Final cleanup for packaging

README.md

@@ -1,17 +1,21 @@
 
-<img src="https://github.com/IKNL/guidelines/blob/master/resources/logos/vantage6.png?raw=true" width=200 align="right">
+<img src="https://github.com/IKNL/guidelines/blob/master/resources/logos/vantage6.png?raw=true" width=180 align="right">
 
+# Vantage6
+> A federated learning solution
+<!--
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+-->
+[![PyPI version](https://badge.fury.io/py/vantage6-common.svg)](https://badge.fury.io/py/vantage6-common)
+This repository is part of the vantage6 solution. Vantage6 allowes to execute computations on federated datasets. This repository contains a common classes, methods, constants that are shared between the packages.
 
-# Introduction
+## :pray: Motivation
 The growing complexity of cancer diagnosis and treatment requires data sets that are larger than currently available in a single hospital or even in cancer registries. However, sharing patient data is difficult due to patient privacy and data protection needs. Federated learning technology has the potential to overcome these limitations. In this approach, organizations can collaborate by exchanging aggregated data and/or statistics while keeping the underlying data safely on site and undisclosed. This repository contains software (and instructions) to setup a federated learning infrastructure.
 
 For an overview of the architecture and information on how to use the infrastructure, please see [https://vantage6.ai](https://vantage6.ai). For documentation, please see [https://docs.distributedlearning.ai/](https://docs.distributedlearning.ai/).
 
 ## Installation
-See the [documentation](https://docs.distributedlearning.ai/) for detailed instructions on how to install the server and nodes. 
-
+See the [documentation](https://docs.distributedlearning.ai/) for detailed instructions on how to install the server and nodes.

requirements.txt

@@ -0,0 +1,9 @@
+appdirs==1.4.3
+certifi==2020.4.5.1
+click==7.1.1
+colorama==0.4.3
+contextlib2==0.5.5
+PyYAML==5.3.1
+schema==0.7.1
+termcolor==1.1.0
+wincertstore==0.2

setup.py

@@ -20,20 +20,20 @@
     description='Vantage6 common',
     long_description=long_description,
     long_description_content_type='text/markdown',
-    url='https://github.com/IKNL/vantage6-client',
+    url='https://github.com/IKNL/vantage6-common',
     packages=find_namespace_packages(),
     python_requires='>=3.6',
     install_requires=[
         'appdirs==1.4.3',
-        'PyYAML==5.3.1',
         'schema==0.7.1',
         'termcolor==1.1.0',
+        'colorama==0.4.3',
         'click==7.1.1',
-        'colorama==0.4.3'
+        'PyYAML==5.3.1'
     ],
     package_data={
-        'vantage6': [
+        'vantage6.common': [
             'common/VERSION'
         ],
     }
-)
+)

vantage6/common/__init__.py

@@ -9,6 +9,7 @@
 # init colorstuff
 init()
 
+
 def logger_name(special__name__):
     log_name = special__name__.split('.')[-1]
     if len(log_name) > 14:
@@ -58,5 +59,6 @@ def warning(msg):
 def error(msg):
     echo(msg, "error")
 
+
 def debug(msg):
     echo(msg, "debug")

vantage6/common/colors.py

@@ -51,6 +51,8 @@
 # THE SOFTWARE.
 
 import logging
+import platform
+
 
 class _AnsiColorStreamHandler(logging.StreamHandler):
     DEFAULT = '\x1b[0m'
@@ -143,8 +145,8 @@ def emit(self, record):
         self._set_color(self.FOREGROUND_WHITE)
 
 # select ColorStreamHandler based on platform
-import platform
+
 if platform.system() == 'Windows':
     ColorStreamHandler = _WinColorStreamHandler
 else:
-    ColorStreamHandler = _AnsiColorStreamHandler
+    ColorStreamHandler = _AnsiColorStreamHandler

vantage6/common/configuration_manager.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 from schema import Schema
 
+
 class Configuration(collections.UserDict):
     """Base to contains a single configuration."""
 
@@ -16,7 +17,10 @@ def __setitem__(self, key, value):
         """ Validation of a single item when put
         """
         # assert key in self.VALIDATORS.keys(), "Invalid Key!"
-        schema = Schema(self.VALIDATORS.get(key,lambda x: True), ignore_extra_keys=True)
+        schema = Schema(
+            self.VALIDATORS.get(key, lambda x: True),
+            ignore_extra_keys=True
+        )
         assert schema.is_valid(value), f"Invalid Value! {value} for {schema}"
         super().__setitem__(key, value)
 
@@ -28,7 +32,8 @@ def __getitem__(self, key):
 
     @property
     def is_valid(self):
-        return Schema(self.VALIDATORS, ignore_extra_keys=True).is_valid(self.data)
+        schema = Schema(self.VALIDATORS, ignore_extra_keys=True)
+        return schema.is_valid(self.data)
 
 
 class ConfigurationManager(object):
@@ -63,7 +68,7 @@ def __init__(self, conf_class=Configuration, name=None):
         self.name = name
         self.conf_class = conf_class
 
-    def put(self, env:str, config: dict):
+    def put(self, env: str, config: dict):
         assert env in self.ENVS
         configuration = self.conf_class(config)
         # only set valid configs
@@ -73,19 +78,19 @@ def put(self, env:str, config: dict):
         #      print(f"config={config}")
         #      print(self.conf_class)
 
-    def get(self, env:str):
+    def get(self, env: str):
         assert env in self.ENVS
         return self.__getattribute__(env)
 
     @property
     def is_empty(self):
-        return not (self.application or self.prod or self.acc \
-            or self.test or self.dev)
+        return not (self.application or self.prod or self.acc
+                    or self.test or self.dev)
 
     @property
     def environments(self):
-        return {"prod":self.prod, "acc":self.acc, "test":self.test,
-            "dev":self.dev, "application": self.application}
+        return {"prod": self.prod, "acc": self.acc, "test": self.test,
+                "dev": self.dev, "application": self.application}
 
     @property
     def has_application(self):
@@ -102,9 +107,9 @@ def available_environments(self):
     def _get_environment_from_dict(self, d, e):
         assert e in self.ENVS
         if e == "application":
-            return d.get("application",{})
+            return d.get("application", {})
         else:
-            return d.get("environments",{}).get(e,{})
+            return d.get("environments", {}).get(e, {})
 
     def load(self, path):
         with open(str(path), 'r') as f:
@@ -121,12 +126,14 @@ def from_file(cls, path, conf_class=Configuration):
         conf.load(path)
         return conf
 
-
     def save(self, path):
 
         config = {"application": dict(self.application), "environments": {
-            "prod": dict(self.prod), "acc": dict(self.acc), "test": dict(self.test),
-            "dev": dict(self.dev)}}
+            "prod": dict(self.prod),
+            "acc": dict(self.acc),
+            "test": dict(self.test),
+            "dev": dict(self.dev)}
+        }
 
         Path(path).parent.mkdir(parents=True, exist_ok=True)
         with open(path, 'w') as f:

vantage6/common/globals.py

@@ -15,4 +15,4 @@
 PACAKAGE_FOLDER = Path(__file__).parent.parent.parent
 
 with open(Path(PACAKAGE_FOLDER) / APPNAME / "common" / "VERSION") as f:
-    VERSION = f.read()
+    VERSION = f.read()

vantage6/common/utest.py

@@ -89,8 +89,8 @@ class TestRunner(unittest.TextTestRunner):
 
     def __init__(self, log, stream=sys.stderr, descriptions=True, verbosity=1,
                  failfast=False, buffer=False, resultclass=None):
-        super(TestRunner, self).__init__(stream, descriptions, verbosity, failfast,
-                                         buffer, resultclass)
+        super(TestRunner, self).__init__(stream, descriptions, verbosity,
+                                         failfast, buffer, resultclass)
         self.log = log
 
     def _makeResult(self):
@@ -112,7 +112,7 @@ def find_tests(path=None):
     # Find test cases
     if path is None:
         path = os.path.abspath(os.path.dirname(__file__))
-    
+
     loader = unittest.TestLoader()
     suites = loader.discover(path)