From e3699c69143151c39028855b742d1f9fc857947b Mon Sep 17 00:00:00 2001 From: Jacob Oldfield Date: Tue, 1 Oct 2024 11:56:03 +1000 Subject: [PATCH 1/2] Update dependencies, update to Pydantic V2 --- .gitignore | 2 + mxcubecore/BaseHardwareObjects.py | 11 +- .../ANSTO/prefect_flows/schemas/grid_scan.py | 2 +- .../ANSTO/prefect_flows/schemas/screening.py | 2 +- .../ESRF/queue_entry/ssx_base_queue_entry.py | 2 +- .../queue_entry/ssx_big_foil_collection.py | 2 +- .../ESRF/queue_entry/ssx_chip_collection.py | 2 +- .../ESRF/queue_entry/ssx_foil_collection.py | 2 +- .../queue_entry/ssx_injector_collection.py | 2 +- .../ESRF/queue_entry/test_collection.py | 2 +- .../HardwareObjects/GenericDiffractometer.py | 2 +- mxcubecore/HardwareObjects/MiniDiff.py | 2 +- .../HardwareObjects/TangoLimaMpegVideo.py | 2 - .../mockup/BeamlineActionsMockup.py | 2 +- .../mockup/DiffractometerMockup.py | 2 +- .../HardwareObjects/mockup/MDCameraMockup.py | 2 - .../ansto/mxcube-web/server.yaml | 2 + mxcubecore/configuration/checkxml.py | 4 +- mxcubecore/model/common.py | 2 +- mxcubecore/model/configmodel.py | 2 +- mxcubecore/model/procedure_model.py | 5 +- poetry.lock | 3606 ++++++++++------- pyproject.toml | 50 +- 23 files changed, 2271 insertions(+), 1441 deletions(-) diff --git a/.gitignore b/.gitignore index b30d0f5be8..978ca6ab3b 100644 --- a/.gitignore +++ b/.gitignore @@ -37,3 +37,5 @@ coverage.xml .DS_Store .vscode/ .python-version + +test/HardwareObjectsMockup.xml/ diff --git a/mxcubecore/BaseHardwareObjects.py b/mxcubecore/BaseHardwareObjects.py index dcd0d97656..423967c521 100644 --- a/mxcubecore/BaseHardwareObjects.py +++ b/mxcubecore/BaseHardwareObjects.py @@ -26,7 +26,6 @@ from collections import OrderedDict import logging from gevent import event, Timeout -import pydantic from typing import ( TYPE_CHECKING, Callable, @@ -43,12 +42,12 @@ ) from typing_extensions import Self, Literal +from pydantic.v1 import BaseModel, Field, create_model from mxcubecore.dispatcher import dispatcher from mxcubecore.CommandContainer import CommandContainer if TYPE_CHECKING: from logging import Logger - from pydantic import BaseModel from .CommandContainer import CommandObject __copyright__ = """ Copyright © 2010-2020 by the MXCuBE collaboration """ @@ -656,11 +655,11 @@ def _get_type_annotations(self) -> None: # Skipp return typehint if _n != "return": self._exports[attr_name].append(_n) - fdict[_n] = (_t, pydantic.Field(alias=_n)) + fdict[_n] = (_t, Field(alias=_n)) _models[attr_name] = ( - pydantic.create_model(attr_name, **fdict), - pydantic.Field(alias=attr_name), + create_model(attr_name, **fdict), + Field(alias=attr_name), ) self._pydantic_models[attr_name] = _models[attr_name][0] @@ -670,7 +669,7 @@ def _get_type_annotations(self) -> None: attr_name ].schema_json() - model = pydantic.create_model(self.__class__.__name__, **_models) + model = create_model(self.__class__.__name__, **_models) self._pydantic_models["all"] = model def execute_exported_command(self, cmd_name: str, args: Dict[str, Any]) -> Any: diff --git a/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/grid_scan.py b/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/grid_scan.py index 489ced272f..9ce4505f35 100644 --- a/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/grid_scan.py +++ b/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/grid_scan.py @@ -1,4 +1,4 @@ -from pydantic import BaseModel +from pydantic.v1 import BaseModel from typing import Optional, Union diff --git a/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/screening.py b/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/screening.py index 68d08bfa04..17a50fc5e8 100644 --- a/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/screening.py +++ b/mxcubecore/HardwareObjects/ANSTO/prefect_flows/schemas/screening.py @@ -1,4 +1,4 @@ -from pydantic import Field, BaseModel +from pydantic.v1 import Field, BaseModel from typing import Union, Optional diff --git a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_base_queue_entry.py b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_base_queue_entry.py index 63572b4d4a..91d3a0a0e8 100644 --- a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_base_queue_entry.py +++ b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_base_queue_entry.py @@ -6,7 +6,7 @@ import gevent from typing_extensions import Literal -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from devtools import debug from mxcubecore import HardwareRepository