Merge pull request #1457 from pyiron/snippets_deprecate

[patch] use deprecate from pyiron_snippets

pyiron_base/__init__.py

@@ -12,7 +12,6 @@
 from pyiron_base.storage.has_stored_traits import HasStoredTraits
 from pyiron_base.storage.inputlist import InputList
 from pyiron_base.storage.parameters import GenericParameters
-from pyiron_base.utils.deprecate import Deprecator, deprecate, deprecate_soon
 from pyiron_base.jobs.job.extension.executable import Executable
 from pyiron_base.project.external import Notebook, load, dump
 from pyiron_base.jobs.dynamic import warn_dynamic_job_classes
@@ -45,9 +44,6 @@
 
 from pyiron_base.jobs.job.toolkit import Toolkit, BaseTools
 
-# Expose snippets references in base API for backwards compatibility
-from pyiron_snippets.import_alarm import ImportAlarm
-
 # Internal init
 from ._version import get_versions
 from pyiron_base.utils.jedi import fix_ipython_autocomplete
@@ -76,10 +72,6 @@
     HasStoredTraits,
     InputList,
     GenericParameters,
-    Deprecator,
-    deprecate,
-    deprecate_soon,
-    ImportAlarm,
     Executable,
     Notebook,
     load,

pyiron_base/database/generic.py

@@ -5,13 +5,13 @@
 DatabaseAccess class deals with accessing the database
 """
 
-from pyiron_base.state.logger import logger
 import numpy as np
 import re
 import os
 from datetime import datetime
-from pyiron_base.utils.deprecate import deprecate
 import pandas
+from pyiron_snippets.deprecate import deprecate
+from pyiron_snippets.logger import logger
 from sqlalchemy import (
     create_engine,
     MetaData,

pyiron_base/database/interface.py

@@ -5,14 +5,14 @@
 DatabaseAccess class deals with accessing the database
 """
 
-from pyiron_base.state.logger import logger
 from abc import ABC, abstractmethod
 from collections.abc import Iterable
 import warnings
 import numpy as np
 import re
-from pyiron_base.utils.deprecate import deprecate
 import pandas
+from pyiron_snippets.deprecate import deprecate
+from pyiron_snippets.logger import logger
 import typing
 import fnmatch
 

pyiron_base/database/manager.py

@@ -6,7 +6,7 @@
 """
 
 from urllib.parse import quote_plus
-from pyiron_base.state.logger import logger
+from pyiron_snippets.logger import logger
 from pyiron_snippets.singleton import Singleton
 from pyiron_base.state.settings import settings as s
 import os

pyiron_base/jobs/datamining.py

@@ -11,11 +11,11 @@
 import os
 import pandas
 from pandas.errors import EmptyDataError
+from pyiron_snippets.deprecate import deprecate
 from tqdm.auto import tqdm
 import types
 from typing import List, Tuple
 
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.jobs.job.generic import GenericJob
 from pyiron_base.jobs.job.extension import jobstatus
 from pyiron_base.storage.hdfio import FileHDFio

pyiron_base/jobs/job/core.py

@@ -12,6 +12,8 @@
 import shutil
 import warnings
 
+from pyiron_snippets.deprecate import deprecate
+
 from pyiron_base.interfaces.has_groups import HasGroups
 from pyiron_base.storage.hdfio import ProjectHDFio
 from pyiron_base.jobs.job.util import (
@@ -33,7 +35,6 @@
     _job_remove_folder,
 )
 from pyiron_base.state import state
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.jobs.job.extension.files import FileBrowser
 
