From d75222f632043cbdfbf670836a9e74f03f606fe7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 6 Mar 2024 15:30:44 +0000
Subject: [PATCH 01/17] Switch to TOML configuration file with further options

---
 .gitignore                    |   1 +
 README.md                     |  10 ++--
 poetry.lock                   |  21 ++++++-
 pyproject.toml                |   1 +
 pytest.ini                    |   3 +
 simvue/config/__init__.py     |   1 +
 simvue/config/parameters.py   |  34 +++++++++++
 simvue/config/user.py         |  67 +++++++++++++++++++++
 simvue/factory/__init__.py    |   6 ++
 simvue/factory/remote.py      |  37 ++++++------
 simvue/run.py                 |  34 ++++++++---
 simvue/utilities.py           | 109 ++++++++++++++++++++++++++--------
 tests/refactor/test_config.py |  98 ++++++++++++++++++++++++++++++
 13 files changed, 364 insertions(+), 58 deletions(-)
 create mode 100644 pytest.ini
 create mode 100644 simvue/config/__init__.py
 create mode 100644 simvue/config/parameters.py
 create mode 100644 simvue/config/user.py
 create mode 100644 tests/refactor/test_config.py

diff --git a/.gitignore b/.gitignore
index e664f5f6..d5e715f2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -134,6 +134,7 @@ dmypy.json
 
 # Simvue files
 simvue.ini
+simvue.toml
 
 # Pyenv
 .python-version
diff --git a/README.md b/README.md
index ab52bd05..23a5f1d4 100644
--- a/README.md
+++ b/README.md
@@ -25,20 +25,20 @@ Collect metadata, metrics and artifacts from simulations, processing and AI/ML t
 
 ## Configuration
 The service URL and token can be defined as environment variables:
-```
+```sh
 export SIMVUE_URL=...
 export SIMVUE_TOKEN=...
 ```
 or a file `simvue.ini` can be created containing:
-```
+```toml
 [server]
-url = ...
-token = ...
+url = "..."
+token = "..."
 ```
 The exact contents of both of the above options can be obtained directly by clicking the **Create new run** button on the web UI. Note that the environment variables have preference over the config file.
 
 ## Usage example
-```
+```python
 from simvue import Run
 
 ...
diff --git a/poetry.lock b/poetry.lock
index ae714864..8f943061 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -1318,6 +1318,23 @@ tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 [package.extras]
 testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
+[[package]]
+name = "pytest-mock"
+version = "3.12.0"
+description = "Thin-wrapper around the mock package for easier use with pytest"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "pytest-mock-3.12.0.tar.gz", hash = "sha256:31a40f038c22cad32287bb43932054451ff5583ff094bca6f675df2f8bc1a6e9"},
+    {file = "pytest_mock-3.12.0-py3-none-any.whl", hash = "sha256:0972719a7263072da3a21c7f4773069bcc7486027d7e8e1f81d98a47e701bc4f"},
+]
+
+[package.dependencies]
+pytest = ">=5.0"
+
+[package.extras]
+dev = ["pre-commit", "pytest-asyncio", "tox"]
+
 [[package]]
 name = "python-dateutil"
 version = "2.8.2"
@@ -1568,4 +1585,4 @@ torch = ["torch"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "5b3598d88f5aeea8176fe1d0ad5f4933ff8643df0c25653f1f7912b8fb4559c3"
+content-hash = "509a248be328cbb62de5b403e34acd2643e77af31c5933c3acdf2721711580aa"
diff --git a/pyproject.toml b/pyproject.toml
index dc4a1368..e8872651 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,6 +33,7 @@ simvue_sender = "simvue.bin.sender:run"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.0.0"
+pytest-mock = "^3.12.0"
 
 [build-system]
 requires = ["poetry-core"]
diff --git a/pytest.ini b/pytest.ini
new file mode 100644
index 00000000..78498523
--- /dev/null
+++ b/pytest.ini
@@ -0,0 +1,3 @@
+[pytest]
+markers =
+    config: tests of simvue configuration
\ No newline at end of file
diff --git a/simvue/config/__init__.py b/simvue/config/__init__.py
new file mode 100644
index 00000000..8da076b2
--- /dev/null
+++ b/simvue/config/__init__.py
@@ -0,0 +1 @@
+from .user import SimvueConfiguration
\ No newline at end of file
diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
new file mode 100644
index 00000000..3d0a0429
--- /dev/null
+++ b/simvue/config/parameters.py
@@ -0,0 +1,34 @@
+import logging
+import pydantic
+import typing
+
+import simvue.models as sv_models
+
+CONFIG_FILE_NAMES: list[str] = [
+    "simvue.toml",
+    ".simvue.toml"
+]
+
+logger = logging.getLogger(__file__)
+
+class ServerSpecifications(pydantic.BaseModel):
+    url: pydantic.AnyHttpUrl
+    token: str
+
+    @pydantic.field_validator("url")
+    @classmethod
+    def url_to_str(cls, v: typing.Any) -> str:
+        return f"{v}"
+
+
+class DefaultRunSpecifications(pydantic.BaseModel):
+    description: typing.Optional[str]=None
+    tags: list[str] | None=None
+    folder: str = pydantic.Field(
+        "/",
+        pattern=sv_models.FOLDER_REGEX
+    )
+
+
+class ClientGeneralOptions(pydantic.BaseModel):
+    debug: bool = False
\ No newline at end of file
diff --git a/simvue/config/user.py b/simvue/config/user.py
new file mode 100644
index 00000000..7395efbc
--- /dev/null
+++ b/simvue/config/user.py
@@ -0,0 +1,67 @@
+import pydantic
+import logging
+import toml
+import typing
+import os
+
+import simvue.utilities as sv_util
+
+from simvue.config.parameters import (
+    ClientGeneralOptions,
+    ServerSpecifications,
+    DefaultRunSpecifications,
+    CONFIG_FILE_NAMES
+)
+
+logger = logging.getLogger(__file__)
+
+class SimvueConfiguration(pydantic.BaseModel):
+    client: ClientGeneralOptions=ClientGeneralOptions()
+    server: ServerSpecifications=pydantic.Field(
+        ...,
+        description="Specifications for Simvue server"
+    )
+    run: DefaultRunSpecifications=DefaultRunSpecifications()
+
+    @classmethod
+    def fetch(
+        cls,
+        server_url: typing.Optional[str]=None,
+        server_token: typing.Optional[str]=None
+    ) -> "SimvueConfiguration":
+        _config_dict: dict[str, dict[str, str]] = {}
+
+        try:
+            logger.info(f"Using config file '{cls.config_file()}'")   
+            _config_dict = toml.load(cls.config_file())
+        except FileNotFoundError:            
+            if not server_token or not server_url:
+                _config_dict = {"server": {}}
+                logger.warning("No config file found, checking environment variables")
+        
+        _config_dict["server"] = _config_dict.get("server", {})
+
+        if server_url:
+            _config_dict["server"]["url"] = server_url
+        if server_token:
+            _config_dict["server"]["token"] = server_token
+
+        _config_dict["server"]["url"] = os.environ.get(
+            "SIMVUE_URL",
+            _config_dict["server"].get("url")
+        )
+        _config_dict["server"]["token"] = os.environ.get(
+            "SIMVUE_TOKEN",
+            _config_dict["server"].get("token")
+        )
+
+        return SimvueConfiguration(**_config_dict)
+
+    @classmethod
+    def config_file(cls) -> str:
+        _config_file: typing.Optional[str] = sv_util.find_first_instance_of_file(CONFIG_FILE_NAMES, check_user_space=True)
+        if not _config_file:
+            raise FileNotFoundError(
+                "Failed to find Simvue configuration file"
+            )
+        return _config_file
\ No newline at end of file
diff --git a/simvue/factory/__init__.py b/simvue/factory/__init__.py
index 5cb001ef..1c3a6059 100644
--- a/simvue/factory/__init__.py
+++ b/simvue/factory/__init__.py
@@ -1,12 +1,18 @@
+import typing
+
 from .remote import Remote
 from .offline import Offline
 from .base import SimvueBaseClass
 
+if typing.TYPE_CHECKING:
+    from simvue.config import SimvueConfiguration
+
 
 def Simvue(
     name: str,
     uniq_id: str,
     mode: str,
+    config: SimvueConfiguration,
     suppress_errors: bool = True
 ) -> SimvueBaseClass:
     if mode == "offline":
diff --git a/simvue/factory/remote.py b/simvue/factory/remote.py
index 7f6470c7..5b761e9c 100644
--- a/simvue/factory/remote.py
+++ b/simvue/factory/remote.py
@@ -2,6 +2,9 @@
 import time
 import typing
 
+if typing.TYPE_CHECKING:
+    from simvue.config import SimvueConfiguration
+
 from simvue.api import post, put, get
 from simvue.utilities import (
     get_auth,
@@ -24,10 +27,10 @@ class Remote(SimvueBaseClass):
     Class which interacts with Simvue REST API
     """
 
-    def __init__(self, name: str, uniq_id: str, suppress_errors: bool = True) -> None:
-        self._url, self._token = get_auth()
+    def __init__(self, name: str, uniq_id: str, config: SimvueConfiguration, suppress_errors: bool = True) -> None:
+        self._config = config
         self._headers: dict[str, str] = {
-            "Authorization": f"Bearer {self._token}",
+            "Authorization": f"Bearer {self._config.server.token}",
             "User-Agent": f"Simvue Python client {__version__}",
         }
         self._headers_mp: dict[str, str] = self._headers | {
@@ -43,7 +46,7 @@ def create_run(self, data) -> tuple[typing.Optional[str], typing.Optional[int]]:
         logger.debug('Creating run with data: "%s"', data)
 
         try:
-            response = post(f"{self._url}/api/runs", self._headers, data)
+            response = post(f"{self._config.server.url}/api/runs", self._headers, data)
         except Exception as err:
             self._error(f"Exception creating run: {str(err)}")
             return (None, None)
@@ -84,7 +87,7 @@ def update(
         logger.debug('Updating run with data: "%s"', data)
 
         try:
-            response = put(f"{self._url}/api/runs", self._headers, data)
+            response = put(f"{self._config.server.url}/api/runs", self._headers, data)
         except Exception as err:
             self._error(f"Exception updating run: {err}")
             return None
@@ -106,11 +109,11 @@ def set_folder_details(self, data, run=None) -> typing.Optional[dict[str, typing
         """
         Set folder details
         """
-        if run is not None and not self._version:
+        if run is not None and not __version__:
             data["name"] = run
 
         try:
-            response = post(f"{self._url}/api/folders", self._headers, data)
+            response = post(f"{self._config.server.url}/api/folders", self._headers, data)
         except Exception as err:
             self._error(f"Exception creatig folder: {err}")
             return None
@@ -127,7 +130,7 @@ def set_folder_details(self, data, run=None) -> typing.Optional[dict[str, typing
         logger.debug('Setting folder details with data: "%s"', data)
 
         try:
-            response = put(f"{self._url}/api/folders", self._headers, data)
+            response = put(f"{self._config.server.url}/api/folders", self._headers, data)
         except Exception as err:
             self._error(f"Exception setting folder details: {err}")
             return None
@@ -156,7 +159,7 @@ def save_file(self, data: dict[str, typing.Any]) -> typing.Optional[dict[str, ty
         # Get presigned URL
         try:
             response = post(
-                f"{self._url}/api/artifacts", self._headers, prepare_for_api(data)
+                f"{self._config.server.url}/api/artifacts", self._headers, prepare_for_api(data)
             )
         except Exception as err:
             self._error(
@@ -238,7 +241,7 @@ def save_file(self, data: dict[str, typing.Any]) -> typing.Optional[dict[str, ty
                     return None
 
