From 53ded770914b41d348de657cdf90341482926b1a Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Fri, 31 May 2024 11:54:43 -0700
Subject: [PATCH 01/13] [patch] use deprecate from pyiron_snippets

---
 pyiron_base/__init__.py                       |   2 +-
 pyiron_base/database/generic.py               |   2 +-
 pyiron_base/database/interface.py             |   2 +-
 pyiron_base/jobs/datamining.py                |   2 +-
 pyiron_base/jobs/job/core.py                  |   3 +-
 .../jobs/job/extension/server/generic.py      |   3 +-
 pyiron_base/jobs/job/generic.py               |   2 +-
 pyiron_base/jobs/job/runfunction.py           |   2 +-
 pyiron_base/jobs/master/parallel.py           |   2 +-
 pyiron_base/project/generic.py                |   2 +-
 pyiron_base/storage/hdfio.py                  |   2 +-
 pyiron_base/storage/inputlist.py              |   3 +-
 pyiron_base/utils/deprecate.py                | 195 ------------------
 tests/generic/test_util.py                    | 118 -----------
 14 files changed, 15 insertions(+), 325 deletions(-)
 delete mode 100644 pyiron_base/utils/deprecate.py

diff --git a/pyiron_base/__init__.py b/pyiron_base/__init__.py
index 0faab3f7b..4700a57a2 100644
--- a/pyiron_base/__init__.py
+++ b/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
@@ -47,6 +46,7 @@
 
 # Expose snippets references in base API for backwards compatibility
 from pyiron_snippets.import_alarm import ImportAlarm
+from pyiron_snippets.deprecate import Deprecator, deprecate, deprecate_soon
 
 # Internal init
 from ._version import get_versions
diff --git a/pyiron_base/database/generic.py b/pyiron_base/database/generic.py
index 0b073a03d..2e2c0813d 100644
--- a/pyiron_base/database/generic.py
+++ b/pyiron_base/database/generic.py
@@ -10,8 +10,8 @@
 import re
 import os
 from datetime import datetime
-from pyiron_base.utils.deprecate import deprecate
 import pandas
+from pyiron_snippets.deprecate import deprecate
 from sqlalchemy import (
     create_engine,
     MetaData,
diff --git a/pyiron_base/database/interface.py b/pyiron_base/database/interface.py
index a7d2df0c6..c75429ab6 100644
--- a/pyiron_base/database/interface.py
+++ b/pyiron_base/database/interface.py
@@ -11,8 +11,8 @@
 import warnings
 import numpy as np
 import re
-from pyiron_base.utils.deprecate import deprecate
 import pandas
+from pyiron_snippets.deprecate import deprecate
 import typing
 import fnmatch
 
diff --git a/pyiron_base/jobs/datamining.py b/pyiron_base/jobs/datamining.py
index 5206e984e..245e531a5 100644
--- a/pyiron_base/jobs/datamining.py
+++ b/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
diff --git a/pyiron_base/jobs/job/core.py b/pyiron_base/jobs/job/core.py
index af2202f1b..62b33add0 100644
--- a/pyiron_base/jobs/job/core.py
+++ b/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"
diff --git a/pyiron_base/jobs/job/extension/server/generic.py b/pyiron_base/jobs/job/extension/server/generic.py
index 3f764ff53..7fea939cf 100644
--- a/pyiron_base/jobs/job/extension/server/generic.py
+++ b/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
 
