Merge branch 'main' into no-tomo-tilt-input

Author: stephen-riggs

.bumpclient.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.17.8"
+current_version = "0.17.9"
 commit = true
 tag = false
 

.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.17.8"
+current_version = "0.17.9"
 commit = true
 tag = true
 

Helm/Chart.yaml

@@ -1,7 +1,7 @@
 apiVersion: v1
 name: murfey-services
 description: Umbrella Helm chart for deploying the servers and daemons needed to enable Murfey to transfer and process data
-version: 0.17.8
+version: 0.17.9
 dependencies:
   - name: murfey-instrument-server-clem
   - name: murfey-instrument-server-tem

Helm/charts/murfey-instrument-server-clem/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-instrument-server-clem
 description: Helm chart for deploying a Murfey instrument server, which executes orders to detect, modify, and transfer files on the instrument PC, and notifies the backend server about transferred files
-version: 0.17.8
+version: 0.17.9

Helm/charts/murfey-rsync/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-rsync
 description: Helm chart for deploying an rsync daemon, which is responsible for executing the transfer of files from the client storage directory to the server storage system
-version: 0.17.8
+version: 0.17.9

Helm/charts/murfey-server/Chart.yaml

@@ -1,4 +1,4 @@
 apiVersion: v1
 name: murfey-server
 description: Helm chart for deploying a Murfey backend server, which is responsible for orchestrating the data transfer and processing workflow between the client PC and the storage system
-version: 0.17.8
+version: 0.17.9

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
 
 [project]
 name = "murfey"
-version = "0.17.8"
+version = "0.17.9"
 description = "Client-Server architecture hauling Cryo-EM data"
 readme = "README.md"
 keywords = [

src/murfey/__init__.py

@@ -1,4 +1,4 @@
 from __future__ import annotations
 
-__version__ = "0.17.8"
-__supported_client_version__ = "0.17.8"
+__version__ = "0.17.9"
+__supported_client_version__ = "0.17.9"

src/murfey/client/__init__.py

@@ -2,8 +2,6 @@
 
 import argparse
 import configparser
-
-# import json
 import logging
 import os
 import platform
@@ -12,57 +10,26 @@
 import time
 import webbrowser
 from datetime import datetime
-from functools import partial
 from pathlib import Path
 from queue import Queue
 from typing import List, Literal
 from urllib.parse import ParseResult, urlparse
 
 import requests
-
-# from multiprocessing import Process, Queue
 from rich.prompt import Confirm
 
-import murfey.client.rsync
 import murfey.client.update
 import murfey.client.watchdir
 import murfey.client.websocket
 from murfey.client.customlogging import CustomHandler, DirectableRichHandler
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.tui.app import MurfeyTUI
 from murfey.client.tui.status_bar import StatusBar
-from murfey.util import _get_visit_list
-
-# from asyncio import Queue
-
-
-# from rich.prompt import Prompt
-
+from murfey.util.client import _get_visit_list, authorised_requests, read_config
 
 log = logging.getLogger("murfey.client")
 
-
-def read_config() -> configparser.ConfigParser:
-    config = configparser.ConfigParser()
-    try:
-        mcch = os.environ.get("MURFEY_CLIENT_CONFIG_HOME")
-        murfey_client_config_home = Path(mcch) if mcch else Path.home()
-        with open(murfey_client_config_home / ".murfey") as configfile:
-            config.read_file(configfile)
-    except FileNotFoundError:
-        log.warning(
-            f"Murfey client configuration file {murfey_client_config_home / '.murfey'} not found"
-        )
-    if "Murfey" not in config:
-        config["Murfey"] = {}
-    return config
-
-
-token = read_config()["Murfey"].get("token", "")
-
-requests.get = partial(requests.get, headers={"Authorization": f"Bearer {token}"})
-requests.post = partial(requests.post, headers={"Authorization": f"Bearer {token}"})
-requests.delete = partial(requests.delete, headers={"Authorization": f"Bearer {token}"})
+requests.get, requests.post, requests.put, requests.delete = authorised_requests()
 
 
 def write_config(config: configparser.ConfigParser):

src/murfey/client/analyser.py

@@ -22,7 +22,7 @@
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 from murfey.client.rsync import RSyncerUpdate, TransferResult
 from murfey.client.tui.forms import FormDependency
-from murfey.util import Observer, get_machine_config_client
+from murfey.util.client import Observer, get_machine_config_client
 from murfey.util.mdoc import get_block
 from murfey.util.models import ProcessingParametersSPA, ProcessingParametersTomo