Malvern app updates

PyStationB/environment.yml

@@ -5,4 +5,4 @@ dependencies:
   - python==3.8.3
   - pip==20.1.1
   - pip:
-    - -r requirements_dev.txt
+    - -r requirements_dev.txt

PyStationB/libraries/ABEX/requirements.txt

@@ -6,6 +6,7 @@ gpy==1.10.0
 matplotlib==3.4.2
 pandas==1.3.1
 param==1.11.1
+psutil==5.7.1
 pydantic==1.8.2
 pydoe==0.3.8
 pyyaml==5.4.1

PyStationB/libraries/PyBCKG/setup.py

@@ -20,7 +20,7 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="",
-    packages=["pyBCKG"],
+    packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",
         "Operating System :: OS Independent",

PyStationB/libraries/Utilities/psbutils/misc.py

@@ -70,7 +70,7 @@ def flatten_list(lst: List[List[Any]]) -> List[Any]:  # pragma: no cover
 
 
 def find_root_directory() -> Path:  # pragma: no cover
-    path = Path(__file__).parent
+    path = Path.cwd()
     while True:
         if (path / "libraries").is_dir() and (path / "projects").is_dir():
             return path.resolve()

PyStationB/projects/Malvern/.amlignore

@@ -0,0 +1,46 @@
+*.egg-info/
+*.ipynb
+*.md
+.amlignore
+.coverage
+.coveragerc
+.flake8
+.git
+.gitattributes
+.github
+.gitignore
+.idea
+.mypy.ini
+.mypy_cache/
+.pre-commit-config.yaml
+.pytest_cache/
+.testmondata
+.vscode/
+/additional_requirements*.txt
+/azure-pipelines/
+/mypy.ini
+/mypy_runner.py
+/node_modules/
+/scripts/
+DATA/
+Data/
+LICENSE
+Makefile
+Notebooks/
+README.txt
+Results/
+SC_RESULTS/
+__pycache__/
+abex-results/
+doc/
+docs/
+libraries/StaticCharacterization
+libraries/UniProt
+make.bat
+projects/Barcoder
+projects/CellSignalling
+projects/OXB_Proteomics
+projects/OXB_Transfection
+slow_tests/
+test_outputs/
+tests/

PyStationB/projects/Malvern/.coveragerc

@@ -0,0 +1,13 @@
+[run]
+parallel = true
+omit = 
+    */setup.py, 
+    */tests/*,
+    /simulator/*
+source =
+    api
+
+[report]
+show_missing = true
+precision = 2
+fail_under = 100.00

PyStationB/projects/Malvern/api/.flaskenv → PyStationB/projects/Malvern/.flaskenv

@@ -1,2 +1,2 @@
-FLASK_APP=api/app.py
+FLASK_APP=api
 FLASK_ENV=development

PyStationB/projects/Malvern/README.md

@@ -1,31 +1,29 @@
 ## Getting started
+
 1. Install [Node.js](https://nodejs.org/en/). This will automatically install Node Package Manager (npm) too.
+
 2. To install the dependencies for our app (specified in package.json):
-```cd app```
-```npm install```
 
-## Setting up the backend (Flask api)
-To create the virtual environment:
+`npm install`
 
-```pyStationB/app/api$ python -m venv MalvernEnv```
+## Setting up the conda envrionment
+Run the following command from the Malvern directory:
 
-## To install the packages:
-```pyStationB/app/api$ python -m pip install -r ../requirements_dev.txt```
-```pyStationB/app/api$ python -m pip install ../../libraries/ABEX```
-```pyStationB/app/api$ python -m pip install ../../libraries/Emukit```
+`conda env create -f environment.yml`
 
-## Install pyBCKG git submodule:
-```pyStationB/app$ cd ../ ```
-```pyStationB$ git submodule update --init --recursive``
+## To Activate the conda env:
 
-## To Activate the virtual env:
+`conda activate malvern`
 
-```pyStationB/app$ api\MalvernEnv\Scripts\activate Malvern``
 
 ## Running the app
 
 ### To start the React app
-`app$ npm run start`
+
+`npm run start`
 
 ### To start the Flask API
-`app$ npm run start-api`
+`npm run start-api`
+
+## Connecting to Azure 
+When you first start the app you will be prompted to login. To do this, enter a connection string in the login tab. Follow the [instructions here](https://docs.microsoft.com/en-us/azure/storage/common/storage-account-keys-manage?toc=%2Fazure%2Fstorage%2Fblobs%2Ftoc.json&tabs=azure-portal#view-account-access-keys) to get the connection string for your storage account

PyStationB/projects/Malvern/api/__init__.py

@@ -0,0 +1,11 @@
+# -------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License (MIT). See LICENSE in the repo root for license information.
+# -------------------------------------------------------------------------------------------
+from flask import Flask
+
+app = Flask(__name__)
+app.config["UPLOADS_DIR"] = "./uploads"
+from api import routes  # type: ignore  # noqa: E402
+
+assert routes is not None  # for flake8