Merge branch 'dev' into 'master'

Release/0.0.0: Make deployable

See merge request windenergie-hsr/aerosense/digital-twin/fsi-twins/panel-codes-twine!2

.dockerignore

@@ -0,0 +1,3 @@
+venv/
+.git
+*.egg-info

.gitlab-ci.yml

@@ -0,0 +1,21 @@
+default:
+  image: python:3.6
+
+build_and_test:
+  variables:
+    TEST_PROJECT_NAME: $TEST_PROJECT_NAME
+    GOOGLE_APPLICATION_CREDENTIALS: $GOOGLE_APPLICATION_CREDENTIALS
+  cache:
+    paths:
+      - requirements-dev.txt
+    when: 'on_success'
+    key: 'build_and_test'
+  script:
+    - apt-get update -y && apt-get install -y --fix-missing build-essential gfortran
+    - python3 -m venv test-venv
+    - bash test-venv/bin/activate
+    - git clone https://github.com/daniel-de-vries/xfoil-python.git && pip install ./xfoil-python
+    - pip install -r requirements-dev.txt
+    - coverage run -m unittest
+    - coverage report
+  coverage: '/TOTAL\s+\d+\s+\d+\s+(\d+%)/'

Dockerfile

@@ -0,0 +1,33 @@
+# xfoil-python only seems to work on python 3.6.
+FROM python:3.6-slim-buster
+
+# Allow statements and log messages to immediately appear in the Knative logs on Google Cloud.
+ENV PYTHONUNBUFFERED True
+
+ENV PROJECT_ROOT=/app
+WORKDIR $PROJECT_ROOT
+
+RUN apt-get update -y && apt-get install -y --fix-missing build-essential gfortran git && rm -rf /var/lib/apt/lists/*
+
+# xfoil-python has to be installed locally from a clone (and only seems to work on python 3.6).
+RUN git clone https://github.com/daniel-de-vries/xfoil-python.git && pip install ./xfoil-python
+
+COPY requirements-dev.txt .
+COPY setup.py .
+COPY . .
+
+RUN pip install --upgrade pip && pip install -r requirements-dev.txt
+
+EXPOSE $PORT
+
+ARG _SERVICE_ID
+ENV SERVICE_ID=$_SERVICE_ID
+
+ARG _GUNICORN_WORKERS=1
+ENV _GUNICORN_WORKERS=$_GUNICORN_WORKERS
+
+ARG _GUNICORN_THREADS=8
+ENV _GUNICORN_THREADS=$_GUNICORN_THREADS
+
+# Timeout is set to 0 to disable the timeouts of the workers to allow Cloud Run to handle instance scaling.
+CMD exec gunicorn --bind :$PORT --workers $_GUNICORN_WORKERS --threads $_GUNICORN_THREADS --timeout 0 octue.cloud.deployment.google.cloud_run:app

README.md

@@ -1,107 +1,21 @@
 # panel-code-twine-python
 A simple twine that runs panel codes. This repository is mirrored to Google Cloud Source Repositories.
 
-## Creating a twine
 
-First, think about:
-- what data you want to flow into and out of the app
-- what kinds of datasets (groups of files) the app might need to access
-- what other applicaitons / twins ('children') you need to use
-- what credentials you might need (e.g. if you're accessing a database or a third party API
 
-The **twine** file secifies all these things and more. First, place an empty `twine.json` file in the root directory of the app.
 
-See [https://twined.readthedocs.io](https://twined.readthedocs.io) for everything there is to know about how to define a twine. If you log in to [octue.com](https://www.octue.com/login) you'll find tools to help you build the twine.
+### Building documents manually
 
-*Note: this example app is not up to date with the current version of twined! Follow or comment on [this issue](https://github.com/octue/octue-app-python/issues/1).*
+**If you did need to build the documentation**
 
-
-## First steps in development
+Install `doxgen`. On a mac, that's `brew install doxygen`; other systems may differ.
 
-If you've not developed python applications before, we strongly recommend the following practices:
-
-- Use an Integrated Development Environment (IDE) to help you. We recommend [Pycharm, by Jetbrains](https://www.jetbrains.com/pycharm/) because it's cross-platform (i.e. for Windows, Mac and Linux), very friendly, and there's a free "Community Edition" which should have all the features you need for now.
-- Ensure Python 3.5 or greater is installed. (Mac users: use [pyenv](https://github.com/pyenv/pyenv), windows users could try [pyenv-win](https://github.com/pyenv-win/pyenv-win)) 
-- [Configure a Virtual Environment](https://www.jetbrains.com/help/pycharm/creating-virtual-environment.html) to ensure you always have a consistent python environment and packages installed.
-
-Once you've set yourself up with Python 3.7+, an IDE and an activated virtual environment, you're ready to go:
-
-- PyCharm will usually do this for you, but if not, install the project dependencies (see `requirements.txt`).
-- Set up a directory containing your input data. How to do this is covered below, in 'Data Directories'.
-
-### Running your app (whilst developing)
-
-`>> python app.py`. Simple as that. You can specify a 
-
-
-### Connecting to the octue platform
-
- 1. Log in to [octue.com](www.octue.com), click `applications > create` in the sidebar, and follow the wizard. Simples!
-
-
-## Data directories
-
-Octue uses a strict folder structure, to help separate input, output, and temporary data. The structure looks like this:
+Install sphinx and other requirements for building the docs:
 ```
-my_data_folder
-    |
-    |- input
-    |    |
-    |    |- config.json
-    |    |- manifest.json
-    |    |- <dataset_xx>
-    |    |    |
-    |    |    |- <file_xxx>
-    |    |    |- <file_xxy>
-    |    |    |- <file_xxz>
-    |    |    |- ...
-    |    | 
-    |    |- <dataset_xy>
-    |    |    |
-    |    |    |- <file_xyx>
-    |    |    |- <file_xyy>
-    |    |    |- <file_xyz>
-    |    |    |- ...
-    |    |
-    |    |- ...
-    |
-    |- logs
-    |    |
-    |    |- ...
-    |
-    |- tmp
-    |    |
-    |    |- ...
-    |
-    |- output
-    |    |
-    |    |- ...
+pip install -r docs/requirements.txt
 ```
 
-- Folder **`input`** contains any input datasets (groups of files). Within each dataset - you can simply dump a load of files created by an instrument or supplied by a third party here. These files should never be altered by the application.
-- Folder **`logs`** will contain log files produced while running the application. You shouldn't need to use these, as all output will be shown either in your terminal or on octue online.
-- Folder **`tmp`** you can write any temporary files (e.g. large cached calculations that are reused but don't form part of the results) here.
-- Folder **`output`** all output files should be saved to this directory. Any output files (like figures) produced by octue are saved here too.
-
-- File **``input/manifest.json``** contains a list of all the files in the input directory, with any tags that are applied (see 'generating the manifest file', below)..
-- File **``input/config.json``** contains a list of options and configuration parameters to use when running the application (see 'generating the config file', below).
-
-
-### Generating the config and manifest files
-
-When a user (you, or someone else) launches an application on octue, they fill in a form (which is generated from the twine). That creates a
-`config.json` file automatically. You can download this for local development.
-
-Connecting datasets to the application creates the `manifest.json`, which you can download too.
-
-But, if you're just testing your own application out, its helpful to generate these files yourself.
-
-The `octue_app_python` repository contains a `schema.json` for the example application. 
-Go to [the octue schema playground](https://www.octue.com/schema/playground), and paste the entire contents of 
-`schema.json` into the top left box.
-
-Fill in the form (it's already populated with defaults) and you'll see your **config** change as you do, in the bottom
-right box. This is what gets pasted into `config.json` (see `octue_app_python/example_data/config.json`). 
-
-You can play around with schema in that playground (if you're having trouble, use the excellent 
-[JSON Editor Online](https://jsoneditoronline.org/) to help debug them if you run into trouble.
+Run the build process:
+```
+sphinx-build -b html docs/source docs/build
+```

app.py

@@ -1,5 +1,7 @@
+import os
 import xfoil_module
 
+REPOSITORY_ROOT = os.path.abspath(os.path.dirname(__file__))
 
 def run(analysis):
     """

