled by default) set the environment variable ``SKINNYWMS_ENABLE_DIMENSION_GROUPING=1``
+
 - development stage: **Alpha**,
 
 
@@ -95,6 +131,14 @@ Magics is available on github https://github.com/ecmwf/magics
 Note that *Magics* support for the Windows operating system is experimental.
 
 
+Start up a local development environment (Docker)
+-----------------------------------------
+
+Make sure you have ``Docker`` and ``docker-compose`` installed. Then run:
+```bash
+docker-compose up
+```
+This will build a dev image and start up a local flask development server (with automatic reload on code changes) at http://localhost:5000 based on the configuration stored in [docker-compose.yml](./docker-compose.yml) and [.env](./.env) and by default try to load all GRIB and NetCDF data stored in [skinnywms/testdata](./skinnywms/testdata).
 
 
 Contributing

docker-compose.yml

@@ -0,0 +1,31 @@
+version: '3.7'
+
+services:
+  skinnywms:
+    build:
+      context: ./
+      dockerfile: Dockerfile
+      args:
+        - PYTHON_IMAGE=python:3.8-slim-buster
+        - http_proxy
+        - https_proxy
+        - no_proxy
+    volumes:
+      - '.:/app/skinnywms:ro'
+      - './skinnywms/testdata:/data:ro'
+    # override the default command to run flask app without uwgsi
+    # to make use of automatic reload on code changes for development purposes
+    command: 
+      - bash 
+      - -c
+      - 'python /app/skinnywms/demo.py --host=${SKINNYWMS_HOST} --port=${SKINNYWMS_PORT} --path=${SKINNYWMS_DATA_PATH}'
+    restart: always
+    ports:
+      - 5000:5000
+    env_file:
+      - ./.env
+    # environment: 
+    #   - SKINNYWMS_DATA_PATH=${SKINNYWMS_DATA_PATH}
+    #   - SKINNYWMS_HOST=${SKINNYWMS_HOST}
+    #   - SKINNYWMS_PORT=${SKINNYWMS_PORT}
+    #   - FLASK_ENV=${FLASK_ENV}