 __author__ = "Jan Janssen"

pyiron_base/jobs/job/extension/server/generic.py

@@ -10,10 +10,11 @@
 import socket
 from typing import Union
 
+from pyiron_snippets.deprecate import deprecate
+
 from pyiron_base.state import state
 from pyiron_base.interfaces.lockable import Lockable, sentinel
 from pyiron_base.interfaces.has_dict import HasDict
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.utils.instance import static_isinstance
 from pyiron_base.jobs.job.extension.server.runmode import Runmode
 

pyiron_base/jobs/job/generic.py

@@ -14,6 +14,7 @@
 import warnings
 
 from h5io_browser.base import _read_hdf, _write_hdf
+from pyiron_snippets.deprecate import deprecate
 
 from pyiron_base.state import state
 from pyiron_base.state.signal import catch_signals
@@ -47,7 +48,6 @@
     _job_reload_after_copy,
 )
 from pyiron_base.utils.instance import static_isinstance, import_class
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.jobs.job.extension.server.generic import Server
 from pyiron_base.database.filetable import FileTable
 from pyiron_base.interfaces.has_dict import HasDict

pyiron_base/jobs/job/runfunction.py

@@ -9,8 +9,8 @@
 import subprocess
 
 from jinja2 import Template
+from pyiron_snippets.deprecate import deprecate
 
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.jobs.job.wrapper import JobWrapper
 from pyiron_base.state import state
 from pyiron_base.state.signal import catch_signals

pyiron_base/jobs/master/parallel.py

@@ -11,6 +11,7 @@
 
 import numpy as np
 import pandas
+from pyiron_snippets.deprecate import deprecate
 import multiprocessing
 import importlib
 from pyiron_base.jobs.job.generic import GenericJob
@@ -21,7 +22,6 @@
 from pyiron_base.state import state
 from pyiron_base.jobs.job.wrapper import job_wrapper_function
 from pyiron_base.jobs.job.util import _get_safe_job_name
-from pyiron_base.utils.deprecate import deprecate
 
 __author__ = "Joerg Neugebauer, Jan Janssen"
 __copyright__ = (

pyiron_base/project/generic.py

@@ -13,6 +13,7 @@
 import stat
 from tqdm.auto import tqdm
 import pandas
+from pyiron_snippets.deprecate import deprecate
 import numpy as np
 
 from pyiron_base.project.jobloader import JobLoader, JobInspector
@@ -27,7 +28,6 @@
     get_job_status,
 )
 from pyiron_base.storage.hdfio import ProjectHDFio
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.interfaces.has_groups import HasGroups
 from pyiron_base.jobs.flex.factory import create_job_factory
 from pyiron_base.jobs.job.util import _special_symbol_replacements, _get_safe_job_name

pyiron_base/state/__init__.py

@@ -14,11 +14,11 @@
 compatibility.
 """
 
-from pyiron_base.state.logger import logger as _logger
 from pyiron_base.database.manager import database as _database
 from pyiron_base.state.publications import publications as _publications
 from pyiron_base.state.queue_adapter import queue_adapters as _queue_adapters
 from pyiron_base.state.settings import settings as _settings
+from pyiron_snippets.logger import logger as _logger
 from pyiron_snippets.singleton import Singleton
 from typing import Dict, Union
 

pyiron_base/state/settings.py

@@ -36,10 +36,10 @@
 import os
 import warnings
 from configparser import ConfigParser
-from pyiron_base.state.logger import logger
 from pyiron_base.state.publications import publications
 from pyiron_base.utils.strtobool import strtobool
 from pathlib import Path
+from pyiron_snippets.logger import logger
 from pyiron_snippets.singleton import Singleton
 from typing import Union, Dict, List
 from copy import deepcopy

pyiron_base/storage/hdfio.py

@@ -17,11 +17,11 @@
 import importlib
 import pandas
 import posixpath
+from pyiron_snippets.deprecate import deprecate
 import numpy as np
 import sys
 from typing import Union, Optional, Any, Tuple
 
-from pyiron_base.utils.deprecate import deprecate
 from pyiron_base.storage.helper_functions import (
     get_h5_path,
     list_groups_and_nodes,

pyiron_base/storage/inputlist.py

@@ -2,8 +2,9 @@
 Backwards compatible way of importing the DataContainer.
 """
 
+from pyiron_snippets.deprecate import deprecate
+
 from pyiron_base.storage.datacontainer import DataContainer
-from pyiron_base.utils.deprecate import deprecate
 
 
 class InputList(DataContainer):