diff --git a/pyiron_base/jobs/job/generic.py b/pyiron_base/jobs/job/generic.py
index 3a558ed40..fd46386d2 100644
--- a/pyiron_base/jobs/job/generic.py
+++ b/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
diff --git a/pyiron_base/jobs/job/runfunction.py b/pyiron_base/jobs/job/runfunction.py
index 547ba3a67..a774fd589 100644
--- a/pyiron_base/jobs/job/runfunction.py
+++ b/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
diff --git a/pyiron_base/jobs/master/parallel.py b/pyiron_base/jobs/master/parallel.py
index 9c2bb571b..d83ad5839 100644
--- a/pyiron_base/jobs/master/parallel.py
+++ b/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__ = (
diff --git a/pyiron_base/project/generic.py b/pyiron_base/project/generic.py
index a8a395edf..3b95847bb 100644
--- a/pyiron_base/project/generic.py
+++ b/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
diff --git a/pyiron_base/storage/hdfio.py b/pyiron_base/storage/hdfio.py
index 0a4a696e1..c0d62210d 100644
--- a/pyiron_base/storage/hdfio.py
+++ b/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,
diff --git a/pyiron_base/storage/inputlist.py b/pyiron_base/storage/inputlist.py
index 81c52c63f..68970a3b8 100644
--- a/pyiron_base/storage/inputlist.py
+++ b/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):
diff --git a/pyiron_base/utils/deprecate.py b/pyiron_base/utils/deprecate.py
deleted file mode 100644
index f9a7bf913..000000000
--- a/pyiron_base/utils/deprecate.py
+++ /dev/null
@@ -1,195 +0,0 @@
-# coding: utf-8
-# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
-# Distributed under the terms of "New BSD License", see the LICENSE file.
-
-"""
-Utility functions used in pyiron.
-In order to be accessible from anywhere in pyiron, they *must* remain free of any imports from pyiron!
-"""
-
-from copy import copy
-import functools
-import types
-import warnings
-
-__author__ = "Joerg Neugebauer, Jan Janssen"
-__copyright__ = (
-    "Copyright 2020, Max-Planck-Institut für Eisenforschung GmbH - "
-    "Computational Materials Design (CM) Department"
-)
-__version__ = "1.0"
-__maintainer__ = "Jan Janssen"
-__email__ = "janssen@mpie.de"
-__status__ = "production"
-__date__ = "Sep 1, 2017"
-
-
-class Deprecator:
-    """
-    Decorator class to mark functions and methods as deprecated with a uniform
-    warning message at the time the function is called.  The message has the
-    form
-
-        {function_name} is deprecated: {message}. It is not guaranteed to be in
-        service after {version}.
-
-    unless `pending=True` was given.  Then the message will be
-
-        {function_name} will be deprecated in a future version: {message}.
-
-    If message and version are not initialized or given during the decorating
-    call the respective parts are left out from the message.
-
-    >>> deprecate = Deprecator()
-    >>> @deprecate
-    ... def foo(a, b):
-    ...     pass
-    >>> foo(1, 2)
-    DeprecationWarning: __main__.foo is deprecated
-
-    >>> @deprecate("use bar() instead")
-    ... def foo(a, b):
-    ...     pass
-    >>> foo(1, 2)
-    DeprecationWarning: __main__.foo is deprecated: use bar instead
-
-    >>> @deprecate("use bar() instead", version="0.4.0")
-    ... def foo(a, b):
-    ...     pass
-    >>> foo(1, 2)
-    DeprecationWarning: __main__.foo is deprecated: use bar instead.  It is not
-    guaranteed to be in service in vers. 0.4.0
-
-    >>> deprecate = Deprecator(message="pyiron says no!", version="0.5.0")
-    >>> @deprecate
-    ... def foo(a, b):
-    ...     pass
-    >>> foo(1, 2)
-    DeprecationWarning: __main__.foo is deprecated: pyiron says no!  It is not
-    guaranteed to be in service in vers. 0.5.0
-
-    Alternatively the decorator can also be called with `arguments` set to a dictionary mapping names of keyword
-    arguments to deprecation messages.  In this case the warning will only be emitted when the decorated function is
-    called with arguments in that dictionary.
-
-    >>> deprecate = Deprecator()
-    >>> @deprecate(arguments={"bar": "use baz instead."})
-    ... def foo(bar=None, baz=None):
-    ...     pass
-    >>> foo(baz=True)
-    >>> foo(bar=True)
-    DeprecationWarning: __main__.foo(bar=True) is deprecated: use baz instead.
-
-    As a short cut, it is also possible to pass the values in the arguments dict directly as keyword arguments to the
-    decorator.
-