         if storage_id:
-            path = f"{self._url}/api/runs/{self._id}/artifacts"
+            path = f"{self._config.server.url}/api/runs/{self._id}/artifacts"
             data["storage"] = storage_id
 
             try:
@@ -268,7 +271,7 @@ def add_alert(self, data, run=None):
         logger.debug('Adding alert with data: "%s"', data)
 
         try:
-            response = post(f"{self._url}/api/alerts", self._headers, data)
+            response = post(f"{self._config.server.url}/api/alerts", self._headers, data)
         except Exception as err:
             self._error(f"Got exception when creating an alert: {str(err)}")
             return False
@@ -292,7 +295,7 @@ def set_alert_state(self, alert_id, status) -> typing.Optional[dict[str, typing.
         """
         data = {"run": self._id, "alert": alert_id, "status": status}
         try:
-            response = put(f"{self._url}/api/alerts/status", self._headers, data)
+            response = put(f"{self._config.server.url}/api/alerts/status", self._headers, data)
         except Exception as err:
             self._error(f"Got exception when setting alert state: {err}")
             return {}
@@ -308,7 +311,7 @@ def list_alerts(self) -> list[dict[str, typing.Any]]:
         List alerts
         """
         try:
-            response = get(f"{self._url}/api/alerts", self._headers)
+            response = get(f"{self._config.server.url}/api/alerts", self._headers)
         except Exception as err:
             self._error(f"Got exception when listing alerts: {str(err)}")
             return []
@@ -328,7 +331,7 @@ def send_metrics(self, data: dict[str, typing.Any]) -> typing.Optional[dict[str,
 
         try:
             response = post(
-                f"{self._url}/api/metrics", self._headers_mp, data, is_json=False
+                f"{self._config.server.url}/api/metrics", self._headers_mp, data, is_json=False
             )
         except Exception as err:
             self._error(f"Exception sending metrics: {str(err)}")
@@ -351,7 +354,7 @@ def send_event(self, data: dict[str, typing.Any]) -> typing.Optional[dict[str, t
 
         try:
             response = post(
-                f"{self._url}/api/events", self._headers_mp, data, is_json=False
+                f"{self._config.server.url}/api/events", self._headers_mp, data, is_json=False
             )
         except Exception as err:
             self._error(f"Exception sending event: {str(err)}")
@@ -374,7 +377,7 @@ def send_heartbeat(self) -> typing.Optional[dict[str, typing.Any]]:
 
         try:
             response = put(
-                f"{self._url}/api/runs/heartbeat", self._headers, {"id": self._id}
+                f"{self._config.server.url}/api/runs/heartbeat", self._headers, {"id": self._id}
             )
         except Exception as err:
             self._error(f"Exception creating run: {str(err)}")
@@ -393,7 +396,7 @@ def check_token(self) -> bool:
         """
         Check token
         """
-        if time.time() - get_expiry(self._token) > 0:
+        if time.time() - get_expiry(self._config.server.token) > 0:
             self._error("Token has expired")
             return False
         return True
diff --git a/simvue/run.py b/simvue/run.py
index c4d4baae..50589706 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -17,6 +17,7 @@
 from .factory import Simvue
 from .serialization import Serializer
 from .models import RunInput
+from .config import SimvueConfiguration
 from .utilities import get_auth, get_expiry, print_nice
 from .executor import Executor
 from pydantic import ValidationError
@@ -165,11 +166,11 @@ def validate_timestamp(timestamp):
     return True
 
 
-class Run(object):
+class Run:
     """
     Track simulation details based on token and URL
     """
-    def __init__(self, mode='online'):
+    def __init__(self, mode='online', server_token=None, server_url=None, debug=False):
         self._uuid = str(uuid.uuid4())
         self._mode = mode
         self._name = None
@@ -187,8 +188,19 @@ def __init__(self, mode='online'):
         self._metrics_queue = None
         self._events_queue = None
         self._active = False
-        self._url, self._token = get_auth()
-        self._headers = {"Authorization": f"Bearer {self._token}"}
+        self._config = SimvueConfiguration.fetch(
+            server_token=server_token,
+            server_url=server_url
+        )
+
+        logging.getLogger(self.__class__.__module__).setLevel(
+            logging.DEBUG
+            if (debug is not None and debug)
+            or (debug is None and self._config.client.debug)
+            else logging.INFO
+        )
+
+        self._headers = {"Authorization": f"Bearer {self._config.server.token}"}
         self._simvue = None
         self._pid = 0
         self._resources_metrics_interval = 30
@@ -226,7 +238,7 @@ def _check_token(self):
         """
         Check if token is valid
         """
-        if self._mode == 'online' and tm.time() - get_expiry(self._token) > 0:
+        if self._mode == 'online' and tm.time() - get_expiry(self._config.server.token) > 0:
             self._error('token has expired or is invalid')
 
     def _start(self, reconnect=False):
@@ -266,7 +278,7 @@ def _start(self, reconnect=False):
                               self._uuid,
                               self._name,
                               self._id,
-                              self._url,
+                              self._config.server.url,
                               self._headers,
                               self._mode,
                               self._pid,
@@ -290,13 +302,17 @@ def init(self, name=None, metadata={}, tags=[], description=None, folder='/', ru
         """
         Initialise a run
         """
+        description = description or self._config.run.description
+        tags = tags or self._config.run.tags
+        folder = folder or self._config.run.folder
+
         if self._mode not in ('online', 'offline', 'disabled'):
             self._error('invalid mode specified, must be online, offline or disabled')
 
         if self._mode == 'disabled':
             return True
 
-        if not self._token or not self._url:
+        if not self._config.server.token or not self._config.run.description:
             self._error('Unable to get URL and token from environment variables or config file')
 
         if name:
@@ -339,7 +355,7 @@ def init(self, name=None, metadata={}, tags=[], description=None, folder='/', ru
         except ValidationError as err:
             self._error(err)
 
-        self._simvue = Simvue(self._name, self._uuid, self._mode, self._suppress_errors)
+        self._simvue = Simvue(self._name, self._uuid, self._mode, self._config, self._suppress_errors)
         name, self._id = self._simvue.create_run(data)
 
         if not name:
@@ -511,7 +527,7 @@ def reconnect(self, run_id, uid=None):
         self._uuid = uid
 
         self._id = run_id
-        self._simvue = Simvue(self._name, self._uuid, self._id, self._mode, self._suppress_errors)
+        self._simvue = Simvue(self._name, self._uuid, self._id, self._mode, self._config, self._suppress_errors)
         self._start(reconnect=True)
 
     def set_pid(self, pid):
diff --git a/simvue/utilities.py b/simvue/utilities.py
index 54fdc00b..9a30b730 100644
--- a/simvue/utilities.py
+++ b/simvue/utilities.py
@@ -3,11 +3,48 @@
 import jwt
 import logging
 import os
-import requests
+import pathlib
 import typing
 
 logger = logging.getLogger(__name__)
 
+
+def find_first_instance_of_file(
+    file_names: typing.Union[list[str], str], check_user_space: bool = True
+) -> typing.Optional[str]:
+    """Traverses a file hierarchy from bottom upwards to find file
+
+    Returns the first instance of 'file_names' found when moving
+    upward from the current directory.
+
+    Parameters
+    ----------
+    file_name: list[str] | str
+        candidate names of file to locate
+    check_user_space: bool, optional
+        check the users home area if current working directory is not
+        within it. Default is True.
+    """
+    if isinstance(file_names, str):
+        file_names = [file_names]
+
+    for root, _, files in os.walk(os.getcwd(), topdown=False):
+        for file_name in file_names:
+            if file_name in files:
+                return os.path.join(root, file_name)
+
+    # If the user is running on different mounted volume or outside
+    # of their user space then the above will not return the file
+    if check_user_space:
+        for file_name in file_names:
+            if os.path.exists(
+                _user_file := os.path.join(pathlib.Path.home(), file_name)
+            ):
+                return _user_file
+
+    return None
+
+
 def check_extra(extra_name: str) -> typing.Callable:
     def decorator(class_func: typing.Callable) -> typing.Callable:
         def wrapper(self, *args, **kwargs) -> typing.Any:
@@ -16,29 +53,37 @@ def wrapper(self, *args, **kwargs) -> typing.Any:
                     import matplotlib
                     import plotly
                 except ImportError:
-                    raise RuntimeError(f"Plotting features require the '{extra_name}' extension to Simvue")
+                    raise RuntimeError(
+                        f"Plotting features require the '{extra_name}' extension to Simvue"
+                    )
             elif extra_name == "torch":
                 try:
                     import torch
                 except ImportError:
-                    raise RuntimeError(f"PyTorch features require the '{extra_name}' extension to Simvue")
+                    raise RuntimeError(
+                        f"PyTorch features require the '{extra_name}' extension to Simvue"
+                    )
             elif extra_name == "dataset":
                 try:
                     import pandas
                     import numpy
                 except ImportError:
-                    raise RuntimeError(f"Dataset features require the '{extra_name}' extension to Simvue")
+                    raise RuntimeError(
+                        f"Dataset features require the '{extra_name}' extension to Simvue"
+                    )
             else:
                 raise RuntimeError(f"Unrecognised extra '{extra_name}'")
             return class_func(self, *args, **kwargs)
+
         return wrapper
+
     return decorator
 
 
 def skip_if_failed(
     failure_attr: str,
     ignore_exc_attr: str,
-    on_failure_return: typing.Optional[typing.Any] = None
+    on_failure_return: typing.Optional[typing.Any] = None,
 ) -> typing.Callable:
     """Decorator for ensuring if Simvue throws an exception any other code continues.
 
@@ -62,13 +107,15 @@ def skip_if_failed(
     typing.Callable
         wrapped class method
     """
+
     def decorator(class_func: typing.Callable) -> typing.Callable:
         def wrapper(self, *args, **kwargs) -> typing.Any:
-            if (
-                getattr(self, failure_attr, None) and 
-                getattr(self, ignore_exc_attr, None)
+            if getattr(self, failure_attr, None) and getattr(
+                self, ignore_exc_attr, None
             ):
-                logger.debug(f"Skipping call to '{class_func.__name__}', client in fail state (see logs).")
+                logger.debug(
+                    f"Skipping call to '{class_func.__name__}', client in fail state (see logs)."
+                )
                 return on_failure_return
             return class_func(self, *args, **kwargs)
 
@@ -85,32 +132,39 @@ def get_auth():
     token = None
 
     # Try reading from config file
-    for filename in (os.path.join(os.path.expanduser("~"), '.simvue.ini'), 'simvue.ini'):
+    for filename in (
+        os.path.join(os.path.expanduser("~"), ".simvue.ini"),
+        "simvue.ini",
+    ):
         try:
             config = configparser.ConfigParser()
             config.read(filename)
-            token = config.get('server', 'token')
-            url = config.get('server', 'url')
+            token = config.get("server", "token")
+            url = config.get("server", "url")
         except:
             pass
 
     # Try environment variables
-    token = os.getenv('SIMVUE_TOKEN', token)
-    url = os.getenv('SIMVUE_URL', url)
+    token = os.getenv("SIMVUE_TOKEN", token)
+    url = os.getenv("SIMVUE_URL", url)
 
     return url, token
 
+
 def get_offline_directory():
     """
     Get directory for offline cache
     """
     directory = None
 
-    for filename in (os.path.join(os.path.expanduser("~"), '.simvue.ini'), 'simvue.ini'):
+    for filename in (
+        os.path.join(os.path.expanduser("~"), ".simvue.ini"),
+        "simvue.ini",
+    ):
         try:
             config = configparser.ConfigParser()
             config.read(filename)
-            directory = config.get('offline', 'cache')
+            directory = config.get("offline", "cache")
         except:
             pass
 
@@ -119,15 +173,17 @@ def get_offline_directory():
 
     return directory
 
+
 def create_file(filename):
     """
     Create an empty file
     """
     try:
-        with open(filename, 'w') as fh:
-            fh.write('')
+        with open(filename, "w") as fh:
+            fh.write("")
     except Exception as err:
-        logger.error('Unable to write file %s due to: %s', filename, str(err))
+        logger.error("Unable to write file %s due to: %s", filename, str(err))
+
 
 def remove_file(filename):
     """
@@ -137,7 +193,8 @@ def remove_file(filename):
         try:
             os.remove(filename)
         except Exception as err:
-            logger.error('Unable to remove file %s due to: %s', filename, str(err))
+            logger.error("Unable to remove file %s due to: %s", filename, str(err))
+
 
 def get_expiry(token):
     """
@@ -145,22 +202,24 @@ def get_expiry(token):
     """
     expiry = 0
     try:
-        expiry = jwt.decode(token, options={"verify_signature": False})['exp']
+        expiry = jwt.decode(token, options={"verify_signature": False})["exp"]
     except:
         pass
     return expiry
 
+
 def prepare_for_api(data_in, all=True):
     """
     Remove references to pickling
     """
     data = data_in.copy()
-    if 'pickled' in data:
-        del data['pickled']
-    if 'pickledFile' in data and all:
-        del data['pickledFile']
+    if "pickled" in data:
+        del data["pickled"]
+    if "pickledFile" in data and all:
+        del data["pickledFile"]
     return data
 
+
 def print_nice(message):
     """
     Log message in a way which hopefully can be distiguished from the user's application
diff --git a/tests/refactor/test_config.py b/tests/refactor/test_config.py
new file mode 100644
index 00000000..42f59b18
--- /dev/null
+++ b/tests/refactor/test_config.py
@@ -0,0 +1,98 @@
+import pytest
+import uuid
+import os.path
+import pydantic
+import pytest_mock
+import tempfile
+import simvue.config as sv_config
+
+
+@pytest.mark.config
+@pytest.mark.parametrize(
+    "use_env", (True, False),
+    ids=("use_env", "no_env")
+)
+@pytest.mark.parametrize(
+    "use_file", (None, "basic", "extended"),
+    ids=("no_file", "basic_file", "extended_file")
+)
+@pytest.mark.parametrize(
+    "use_args", (True, False),
+    ids=("args", "no_args")
+)
+def test_config_setup(
+    use_env: bool,
+    use_file: str | None,
+    use_args: bool,
+    monkeypatch: pytest.MonkeyPatch,
+    mocker: pytest_mock.MockerFixture
+) -> None:
+    _token: str = f"{uuid.uuid4()}".replace('-', '')
+    _other_token: str = f"{uuid.uuid4()}".replace('-', '')
+    _arg_token: str = f"{uuid.uuid4()}".replace('-', '')
+    _url: str = "https://simvue.example.com/"
+    _other_url: str = "http://simvue.example.com/"
+    _arg_url: str = "http://simvue.example.io/"
+    _description: str = "test case for runs"
+    _folder: str = "/test-case"
+    _tags: list[str] = ["tag-test", "other-tag"]
+
+    if use_env:
+        monkeypatch.setenv("SIMVUE_TOKEN", _other_token)
+        monkeypatch.setenv("SIMVUE_URL", _other_url)
+    else:
+        monkeypatch.delenv("SIMVUE_TOKEN", False)
+        monkeypatch.delenv("SIMVUE_URL", False)
+
+    with tempfile.TemporaryDirectory() as temp_d:
+        mocker.patch("pathlib.Path.home", lambda: temp_d)
+        if use_file:
+            with open(_config_file := os.path.join(temp_d, "simvue.toml"), "w") as out_f:
+                _lines: str = f"""
+[server]
+url = "{_url}"
+token = "{_token}"
+"""
+                if use_file == "extended":
+                    _lines += f"""
+[run]
+description = "{_description}"
+folder = "{_folder}"
+tags = {_tags}
+"""
+                out_f.write(_lines)
+        os.chdir(temp_d)
+
+        if not use_file and not use_env and not use_args:
+            with pytest.raises(pydantic.ValidationError):
+                sv_config.SimvueConfiguration.fetch()
+            return
+        elif use_args:
+            _config = sv_config.SimvueConfiguration.fetch(
+                server_url=_arg_url,
+                server_token=_arg_token
+            )
+        else:
+            _config = sv_config.SimvueConfiguration.fetch()
+
+        if use_file:
+            assert _config.config_file() == _config_file
+
+        if use_env:
+            assert _config.server.url == _other_url
+            assert _config.server.token == _other_token
+        elif use_args:
+            assert _config.server.url == _arg_url
+            assert _config.server.token == _arg_token
+        elif use_file:
+            assert _config.server.url == _url
+            assert _config.server.token == _token
+
+        if use_file == "extended":
+            assert _config.run.description == _description
+            assert _config.run.folder == _folder
+            assert _config.run.tags == _tags
+        elif use_file:
+            assert _config.run.folder == "/"
+            assert not _config.run.description
+            assert not _config.run.tags
\ No newline at end of file

From f1978c6f0e92bbb59139a769fe063e9e37408127 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Mon, 5 Aug 2024 13:35:14 +0100
Subject: [PATCH 02/17] Add legacy config support

---
 poetry.lock                        | 245 ++++++++++++++++-------------
 simvue/config/parameters.py        |  33 ++--
 simvue/config/user.py              |  74 +++++++--
 simvue/factory/proxy/__init__.py   |  13 +-
 simvue/factory/proxy/offline.py    |   3 +
 simvue/factory/proxy/remote.py     |  17 +-
 simvue/run.py                      |   8 +-
 simvue/utilities.py                |  13 +-
 tests/refactor/test_config.py      |  39 +++--
 tests/refactor/test_executor.py    |   1 -
 tests/unit/test_suppress_errors.py |   3 +-
 11 files changed, 272 insertions(+), 177 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 87dbb35d..bf2c229a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -211,63 +211,83 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
-version = "7.6.0"
+version = "7.6.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "coverage-7.6.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:a8659fd33ee9e6ca03950cfdcdf271d645cf681609153f218826dd9805ab585c"},
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+    {file = "matplotlib-3.9.0.tar.gz", hash = "sha256:e6d29ea6c19e34b30fb7d88b7081f869a03014f66fe06d62cc77d5a6ea88ed7a"},
 ]
 
 [package.dependencies]
@@ -1234,19 +1254,19 @@ typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
 
 [[package]]
 name = "pyjwt"
-version = "2.8.0"
+version = "2.9.0"
 description = "JSON Web Token implementation in Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "PyJWT-2.8.0-py3-none-any.whl", hash = "sha256:59127c392cc44c2da5bb3192169a91f429924e17aff6534d70fdc02ab3e04320"},
-    {file = "PyJWT-2.8.0.tar.gz", hash = "sha256:57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de"},
+    {file = "PyJWT-2.9.0-py3-none-any.whl", hash = "sha256:3b02fb0f44517787776cf48f2ae25d8e14f300e6d7545a4315cee571a415e850"},
+    {file = "pyjwt-2.9.0.tar.gz", hash = "sha256:7e1e5b56cc735432a7369cbfa0efe50fa113ebecdc04ae6922deba8b84582d0c"},
 ]
 
 [package.extras]
 crypto = ["cryptography (>=3.4.0)"]
-dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"]
-docs = ["sphinx (>=4.5.0,<5.0.0)", "sphinx-rtd-theme", "zope.interface"]
+dev = ["coverage[toml] (==5.0.4)", "cryptography (>=3.4.0)", "pre-commit", "pytest (>=6.0.0,<7.0.0)", "sphinx", "sphinx-rtd-theme", "zope.interface"]
+docs = ["sphinx", "sphinx-rtd-theme", "zope.interface"]
 tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 
 [[package]]
@@ -1445,45 +1465,46 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "ruff"
-version = "0.5.5"
+version = "0.5.6"
 description = "An extremely fast Python linter and code formatter, written in Rust."
 optional = false
 python-versions = ">=3.7"
 files = [
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+    {file = "ruff-0.5.6-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:94fe60869bfbf0521e04fd62b74cbca21cbc5beb67cbb75ab33fe8c174f54414"},
+    {file = "ruff-0.5.6-py3-none-win32.whl", hash = "sha256:e6a584c1de6f8591c2570e171cc7ce482bb983d49c70ddf014393cd39e9dfaed"},
+    {file = "ruff-0.5.6-py3-none-win_amd64.whl", hash = "sha256:d7fe7dccb1a89dc66785d7aa0ac283b2269712d8ed19c63af908fdccca5ccc1a"},
+    {file = "ruff-0.5.6-py3-none-win_arm64.whl", hash = "sha256:57c6c0dd997b31b536bff49b9eee5ed3194d60605a4427f735eeb1f9c1b8d264"},
+    {file = "ruff-0.5.6.tar.gz", hash = "sha256:07c9e3c2a8e1fe377dd460371c3462671a728c981c3205a5217291422209f642"},
 ]
 
 [[package]]
 name = "setuptools"
-version = "70.3.0"
+version = "72.1.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-70.3.0-py3-none-any.whl", hash = "sha256:fe384da74336c398e0d956d1cae0669bc02eed936cdb1d49b57de1990dc11ffc"},
-    {file = "setuptools-70.3.0.tar.gz", hash = "sha256:f171bab1dfbc86b132997f26a119f6056a57950d058587841a0082e8830f9dc5"},
+    {file = "setuptools-72.1.0-py3-none-any.whl", hash = "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1"},
+    {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"},
 ]
 
 [package.extras]
+core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.text (>=3.7)", "more-itertools (>=8.8)", "ordered-set (>=3.1.1)", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.10.0)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 3d0a0429..ba05e92e 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -1,34 +1,45 @@
 import logging
+import time
 import pydantic
 import typing
+import pathlib
 
 import simvue.models as sv_models
+from simvue.utilities import get_expiry
 
-CONFIG_FILE_NAMES: list[str] = [
-    "simvue.toml",
-    ".simvue.toml"
+CONFIG_FILE_NAMES: list[str] = ["simvue.toml", ".simvue.toml"]
+
+CONFIG_INI_FILE_NAMES: list[str] = [
+    f'{pathlib.Path.cwd().joinpath("simvue.ini")}',
+    f'{pathlib.Path.home().joinpath(".simvue.ini")}',
 ]
 
 logger = logging.getLogger(__file__)
 
+
 class ServerSpecifications(pydantic.BaseModel):
     url: pydantic.AnyHttpUrl
-    token: str
+    token: pydantic.SecretStr
 
     @pydantic.field_validator("url")
     @classmethod
     def url_to_str(cls, v: typing.Any) -> str:
         return f"{v}"
 