as HWR diff --git a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_big_foil_collection.py b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_big_foil_collection.py index 350002fea1..2d78ef104e 100644 --- a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_big_foil_collection.py +++ b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_big_foil_collection.py @@ -2,7 +2,7 @@ from typing_extensions import Literal -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from devtools import debug from mxcubecore.model.common import ( diff --git a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_chip_collection.py b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_chip_collection.py index 600d8214a8..36c459094d 100644 --- a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_chip_collection.py +++ b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_chip_collection.py @@ -3,7 +3,7 @@ import contextlib import enum import subprocess -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from devtools import debug from mxcubecore import HardwareRepository as HWR diff --git a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_foil_collection.py b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_foil_collection.py index bdc938eab2..f694579024 100644 --- a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_foil_collection.py +++ b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_foil_collection.py @@ -4,7 +4,7 @@ from typing_extensions import Literal -from pydantic import Field +from pydantic.v1 import Field from devtools import debug from mxcubecore.model.common import ( diff --git a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_injector_collection.py b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_injector_collection.py index 620c71ce4f..a43e777851 100644 --- a/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_injector_collection.py +++ b/mxcubecore/HardwareObjects/ESRF/queue_entry/ssx_injector_collection.py @@ -2,7 +2,7 @@ import time import enum -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from devtools import debug from mxcubecore import HardwareRepository as HWR diff --git a/mxcubecore/HardwareObjects/ESRF/queue_entry/test_collection.py b/mxcubecore/HardwareObjects/ESRF/queue_entry/test_collection.py index de378d9acb..8ae771c4d4 100644 --- a/mxcubecore/HardwareObjects/ESRF/queue_entry/test_collection.py +++ b/mxcubecore/HardwareObjects/ESRF/queue_entry/test_collection.py @@ -3,7 +3,7 @@ from typing_extensions import Literal -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from devtools import debug from mxcubecore import HardwareRepository as HWR diff --git a/mxcubecore/HardwareObjects/GenericDiffractometer.py b/mxcubecore/HardwareObjects/GenericDiffractometer.py index 9af73f2052..fc6004eb44 100755 --- a/mxcubecore/HardwareObjects/GenericDiffractometer.py +++ b/mxcubecore/HardwareObjects/GenericDiffractometer.py @@ -33,7 +33,7 @@ import enum from typing import List, Tuple, Union, Dict -from pydantic import BaseModel, Field, ValidationError +from pydantic.v1 import BaseModel, Field, ValidationError from mxcubecore.HardwareObjects import sample_centring from mxcubecore.model import queue_model_objects diff --git a/mxcubecore/HardwareObjects/MiniDiff.py b/mxcubecore/HardwareObjects/MiniDiff.py index 36859b000b..7103aa94c5 100644 --- a/mxcubecore/HardwareObjects/MiniDiff.py +++ b/mxcubecore/HardwareObjects/MiniDiff.py @@ -9,7 +9,7 @@ import json from typing import Union -from pydantic import ValidationError +from pydantic.v1 import ValidationError from mxcubecore.BaseHardwareObjects import Equipment from mxcubecore.TaskUtils import task diff --git a/mxcubecore/HardwareObjects/TangoLimaMpegVideo.py b/mxcubecore/HardwareObjects/TangoLimaMpegVideo.py index 65eb2eb47b..2cc2e03bc9 100644 --- a/mxcubecore/HardwareObjects/TangoLimaMpegVideo.py +++ b/mxcubecore/HardwareObjects/TangoLimaMpegVideo.py @@ -73,8 +73,6 @@ def start_video_stream_process(self, port): self._video_stream_process = subprocess.Popen( [ "video-streamer", - "-tu", - self.get_property("tangoname").strip(), "-hs", "localhost", "-p", diff --git a/mxcubecore/HardwareObjects/mockup/BeamlineActionsMockup.py b/mxcubecore/HardwareObjects/mockup/BeamlineActionsMockup.py index bb26f75eed..2e168ccaa8 100644 --- a/mxcubecore/HardwareObjects/mockup/BeamlineActionsMockup.py +++ b/mxcubecore/HardwareObjects/mockup/BeamlineActionsMockup.py @@ -1,6 +1,6 @@ from typing_extensions import