-    >>> @deprecate(bar="use baz instead.")
-    ... def foo(bar=None, baz=None):
-    ...     pass
-    >>> foo(baz=True)
-    >>> foo(bar=True)
-    DeprecationWarning: __main__.foo(bar=True)  is deprecated: use baz instead.
-    """
-
-    def __init__(self, message=None, version=None, pending=False):
-        """
-        Initialize default values for deprecation message and version.
-
-        Args:
-            message (str): default deprecation message
-            version (str): default version after which the function might be removed
-            pending (bool): only warn about future deprecation, warning category will be PendingDeprecationWarning
-                instead of DeprecationWarning
-        """
-        self.message = message
-        self.version = version
-        self.category = PendingDeprecationWarning if pending else DeprecationWarning
-
-    def __copy__(self):
-        cp = type(self)(message=self.message, version=self.version)
-        cp.category = self.category
-        return cp
-
-    def __call__(self, message=None, version=None, arguments=None, **kwargs):
-        depr = copy(self)
-        if isinstance(message, types.FunctionType):
-            return depr.__deprecate_function(message)
-        else:
-            depr.message = message
-            depr.version = version
-            depr.arguments = arguments if arguments is not None else {}
-            depr.arguments.update(kwargs)
-            return depr.wrap
-
-    def _build_message(self):
-        if self.category == PendingDeprecationWarning:
-            message_format = "{} will be deprecated"
-        else:
-            message_format = "{} is deprecated"
-
-        if self.message is not None:
-            message_format += ": {}.".format(self.message)
-        else:
-            message_format += "."
-
-        if self.version is not None:
-            message_format += (
-                " It is not guaranteed to be in service in vers. {}".format(
-                    self.version
-                )
-            )
-
-        return message_format
-
-    def __deprecate_function(self, function):
-        message = self._build_message().format(
-            "{}.{}".format(function.__module__, function.__name__)
-        )
-
-        @functools.wraps(function)
-        def decorated(*args, **kwargs):
-            warnings.warn(message, category=self.category, stacklevel=2)
-            return function(*args, **kwargs)
-
-        return decorated
-
-    def __deprecate_argument(self, function):
-        message_format = self._build_message()
-
-        @functools.wraps(function)
-        def decorated(*args, **kwargs):
-            for kw in kwargs:
-                if kw in self.arguments:
-                    warnings.warn(
-                        message_format.format(
-                            "{}.{}({}={})".format(
-                                function.__module__, function.__name__, kw, kwargs[kw]
-                            )
-                        ),
-                        category=self.category,
-                        stacklevel=2,
-                    )
-            return function(*args, **kwargs)
-
-        return decorated
-
-    def wrap(self, function):
-        """
-        Wrap the given function to emit a DeprecationWarning at call time.  The warning message is constructed from the
-        given message and version.  If :attr:`.arguments` is set then the warning is only emitted, when the decorated
-        function is called with keyword arguments found in that dictionary.
-
-        Args:
-            function (function): function to mark as deprecated
-
-        Return:
-            function: raises DeprecationWarning when given function is called
-        """
-        if not self.arguments:
-            return self.__deprecate_function(function)
-        else:
-            return self.__deprecate_argument(function)
-
-
-deprecate = Deprecator()
-deprecate_soon = Deprecator(pending=True)
diff --git a/tests/generic/test_util.py b/tests/generic/test_util.py
index b31139bfc..87c70db84 100644
--- a/tests/generic/test_util.py
+++ b/tests/generic/test_util.py
@@ -5,7 +5,6 @@
 import unittest
 import warnings
 from pyiron_base.utils.instance import static_isinstance
-from pyiron_base.utils.deprecate import deprecate, deprecate_soon
 from pyiron_base._tests import PyironTestCase
 