+    @pydantic.field_validator("token")
+    def check_token(cls, v: typing.Any) -> bool:
+        if not (expiry := get_expiry(v)):
+            raise AssertionError("Failed to parse Simvue token - invalid token form")
+        if time.time() - expiry > 0:
+            raise AssertionError("Simvue token has expired")
+        return v
+
 
 class DefaultRunSpecifications(pydantic.BaseModel):
-    description: typing.Optional[str]=None
-    tags: list[str] | None=None
-    folder: str = pydantic.Field(
-        "/",
-        pattern=sv_models.FOLDER_REGEX
-    )
+    description: typing.Optional[str] = None
+    tags: list[str] | None = None
+    folder: str = pydantic.Field("/", pattern=sv_models.FOLDER_REGEX)
 
 
 class ClientGeneralOptions(pydantic.BaseModel):
-    debug: bool = False
\ No newline at end of file
+    debug: bool = False
diff --git a/simvue/config/user.py b/simvue/config/user.py
index 49026b01..fdc2eecf 100644
--- a/simvue/config/user.py
+++ b/simvue/config/user.py
@@ -2,6 +2,10 @@
 import logging
 import os
 import typing
+import pathlib
+import configparser
+import contextlib
+import warnings
 
 import pydantic
 import toml
@@ -9,6 +13,7 @@
 import simvue.utilities as sv_util
 from simvue.config.parameters import (
     CONFIG_FILE_NAMES,
+    CONFIG_INI_FILE_NAMES,
     ClientGeneralOptions,
     DefaultRunSpecifications,
     ServerSpecifications,
@@ -18,12 +23,37 @@
 
 
 class SimvueConfiguration(pydantic.BaseModel):
+    # Hide values as they contain token and URL
+    model_config = pydantic.ConfigDict(hide_input_in_errors=True)
     client: ClientGeneralOptions = ClientGeneralOptions()
     server: ServerSpecifications = pydantic.Field(
         ..., description="Specifications for Simvue server"
     )
     run: DefaultRunSpecifications = DefaultRunSpecifications()
 
+    @classmethod
+    def _parse_ini_config(cls, ini_file: pathlib.Path) -> dict[str, dict[str, str]]:
+        """Parse a legacy INI config file if found."""
+        # NOTE: Legacy INI support, this will be removed
+        warnings.warn(
+            "Support for legacy INI based configuration files will be dropped in simvue>=1.2, "
+            "please switch to TOML based configuration.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+
+        config_dict: dict[str, dict[str, str]] = {"server": {}}
+
+        with contextlib.suppress(Exception):
+            parser = configparser.ConfigParser()
+            parser.read(f"{ini_file}")
+            if token := parser.get("server", "token"):
+                config_dict["server"]["token"] = token
+            if url := parser.get("server", "url"):
+                config_dict["server"]["url"] = url
+
+        return config_dict
+
     @classmethod
     def fetch(
         cls,
@@ -34,7 +64,13 @@ def fetch(
 
         try:
             logger.info(f"Using config file '{cls.config_file()}'")
-            _config_dict = toml.load(cls.config_file())
+
+            # NOTE: Legacy INI support, this will be removed
+            if cls.config_file().suffix == ".toml":
+                _config_dict = toml.load(cls.config_file())
+            else:
+                _config_dict = cls._parse_ini_config(cls.config_file())
+
         except FileNotFoundError:
             if not server_token or not server_url:
                 _config_dict = {"server": {}}
@@ -42,32 +78,46 @@ def fetch(
 
         _config_dict["server"] = _config_dict.get("server", {})
 
-        _server_url = os.environ.get("SIMVUE_URL", _config_dict["server"].get("url"))
-
-        if not _server_url:
-            raise RuntimeError("No server URL was specified")
+        # Ranking of configurations for token and URl is:
+        # Envionment Variables > Run Definition > Configuration File
 
-        _config_dict["server"]["url"] = _server_url
+        _server_url = os.environ.get(
+            "SIMVUE_URL", server_url or _config_dict["server"].get("url")
+        )
 
         _server_token = os.environ.get(
-            "SIMVUE_TOKEN", _config_dict["server"].get("token")
+            "SIMVUE_TOKEN", server_token or _config_dict["server"].get("token")
         )
 
+        if not _server_url:
+            raise RuntimeError("No server URL was specified")
+
         if not _server_token:
             raise RuntimeError("No server token was specified")
 
         _config_dict["server"]["token"] = _server_token
+        _config_dict["server"]["url"] = _server_url
 
         return SimvueConfiguration(**_config_dict)
 
     @classmethod
     @functools.lru_cache
-    def config_file(cls) -> str:
-        _config_file: typing.Optional[str] = sv_util.find_first_instance_of_file(
-            CONFIG_FILE_NAMES, check_user_space=True
+    def config_file(cls) -> pathlib.Path:
+        _config_file: typing.Optional[pathlib.Path] = (
+            sv_util.find_first_instance_of_file(
+                CONFIG_FILE_NAMES, check_user_space=True
+            )
         )
+
+        # NOTE: Legacy INI support, this will be removed
+        if not _config_file:
+            _config_file: typing.Optional[pathlib.Path] = (
+                sv_util.find_first_instance_of_file(
+                    CONFIG_INI_FILE_NAMES, check_user_space=True
+                )
+            )
+
         if not _config_file:
             raise FileNotFoundError("Failed to find Simvue configuration file")
-        else:
-            logger.debug(f"Using config file '{_config_file}'")
+
         return _config_file
diff --git a/simvue/factory/proxy/__init__.py b/simvue/factory/proxy/__init__.py
index 0f3267d1..91065558 100644
--- a/simvue/factory/proxy/__init__.py
+++ b/simvue/factory/proxy/__init__.py
@@ -9,15 +9,22 @@
 
 if typing.TYPE_CHECKING:
     from .base import SimvueBaseClass
+    from simvue.config import SimvueConfiguration
 
 from .offline import Offline
 from .remote import Remote
 
 
 def Simvue(
-    name: typing.Optional[str], uniq_id: str, mode: str, suppress_errors: bool = True
+    name: typing.Optional[str],
+    uniq_id: str,
+    mode: str,
+    config: "SimvueConfiguration",
+    suppress_errors: bool = True,
 ) -> "SimvueBaseClass":
     if mode == "offline":
-        return Offline(name, uniq_id, suppress_errors)
+        return Offline(name=name, uniq_id=uniq_id, suppress_errors=suppress_errors)
     else:
-        return Remote(name, uniq_id, suppress_errors)
+        return Remote(
+            name=name, uniq_id=uniq_id, config=config, suppress_errors=suppress_errors
+        )
diff --git a/simvue/factory/proxy/offline.py b/simvue/factory/proxy/offline.py
index 31f20e3f..4d4034e5 100644
--- a/simvue/factory/proxy/offline.py
+++ b/simvue/factory/proxy/offline.py
@@ -16,6 +16,9 @@
     skip_if_failed,
 )
 
+if typing.TYPE_CHECKING:
+    pass
+
 logger = logging.getLogger(__name__)
 
 
diff --git a/simvue/factory/proxy/remote.py b/simvue/factory/proxy/remote.py
index 3656c8e4..523c17da 100644
--- a/simvue/factory/proxy/remote.py
+++ b/simvue/factory/proxy/remote.py
@@ -1,5 +1,4 @@
 import logging
-import time
 import typing
 
 if typing.TYPE_CHECKING:
@@ -7,7 +6,7 @@
 
 from simvue.api import get, post, put
 from simvue.factory.proxy.base import SimvueBaseClass
-from simvue.utilities import get_expiry, prepare_for_api, skip_if_failed
+from simvue.utilities import prepare_for_api, skip_if_failed
 from simvue.version import __version__
 
 logger = logging.getLogger(__name__)
@@ -478,20 +477,6 @@ def send_heartbeat(self) -> typing.Optional[dict[str, typing.Any]]:
         self._error(f"Got status code {response.status_code} when sending heartbeat")
         return None
 
-    @skip_if_failed("_aborted", "_suppress_errors", False)
-    def check_token(self) -> bool:
-        """
-        Check token
-        """
-        if not (expiry := get_expiry(self._config.server.token)):
-            self._error("Failed to parse user token")
-            return False
-
-        if time.time() - expiry > 0:
-            self._error("Token has expired")
-            return False
-        return True
-
     @skip_if_failed("_aborted", "_suppress_errors", False)
     def get_abort_status(self) -> bool:
         logger.debug("Retrieving alert status")
diff --git a/simvue/run.py b/simvue/run.py
index 973dbe35..82a343bd 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -90,9 +90,9 @@ class Run:
     @pydantic.validate_call
     def __init__(
         self,
+        mode: typing.Literal["online", "offline", "disabled"] = "online",
         server_token: typing.Optional[str] = None,
         server_url: typing.Optional[str] = None,
-        mode: typing.Literal["online", "offline", "disabled"] = "online",
         debug: bool = False,
     ) -> None:
         """Initialise a new Simvue run
@@ -644,7 +644,11 @@ def init(
             return False
 
         self._simvue = Simvue(
-            self._name, self._uuid, self._mode, self._config, self._suppress_errors
+            name=self._name,
+            uniq_id=self._uuid,
+            mode=self._mode,
+            config=self._config,
+            suppress_errors=self._suppress_errors,
         )
         name, self._id = self._simvue.create_run(data)
 
diff --git a/simvue/utilities.py b/simvue/utilities.py
index 05d4c0af..de6c4d2b 100644
--- a/simvue/utilities.py
+++ b/simvue/utilities.py
@@ -25,7 +25,7 @@
 
 def find_first_instance_of_file(
     file_names: typing.Union[list[str], str], check_user_space: bool = True
-) -> typing.Optional[str]:
+) -> typing.Optional[pathlib.Path]:
     """Traverses a file hierarchy from bottom upwards to find file
 
     Returns the first instance of 'file_names' found when moving
@@ -38,6 +38,11 @@ def find_first_instance_of_file(
     check_user_space: bool, optional
         check the users home area if current working directory is not
         within it. Default is True.
+
+    Returns
+    -------
+    pathlib.Path | None
+        first matching file if found
     """
     if isinstance(file_names, str):
         file_names = [file_names]
@@ -45,15 +50,13 @@ def find_first_instance_of_file(
     for root, _, files in os.walk(os.getcwd(), topdown=False):
         for file_name in file_names:
             if file_name in files:
-                return os.path.join(root, file_name)
+                return pathlib.Path(root).joinpath(file_name)
 
     # If the user is running on different mounted volume or outside
     # of their user space then the above will not return the file
     if check_user_space:
         for file_name in file_names:
-            if os.path.exists(
-                _user_file := os.path.join(pathlib.Path.home(), file_name)
-            ):
+            if os.path.exists(_user_file := pathlib.Path.home().joinpath(file_name)):
                 return _user_file
 
     return None
diff --git a/tests/refactor/test_config.py b/tests/refactor/test_config.py
index 42f59b18..0a99eb26 100644
--- a/tests/refactor/test_config.py
+++ b/tests/refactor/test_config.py
@@ -1,10 +1,10 @@
 import pytest
 import uuid
-import os.path
+import pathlib
 import pydantic
 import pytest_mock
 import tempfile
-import simvue.config as sv_config
+import simvue.config
 
 
 @pytest.mark.config
@@ -13,8 +13,8 @@
     ids=("use_env", "no_env")
 )
 @pytest.mark.parametrize(
-    "use_file", (None, "basic", "extended"),
-    ids=("no_file", "basic_file", "extended_file")
+    "use_file", (None, "basic", "extended", "ini"),
+    ids=("no_file", "basic_file", "extended_file", "legacy_file")
 )
 @pytest.mark.parametrize(
     "use_args", (True, False),
@@ -45,14 +45,22 @@ def test_config_setup(
         monkeypatch.delenv("SIMVUE_URL", False)
 
     with tempfile.TemporaryDirectory() as temp_d:
-        mocker.patch("pathlib.Path.home", lambda: temp_d)
+        _config_file = None
         if use_file:
-            with open(_config_file := os.path.join(temp_d, "simvue.toml"), "w") as out_f:
-                _lines: str = f"""
+            with open(_config_file := pathlib.Path(temp_d).joinpath(f"simvue.{'toml' if use_file != 'ini' else 'ini'}"), "w") as out_f:
+                if use_file != "ini":
+                    _lines: str = f"""
 [server]
 url = "{_url}"
 token = "{_token}"
 """
+                else:
+                    _lines = f"""
+[server]
+url = {_url}
+token = {_token}
+"""
+
                 if use_file == "extended":
                     _lines += f"""
 [run]
@@ -61,19 +69,21 @@ def test_config_setup(
 tags = {_tags}
 """
                 out_f.write(_lines)
-        os.chdir(temp_d)
+            simvue.config.SimvueConfiguration.config_file.cache_clear()
+        
+        mocker.patch("simvue.config.user.sv_util.find_first_instance_of_file", lambda *_, **__: _config_file)
 
         if not use_file and not use_env and not use_args:
-            with pytest.raises(pydantic.ValidationError):
-                sv_config.SimvueConfiguration.fetch()
+            with pytest.raises(RuntimeError):
+                simvue.config.SimvueConfiguration.fetch()
             return
         elif use_args:
-            _config = sv_config.SimvueConfiguration.fetch(
+            _config = simvue.config.SimvueConfiguration.fetch(
                 server_url=_arg_url,
                 server_token=_arg_token
             )
         else:
-            _config = sv_config.SimvueConfiguration.fetch()
+            _config = simvue.config.SimvueConfiguration.fetch()
 
         if use_file:
             assert _config.config_file() == _config_file
@@ -95,4 +105,7 @@ def test_config_setup(
         elif use_file:
             assert _config.run.folder == "/"
             assert not _config.run.description
-            assert not _config.run.tags
\ No newline at end of file
+            assert not _config.run.tags
+
+        simvue.config.SimvueConfiguration.config_file.cache_clear()
+
diff --git a/tests/refactor/test_executor.py b/tests/refactor/test_executor.py
index d5a16fae..05f5ce26 100644
--- a/tests/refactor/test_executor.py
+++ b/tests/refactor/test_executor.py
@@ -131,7 +131,6 @@ def test_add_process_command_assembly(request: pytest.FixtureRequest) -> None:
 def test_completion_callbacks_var_change(request: pytest.FixtureRequest) -> None:
     success: dict[str, bool] = {"complete": False}
     def completion_callback(*_, success: dict[str, bool]=success, **__):
-        print("YH BOI")
         success["complete"] = True
 
     with simvue.Run() as run:
diff --git a/tests/unit/test_suppress_errors.py b/tests/unit/test_suppress_errors.py
index 650ba16c..8a1b9f29 100644
--- a/tests/unit/test_suppress_errors.py
+++ b/tests/unit/test_suppress_errors.py
@@ -13,7 +13,6 @@ def test_suppress_errors_false():
             suppress_errors=False,
             disable_resources_metrics=123,
         )
-    print(e.value)
     assert "Input should be a valid boolean, unable to interpret input" in f"{e.value}"
         
 def test_suppress_errors_true(caplog):
@@ -44,4 +43,4 @@ def test_suppress_errors_default(caplog):
     
     caplog.set_level(logging.ERROR)
     
-    assert "Input should be a valid boolean, unable to interpret input" in caplog.text
\ No newline at end of file
+    assert "Input should be a valid boolean, unable to interpret input" in caplog.text

From 0c3e61793f1fa740894d656d6f98cfe4ad61c3a9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Mon, 5 Aug 2024 15:36:42 +0100
Subject: [PATCH 03/17] Fix tests for config updates

---
 simvue/config/parameters.py     |  6 +++---
 simvue/factory/proxy/base.py    |  4 ----
 simvue/factory/proxy/offline.py |  4 ----
 simvue/factory/proxy/remote.py  |  5 +++--
 simvue/run.py                   |  3 ---
 simvue/sender.py                | 17 +++++++++--------
 tests/refactor/conftest.py      |  1 +
 tests/refactor/test_config.py   |  9 ++++++---
 8 files changed, 22 insertions(+), 27 deletions(-)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index ba05e92e..97a90ca5 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -27,12 +27,12 @@ def url_to_str(cls, v: typing.Any) -> str:
         return f"{v}"
 
     @pydantic.field_validator("token")
-    def check_token(cls, v: typing.Any) -> bool:
-        if not (expiry := get_expiry(v)):
+    def check_token(cls, v: pydantic.SecretStr) -> str:
+        if not (expiry := get_expiry(v.get_secret_value())):
             raise AssertionError("Failed to parse Simvue token - invalid token form")
         if time.time() - expiry > 0:
             raise AssertionError("Simvue token has expired")
-        return v
+        return v.get_secret_value()
 
 
 class DefaultRunSpecifications(pydantic.BaseModel):
diff --git a/simvue/factory/proxy/base.py b/simvue/factory/proxy/base.py
index 1ca9060c..2dc3c13d 100644
--- a/simvue/factory/proxy/base.py
+++ b/simvue/factory/proxy/base.py
@@ -86,10 +86,6 @@ def send_event(
     def send_heartbeat(self) -> typing.Optional[dict[str, typing.Any]]:
         pass
 
-    @abc.abstractmethod
-    def check_token(self) -> bool:
-        pass
-
     @abc.abstractmethod
     def get_abort_status(self) -> bool:
         pass
diff --git a/simvue/factory/proxy/offline.py b/simvue/factory/proxy/offline.py
index 4d4034e5..5ec1ccc6 100644
--- a/simvue/factory/proxy/offline.py
+++ b/simvue/factory/proxy/offline.py
@@ -219,7 +219,3 @@ def send_heartbeat(self) -> typing.Optional[dict[str, typing.Any]]:
         )
         pathlib.Path(os.path.join(self._directory, "heartbeat")).touch()
         return {"success": True}
-
-    @skip_if_failed("_aborted", "_suppress_errors", False)
-    def check_token(self) -> bool:
-        return True
diff --git a/simvue/factory/proxy/remote.py b/simvue/factory/proxy/remote.py
index 523c17da..f52900f0 100644
--- a/simvue/factory/proxy/remote.py
+++ b/simvue/factory/proxy/remote.py
@@ -37,7 +37,6 @@ def __init__(
             "Content-Type": "application/msgpack"
         }
         super().__init__(name, uniq_id, suppress_errors)
-        self.check_token()
 
         self._id = uniq_id
 
@@ -45,7 +44,9 @@ def __init__(
     def list_tags(self) -> list[str]:
         logger.debug("Retrieving existing tags")
         try:
-            response = get(f"{self._url}/api/runs/{self._id}", self._headers)
+            response = get(
+                f"{self._config.server.url}/api/runs/{self._id}", self._headers
+            )
         except Exception as err:
             self._error(f"Exception retrieving tags: {str(err)}")
             return []
diff --git a/simvue/run.py b/simvue/run.py
index 0b654879..f159dea2 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -434,9 +434,6 @@ def _start(self, reconnect: bool = False) -> bool:
 
         logger.debug("Starting run")
 
-        if self._simvue and not self._simvue.check_token():
-            return False
-
         data: dict[str, typing.Any] = {"status": self._status}
 
         if reconnect:
diff --git a/simvue/sender.py b/simvue/sender.py
index 8bee03d7..7a95b610 100644
--- a/simvue/sender.py
+++ b/simvue/sender.py
@@ -8,6 +8,8 @@
 
 import msgpack
 
+from simvue.config.user import SimvueConfiguration
+
 from .factory.proxy.remote import Remote
 from .utilities import create_file, get_offline_directory, remove_file
 
@@ -170,11 +172,11 @@ def process(run):
     # Create run if it hasn't previously been created
     created_file = f"{current}/init"
     name = None
+    config = SimvueConfiguration()
     if not os.path.isfile(created_file):
-        remote = Remote(run_init["name"], id, suppress_errors=False)
-
-        # Check token
-        remote.check_token()
+        remote = Remote(
+            name=run_init["name"], uniq_id=id, config=config, suppress_errors=False
+        )
 
         name, run_id = remote.create_run(run_init)
         if name:
@@ -187,10 +189,9 @@ def process(run):
     else:
         name, run_id = get_details(created_file)
         run_init["name"] = name
-        remote = Remote(run_init["name"], run_id, suppress_errors=False)
-
-        # Check token
-        remote.check_token()
+        remote = Remote(
+            name=run_init["name"], uniq_id=run_id, config=config, suppress_errors=False
+        )
 
     if status == "running":
         # Check for recent heartbeat
diff --git a/tests/refactor/conftest.py b/tests/refactor/conftest.py
index 09928da0..778d29cc 100644
--- a/tests/refactor/conftest.py
+++ b/tests/refactor/conftest.py
@@ -138,3 +138,4 @@ def setup_test_run(run: sv_run.Run, create_objects: bool, request: pytest.Fixtur
 
     time.sleep(1.)
     return TEST_DATA
+
diff --git a/tests/refactor/test_config.py b/tests/refactor/test_config.py
index 0a99eb26..30e1d412 100644
--- a/tests/refactor/test_config.py
+++ b/tests/refactor/test_config.py
@@ -1,10 +1,10 @@
 import pytest
+import typing
 import uuid
 import pathlib
-import pydantic
 import pytest_mock
 import tempfile
-import simvue.config
+from simvue.config import SimvueConfiguration
 
 
 @pytest.mark.config
@@ -69,10 +69,13 @@ def test_config_setup(
 tags = {_tags}
 """
                 out_f.write(_lines)
-            simvue.config.SimvueConfiguration.config_file.cache_clear()
+            SimvueConfiguration.config_file.cache_clear()
         
+        mocker.patch("simvue.config.parameters.get_expiry", lambda *_, **__: 1e10)
         mocker.patch("simvue.config.user.sv_util.find_first_instance_of_file", lambda *_, **__: _config_file)
 
+        import simvue.config
+
         if not use_file and not use_env and not use_args:
             with pytest.raises(RuntimeError):
                 simvue.config.SimvueConfiguration.fetch()

From 4fbd2381460ecf82481179ac6eea25085fc2680d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Mon, 5 Aug 2024 15:56:07 +0100
Subject: [PATCH 04/17] Fixed all references to self._url in Run

---
 simvue/factory/proxy/remote.py   | 4 +++-
 tests/refactor/test_run_class.py | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/simvue/factory/proxy/remote.py b/simvue/factory/proxy/remote.py
index f52900f0..75a297ed 100644
--- a/simvue/factory/proxy/remote.py
+++ b/simvue/factory/proxy/remote.py
@@ -483,7 +483,9 @@ def get_abort_status(self) -> bool:
         logger.debug("Retrieving alert status")
 
         try:
-            response = get(f"{self._url}/api/runs/{self._id}/abort", self._headers_mp)
+            response = get(
+                f"{self._config.server.url}/api/runs/{self._id}/abort", self._headers_mp
+            )
         except Exception as err:
             self._error(f"Exception retrieving abort status: {str(err)}")
             return False
diff --git a/tests/refactor/test_run_class.py b/tests/refactor/test_run_class.py
index 106f9983..83a074ad 100644
--- a/tests/refactor/test_run_class.py
+++ b/tests/refactor/test_run_class.py
@@ -481,6 +481,7 @@ def testing_exit(status: int) -> None:
     client = sv_cl.Client()
     client.abort_run(run._id, reason="testing abort")
     time.sleep(4)
+    assert run._resources_metrics_interval == 1
     for child in child_processes:
         assert not child.is_running()
     if not run._status == "terminated":

