Refactor feedback-callback and update package dependencies (#688)

* Migrated the following feedback-callback logic blocks into individual modules, and added unit tests:
  * 'atlas_update'
  * 'data_collection'
  * 'data_collection_group'
  * 'processing_job'
* Modified `feedback_callback` entry points to return dictionary instead of boolean
* Updated project package dependencies**
  * Removed the version lock on `stomp-py` from when `8.1.1` caused us issues
  * Removed the FastAPI version lock from when there were conflicting `httpx` version dependencies
  * Added `graypy` as an explicit package dependency, since we use it directly
  * Removed `backports.entry_points_selectable` now that Python 3.9 has been dropped

Author: tieneupin

pyproject.toml

@@ -29,7 +29,6 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-    "backports.entry_points_selectable",
     "defusedxml", # For safely parsing XML files
     "pydantic>=2",
     "pydantic-settings",
@@ -55,13 +54,14 @@ developer = [
 ]
 instrument-server = [
     "aiohttp",
-    "fastapi[standard]<0.116.0",
+    "fastapi[standard-no-fastapi-cloud-cli]>=0.116.0",
     "python-jose",
 ]
 server = [
     "aiohttp",
     "cryptography",
-    "fastapi[standard]<0.116.0",
+    "fastapi[standard-no-fastapi-cloud-cli]>=0.116.0",
+    "graypy",
     "ispyb>=10.2.4", # Responsible for setting requirements for SQLAlchemy and mysql-connector-python;
     "jinja2",
     "mrcfile",
@@ -73,7 +73,7 @@ server = [
     "python-jose[cryptography]",
     "sqlalchemy[postgresql]", # Add as explicit dependency
     "sqlmodel",
-    "stomp-py<=8.1.0", # 8.1.1 (released 2024-04-06) doesn't work with our project
+    "stomp-py>8.1.1", # 8.1.1 (released 2024-04-06) doesn't work with our project
     "zocalo>=1",
 ]
 [project.urls]
@@ -100,14 +100,18 @@ GitHub = "https://github.com/DiamondLightSource/python-murfey"
 [project.entry-points."murfey.config.extraction"]
 "murfey_machine" = "murfey.util.config:get_extended_machine_config"
 [project.entry-points."murfey.workflows"]
+"atlas_update" = "murfey.workflows.register_atlas_update:run"
 "clem.align_and_merge" = "murfey.workflows.clem.align_and_merge:submit_cluster_request"
 "clem.process_raw_lifs" = "murfey.workflows.clem.process_raw_lifs:zocalo_cluster_request"
 "clem.process_raw_tiffs" = "murfey.workflows.clem.process_raw_tiffs:zocalo_cluster_request"
 "clem.register_align_and_merge_result" = "murfey.workflows.clem.register_align_and_merge_results:register_align_and_merge_result"
 "clem.register_preprocessing_result" = "murfey.workflows.clem.register_preprocessing_results:run"
+"data_collection" = "murfey.workflows.register_data_collection:run"
+"data_collection_group" = "murfey.workflows.register_data_collection_group:run"
 "pato" = "murfey.workflows.notifications:notification_setup"
 "picked_particles" = "murfey.workflows.spa.picking:particles_picked"
 "picked_tomogram" = "murfey.workflows.tomo.picking:picked_tomogram"
+"processing_job" = "murfey.workflows.register_processing_job:run"
 "spa.flush_spa_preprocess" = "murfey.workflows.spa.flush_spa_preprocess:flush_spa_preprocess"
 
 [tool.setuptools]

src/murfey/client/context.py

@@ -1,11 +1,10 @@
 from __future__ import annotations
 
 import logging
+from importlib.metadata import entry_points
 from pathlib import Path
 from typing import Any, Dict, List, NamedTuple
 
-from backports.entry_points_selectable import entry_points
-
 from murfey.client.instance_environment import MurfeyInstanceEnvironment
 
 logger = logging.getLogger("murfey.client.context")

src/murfey/server/api/clem.py

@@ -3,12 +3,14 @@
 import re
 import traceback
 from ast import literal_eval
-from importlib.metadata import EntryPoint  # type hinting only
+from importlib.metadata import (
+    EntryPoint,  # type hinting only
+    entry_points,
+)
 from logging import getLogger
 from pathlib import Path
 from typing import Literal, Optional, Type, Union
 
-from backports.entry_points_selectable import entry_points
 from fastapi import APIRouter
 from pydantic import BaseModel, field_validator
 from sqlalchemy.exc import NoResultFound
@@ -752,9 +754,7 @@ def process_raw_lifs(
     try:
         # Try and load relevant Murfey workflow
         workflow: EntryPoint = list(
-            entry_points().select(
-                group="murfey.workflows", name="clem.process_raw_lifs"
-            )
+            entry_points(group="murfey.workflows", name="clem.process_raw_lifs")
         )[0]
     except IndexError:
         raise RuntimeError("The relevant Murfey workflow was not found")
@@ -792,9 +792,7 @@ def process_raw_tiffs(
     try:
         # Try and load relevant Murfey workflow
         workflow: EntryPoint = list(
-            entry_points().select(
-                group="murfey.workflows", name="clem.process_raw_tiffs"
-            )
+            entry_points(group="murfey.workflows", name="clem.process_raw_tiffs")
         )[0]
     except IndexError:
         raise RuntimeError("The relevant Murfey workflow was not found")
@@ -853,7 +851,7 @@ def align_and_merge_stacks(
     try:
         # Try and load relevant Murfey workflow
         workflow: EntryPoint = list(
-            entry_points().select(group="murfey.workflows", name="clem.align_and_merge")
+            entry_points(group="murfey.workflows", name="clem.align_and_merge")
         )[0]
     except IndexError:
         raise RuntimeError("The relevant Murfey workflow was not found")