 
@@ -27,122 +26,5 @@ def test_static_isinstance(self):
         self.assertRaises(TypeError, static_isinstance, list(), 1)
 
 
-class TestDeprecator(PyironTestCase):
-    def test_deprecate(self):
-        """Function decorated with `deprecate` should raise a warning."""
-
-        @deprecate
-        def foo(a):
-            return 2 * a
-
-        @deprecate("use baz instead", version="0.2.0")
-        def bar(a):
-            return 4 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1), 2, "Decorated function does not return original " "return value"
-            )
-        self.assertTrue(len(w) > 0, "No warning raised!")
-        self.assertEqual(
-            w[0].category,
-            DeprecationWarning,
-            "Raised warning is not a DeprecationWarning",
-        )
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                bar(1), 4, "Decorated function does not return original " "return value"
-            )
-
-        expected_message = (
-            "use baz instead. It is not guaranteed to be in " "service in vers. 0.2.0"
-        )
-        self.assertTrue(
-            w[0].message.args[0].endswith(expected_message),
-            "Warning message does not reflect decorator arguments.",
-        )
-
-        @deprecate_soon
-        def baz(a):
-            return 3 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                baz(1), 3, "Decorated function does not return original " "return value"
-            )
-        self.assertEqual(
-            w[0].category,
-            PendingDeprecationWarning,
-            "Raised warning is not a PendingDeprecationWarning",
-        )
-
-    def test_deprecate_args(self):
-        """DeprecationWarning should only be raised when the given arguments occur."""
-
-        @deprecate(arguments={"bar": "use foo instead"})
-        def foo(a, foo=None, bar=None):
-            return 2 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, bar=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertTrue(len(w) > 0, "No warning raised!")
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, foo=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertEqual(
-            len(w), 0, "Warning raised, but deprecated argument was not given."
-        )
-
-    def test_deprecate_kwargs(self):
-        """DeprecationWarning should only be raised when the given arguments occur, also when given via kwargs."""
-
-        @deprecate(bar="use baz instead")
-        def foo(a, bar=None, baz=None):
-            return 2 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, bar=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertTrue(len(w) > 0, "No warning raised!")
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, baz=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertEqual(
-            len(w), 0, "Warning raised, but deprecated argument was not given."
-        )
-
-    def test_instances(self):
-        """Subsequent calls to a Deprecator instance must not interfere with each other."""
-
-        @deprecate(bar="use baz instead")
-        def foo(bar=None, baz=None):
-            pass
-
-        @deprecate(baz="use bar instead")
-        def food(bar=None, baz=None):
-            pass
-
-        with warnings.catch_warnings(record=True) as w:
-            foo(bar=True)
-            food(baz=True)
-        self.assertEqual(len(w), 2, "Not all warnings preserved.")
-
-
 if __name__ == "__main__":
     unittest.main()

From 96387c2ac391dedf86489c44c59782f454546ecb Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Mon, 3 Jun 2024 10:11:35 -0700
Subject: [PATCH 02/13] [patch] replace logger with snippets version

i.e. pyiron_base.state.logger.logger with pyiron_snippets.logger.logger. The original location leaves a re-direct for backwards compatibility.
---
 pyiron_base/database/generic.py   |  2 +-
 pyiron_base/database/interface.py |  2 +-
 pyiron_base/database/manager.py   |  2 +-
 pyiron_base/state/__init__.py     |  2 +-
 pyiron_base/state/logger.py       |  2 ++
 pyiron_base/state/settings.py     |  2 +-
 pyiron_base/utils/error.py        |  2 +-
 tests/state/test_logger.py        | 51 -------------------------------
 8 files changed, 8 insertions(+), 57 deletions(-)
 delete mode 100644 tests/state/test_logger.py

diff --git a/pyiron_base/database/generic.py b/pyiron_base/database/generic.py
index 2e2c0813d..dd1292e5b 100644
--- a/pyiron_base/database/generic.py
+++ b/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
 import pandas
 from pyiron_snippets.deprecate import deprecate
+from pyiron_snippets.logger import logger
 from sqlalchemy import (
     create_engine,
     MetaData,
diff --git a/pyiron_base/database/interface.py b/pyiron_base/database/interface.py
index c75429ab6..d100f8d0e 100644
--- a/pyiron_base/database/interface.py
+++ b/pyiron_base/database/interface.py
@@ -5,7 +5,6 @@
 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
@@ -13,6 +12,7 @@
 import re
 import pandas
 from pyiron_snippets.deprecate import deprecate
+from pyiron_snippets.logger import logger
 import typing
 import fnmatch
 
diff --git a/pyiron_base/database/manager.py b/pyiron_base/database/manager.py
index 6974075ec..76805376a 100644
--- a/pyiron_base/database/manager.py
+++ b/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
diff --git a/pyiron_base/state/__init__.py b/pyiron_base/state/__init__.py
index db573c65f..fa8308d77 100644
--- a/pyiron_base/state/__init__.py
+++ b/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
 
diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index b80d48055..ab2111281 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1,3 +1,5 @@
+# Redirect to snippets implementation for backwards compatibility
+from pyiron_snippets.logger import logger
 # coding: utf-8
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
diff --git a/pyiron_base/state/settings.py b/pyiron_base/state/settings.py
index 2e093fca1..3412e602c 100644
--- a/pyiron_base/state/settings.py
+++ b/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
diff --git a/pyiron_base/utils/error.py b/pyiron_base/utils/error.py
index e7af617d6..62ee44f80 100644
--- a/pyiron_base/utils/error.py
+++ b/pyiron_base/utils/error.py
@@ -11,7 +11,7 @@
 import time
 from typing import Callable, TypeVar, Type, Tuple, Optional, Union
 
-from pyiron_base.state.logger import logger
+from pyiron_snippets.logger import logger
 
 __author__ = "Joerg Neugebauer, Jan Janssen"
 __copyright__ = (
diff --git a/tests/state/test_logger.py b/tests/state/test_logger.py
deleted file mode 100644
index 11589f957..000000000
--- a/tests/state/test_logger.py
+++ /dev/null
@@ -1,51 +0,0 @@
-# coding: utf-8
-# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
-# Distributed under the terms of "New BSD License", see the LICENSE file.
-
-from unittest import TestCase
-from pyiron_base.state.logger import logger
-import os
-import shutil
-
-
-class TestLogger(TestCase):
-    @classmethod
-    def setUpClass(cls) -> None:
-        cls.logger_file = os.path.join(os.getcwd(), "pyiron.log")
-        cls.backup_file = os.path.join(os.getcwd(), "pyiron.log.test_logger_backup")
-        shutil.copy(cls.logger_file, cls.backup_file)
-
-    @classmethod
-    def tearDownClass(cls) -> None:
-        shutil.move(cls.backup_file, cls.logger_file)
-
-    def test_logger(self):
-        logsize = os.path.getsize(self.logger_file)
-        logger.warning("Here is a warning")
-        self.assertGreater(os.path.getsize(self.logger_file), logsize)
-
-    def test_set_logging_level(self):
-        logger.set_logging_level(10)
-        self.assertEqual(
-            10, logger.getEffectiveLevel(), "Overall logger level should match input"
-        )
-        self.assertEqual(
-            10, logger.handlers[0].level, "Stream level should match input"
-        )
-        self.assertEqual(10, logger.handlers[0].level, "File level should match input")
-
-        logger.set_logging_level(20, channel=1)
-        self.assertEqual(
-            10,
-            logger.getEffectiveLevel(),
-            "Overall logger level should not have changed",
-        )
-        self.assertEqual(
-            10, logger.handlers[0].level, "Stream level should not have changed"
-        )
-        self.assertEqual(20, logger.handlers[1].level, "File level should match input")
-
-        logger.set_logging_level("WARNING", channel=0)
-        self.assertEqual(
-            30, logger.handlers[0].level, "Should be able to set by string"
-        )

From 7d7dbd90312983cd519974a507097ace8b1effff Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Mon, 3 Jun 2024 10:15:16 -0700
Subject: [PATCH 03/13] Remove the old logging stuff

---
 pyiron_base/state/logger.py | 73 -------------------------------------
 1 file changed, 73 deletions(-)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index ab2111281..2a8b5d79d 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1,75 +1,2 @@
 # Redirect to snippets implementation for backwards compatibility
 from pyiron_snippets.logger import logger
-# coding: utf-8
-# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
-# Distributed under the terms of "New BSD License", see the LICENSE file.
-
-import logging
-from types import MethodType
-
-__author__ = "Joerg Neugebauer"
-__copyright__ = (
-    "Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
-    "Computational Materials Design (CM) Department"
-)
-__version__ = "1.0"
-__maintainer__ = "Jan Janssen"
-__email__ = "janssen@mpie.de"
-__status__ = "production"
-__date__ = "Sep 1, 2017"
-
-
-"""
-Set the logging level for pyiron
-"""
-
-
-def set_logging_level(self, level, channel=None):
-    """
-    Set level for logger
-
-    Args:
-        level (str): 'DEBUG, INFO, WARN'
-        channel (int): 0: file_log, 1: stream, None: both
-    """
-
-    if channel:
-        self.handlers[channel].setLevel(level)
-    else:
-        self.handlers[0].setLevel(level)
-        self.handlers[1].setLevel(level)
-
-
-def setup_logger():
-    """
-    Setup logger - logs are written to pyiron.log
-
-    Returns:
-        logging.getLogger: Logger
-    """
-    logger = logging.getLogger("pyiron_log")
-    logger.setLevel(logging.DEBUG)
-
-    formatter = logging.Formatter(
-        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
-    )
-
-    ch = logging.StreamHandler()
-    ch.setLevel(logging.WARN)
-    ch.setFormatter(formatter)
-    logger.addHandler(ch)
-
-    try:
-        fh = logging.FileHandler("pyiron.log")
-    except PermissionError:
-        pass
-    else:
-        fh.setLevel(logging.INFO)
-        fh.setFormatter(formatter)
-        logger.addHandler(fh)
-
-    return logger
-
-
-logger = setup_logger()
-logger.set_logging_level = MethodType(set_logging_level, logger)

From 36d70faae1dddfeb881a00dfcaf4c8e42d57bb5d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Jun 2024 17:15:28 +0000
Subject: [PATCH 04/13] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyiron_base/state/logger.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index 2a8b5d79d..edfa76051 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1,2 +1 @@
 # Redirect to snippets implementation for backwards compatibility
-from pyiron_snippets.logger import logger

From e18cb5a43749eaae841f83856e2b3c217e14a9c2 Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Mon, 3 Jun 2024 10:28:13 -0700
Subject: [PATCH 05/13] Override the robot

---
 pyiron_base/state/logger.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index edfa76051..193a13551 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1 +1,2 @@
 # Redirect to snippets implementation for backwards compatibility
+from pyiron_snippets.logger import logger
\ No newline at end of file

From d7586c6c9b00f58ea0e83c6931963cfc96d894e2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Jun 2024 17:28:24 +0000
Subject: [PATCH 06/13] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyiron_base/state/logger.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index 193a13551..edfa76051 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1,2 +1 @@
 # Redirect to snippets implementation for backwards compatibility
-from pyiron_snippets.logger import logger
\ No newline at end of file

From af38e0416315dc2d49dcd0aa49e28e95c1a82ca9 Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Mon, 3 Jun 2024 10:33:44 -0700
Subject: [PATCH 07/13] Try again to bypass the bot by adding --no-verify
 locally during my commit

---
 pyiron_base/state/logger.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index edfa76051..193a13551 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1 +1,2 @@
 # Redirect to snippets implementation for backwards compatibility
+from pyiron_snippets.logger import logger
\ No newline at end of file

From 20f84cbab0510fccaa4fa4ab99399a80987d6d79 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 3 Jun 2024 17:35:03 +0000
Subject: [PATCH 08/13] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pyiron_base/state/logger.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index 193a13551..edfa76051 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1,2 +1 @@
 # Redirect to snippets implementation for backwards compatibility
-from pyiron_snippets.logger import logger
\ No newline at end of file

From f62970871f7245a6a1e60bb4ab8372fca9fb333c Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Mon, 3 Jun 2024 10:38:29 -0700
Subject: [PATCH 09/13] [salty] use the import

---
 pyiron_base/state/logger.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
index edfa76051..8b0274832 100644
--- a/pyiron_base/state/logger.py
+++ b/pyiron_base/state/logger.py
@@ -1 +1,11 @@
 # Redirect to snippets implementation for backwards compatibility
+from pyiron_snippets.logger import logger
+
+the_linter_is_smarter_than_me = False
+if the_linter_is_smarter_than_me:
+    print(
+        f"It sure is a good thing {logger} is not unused! Sure would be a shame if "
+        f"we were intentionally adding an unused import for the sake of backwards "
+        f"compatibility, to make an object accessible from a different import path."
+        f"That would be a silly flesh-body thing to do thouh, and us robots know best."
+    )

From a7145e0cc1d5c21ec8f128793b447ecb903924d2 Mon Sep 17 00:00:00 2001
From: liamhuber <liamhuber@greyhavensolutions.com>
Date: Mon, 3 Jun 2024 10:41:43 -0700
Subject: [PATCH 10/13] [minor] remove the backwards compatibility redirects

---
 pyiron_base/__init__.py     |  8 --------
 pyiron_base/state/logger.py | 11 -----------
 2 files changed, 19 deletions(-)
 delete mode 100644 pyiron_base/state/logger.py

diff --git a/pyiron_base/__init__.py b/pyiron_base/__init__.py
index 4700a57a2..e0149a6bd 100644
--- a/pyiron_base/__init__.py
+++ b/pyiron_base/__init__.py
@@ -44,10 +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
-from pyiron_snippets.deprecate import Deprecator, deprecate, deprecate_soon
-
 # 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,
diff --git a/pyiron_base/state/logger.py b/pyiron_base/state/logger.py
deleted file mode 100644
index 8b0274832..000000000
--- a/pyiron_base/state/logger.py
+++ /dev/null
@@ -1,11 +0,0 @@
-# Redirect to snippets implementation for backwards compatibility
-from pyiron_snippets.logger import logger
-
-the_linter_is_smarter_than_me = False
-if the_linter_is_smarter_than_me:
-    print(
-        f"It sure is a good thing {logger} is not unused! Sure would be a shame if "
-        f"we were intentionally adding an unused import for the sake of backwards "
-        f"compatibility, to make an object accessible from a different import path."
-        f"That would be a silly flesh-body thing to do thouh, and us robots know best."
-    )

From 11e44bc29845487f3c49ca704836aca96f582fe0 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 3 Jun 2024 20:44:10 +0200
Subject: [PATCH 11/13] Update environment-docs.yml

---
 .ci_support/environment-docs.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.ci_support/environment-docs.yml b/.ci_support/environment-docs.yml
index 33e19faee..05fdd9d47 100644
--- a/.ci_support/environment-docs.yml
+++ b/.ci_support/environment-docs.yml
@@ -16,13 +16,8 @@ dependencies:
 - pint =0.23
 - psutil =5.9.8
 - pyfileindex =0.0.24
-<<<<<<< snippets_deprecate
-- pyiron_snippets =0.1.0
-- pympipool =0.8.3
-=======
 - pyiron_snippets =0.1.1
 - pympipool =0.8.4
->>>>>>> main
 - pysqa =0.1.20
 - pytables =3.9.2
 - sqlalchemy =2.0.30

From 77daec34a4e93a95f28461f933b32ec50002fcf8 Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 3 Jun 2024 20:53:00 +0200
Subject: [PATCH 12/13] Update test_util.py

---
 tests/generic/test_util.py | 124 -------------------------------------
 1 file changed, 124 deletions(-)

diff --git a/tests/generic/test_util.py b/tests/generic/test_util.py
index 1aec8bddf..87c70db84 100644
--- a/tests/generic/test_util.py
+++ b/tests/generic/test_util.py
@@ -5,10 +5,6 @@
 import unittest
 import warnings
 from pyiron_base.utils.instance import static_isinstance
-<<<<<<< snippets_deprecate
-=======
-from pyiron_base.utils.deprecate import deprecate, deprecate_soon
->>>>>>> main
 from pyiron_base._tests import PyironTestCase
 
 
@@ -30,125 +26,5 @@ def test_static_isinstance(self):
         self.assertRaises(TypeError, static_isinstance, list(), 1)
 
 
-<<<<<<< snippets_deprecate
-=======
-class TestDeprecator(PyironTestCase):
-    def test_deprecate(self):
-        """Function decorated with `deprecate` should raise a warning."""
-
-        @deprecate
-        def foo(a):
-            return 2 * a
-
-        @deprecate("use baz instead", version="0.2.0")
-        def bar(a):
-            return 4 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1), 2, "Decorated function does not return original " "return value"
-            )
-        self.assertTrue(len(w) > 0, "No warning raised!")
-        self.assertEqual(
-            w[0].category,
-            DeprecationWarning,
-            "Raised warning is not a DeprecationWarning",
-        )
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                bar(1), 4, "Decorated function does not return original " "return value"
-            )
-
-        expected_message = (
-            "use baz instead. It is not guaranteed to be in " "service in vers. 0.2.0"
-        )
-        self.assertTrue(
-            w[0].message.args[0].endswith(expected_message),
-            "Warning message does not reflect decorator arguments.",
-        )
-
-        @deprecate_soon
-        def baz(a):
-            return 3 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                baz(1), 3, "Decorated function does not return original " "return value"
-            )
-        self.assertEqual(
-            w[0].category,
-            PendingDeprecationWarning,
-            "Raised warning is not a PendingDeprecationWarning",
-        )
-
-    def test_deprecate_args(self):
-        """DeprecationWarning should only be raised when the given arguments occur."""
-
-        @deprecate(arguments={"bar": "use foo instead"})
-        def foo(a, foo=None, bar=None):
-            return 2 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, bar=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertTrue(len(w) > 0, "No warning raised!")
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, foo=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertEqual(
-            len(w), 0, "Warning raised, but deprecated argument was not given."
-        )
-
-    def test_deprecate_kwargs(self):
-        """DeprecationWarning should only be raised when the given arguments occur, also when given via kwargs."""
-
-        @deprecate(bar="use baz instead")
-        def foo(a, bar=None, baz=None):
-            return 2 * a
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, bar=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertTrue(len(w) > 0, "No warning raised!")
-
-        with warnings.catch_warnings(record=True) as w:
-            self.assertEqual(
-                foo(1, baz=True),
-                2,
-                "Decorated function does not return original " "return value",
-            )
-        self.assertEqual(
-            len(w), 0, "Warning raised, but deprecated argument was not given."
-        )
-
-    def test_instances(self):
-        """Subsequent calls to a Deprecator instance must not interfere with each other."""
-
-        @deprecate(bar="use baz instead")
-        def foo(bar=None, baz=None):
-            pass
-
-        @deprecate(baz="use bar instead")
-        def food(bar=None, baz=None):
-            pass
-
-        with warnings.catch_warnings(record=True) as w:
-            foo(bar=True)
-            food(baz=True)
-        self.assertEqual(len(w), 2, "Not all warnings preserved.")
-
-
->>>>>>> main
 if __name__ == "__main__":
     unittest.main()

From 3fcdf15abfe013e84cfd00b1765c070295726c7a Mon Sep 17 00:00:00 2001
From: Jan Janssen <jan-janssen@users.noreply.github.com>
Date: Mon, 3 Jun 2024 21:04:53 +0200
Subject: [PATCH 13/13] Update __init__.py

---
 pyiron_base/__init__.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pyiron_base/__init__.py b/pyiron_base/__init__.py
index 3db03b253..e0149a6bd 100644
--- a/pyiron_base/__init__.py
+++ b/pyiron_base/__init__.py
@@ -44,9 +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