From 11723df57aabb3a4e949cfdf1cdc8802ec7c0e60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 11 Sep 2024 13:11:18 +0100
Subject: [PATCH 05/17] Fix linting issues

---
 simvue/config/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/simvue/config/__init__.py b/simvue/config/__init__.py
index 8da076b2..c3a62b8a 100644
--- a/simvue/config/__init__.py
+++ b/simvue/config/__init__.py
@@ -1 +1 @@
-from .user import SimvueConfiguration
\ No newline at end of file
+from .user import SimvueConfiguration as SimvueConfiguration

From b01005f927993693485fb831fbc3273f6439512e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 25 Sep 2024 15:10:00 +0100
Subject: [PATCH 06/17] Move token server check to validation

---
 simvue/config/parameters.py    | 31 ++++++++++++++++++++++++++++---
 simvue/factory/proxy/remote.py | 33 +--------------------------------
 2 files changed, 29 insertions(+), 35 deletions(-)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 97a90ca5..4ce414a4 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -3,9 +3,12 @@
 import pydantic
 import typing
 import pathlib
+import http
 
 import simvue.models as sv_models
 from simvue.utilities import get_expiry
+from simvue.version import __version__
+from simvue.api import get
 
 CONFIG_FILE_NAMES: list[str] = ["simvue.toml", ".simvue.toml"]
 
@@ -27,12 +30,34 @@ def url_to_str(cls, v: typing.Any) -> str:
         return f"{v}"
 
     @pydantic.field_validator("token")
-    def check_token(cls, v: pydantic.SecretStr) -> str:
-        if not (expiry := get_expiry(v.get_secret_value())):
+    def check_token(cls, v: typing.Any) -> str:
+        if not (expiry := get_expiry(v)):
             raise AssertionError("Failed to parse Simvue token - invalid token form")
         if time.time() - expiry > 0:
             raise AssertionError("Simvue token has expired")
-        return v.get_secret_value()
+        return v
+
+    @pydantic.model_validator(mode="after")
+    def check_valid_server(cls, values: dict) -> bool:
+        url = values["url"]
+        token = values["token"]
+        headers: dict[str, str] = {
+            "Authorization": f"Bearer {token}",
+            "User-Agent": f"Simvue Python client {__version__}",
+        }
+        try:
+            response = get(f"{url}/api/version", headers)
+
+            if response.status_code != http.HTTPStatus.OK or not response.json().get(
+                "version"
+            ):
+                raise AssertionError
+
+            if response.status_code == http.HTTPStatus.UNAUTHORIZED:
+                raise AssertionError("Unauthorised token")
+
+        except Exception as err:
+            raise AssertionError(f"Exception retrieving server version: {str(err)}")
 
 
 class DefaultRunSpecifications(pydantic.BaseModel):
diff --git a/simvue/factory/proxy/remote.py b/simvue/factory/proxy/remote.py
index 69812ea7..f61ed0d3 100644
--- a/simvue/factory/proxy/remote.py
+++ b/simvue/factory/proxy/remote.py
@@ -1,14 +1,13 @@
 import logging
 import typing
 import http
-import time
 
 if typing.TYPE_CHECKING:
     from simvue.config import SimvueConfiguration
 
 from simvue.api import get, post, put
 from simvue.factory.proxy.base import SimvueBaseClass
-from simvue.utilities import prepare_for_api, skip_if_failed, get_expiry
+from simvue.utilities import prepare_for_api, skip_if_failed
 from simvue.version import __version__
 
 logger = logging.getLogger(__name__)
@@ -483,36 +482,6 @@ def send_heartbeat(self) -> typing.Optional[dict[str, typing.Any]]:
         self._error(f"Got status code {response.status_code} when sending heartbeat")
         return None
 
-    @skip_if_failed("_aborted", "_suppress_errors", False)
-    def check_token(self) -> bool:
-        """
-        Check token
-        """
-        if not (expiry := get_expiry(self._token)):
-            self._error("Failed to parse user token")
-            return False
-
-        if time.time() - expiry > 0:
-            self._error("Token has expired")
-            return False
-
-        try:
-            response = get(f"{self._url}/api/version", self._headers)
-
-            if response.status_code != http.HTTPStatus.OK or not response.json().get(
-                "version"
-            ):
-                raise AssertionError
-
-            if response.status_code == http.HTTPStatus.UNAUTHORIZED:
-                self._error("Unauthorised token")
-                return False
-
-        except Exception as err:
-            self._error(f"Exception retrieving server version: {str(err)}")
-            return False
-        return True
-
     @skip_if_failed("_aborted", "_suppress_errors", False)
     def get_abort_status(self) -> bool:
         logger.debug("Retrieving alert status")

From bbafb5f048e905c8c606b804ea8bbd5136a889fd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Thu, 26 Sep 2024 10:54:20 +0100
Subject: [PATCH 07/17] Fix token processing in validation

---
 simvue/config/parameters.py | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 4ce414a4..772859f8 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -31,22 +31,22 @@ def url_to_str(cls, v: typing.Any) -> str:
 
     @pydantic.field_validator("token")
     def check_token(cls, v: typing.Any) -> str:
-        if not (expiry := get_expiry(v)):
+        value = v.get_secret_value()
+        if not (expiry := get_expiry(value)):
             raise AssertionError("Failed to parse Simvue token - invalid token form")
         if time.time() - expiry > 0:
             raise AssertionError("Simvue token has expired")
-        return v
+        return value
 
     @pydantic.model_validator(mode="after")
-    def check_valid_server(cls, values: dict) -> bool:
-        url = values["url"]
-        token = values["token"]
+    @classmethod
+    def check_valid_server(cls, values: "ServerSpecifications") -> bool:
         headers: dict[str, str] = {
-            "Authorization": f"Bearer {token}",
+            "Authorization": f"Bearer {values.token}",
             "User-Agent": f"Simvue Python client {__version__}",
         }
         try:
-            response = get(f"{url}/api/version", headers)
+            response = get(f"{values.url}/api/version", headers)
 
             if response.status_code != http.HTTPStatus.OK or not response.json().get(
                 "version"
@@ -59,6 +59,8 @@ def check_valid_server(cls, values: dict) -> bool:
         except Exception as err:
             raise AssertionError(f"Exception retrieving server version: {str(err)}")
 
+        return values
+
 
 class DefaultRunSpecifications(pydantic.BaseModel):
     description: typing.Optional[str] = None

From b4438faa78ea118e6f63df5cdc1184d5ca112b1d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Fri, 27 Sep 2024 08:21:34 +0100
Subject: [PATCH 08/17] Added URL check deactivation environment variable

---
 simvue/config/parameters.py   | 4 ++++
 tests/refactor/test_config.py | 6 +++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 772859f8..9f241c59 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -1,4 +1,5 @@
 import logging
+import os
 import time
 import pydantic
 import typing
@@ -41,6 +42,9 @@ def check_token(cls, v: typing.Any) -> str:
     @pydantic.model_validator(mode="after")
     @classmethod
     def check_valid_server(cls, values: "ServerSpecifications") -> bool:
+        if os.environ.get("SIMVUE_NO_SERVER_CHECK"):
+            return values
+
         headers: dict[str, str] = {
             "Authorization": f"Bearer {values.token}",
             "User-Agent": f"Simvue Python client {__version__}",
diff --git a/tests/refactor/test_config.py b/tests/refactor/test_config.py
index 30e1d412..f7236a1d 100644
--- a/tests/refactor/test_config.py
+++ b/tests/refactor/test_config.py
@@ -1,5 +1,6 @@
 import pytest
 import typing
+import os
 import uuid
 import pathlib
 import pytest_mock
@@ -37,6 +38,9 @@ def test_config_setup(
     _folder: str = "/test-case"
     _tags: list[str] = ["tag-test", "other-tag"]
 
+    # Deactivate the server checks for this test
+    monkeypatch.setenv("SIMVUE_NO_SERVER_CHECK", True)
+
     if use_env:
         monkeypatch.setenv("SIMVUE_TOKEN", _other_token)
         monkeypatch.setenv("SIMVUE_URL", _other_url)
@@ -70,7 +74,7 @@ def test_config_setup(
 """
                 out_f.write(_lines)
             SimvueConfiguration.config_file.cache_clear()
-        
+
         mocker.patch("simvue.config.parameters.get_expiry", lambda *_, **__: 1e10)
         mocker.patch("simvue.config.user.sv_util.find_first_instance_of_file", lambda *_, **__: _config_file)
 

From d91487fe07133a33caef71a4ef127848ac167471 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Fri, 27 Sep 2024 08:47:16 +0100
Subject: [PATCH 09/17] Remove outdated test

---
 tests/refactor/test_proxies.py | 15 ---------------
 1 file changed, 15 deletions(-)
 delete mode 100644 tests/refactor/test_proxies.py

diff --git a/tests/refactor/test_proxies.py b/tests/refactor/test_proxies.py
deleted file mode 100644
index 00a09c3b..00000000
--- a/tests/refactor/test_proxies.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import pytest
-
-from simvue.factory.proxy import Simvue
-
-@pytest.mark.proxy
-def test_simvue_url_check() -> None:
-    """Checks the Token/URL checker"""
-    remote = Simvue(
-        name="",
-        uniq_id="",
-        mode="online",
-        suppress_errors=False
-    )
-    assert remote.check_token()
-

From ed7dfe76aaf181d595974c5b55022aa849c6e434 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 10:28:56 +0100
Subject: [PATCH 10/17] Remove remnants of legacy token retrieval

---
 simvue/client.py           | 64 ++++++++++++++++++++++----------------
 simvue/run.py              | 10 +++---
 simvue/utilities.py        | 39 -----------------------
 tests/refactor/conftest.py |  2 +-
 4 files changed, 43 insertions(+), 72 deletions(-)

diff --git a/simvue/client.py b/simvue/client.py
index 713f457a..38331c28 100644
--- a/simvue/client.py
+++ b/simvue/client.py
@@ -24,8 +24,9 @@
 )
 from .serialization import deserialize_data
 from .simvue_types import DeserializedContent
-from .utilities import check_extra, get_auth, prettify_pydantic
+from .utilities import check_extra, prettify_pydantic
 from .models import FOLDER_REGEX, NAME_REGEX
+from .config import SimvueConfiguration
 
 if typing.TYPE_CHECKING:
     pass
@@ -90,18 +91,29 @@ class Client:
     Class for querying Simvue
     """
 
-    def __init__(self) -> None:
-        """Initialise an instance of the Simvue client"""
-        self._url: typing.Optional[str]
-        self._token: typing.Optional[str]
+    def __init__(
+        self,
+        server_token: typing.Optional[str]=None,
+        server_url: typing.Optional[str]=None
+    ) -> None:
+        """Initialise an instance of the Simvue client
 
-        self._url, self._token = get_auth()
+        Parameters
+        ----------
+        server_token : str, optional
+            specify token, if unset this is read from the config file
+        server_url : str, optional
+            specify URL, if unset this is read from the config file
+        """
+        self._config = SimvueConfiguration.fetch(
+            server_token=server_token, server_url=server_url
+        )
 
-        for label, value in zip(("URL", "API token"), (self._url, self._token)):
+        for label, value in zip(("URL", "API token"), (self._config.server.url, self._config.server.url)):
             if not value:
                 logger.warning(f"No {label} specified")
 
-        self._headers: dict[str, str] = {"Authorization": f"Bearer {self._token}"}
+        self._headers: dict[str, str] = {"Authorization": f"Bearer {self._config.server.token}"}
 
     def _get_json_from_response(
         self,
@@ -165,7 +177,7 @@ def get_run_id_from_name(
         params: dict[str, str] = {"filters": json.dumps([f"name == {name}"])}
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/runs", headers=self._headers, params=params
+            f"{self._config.server.url}/api/runs", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -215,7 +227,7 @@ def get_run(self, run_id: str) -> typing.Optional[dict[str, typing.Any]]:
         """
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/runs/{run_id}", headers=self._headers
+            f"{self._config.server.url}/api/runs/{run_id}", headers=self._headers
         )
 
         json_response = self._get_json_from_response(
@@ -331,7 +343,7 @@ def get_runs(
         }
 
         response = requests.get(
-            f"{self._url}/api/runs", headers=self._headers, params=params
+            f"{self._config.server.url}/api/runs", headers=self._headers, params=params
         )
 
         response.raise_for_status()
@@ -380,7 +392,7 @@ def delete_run(self, run_identifier: str) -> typing.Optional[dict]:
         """
 
         response = requests.delete(
-            f"{self._url}/api/runs/{run_identifier}", headers=self._headers
+            f"{self._config.server.url}/api/runs/{run_identifier}", headers=self._headers
         )
 
         json_response = self._get_json_from_response(
@@ -415,7 +427,7 @@ def _get_folder_id_from_path(self, path: str) -> typing.Optional[str]:
         params: dict[str, str] = {"filters": json.dumps([f"path == {path}"])}
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/folders", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders", headers=self._headers, params=params
         )
 
         if (
@@ -458,7 +470,7 @@ def delete_runs(
         params: dict[str, bool] = {"runs_only": True, "runs": True}
 
         response = requests.delete(
-            f"{self._url}/api/folders/{folder_id}", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders/{folder_id}", headers=self._headers, params=params
         )
 
         if response.status_code == http.HTTPStatus.OK:
@@ -522,7 +534,7 @@ def delete_folder(
         params |= {"recursive": recursive}
 
         response = requests.delete(
-            f"{self._url}/api/folders/{folder_id}", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders/{folder_id}", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -551,7 +563,7 @@ def delete_alert(self, alert_id: str) -> None:
             the unique identifier for the alert
         """
         response = requests.delete(
-            f"{self._url}/api/alerts/{alert_id}", headers=self._headers
+            f"{self._config.server.url}/api/alerts/{alert_id}", headers=self._headers
         )
 
         if response.status_code == http.HTTPStatus.OK:
@@ -586,7 +598,7 @@ def list_artifacts(self, run_id: str) -> list[dict[str, typing.Any]]:
         params: dict[str, str] = {"runs": json.dumps([run_id])}
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/artifacts", headers=self._headers, params=params
+            f"{self._config.server.url}/api/artifacts", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -610,7 +622,7 @@ def _retrieve_artifact_from_server(
         params: dict[str, str | None] = {"name": name}
 
         response = requests.get(
-            f"{self._url}/api/runs/{run_id}/artifacts",
+            f"{self._config.server.url}/api/runs/{run_id}/artifacts",
             headers=self._headers,
             params=params,
         )
@@ -649,7 +661,7 @@ def abort_run(self, run_id: str, reason: str) -> typing.Union[dict, list]:
         body: dict[str, str | None] = {"id": run_id, "reason": reason}
 
         response = requests.put(
-            f"{self._url}/api/runs/abort",
+            f"{self._config.server.url}/api/runs/abort",
             headers=self._headers,
             json=body,
         )
@@ -843,7 +855,7 @@ def get_artifacts_as_files(
         params: dict[str, typing.Optional[str]] = {"category": category}
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/runs/{run_id}/artifacts",
+            f"{self._config.server.url}/api/runs/{run_id}/artifacts",
             headers=self._headers,
             params=params,
         )
@@ -935,7 +947,7 @@ def get_folders(
         }
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/folders", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -980,7 +992,7 @@ def get_metrics_names(self, run_id: str) -> list[str]:
         params = {"runs": json.dumps([run_id])}
 
         response: requests.Response = requests.get(
-            f"{self._url}/api/metrics/names", headers=self._headers, params=params
+            f"{self._config.server.url}/api/metrics/names", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -1014,7 +1026,7 @@ def _get_run_metrics_from_server(
         }
 
         metrics_response: requests.Response = requests.get(
-            f"{self._url}/api/metrics", headers=self._headers, params=params
+            f"{self._config.server.url}/api/metrics", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -1271,7 +1283,7 @@ def get_events(
         }
 
         response = requests.get(
-            f"{self._url}/api/events", headers=self._headers, params=params
+            f"{self._config.server.url}/api/events", headers=self._headers, params=params
         )
 
         json_response = self._get_json_from_response(
@@ -1317,7 +1329,7 @@ def get_alerts(
             if there was a failure retrieving data from the server
         """
         if not run_id:
-            response = requests.get(f"{self._url}/api/alerts/", headers=self._headers)
+            response = requests.get(f"{self._config.server.url}/api/alerts/", headers=self._headers)
 
             json_response = self._get_json_from_response(
                 expected_status=[http.HTTPStatus.OK],
@@ -1326,7 +1338,7 @@ def get_alerts(
             )
         else:
             response = requests.get(
-                f"{self._url}/api/runs/{run_id}", headers=self._headers
+                f"{self._config.server.url}/api/runs/{run_id}", headers=self._headers
             )
 
             json_response = self._get_json_from_response(
diff --git a/simvue/run.py b/simvue/run.py
index 2440536c..6c3658b9 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -47,7 +47,6 @@
     calculate_sha256,
     compare_alerts,
     skip_if_failed,
-    get_auth,
     get_offline_directory,
     validate_timestamp,
     simvue_timestamp,
@@ -163,9 +162,8 @@ def __init__(
         )
 
         self._aborted: bool = False
-        self._url, self._token = get_auth()
         self._resources_metrics_interval: typing.Optional[int] = HEARTBEAT_INTERVAL
-        self._headers: dict[str, str] = {"Authorization": f"Bearer {self._token}"}
+        self._headers: dict[str, str] = {"Authorization": f"Bearer {self._config.server.token}"}
         self._simvue: typing.Optional[SimvueBaseClass] = None
         self._pid: typing.Optional[int] = 0
         self._shutdown_event: typing.Optional[threading.Event] = None
@@ -298,7 +296,7 @@ def _create_heartbeat_callback(
         self,
     ) -> typing.Callable[[threading.Event], None]:
         if (
-            self._mode == "online" and (not self._url or not self._id)
+            self._mode == "online" and (not self._config.server.url or not self._id)
         ) or not self._heartbeat_termination_trigger:
             raise RuntimeError("Could not commence heartbeat, run not initialised")
 
@@ -380,7 +378,7 @@ def _create_dispatch_callback(
         if self._mode == "online" and not self._id:
             raise RuntimeError("Expected identifier for run")
 
-        if not self._url:
+        if not self._config.server.url:
             raise RuntimeError("Cannot commence dispatch, run not initialised")
 
         def _offline_dispatch_callback(
@@ -415,7 +413,7 @@ def _offline_dispatch_callback(
         def _online_dispatch_callback(
             buffer: list[typing.Any],
             category: str,
-            url: str = self._url,
+            url: str = self._config.server.url,
             run_id: typing.Optional[str] = self._id,
             headers: dict[str, str] = self._headers,
         ) -> None:
diff --git a/simvue/utilities.py b/simvue/utilities.py
index b711ed93..f7bc0724 100644
--- a/simvue/utilities.py
+++ b/simvue/utilities.py
@@ -249,45 +249,6 @@ def wrapper(self, *args, **kwargs) -> typing.Any:
     return wrapper
 
 
-def get_auth() -> tuple[str, str]:
-    """
-    Get the URL and access token
-    """
-    url: typing.Optional[str] = None
-    token: typing.Optional[str] = None
-    token_source: str = ""
-    url_source: str = ""
-
-    # Try reading from config file
-    for filename in (
-        os.path.join(os.path.expanduser("~"), ".simvue.ini"),
-        "simvue.ini",
-    ):
-        with contextlib.suppress(Exception):
-            config = configparser.ConfigParser()
-            config.read(filename)
-            token = config.get("server", "token")
-            token_source = filename
-            url = config.get("server", "url")
-            url_source = filename
-
-    # Try environment variables
-    if not token and (token := os.getenv("SIMVUE_TOKEN")):
-        token_source = "env:SIMVUE_TOKEN"
-    if not url and (url := os.getenv("SIMVUE_URL")):
-        url_source = "env:SIMVUE_URL"
-
-    if not token:
-        raise ValueError("No Simvue server token was specified")
-    if not url:
-        raise ValueError("No Simvue server URL was specified")
-
-    logger.info(f"Using '{token_source}' as source for Simvue token")
-    logger.info(f"Using '{url_source}' as source for Simvue URL")
-
-    return url, token
-
-
 def get_offline_directory() -> str:
     """
     Get directory for offline cache
diff --git a/tests/refactor/conftest.py b/tests/refactor/conftest.py
index b56f81cf..61214b10 100644
--- a/tests/refactor/conftest.py
+++ b/tests/refactor/conftest.py
@@ -113,7 +113,7 @@ def setup_test_run(run: sv_run.Run, create_objects: bool, request: pytest.Fixtur
         TEST_DATA["metrics"] = ("metric_counter", "metric_val")
     TEST_DATA["run_id"] = run._id
     TEST_DATA["run_name"] = run._name
-    TEST_DATA["url"] = run._url
+    TEST_DATA["url"] = run._config.server.url
     TEST_DATA["headers"] = run._headers
     TEST_DATA["pid"] = run._pid
     TEST_DATA["resources_metrics_interval"] = run._resources_metrics_interval

From 922ce0a86b4c989e71530d41f2375f03844d90d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 10:50:35 +0100
Subject: [PATCH 11/17] Handle folder defaults correctly

---
 simvue/run.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/simvue/run.py b/simvue/run.py
index 6c3658b9..91f6afc9 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -163,7 +163,9 @@ def __init__(
 
         self._aborted: bool = False
         self._resources_metrics_interval: typing.Optional[int] = HEARTBEAT_INTERVAL
-        self._headers: dict[str, str] = {"Authorization": f"Bearer {self._config.server.token}"}
+        self._headers: dict[str, str] = {
+            "Authorization": f"Bearer {self._config.server.token}"
+        }
         self._simvue: typing.Optional[SimvueBaseClass] = None
         self._pid: typing.Optional[int] = 0
         self._shutdown_event: typing.Optional[threading.Event] = None
@@ -561,7 +563,9 @@ def init(
         metadata: typing.Optional[dict[str, typing.Any]] = None,
         tags: typing.Optional[list[str]] = None,
         description: typing.Optional[str] = None,
-        folder: typing.Annotated[str, pydantic.Field(pattern=FOLDER_REGEX)] = "/",
+        folder: typing.Annotated[
+            str, pydantic.Field(None, pattern=FOLDER_REGEX)
+        ] = None,
         running: bool = True,
         retention_period: typing.Optional[str] = None,
         timeout: typing.Optional[int] = 180,
@@ -614,7 +618,7 @@ def init(
 
         description = description or self._config.run.description
         tags = tags or self._config.run.tags
-        folder = folder or self._config.run.folder
+        folder = folder or self._config.run.folder or "/"
 
         self._term_color = not no_color
 

From beb624cf8078960c722ebae91d98444c4b57f86d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 11:00:44 +0100
Subject: [PATCH 12/17] Add 'name' to config file