cloudbuild.yaml

@@ -0,0 +1,47 @@
+steps:
+  - name: gcr.io/cloud-builders/docker
+    args:
+      - build
+      - '--no-cache'
+      - '-t'
+      - '$_GCR_HOSTNAME/$PROJECT_ID/$REPO_NAME/$_SERVICE_NAME:$COMMIT_SHA'
+      -  --build-arg
+      - _SERVICE_ID=$_SERVICE_ID
+      - .
+      - '-f'
+      - Dockerfile
+    id: Build
+  - name: gcr.io/cloud-builders/docker
+    args:
+      - push
+      - '$_GCR_HOSTNAME/$PROJECT_ID/$REPO_NAME/$_SERVICE_NAME:$COMMIT_SHA'
+    id: Push
+  - name: 'gcr.io/google.com/cloudsdktool/cloud-sdk:slim'
+    args:
+      - run
+      - services
+      - update
+      - $_SERVICE_NAME
+      - '--platform=managed'
+      - '--image=$_GCR_HOSTNAME/$PROJECT_ID/$REPO_NAME/$_SERVICE_NAME:$COMMIT_SHA'
+      - >-
+        --labels=managed-by=gcp-cloud-build-deploy-cloud-run,commit-sha=$COMMIT_SHA,gcb-build-id=$BUILD_ID,gcb-trigger-id=$_TRIGGER_ID,$_LABELS
+      - '--region=$_DEPLOY_REGION'
+      - '--quiet'
+    id: Deploy
+    entrypoint: gcloud
+images:
+  - '$_GCR_HOSTNAME/$PROJECT_ID/$REPO_NAME/$_SERVICE_NAME:$COMMIT_SHA'
+options:
+  substitutionOption: ALLOW_LOOSE
+substitutions:
+  _GCR_HOSTNAME: eu.gcr.io
+  _PLATFORM: managed
+  _SERVICE_NAME: panel-codes-twine
+  _LABELS: gcb-trigger-id=c11b2517-2b8b-435b-9a30-8213e322851b
+  _TRIGGER_ID: c11b2517-2b8b-435b-9a30-8213e322851b
+  _DEPLOY_REGION: europe-north1
+tags:
+  - gcp-cloud-build-deploy-cloud-run
+  - gcp-cloud-build-deploy-cloud-run-managed
+  - panel-codes-twine

data/input/manifest.json

@@ -1,29 +1,32 @@
 {
   "id": "8ead7669-8162-4f64-8cd5-4abe92509e17",
+  "keys": {"aerofoil_shape_data": 0},
   "type" : "dataset",
   "datasets": [
     {
       "id": "7ead7669-8162-4f64-8cd5-4abe92509e18",
       "name": "aerofoil_shape_data",
-      "tags": "naca_0012",
+      "tags": ["series:naca"],
       "files": [
         {
-          "path": "input/datasets/aerofoil_shape_file/naca_2412.dat",
+          "path": "naca_2412.dat",
           "cluster": 0,
           "sequence": 0,
           "extension": "dat",
-          "tags": "",
+          "tags": ["name:naca-2412"],
+          "timestamp": 0,
           "id": "abff07bc-7c19-4ed5-be6d-a6546eae8f86",
           "last_modified": "2019-02-28T22:40:30.533005Z",
           "name": "naca_2412.dat",
           "size_bytes": 59684813
         },
         {
-          "path": "input/datasets/aerofoil_shape_file/naca_0012.dat",
+          "path": "naca_0012.dat",
           "cluster": 0,
           "sequence": 1,
           "extension": "dat",
-          "tags": "naca_0012",
+          "tags": ["name:naca-0012"],
+          "timestamp": 0,
           "id": "abff07bc-7c19-4ed5-be6d-a6546eae8f87",
           "last_modified": "2019-02-28T22:40:30.533005Z",
           "name": "naca_0012.dat"

data/input/values.json

@@ -1,4 +1,5 @@
 {
+  "airfoil_name": "naca-0012",
   "alpha_range": [0, 6, 1],
   "inflow_speed": 1,
   "kinematic_viscosity": 1e-5,

deployment_configuration.json

@@ -0,0 +1,8 @@
+{
+    "app_dir": ".",
+    "twine": "twine.json",
+    "configuration_values": {
+        "analysis_program": "xfoil",
+        "max_iterations": 20
+    }
+}

docs/.gitignore

@@ -0,0 +1,4 @@
+doctrees
+html
+source/doxyoutput*
+source/library_api*

docs/requirements.txt

@@ -0,0 +1,6 @@
+# Required by the python script for building documentation
+Sphinx>=2,<3
+sphinx-rtd-theme==0.5.0
+sphinx-tabs==1.2.1
+octue==0.1.12
+pyserial==3.5

docs/source/api.rst

@@ -0,0 +1,14 @@
+.. _api:
+
+===
+API
+===
+
+
+.. _api_xfoil:
+
+X-Foil Module
+=============
+
+.. automodule:: xfoil_module.routines
+    :members: