vantage6 5.0.0a26__py3-none-any.whl → 5.0.0a29__py3-none-any.whl

tests_cli/test_server_cli.py

@@ -1,18 +1,19 @@
 import unittest
-
-from unittest.mock import MagicMock, patch
 from pathlib import Path
+from unittest.mock import MagicMock, patch
+
 from click.testing import CliRunner
 
 from vantage6.common.globals import APPNAME, InstanceType
+
 from vantage6.cli.common.utils import attach_logs
-from vantage6.cli.server.start import cli_server_start
-from vantage6.cli.server.list import cli_server_configuration_list
+from vantage6.cli.server.attach import cli_server_attach
 from vantage6.cli.server.files import cli_server_files
 from vantage6.cli.server.import_ import cli_server_import
+from vantage6.cli.server.list import cli_server_configuration_list
 from vantage6.cli.server.new import cli_server_new
+from vantage6.cli.server.start import cli_server_start
 from vantage6.cli.server.stop import cli_server_stop
-from vantage6.cli.server.attach import cli_server_attach
 
 
 class ServerCLITest(unittest.TestCase):
@@ -133,7 +134,7 @@ class ServerCLITest(unittest.TestCase):
         """Stop server without errors."""
 
         container1 = MagicMock()
-        container1.name = f"{APPNAME}-iknl-system-{InstanceType.SERVER.value}"
+        container1.name = f"{APPNAME}-iknl-system-{InstanceType.SERVER}"
         containers.containers.list.return_value = [container1]
 
         runner = CliRunner()

tests_cli/test_wizard.py

@@ -1,15 +1,15 @@
 import unittest
-
 from pathlib import Path
-from unittest.mock import patch, MagicMock
+from unittest.mock import MagicMock, patch
+
+from vantage6.common.globals import InstanceType, NodePolicy
 
 from vantage6.cli.configuration_wizard import (
-    node_configuration_questionaire,
-    server_configuration_questionaire,
     configuration_wizard,
+    node_configuration_questionaire,
     select_configuration_questionaire,
+    server_configuration_questionaire,
 )
-from vantage6.common.globals import InstanceType, NodePolicy
 
 module_path = "vantage6.cli.configuration_wizard"
 
@@ -70,8 +70,8 @@ class WizardTest(unittest.TestCase):
         for key in keys:
             self.assertIn(key, config)
         nested_keys = [
-            ["policies", NodePolicy.ALLOWED_ALGORITHMS],
-            ["policies", NodePolicy.ALLOWED_ALGORITHM_STORES],
+            ["policies", NodePolicy.ALLOWED_ALGORITHMS.value],
+            ["policies", NodePolicy.ALLOWED_ALGORITHM_STORES.value],
         ]
         for nesting in nested_keys:
             current_config = config

vantage6/cli/__build__

@@ -1 +1 @@
-26
+29

vantage6/cli/algorithm/generate_algorithm_json.py

@@ -1,27 +1,27 @@
-import os
-import sys
 import importlib
 import inspect
 import json
-
-from enum import Enum
+import os
+import sys
 from inspect import getmembers, isfunction, ismodule, signature
 from pathlib import Path
 from types import ModuleType, UnionType
 from typing import Any, OrderedDict
 
 import click
-import questionary as q
 import pandas as pd
+import questionary as q
 
-from vantage6.algorithm.client import AlgorithmClient
-from vantage6.algorithm.tools import DecoratorStepType
 from vantage6.common import error, info, warning
-from vantage6.common.enum import AlgorithmArgumentType, AlgorithmStepType
 from vantage6.common.algorithm_function import (
     get_vantage6_decorator_type,
     is_vantage6_algorithm_func,
 )
+from vantage6.common.enum import AlgorithmArgumentType, AlgorithmStepType, StrEnumBase
+
+from vantage6.algorithm.tools import DecoratorStepType
+
+from vantage6.algorithm.client import AlgorithmClient
 from vantage6.algorithm.preprocessing.algorithm_json_data import (
     PREPROCESSING_FUNCTIONS_JSON_DATA,
 )
@@ -54,7 +54,7 @@ class MergePreference:
         cls._prefer_existing = None
 
 
-class FunctionArgumentType(Enum):
+class FunctionArgumentType(StrEnumBase):
     """Type of the function argument"""
 
     PARAMETER = "parameter"
@@ -80,7 +80,7 @@ class Function:
             "display_name": self._pretty_print_name(self.name),
             "standalone": True,
             "description": self._extract_headline_of_docstring(),
-            "step_type": self.step_type,
+            "step_type": self.step_type.value if self.step_type else None,
             "ui_visualizations": [],
             "arguments": [],
             "databases": [],
@@ -91,7 +91,7 @@ class Function:
         # if the function is a data extraction function, the first argument is a dict
         # with database connection details. This argument should not be added to the
         # function json. Instead, a database should be added to the function json.
-        if self.step_type == AlgorithmStepType.DATA_EXTRACTION.value:
+        if self.step_type == AlgorithmStepType.DATA_EXTRACTION:
             function_json["databases"].append(
                 {
                     "name": "Database",
@@ -211,11 +211,12 @@ class Function:
             }, FunctionArgumentType.DATAFRAME
         else:
             # This is a regular function parameter
+            type_ = self._get_argument_type(param, name)
             arg_json = {
                 "name": name,
                 "display_name": self._pretty_print_name(name),
                 "description": self._extract_parameter_description(name),
-                "type": self.get_argument_type(param, name),
+                "type": type_.value if type_ else None,
                 "required": param.default == inspect.Parameter.empty,
                 "has_default_value": param.default != inspect.Parameter.empty,
                 "is_frontend_only": False,
@@ -247,7 +248,9 @@ class Function:
                 "will not be added."
             )
 
-    def get_argument_type(self, param: inspect.Parameter, name: str) -> str:
+    def _get_argument_type(
+        self, param: inspect.Parameter, name: str
+    ) -> AlgorithmArgumentType | None:
         """Get the type of the argument"""
         if isinstance(param.annotation, UnionType):
             # Arguments with default values may have type 'str | None'. If that is the
@@ -276,23 +279,23 @@ class Function:
             type_ = param.annotation
 
         if type_ == str:
-            return AlgorithmArgumentType.STRING.value
+            return AlgorithmArgumentType.STRING
         elif type_ == dict:
-            return AlgorithmArgumentType.JSON.value
+            return AlgorithmArgumentType.JSON
         elif type_ == int:
-            return AlgorithmArgumentType.INTEGER.value
+            return AlgorithmArgumentType.INTEGER
         elif type_ == float:
-            return AlgorithmArgumentType.FLOAT.value
+            return AlgorithmArgumentType.FLOAT
         elif type_ == bool:
-            return AlgorithmArgumentType.BOOLEAN.value
+            return AlgorithmArgumentType.BOOLEAN
         elif type_ == list:
-            return AlgorithmArgumentType.STRINGS.value
+            return AlgorithmArgumentType.STRINGS
         elif type_ == list[str]:
-            return AlgorithmArgumentType.STRINGS.value
+            return AlgorithmArgumentType.STRINGS
         elif type_ == list[int]:
-            return AlgorithmArgumentType.INTEGERS.value
+            return AlgorithmArgumentType.INTEGERS
         elif type_ == list[float]:
-            return AlgorithmArgumentType.FLOATS.value
+            return AlgorithmArgumentType.FLOATS
         else:
             warning(
                 f"Unsupported argument type: {param.annotation} for argument {name} "
@@ -321,21 +324,20 @@ class Function:
         header = " ".join(line.strip() for line in lines if line.strip() != "")
         return header
 
-    def _get_step_type(self) -> str:
+    def _get_step_type(self) -> AlgorithmStepType | None:
         """Get the step type of the function"""
         decorator_type = get_vantage6_decorator_type(self.func)
         if decorator_type == DecoratorStepType.FEDERATED:
-            return AlgorithmStepType.FEDERATED_COMPUTE.value
+            return AlgorithmStepType.FEDERATED_COMPUTE
         elif decorator_type == DecoratorStepType.CENTRAL:
-            return AlgorithmStepType.CENTRAL_COMPUTE.value
+            return AlgorithmStepType.CENTRAL_COMPUTE
         elif decorator_type == DecoratorStepType.PREPROCESSING:
-            return AlgorithmStepType.PREPROCESSING.value
+            return AlgorithmStepType.PREPROCESSING
         elif decorator_type == DecoratorStepType.DATA_EXTRACTION:
-            return AlgorithmStepType.DATA_EXTRACTION.value
+            return AlgorithmStepType.DATA_EXTRACTION
         else:
             warning(
-                f"Unsupported decorator type: {decorator_type} for function "
-                f"{self.name}"
+                f"Unsupported decorator type: {decorator_type} for function {self.name}"
             )
             return None
 

vantage6/cli/algostore/list.py

@@ -2,6 +2,7 @@ import click
 
 from vantage6.common.docker.addons import check_docker_running
 from vantage6.common.globals import InstanceType
+
 from vantage6.cli.common.utils import get_server_configuration_list
 
 
@@ -12,4 +13,4 @@ def cli_algo_store_configuration_list() -> None:
     """
     check_docker_running()
 
-    get_server_configuration_list(InstanceType.ALGORITHM_STORE.value)
+    get_server_configuration_list(InstanceType.ALGORITHM_STORE)

vantage6/cli/algostore/start.py

@@ -7,6 +7,8 @@ from vantage6.common.globals import (
     InstanceType,
     Ports,
 )
+
+from vantage6.cli.common.decorator import click_insert_context
 from vantage6.cli.common.start import (
     attach_logs,
     check_for_start,
@@ -17,7 +19,6 @@ from vantage6.cli.common.start import (
     pull_infra_image,
 )
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
-from vantage6.cli.common.decorator import click_insert_context
 
 
 @click.command()
@@ -27,13 +28,12 @@ from vantage6.cli.common.decorator import click_insert_context
 @click.option(
     "--keep/--auto-remove",
     default=False,
-    help="Keep image after algorithm store has been stopped. Useful " "for debugging",
+    help="Keep image after algorithm store has been stopped. Useful for debugging",
 )
 @click.option(
     "--mount-src",
     default="",
-    help="Override vantage6 source code in container with the source"
-    " code in this path",
+    help="Override vantage6 source code in container with the source code in this path",
 )
 @click.option(
     "--attach/--detach",
@@ -54,7 +54,7 @@ def cli_algo_store_start(
     Start the algorithm store server.
     """
     info("Starting algorithm store...")
-    docker_client = check_for_start(ctx, InstanceType.ALGORITHM_STORE.value)
+    docker_client = check_for_start(ctx, InstanceType.ALGORITHM_STORE)
 
     image = get_image(image, ctx, "algorithm-store", DEFAULT_ALGO_STORE_IMAGE)
 
@@ -84,7 +84,7 @@ def cli_algo_store_start(
     info(cmd)
 
     info("Run Docker container")
-    port_ = str(port or ctx.config["port"] or Ports.DEV_ALGO_STORE.value)
+    port_ = str(port or ctx.config["port"] or Ports.DEV_ALGO_STORE)
     container = docker_client.containers.run(
         image,
         command=cmd,

vantage6/cli/algostore/stop.py

@@ -2,12 +2,13 @@ import click
 import docker
 from colorama import Fore, Style
 
-from vantage6.common import info, warning, error
+from vantage6.common import error, info, warning
 from vantage6.common.docker.addons import (
     check_docker_running,
     remove_container_if_exists,
 )
 from vantage6.common.globals import APPNAME, InstanceType
+
 from vantage6.cli.common.decorator import click_insert_context
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
 
@@ -23,7 +24,7 @@ def cli_algo_store_stop(ctx: AlgorithmStoreContext, all_stores: bool):
     client = docker.from_env()
 
     running_stores = client.containers.list(
-        filters={"label": f"{APPNAME}-type={InstanceType.ALGORITHM_STORE.value}"}
+        filters={"label": f"{APPNAME}-type={InstanceType.ALGORITHM_STORE}"}
     )
 
     if not running_stores:

vantage6/cli/common/decorator.py

@@ -1,11 +1,13 @@
 from functools import wraps
 from pathlib import Path
+
 import click
 
 from vantage6.common import error
 from vantage6.common.globals import InstanceType
+
 from vantage6.cli.configuration_wizard import select_configuration_questionaire
-from vantage6.cli.context import select_context_class, get_context
+from vantage6.cli.context import get_context, select_context_class
 
 
 def click_insert_context(

vantage6/cli/common/start.py

@@ -33,8 +33,8 @@ from vantage6.cli.common.utils import print_log_worker
 from vantage6.cli.context import AlgorithmStoreContext, ServerContext
 from vantage6.cli.globals import AlgoStoreGlobals, ServerGlobals
 from vantage6.cli.utils import (
-    validate_input_cmd_args,
     check_config_name_allowed,
+    validate_input_cmd_args,
 )
 
 
@@ -69,7 +69,7 @@ def check_for_start(ctx: AppContext, type_: InstanceType) -> DockerClient:
     )
     for server in running_servers:
         if server.name == f"{APPNAME}-{ctx.name}-{ctx.scope}-{type_}":
-            error(f"Server {Fore.RED}{ctx.name}{Style.RESET_ALL} " "is already running")
+            error(f"Server {Fore.RED}{ctx.name}{Style.RESET_ALL} is already running")
             exit(1)
     return docker_client
 
@@ -304,8 +304,6 @@ def attach_logs(container: Container, type_: InstanceType) -> None:
     type_ : InstanceType
         The type of instance to attach the logs for
     """
-    if isinstance(type_, enum.Enum):
-        type_ = type_.value
     logs = container.attach(stream=True, logs=True, stdout=True)
     Thread(target=print_log_worker, args=(logs,), daemon=True).start()
     while True:

vantage6/cli/common/utils.py

@@ -78,7 +78,7 @@ def get_running_servers(
     return [server.name for server in running_servers]
 
 
-def get_server_configuration_list(instance_type: InstanceType.SERVER) -> None:
+def get_server_configuration_list(instance_type: InstanceType) -> None:
     """
     Print list of available server configurations.
 
@@ -90,11 +90,7 @@ def get_server_configuration_list(instance_type: InstanceType.SERVER) -> None:
     client = docker.from_env()
     ctx_class = select_context_class(instance_type)
 
-    instance_type_value = (
-        instance_type.value if isinstance(instance_type, enum.Enum) else instance_type
-    )
-
-    running_server_names = get_running_servers(client, instance_type_value)
+    running_server_names = get_running_servers(client, instance_type)
     header = "\nName" + (21 * " ") + "Status" + (10 * " ") + "System/User"
 
     click.echo(header)
@@ -108,26 +104,24 @@ def get_server_configuration_list(instance_type: InstanceType.SERVER) -> None:
     for config in configs:
         status = (
             running
-            if f"{APPNAME}-{config.name}-system-{instance_type_value}"
-            in running_server_names
+            if f"{APPNAME}-{config.name}-system-{instance_type}" in running_server_names
             else stopped
         )
-        click.echo(f"{config.name:25}" f"{status:25} System ")
+        click.echo(f"{config.name:25}{status:25} System ")
 
     # user folders
     configs, f2 = ctx_class.available_configurations(system_folders=False)
     for config in configs:
         status = (
             running
-            if f"{APPNAME}-{config.name}-user-{instance_type_value}"
-            in running_server_names
+            if f"{APPNAME}-{config.name}-user-{instance_type}" in running_server_names
             else stopped
         )
-        click.echo(f"{config.name:25}" f"{status:25} User   ")
+        click.echo(f"{config.name:25}{status:25} User   ")
 
     click.echo("-" * 85)
     if len(f1) + len(f2):
-        warning(f"{Fore.RED}Failed imports: {len(f1)+len(f2)}{Style.RESET_ALL}")
+        warning(f"{Fore.RED}Failed imports: {len(f1) + len(f2)}{Style.RESET_ALL}")
 
 
 def print_log_worker(logs_stream: Iterable[bytes]) -> None:

vantage6/cli/configuration_manager.py

@@ -1,4 +1,6 @@
-from schema import And, Or, Use, Optional
+from typing import Self
+
+from schema import And, Optional, Or, Use
 
 from vantage6.common.configuration_manager import Configuration, ConfigurationManager
 
@@ -63,7 +65,7 @@ class NodeConfigurationManager(ConfigurationManager):
         super().__init__(conf_class=NodeConfiguration, name=name)
 
     @classmethod
-    def from_file(cls, path: str) -> "NodeConfigurationManager":
+    def from_file(cls, path: str) -> Self:
         """
         Create a new instance of the NodeConfigurationManager from a
         configuration file.
@@ -95,7 +97,7 @@ class ServerConfigurationManager(ConfigurationManager):
         super().__init__(conf_class=ServerConfiguration, name=name)
 
     @classmethod
-    def from_file(cls, path) -> "ServerConfigurationManager":
+    def from_file(cls, path) -> Self:
         """
         Create a new instance of the ServerConfigurationManager from a
         configuration file.

vantage6/cli/configuration_wizard.py

@@ -56,9 +56,9 @@ def node_configuration_questionaire(dirs: dict, instance_name: str) -> dict:
 
     # set default port to the https port if server_url is https
     default_port = (
-        str(Ports.HTTPS.value)
+        str(Ports.HTTPS)
         if config["server_url"].startswith("https")
-        else str(Ports.DEV_SERVER.value)
+        else str(Ports.DEV_SERVER)
     )
 
     config = config | q.unsafe_prompt(
@@ -184,8 +184,7 @@ def node_configuration_questionaire(dirs: dict, instance_name: str) -> dict:
         error(f"Could not authenticate with server: {e}")
         error("Please check (1) your API key and (2) if your server is online")
         warning(
-            "If you continue, you should provide your collaboration "
-            "settings manually."
+            "If you continue, you should provide your collaboration settings manually."
         )
         if q.confirm("Do you want to abort?", default=True).unsafe_ask():
             exit(0)
@@ -314,10 +313,9 @@ def _get_common_server_config(instance_type: InstanceType, instance_name: str) -
                 "name": "port",
                 "message": "Enter port to which the server listens:",
                 "default": (
-                    # Note that .value is required in YAML to get proper str value
-                    str(Ports.DEV_SERVER.value)
+                    str(Ports.DEV_SERVER)
                     if instance_type == InstanceType.SERVER
-                    else str(Ports.DEV_ALGO_STORE.value)
+                    else str(Ports.DEV_ALGO_STORE)
                 ),
             },
         ]
@@ -454,9 +452,7 @@ def algo_store_configuration_questionaire(instance_name: str) -> dict:
     """
     config = _get_common_server_config(InstanceType.ALGORITHM_STORE, instance_name)
 
-    default_v6_server_uri = (
-        f"http://localhost:{Ports.DEV_SERVER.value}{DEFAULT_API_PATH}"
-    )
+    default_v6_server_uri = f"http://localhost:{Ports.DEV_SERVER}{DEFAULT_API_PATH}"
     default_root_username = "admin"
 
     v6_server_uri = q.text(

vantage6/cli/context/__init__.py

@@ -10,8 +10,9 @@ more.
 
 from colorama import Fore, Style
 
-from vantage6.common.globals import InstanceType
 from vantage6.common import error
+from vantage6.common.globals import InstanceType
+
 from vantage6.cli.context.algorithm_store import AlgorithmStoreContext
 from vantage6.cli.context.node import NodeContext
 from vantage6.cli.context.server import ServerContext

vantage6/cli/context/algorithm_store.py

@@ -1,14 +1,15 @@
 from __future__ import annotations
 
 from vantage6.common.globals import APPNAME, InstanceType
+
+from vantage6.cli._version import __version__
 from vantage6.cli.configuration_manager import ServerConfigurationManager
+from vantage6.cli.context.base_server import BaseServerContext
 from vantage6.cli.globals import (
     DEFAULT_SERVER_SYSTEM_FOLDERS as S_FOL,
-    ServerType,
     AlgoStoreGlobals,
+    ServerType,
 )
-from vantage6.cli._version import __version__
-from vantage6.cli.context.base_server import BaseServerContext
 
 
 class AlgorithmStoreContext(BaseServerContext):
@@ -28,7 +29,9 @@ class AlgorithmStoreContext(BaseServerContext):
 
     def __init__(self, instance_name: str, system_folders: bool = S_FOL):
         super().__init__(
-            InstanceType.ALGORITHM_STORE, instance_name, system_folders=system_folders
+            InstanceType.ALGORITHM_STORE,
+            instance_name,
+            system_folders=system_folders,
         )
         self.log.info("vantage6 version '%s'", __version__)
 
@@ -41,7 +44,7 @@ class AlgorithmStoreContext(BaseServerContext):
         str
             string representation of the database uri
         """
-        return super().get_database_uri(AlgoStoreGlobals.DB_URI_ENV_VAR)
+        return super().get_database_uri(AlgoStoreGlobals.DB_URI_ENV_VAR.value)
 
     @property
     def docker_container_name(self) -> str:
@@ -53,7 +56,7 @@ class AlgorithmStoreContext(BaseServerContext):
         str
             Server's docker container name
         """
-        return f"{APPNAME}-{self.name}-{self.scope}-{ServerType.ALGORITHM_STORE.value}"
+        return f"{APPNAME}-{self.name}-{self.scope}-{ServerType.ALGORITHM_STORE}"
 
     @classmethod
     def from_external_config_file(
@@ -79,7 +82,7 @@ class AlgorithmStoreContext(BaseServerContext):
         return super().from_external_config_file(
             path,
             ServerType.ALGORITHM_STORE,
-            AlgoStoreGlobals.CONFIG_NAME_ENV_VAR,
+            AlgoStoreGlobals.CONFIG_NAME_ENV_VAR.value,
             system_folders,
         )
 

vantage6/cli/context/node.py

@@ -2,14 +2,14 @@ from __future__ import annotations
 
 import hashlib
 import os.path
-
 from pathlib import Path
 
 from vantage6.common.context import AppContext
 from vantage6.common.globals import APPNAME, STRING_ENCODING, InstanceType
+
+from vantage6.cli._version import __version__
 from vantage6.cli.configuration_manager import NodeConfigurationManager
 from vantage6.cli.globals import DEFAULT_NODE_SYSTEM_FOLDERS as N_FOL
-from vantage6.cli._version import __version__
 
 
 class NodeContext(AppContext):
@@ -40,12 +40,7 @@ class NodeContext(AppContext):
         logger_prefix: str = "",
     ):
         super().__init__(
-            InstanceType.NODE,
-            instance_name,
-            system_folders,
-            config_file,
-            print_log_header,
-            logger_prefix,
+            InstanceType.NODE, instance_name, system_folders=system_folders
         )
         if print_log_header:
             self.log.info("vantage6 version '%s'", __version__)
@@ -133,7 +128,7 @@ class NodeContext(AppContext):
         Path
             Path to the data folder
         """
-        return AppContext.type_data_folder(InstanceType.NODE.value, system_folders)
+        return AppContext.type_data_folder(InstanceType.NODE, system_folders)
 
     @property
     def databases(self) -> dict:

vantage6/cli/context/server.py

@@ -1,16 +1,18 @@
 from __future__ import annotations
+
 from pathlib import Path
 
 from vantage6.common.globals import APPNAME, InstanceType
+
+from vantage6.cli._version import __version__
 from vantage6.cli.configuration_manager import ServerConfigurationManager
+from vantage6.cli.context.base_server import BaseServerContext
 from vantage6.cli.globals import (
     DEFAULT_SERVER_SYSTEM_FOLDERS as S_FOL,
     PROMETHEUS_DIR,
-    ServerType,
     ServerGlobals,
+    ServerType,
 )
-from vantage6.cli._version import __version__
-from vantage6.cli.context.base_server import BaseServerContext
 
 
 class ServerContext(BaseServerContext):
@@ -45,7 +47,7 @@ class ServerContext(BaseServerContext):
         str
             string representation of the database uri
         """
-        return super().get_database_uri(ServerGlobals.DB_URI_ENV_VAR)
+        return super().get_database_uri(ServerGlobals.DB_URI_ENV_VAR.value)
 
     @property
     def docker_container_name(self) -> str:
@@ -105,7 +107,10 @@ class ServerContext(BaseServerContext):
             Server context object
         """
         return super().from_external_config_file(
-            path, ServerType.V6SERVER, ServerGlobals.CONFIG_NAME_ENV_VAR, system_folders
+            path,
+            ServerType.V6SERVER,
+            ServerGlobals.CONFIG_NAME_ENV_VAR.value,
+            system_folders,
         )
 
     @classmethod