---
 simvue/config/parameters.py | 1 +
 simvue/run.py               | 1 +
 2 files changed, 2 insertions(+)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 9f241c59..ee468553 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -67,6 +67,7 @@ def check_valid_server(cls, values: "ServerSpecifications") -> bool:
 
 
 class DefaultRunSpecifications(pydantic.BaseModel):
+    name: typing.Optional[str] = None
     description: typing.Optional[str] = None
     tags: list[str] | None = None
     folder: str = pydantic.Field("/", pattern=sv_models.FOLDER_REGEX)
diff --git a/simvue/run.py b/simvue/run.py
index 91f6afc9..30841bf0 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -619,6 +619,7 @@ def init(
         description = description or self._config.run.description
         tags = tags or self._config.run.tags
         folder = folder or self._config.run.folder or "/"
+        name = name or self._config.run.name
 
         self._term_color = not no_color
 

From 34d25fc08aa5864516318a777a991bf67c7f5025 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 11:01:36 +0100
Subject: [PATCH 13/17] Reformat with Ruff

---
 simvue/client.py | 51 +++++++++++++++++++++++++++++++++++-------------
 1 file changed, 37 insertions(+), 14 deletions(-)

diff --git a/simvue/client.py b/simvue/client.py
index 38331c28..28f448df 100644
--- a/simvue/client.py
+++ b/simvue/client.py
@@ -93,8 +93,8 @@ class Client:
 
     def __init__(
         self,
-        server_token: typing.Optional[str]=None,
-        server_url: typing.Optional[str]=None
+        server_token: typing.Optional[str] = None,
+        server_url: typing.Optional[str] = None,
     ) -> None:
         """Initialise an instance of the Simvue client
 
@@ -109,11 +109,15 @@ def __init__(
             server_token=server_token, server_url=server_url
         )
 
-        for label, value in zip(("URL", "API token"), (self._config.server.url, self._config.server.url)):
+        for label, value in zip(
+            ("URL", "API token"), (self._config.server.url, self._config.server.url)
+        ):
             if not value:
                 logger.warning(f"No {label} specified")
 
-        self._headers: dict[str, str] = {"Authorization": f"Bearer {self._config.server.token}"}
+        self._headers: dict[str, str] = {
+            "Authorization": f"Bearer {self._config.server.token}"
+        }
 
     def _get_json_from_response(
         self,
@@ -392,7 +396,8 @@ def delete_run(self, run_identifier: str) -> typing.Optional[dict]:
         """
 
         response = requests.delete(
-            f"{self._config.server.url}/api/runs/{run_identifier}", headers=self._headers
+            f"{self._config.server.url}/api/runs/{run_identifier}",
+            headers=self._headers,
         )
 
         json_response = self._get_json_from_response(
@@ -427,7 +432,9 @@ def _get_folder_id_from_path(self, path: str) -> typing.Optional[str]:
         params: dict[str, str] = {"filters": json.dumps([f"path == {path}"])}
 
         response: requests.Response = requests.get(
-            f"{self._config.server.url}/api/folders", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders",
+            headers=self._headers,
+            params=params,
         )
 
         if (
@@ -470,7 +477,9 @@ def delete_runs(
         params: dict[str, bool] = {"runs_only": True, "runs": True}
 
         response = requests.delete(
-            f"{self._config.server.url}/api/folders/{folder_id}", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders/{folder_id}",
+            headers=self._headers,
+            params=params,
         )
 
         if response.status_code == http.HTTPStatus.OK:
@@ -534,7 +543,9 @@ def delete_folder(
         params |= {"recursive": recursive}
 
         response = requests.delete(
-            f"{self._config.server.url}/api/folders/{folder_id}", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders/{folder_id}",
+            headers=self._headers,
+            params=params,
         )
 
         json_response = self._get_json_from_response(
@@ -598,7 +609,9 @@ def list_artifacts(self, run_id: str) -> list[dict[str, typing.Any]]:
         params: dict[str, str] = {"runs": json.dumps([run_id])}
 
         response: requests.Response = requests.get(
-            f"{self._config.server.url}/api/artifacts", headers=self._headers, params=params
+            f"{self._config.server.url}/api/artifacts",
+            headers=self._headers,
+            params=params,
         )
 
         json_response = self._get_json_from_response(
@@ -947,7 +960,9 @@ def get_folders(
         }
 
         response: requests.Response = requests.get(
-            f"{self._config.server.url}/api/folders", headers=self._headers, params=params
+            f"{self._config.server.url}/api/folders",
+            headers=self._headers,
+            params=params,
         )
 
         json_response = self._get_json_from_response(
@@ -992,7 +1007,9 @@ def get_metrics_names(self, run_id: str) -> list[str]:
         params = {"runs": json.dumps([run_id])}
 
         response: requests.Response = requests.get(
-            f"{self._config.server.url}/api/metrics/names", headers=self._headers, params=params
+            f"{self._config.server.url}/api/metrics/names",
+            headers=self._headers,
+            params=params,
         )
 
         json_response = self._get_json_from_response(
@@ -1026,7 +1043,9 @@ def _get_run_metrics_from_server(
         }
 
         metrics_response: requests.Response = requests.get(
-            f"{self._config.server.url}/api/metrics", headers=self._headers, params=params
+            f"{self._config.server.url}/api/metrics",
+            headers=self._headers,
+            params=params,
         )
 
         json_response = self._get_json_from_response(
@@ -1283,7 +1302,9 @@ def get_events(
         }
 
         response = requests.get(
-            f"{self._config.server.url}/api/events", headers=self._headers, params=params
+            f"{self._config.server.url}/api/events",
+            headers=self._headers,
+            params=params,
         )
 
         json_response = self._get_json_from_response(
@@ -1329,7 +1350,9 @@ def get_alerts(
             if there was a failure retrieving data from the server
         """
         if not run_id:
-            response = requests.get(f"{self._config.server.url}/api/alerts/", headers=self._headers)
+            response = requests.get(
+                f"{self._config.server.url}/api/alerts/", headers=self._headers
+            )
 
             json_response = self._get_json_from_response(
                 expected_status=[http.HTTPStatus.OK],

From f844a3c57521812697a15088956dc499f76667ab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 11:12:44 +0100
Subject: [PATCH 14/17] Add metadata to config, combine config tags with
 session tags

---
 simvue/config/parameters.py | 3 ++-
 simvue/config/user.py       | 1 +
 simvue/run.py               | 5 +++--
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index ee468553..7b3bd04a 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -69,8 +69,9 @@ def check_valid_server(cls, values: "ServerSpecifications") -> bool:
 class DefaultRunSpecifications(pydantic.BaseModel):
     name: typing.Optional[str] = None
     description: typing.Optional[str] = None
-    tags: list[str] | None = None
+    tags: typing.Optional[list[str]] = None
     folder: str = pydantic.Field("/", pattern=sv_models.FOLDER_REGEX)
+    metadata: typing.Optional[dict[str, str]] = None
 
 
 class ClientGeneralOptions(pydantic.BaseModel):
diff --git a/simvue/config/user.py b/simvue/config/user.py
index fdc2eecf..44f15957 100644
--- a/simvue/config/user.py
+++ b/simvue/config/user.py
@@ -55,6 +55,7 @@ def _parse_ini_config(cls, ini_file: pathlib.Path) -> dict[str, dict[str, str]]:
         return config_dict
 
     @classmethod
+    @sv_util.prettify_pydantic
     def fetch(
         cls,
         server_url: typing.Optional[str] = None,
diff --git a/simvue/run.py b/simvue/run.py
index 30841bf0..c67661ac 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -617,9 +617,10 @@ def init(
             return True
 
         description = description or self._config.run.description
-        tags = tags or self._config.run.tags
-        folder = folder or self._config.run.folder or "/"
+        tags = (tags or []) + (self._config.run.tags or [])
+        folder = folder or self._config.run.folder
         name = name or self._config.run.name
+        metadata = (metadata or {}) | (self._config.run.metadata or {})
 
         self._term_color = not no_color
 

From c3485bf9cd3e131776a440b4d5dffb3046b68556 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 11:18:02 +0100
Subject: [PATCH 15/17] Add headers to files

---
 simvue/config/__init__.py   | 8 ++++++++
 simvue/config/parameters.py | 8 ++++++++
 simvue/config/user.py       | 8 ++++++++
 3 files changed, 24 insertions(+)

diff --git a/simvue/config/__init__.py b/simvue/config/__init__.py
index c3a62b8a..db386d99 100644
--- a/simvue/config/__init__.py
+++ b/simvue/config/__init__.py
@@ -1 +1,9 @@
+"""
+Simvue Configuration
+====================
+
+This module contains definitions for the Simvue configuration options
+
+"""
+
 from .user import SimvueConfiguration as SimvueConfiguration
diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 7b3bd04a..4d7f4193 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -1,3 +1,11 @@
+"""
+Simvue Configuration File Models
+================================
+
+Pydantic models for elements of the Simvue configuration file
+
+"""
+
 import logging
 import os
 import time
diff --git a/simvue/config/user.py b/simvue/config/user.py
index 44f15957..b0ab6d8e 100644
--- a/simvue/config/user.py
+++ b/simvue/config/user.py
@@ -1,3 +1,11 @@
+"""
+Simvue Configuration File Model
+===============================
+
+Pydantic model for the Simvue TOML configuration file
+
+"""
+
 import functools
 import logging
 import os

From f3e368fea7f47ee918cc8904d9447ec9442807a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 11:27:15 +0100
Subject: [PATCH 16/17] Allow str, int, float, bool for metadata

---
 simvue/config/parameters.py | 2 +-
 simvue/run.py               | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/simvue/config/parameters.py b/simvue/config/parameters.py
index 4d7f4193..7b378d72 100644
--- a/simvue/config/parameters.py
+++ b/simvue/config/parameters.py
@@ -79,7 +79,7 @@ class DefaultRunSpecifications(pydantic.BaseModel):
     description: typing.Optional[str] = None
     tags: typing.Optional[list[str]] = None
     folder: str = pydantic.Field("/", pattern=sv_models.FOLDER_REGEX)
-    metadata: typing.Optional[dict[str, str]] = None
+    metadata: typing.Optional[dict[str, typing.Union[str, int, float, bool]]] = None
 
 
 class ClientGeneralOptions(pydantic.BaseModel):
diff --git a/simvue/run.py b/simvue/run.py
index c67661ac..16fd4e47 100644
--- a/simvue/run.py
+++ b/simvue/run.py
@@ -560,7 +560,9 @@ def init(
             typing.Annotated[str, pydantic.Field(pattern=NAME_REGEX)]
         ] = None,
         *,
-        metadata: typing.Optional[dict[str, typing.Any]] = None,
+        metadata: typing.Optional[
+            dict[str, typing.Union[str, int, float, bool]]
+        ] = None,
         tags: typing.Optional[list[str]] = None,
         description: typing.Optional[str] = None,
         folder: typing.Annotated[

From aa205aea2f1040690216f4f526f486686f793365 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kristian=20Zar=C4=99bski?= <kristian.zarebski@ukaea.uk>
Date: Wed, 9 Oct 2024 14:34:06 +0100
Subject: [PATCH 17/17] Try lengthening wait for test

---
 tests/refactor/test_run_class.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/refactor/test_run_class.py b/tests/refactor/test_run_class.py
index 3b5fed56..8ff44a89 100644
--- a/tests/refactor/test_run_class.py
+++ b/tests/refactor/test_run_class.py
@@ -529,10 +529,10 @@ def testing_exit(status: int) -> None:
         if i == 4:
             client.abort_run(run._id, reason="testing abort")
         i += 1
-        if abort_set.is_set() or i > 9:
+        if abort_set.is_set() or i > 11:
             break
 
-    assert i < 7
+    assert i < 10
     assert run._status == "terminated"