Literal -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field from mxcubecore.TaskUtils import task from mxcubecore.CommandContainer import CommandObject from mxcubecore.HardwareObjects.BeamlineActions import ( diff --git a/mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py b/mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py index e71bcd9c75..3d190aad25 100644 --- a/mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py +++ b/mxcubecore/HardwareObjects/mockup/DiffractometerMockup.py @@ -22,7 +22,7 @@ import random import warnings -from pydantic import ValidationError +from pydantic.v1 import ValidationError from mxcubecore.HardwareObjects.GenericDiffractometer import ( GenericDiffractometer, diff --git a/mxcubecore/HardwareObjects/mockup/MDCameraMockup.py b/mxcubecore/HardwareObjects/mockup/MDCameraMockup.py index 166cdec16a..f9d008dbb8 100644 --- a/mxcubecore/HardwareObjects/mockup/MDCameraMockup.py +++ b/mxcubecore/HardwareObjects/mockup/MDCameraMockup.py @@ -115,8 +115,6 @@ def start_video_stream_process(self, size): self._video_stream_process = subprocess.Popen( [ "video-streamer", - "-tu", - "test", "-hs", "localhost", "-p", diff --git a/mxcubecore/configuration/ansto/mxcube-web/server.yaml b/mxcubecore/configuration/ansto/mxcube-web/server.yaml index b59005f49e..d072e3ab71 100644 --- a/mxcubecore/configuration/ansto/mxcube-web/server.yaml +++ b/mxcubecore/configuration/ansto/mxcube-web/server.yaml @@ -12,7 +12,9 @@ server: - "http://localhost:3000" - "ws://localhost:8000" - "https://mxcube.mx3.beamline.synchrotron.org.au" + - "wss://mxcube.mx3.beamline.synchrotron.org.au" - "http://mxcube.mx3.beamline.synchrotron.org.au" + - "ws://mxcube.mx3.beamline.synchrotron.org.au" mxcube: USE_EXTERNAL_STREAMER: False diff --git a/mxcubecore/configuration/checkxml.py b/mxcubecore/configuration/checkxml.py index 1e29245efe..64ed5b56bf 100644 --- a/mxcubecore/configuration/checkxml.py +++ b/mxcubecore/configuration/checkxml.py @@ -2,7 +2,7 @@ import xmltodict import argparse import pprint -import pydantic +from pydantic.v1 import ValidationError from colorama import Fore, Back, Style from mxcubecore.model import configmodel @@ -40,7 +40,7 @@ def check_xml(rpath="."): if config_model: try: config_model(**_data_to_validate) - except pydantic.ValidationError as ex: + except ValidationError as ex: print(f"{Fore.RED}WARNING in: {fpath}") print(f"{str(ex)}") print(Style.RESET_ALL) diff --git a/mxcubecore/model/common.py b/mxcubecore/model/common.py index f862b26e37..f0c53d4400 100644 --- a/mxcubecore/model/common.py +++ b/mxcubecore/model/common.py @@ -1,6 +1,6 @@ from datetime import datetime from typing import Optional, Union -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field class CommonCollectionParamters(BaseModel): diff --git a/mxcubecore/model/configmodel.py b/mxcubecore/model/configmodel.py index f82fbc11c2..a014abbcb0 100644 --- a/mxcubecore/model/configmodel.py +++ b/mxcubecore/model/configmodel.py @@ -1,4 +1,4 @@ -from pydantic import BaseModel, Field +from pydantic.v1 import BaseModel, Field class ExporterNStateConfigModel(BaseModel): diff --git a/mxcubecore/model/procedure_model.py b/mxcubecore/model/procedure_model.py index ea3717c0e2..796c3b9559 100644 --- a/mxcubecore/model/procedure_model.py +++ b/mxcubecore/model/procedure_model.py @@ -1,14 +1,13 @@ # -*- coding: utf-8 -*- -import pydantic -from pydantic import Field +from pydantic.v1 import BaseModel, Field class ValidationError(Exception): pass -class BaseModel(pydantic.BaseModel): +class BaseModel(BaseModel): def __init__(self, *args, **kwargs): try: super(BaseModel, self).__init__(*args, **kwargs) diff --git a/poetry.lock b/poetry.lock index 5432ba1723..5b6417b007 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,15 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. + +[[package]] +name = "aiofiles" +version = "24.1.0" +description = "File support for asyncio." +optional = false +python-versions = ">=3.8" +files = [ + {file = "aiofiles-24.1.0-py3-none-any.whl", hash = "sha256:b4ec55f4195e3eb5d7abd1bf7e061763e864dd4954231fb8539a0ef8bb8260e5"}, + {file = "aiofiles-24.1.0.tar.gz", hash = "sha256:22a075c9e5a3810f0c2e48f3008c94d68c65d763b9b03857924c99e57355166c"}, +] [[package]] name = "aiosqlite" @@ -31,13 +42,13 @@ files = [ [[package]] name = "alembic" -version = "1.13.1" +version = "1.13.2" description = "A database migration tool for SQLAlchemy." optional = true python-versions = ">=3.8" files = [ - {file = "alembic-1.13.1-py3-none-any.whl", hash = "sha256:2edcc97bed0bd3272611ce3a98d98279e9c209e7186e43e75bbb1b2bdfdbcc43"}, - {file = "alembic-1.13.1.tar.gz", hash = "sha256:4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595"}, + {file = "alembic-1.13.2-py3-none-any.whl", hash = "sha256:6b8733129a6224a9a711e17c99b08462dbf7cc9670ba8f2e2ae9af860ceb1953"}, + {file = "alembic-1.13.2.tar.gz", hash = "sha256:1ff0ae32975f4fd96028c39ed9bb3c867fe3af956bd7bb37343b54c9fe7445ef"}, ] [package.dependencies] @@ -50,11 +61,25 @@ typing-extensions = ">=4" [package.extras] tz = ["backports.zoneinfo"] +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] + +[package.dependencies] +typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.9\""} + [[package]] name = "anyio" version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" -optional = true +optional = false python-versions = ">=3.7" files = [ {file = "anyio-3.7.1-py3-none-any.whl", hash = "sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5"}, @@ -71,15 +96,26 @@ doc = ["Sphinx", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd- test = ["anyio[trio]", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] trio = ["trio (<0.22)"] +[[package]] +name = "appdirs" +version = "1.4.4" +description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +optional = false +python-versions = "*" +files = [ + {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"}, + {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"}, +] + [[package]] name = "apprise" -version = "1.7.2" +version = "1.9.0" description = "Push Notifications that work with just about every platform!" optional = true python-versions = ">=3.6" files = [ - {file = "apprise-1.7.2-py3-none-any.whl", hash = "sha256:f3192e62924e54334d4ca0c5723d7de9293500e1a0fbf3a890433ea5b6b56df8"}, - {file = "apprise-1.7.2.tar.gz", hash = "sha256:09e159b29008e6c8e93d7ffc3c15d419c0bbae41620405f8f2d3432b72a2e9bf"}, + {file = "apprise-1.9.0-py3-none-any.whl", hash = "sha256:7192c953eeb282a7afee012512d3de0104b5a6a11bdda29283435df5a79dfe7f"}, + {file = "apprise-1.9.0.tar.gz", hash = "sha256:b5c93afd6331afe4b63a55d1cea9076e47becb4ba89b562b181c13e25bb0c7d6"}, ] [package.dependencies] @@ -104,22 +140,6 @@ files = [ [package.dependencies] sniffio = "*" -[[package]] -name = "astroid" -version = "2.15.8" -description = "An abstract syntax tree for Python with inference support." -optional = false -python-versions = ">=3.7.2" -files = [ - {file = "astroid-2.15.8-py3-none-any.whl", hash = "sha256:1aa149fc5c6589e3d0ece885b4491acd80af4f087baafa3fb5203b113e68cd3c"}, - {file = "astroid-2.15.8.tar.gz", hash = "sha256:6c107453dffee9055899705de3c9ead36e74119cee151e5a9aaf7f0b0e020a6a"}, -] - -[package.dependencies] -lazy-object-proxy = ">=1.4.0" -typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} -wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""} - [[package]] name = "astunparse" version = "1.6.3" @@ -139,7 +159,7 @@ wheel = ">=0.23.0,<1.0" name = "async-timeout" version = "4.0.3" description = "Timeout context manager for asyncio programs" -optional = true +optional = false python-versions = ">=3.7" files = [ {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"}, @@ -205,32 +225,32 @@ test = ["flake8 (>=6.1,<7.0)", "uvloop (>=0.15.3)"] [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"}, - {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"}, + {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"}, + {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"}, ] [package.extras] -cov = ["attrs[tests]", "coverage[toml] (>=5.3)"] -dev = ["attrs[tests]", "pre-commit"] -docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", 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6379) - rdb = self.get_property("db", 11) + rhost = self.get_property( + "host", + environ.get("MXCUBE_REDIS_HOST", "localhost"), + ) + rport = self.get_property( + "port", + int(environ.get("MXCUBE_REDIS_PORT", "6379")), + ) + username = self.get_property( + "username", + environ.get("MXCUBE_REDIS_USERNAME"), + ) + password = self.get_property( + "password", + environ.get("MXCUBE_REDIS_PASSWORD"), + ) + rdb = self.get_property( + "db", + int(environ.get("MXCUBE_REDIS_DB", "11")), + ) self._r = redis.Redis( - host=rhost, port=rport, db=rdb, charset="utf-8", decode_responses=True + host=rhost, + port=rport, + username=username, + password=password, + db=rdb, + charset="utf-8", + decode_responses=True, ) if not self._subsribe_task: