Release 0.9.0 (#217)

The 0.9.0 release PR containing additional prior maintenance PRs (#198, #211)
emdgroup · May 21, 2024 · 3a67df4 · 3a67df4
2 parents ae5bad0 + f4d0ae8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,25 +4,25 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Unreleased
+## [0.9.0] - 2024-05-21
 ### Added
-- `mypy` for search space and objectives
 - Class hierarchy for objectives
-- Deserialization is now also possible from optional class name abbreviations
 - `AdditiveKernel`, `LinearKernel`, `MaternKernel`, `PeriodicKernel`, 
   `PiecewisePolynomialKernel`, `PolynomialKernel`, `ProductKernel`, `RBFKernel`, 
-  `RFFKernel`, `RQKernel`, `ScaleKernel` classes for specifying kernels
-- `GammaPrior`, `HalfCauchyPrior`, `NormalPrior`, `HalfNormalPrior`, `LogNormalPrior`
-  and `SmoothedBoxPrior` classes for specifying priors 
+  `RFFKernel`, `RQKernel`, `ScaleKernel` classes
 - `KernelFactory` protocol enabling context-dependent construction of kernels
 - Preset mechanism for `GaussianProcessSurrogate`
 - `hypothesis` strategies and roundtrip test for kernels, constraints, objectives,
   priors and acquisition functions
 - New acquisition functions: `qSR`, `qNEI`, `LogEI`, `qLogEI`, `qLogNEI`
-- Serialization user guide
+- `GammaPrior`, `HalfCauchyPrior`, `NormalPrior`, `HalfNormalPrior`, `LogNormalPrior`
+  and `SmoothedBoxPrior` classes
+- Possibility to deserialize classes from optional class name abbreviations
 - Basic deserialization tests using different class type specifiers
+- Serialization user guide
 - Environment variables user guide
 - Utility for estimating memory requirements of discrete product search space
+- `mypy` for search space and objectives
 
 ### Changed
 - Reorganized acquisition.py into `acquisition` subpackage
@@ -61,6 +61,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `acquisition_function_cls` constructor parameter for `BayesianRecommender`
 - `VarUCB` and `qVarUCB` acquisition functions
 
+### Expired Deprecations (from 0.6.*)
+- `BayBE` class
+- `baybe.surrogate` module
+- `baybe.targets.Objective` class
+- `baybe.strategies.Strategy` class
+
 ## [0.8.2] - 2024-03-27
 ### Added
 - Simulation user guide

diff --git a/README.md b/README.md
@@ -72,7 +72,7 @@ In cases where we are confronted with multiple (potentially conflicting) targets
 the `DesirabilityObjective` can be used instead. It allows to define additional
 settings, such as how these targets should be balanced.
 For more details, see the
-[objectives section](https://emdgroup.github.io/baybe/userguide/objective.html)
+[objectives section](https://emdgroup.github.io/baybe/userguide/objectives.html)
 of the user guide.
 
 ### Defining the Search Space
@@ -307,7 +307,7 @@ host machine names are anonymized with via truncated hashing.
   `telemetry` module.
 - You can always deactivate all telemetry by setting the environment variable 
   `BAYBE_TELEMETRY_ENABLED` to `false` or `off`. For details please consult
-  [this page](https://emdgroup.github.io/baybe/_autosummary/baybe.telemetry.html).
+  [this page](https://emdgroup.github.io/baybe/userguide/envvars.html#telemetry).
 - If you want to be absolutely sure, you can uninstall internet related packages such
   as `opentelemetry*` or its secondary dependencies from the environment. Due to the
   inability of specifying opt-out dependencies, these are installed by default, but the

diff --git a/baybe/__init__.py b/baybe/__init__.py
@@ -3,7 +3,6 @@
 import warnings
 
 from baybe.campaign import Campaign
-from baybe.deprecation import BayBE
 
 # Show deprecation warnings
 warnings.filterwarnings("default", category=DeprecationWarning, module="baybe")
@@ -52,7 +51,6 @@ def infer_version() -> str:  # pragma: no cover
 __version__ = infer_version()
 __all__ = [
     "__version__",
-    "BayBE",
     "Campaign",
 ]
 

diff --git a/baybe/deprecation.py b/baybe/deprecation.py
@@ -2,22 +2,6 @@
 
 import warnings
 
-from attrs import define
-
-from baybe import Campaign
-
-
-@define
-class BayBE(Campaign):
-    """A :class:`baybe.campaign.Campaign` alias for backward compatibility."""
-
-    def __attrs_pre_init__(self):
-        warnings.warn(
-            "The 'BayBE' class is deprecated and will be removed in a future version. "
-            "Please use the 'Campaign' class instead.",
-            DeprecationWarning,
-        )
-
 
 def compatibilize_config(config: dict) -> dict:
     """Turn a legacy-format config into the new format."""

diff --git a/baybe/strategies/__init__.py b/baybe/strategies/__init__.py
@@ -2,7 +2,6 @@
 
 from baybe.strategies.deprecation import (
     SequentialStrategy,
-    Strategy,
     StreamingSequentialStrategy,
     TwoPhaseStrategy,
 )
@@ -11,5 +10,4 @@
     "SequentialStrategy",
     "StreamingSequentialStrategy",
     "TwoPhaseStrategy",
-    "Strategy",
 ]
diff --git a/baybe/strategies/deprecation.py b/baybe/strategies/deprecation.py
@@ -9,18 +9,6 @@
 )
 
 
-def Strategy(*args, **kwargs) -> TwoPhaseMetaRecommender:
-    """A ``Strategy`` alias for backward compatibility."""  # noqa: D401 (imperative mood)
-    warnings.warn(
-        f"Using 'Strategy' directly is deprecated and will be removed in a future "
-        f"version. Please use 'recommenders.{TwoPhaseMetaRecommender.__name__}' class "
-        f"instead.",
-        DeprecationWarning,
-    )
-
-    return TwoPhaseMetaRecommender(*args, **kwargs)
-
-
 def TwoPhaseStrategy(*args, **kwargs) -> TwoPhaseMetaRecommender:
     """A ``TwoPhaseStrategy`` alias for backward compatibility."""  # noqa: D401 (imperative mood)
     warnings.warn(

diff --git a/baybe/surrogate.py b/baybe/surrogate.py
diff --git a/baybe/targets/__init__.py b/baybe/targets/__init__.py
@@ -1,12 +1,10 @@
 """BayBE targets."""
 
-from baybe.targets.deprecation import Objective
 from baybe.targets.enum import TargetMode, TargetTransformation
 from baybe.targets.numerical import NumericalTarget
 
 __all__ = [
     "NumericalTarget",
-    "Objective",
     "TargetMode",
     "TargetTransformation",
 ]
diff --git a/baybe/targets/deprecation.py b/baybe/targets/deprecation.py
diff --git a/baybe/telemetry.py b/baybe/telemetry.py
@@ -1,4 +1,7 @@
-"""Telemetry functionality for BayBE."""
+"""Telemetry functionality for BayBE.
+
+For more details, see https://emdgroup.github.io/baybe/userguide/envvars.html#telemetry
+"""
 
 import getpass
 import hashlib

diff --git a/docs/templates/custom-module-template.rst b/docs/templates/custom-module-template.rst
@@ -61,7 +61,7 @@
    :template: custom-module-template.rst
    :recursive:
 {% for item in modules %}
-{% if not item in ("baybe.deprecation", "baybe.surrogate", "baybe.strategies.deprecation", "baybe.targets.deprecation", "baybe.objectives.deprecation") %}
+{% if not item in ("baybe.deprecation", "baybe.strategies.deprecation", "baybe.objectives.deprecation") %}
    {{ item }}
 {%- endif %}
 {%- endfor %}

diff --git a/docs/userguide/campaigns.md b/docs/userguide/campaigns.md
@@ -22,7 +22,7 @@ describe the underlying optimization problem at hand:
 
 | Campaign Specification                     | BayBE Class                                                                               |
 |:-------------------------------------------|:------------------------------------------------------------------------------------------|
-| What should be optimized in the campaign?  | `Objective` ([class](baybe.objectives.base.Objective) / [user guide](./objective))              |
+| What should be optimized in the campaign?  | `Objective` ([class](baybe.objectives.base.Objective) / [user guide](./objectives))              |
 | Which experimental factors can be altered? | `SearchSpace` ([class](baybe.searchspace.core.SearchSpace) / [user guide](./searchspace)) |
 
 Apart from this basic configuration, it is possible to further define the specific

diff --git a/docs/userguide/objective.md → docs/userguide/objectives.md b/docs/userguide/objective.md → docs/userguide/objectives.md
diff --git a/docs/userguide/targets.md b/docs/userguide/targets.md
@@ -5,7 +5,7 @@ experiment and the machine learning core behind BayBE.
 In general, it is expected that you create one [`Target`](baybe.targets.base.Target)
 object for each of your observables.
 The way BayBE treats multiple targets is then controlled via the 
-[`Objective`](../../userguide/objective).
+[`Objective`](../../userguide/objectives).
 
 ## NumericalTarget
 Besides the `name`, a [`NumericalTarget`](baybe.targets.numerical.NumericalTarget)

diff --git a/docs/userguide/userguide.md b/docs/userguide/userguide.md
@@ -4,7 +4,7 @@
 Campaigns <campaigns>
 Constraints <constraints>
 Environment Vars <envvars>
-Objective <objective>
+Objectives <objectives>
 Parameters <parameters>
 Recommenders <recommenders>
 Search Spaces <searchspace>

diff --git a/examples/Multi_Target/Multi_Target_Header.md b/examples/Multi_Target/Multi_Target_Header.md
@@ -1,4 +1,4 @@
 # Multi Target
 
 These examples demonstrate BayBE's
-{doc}`Multi-Target Capabilities </userguide/objective>`.
+{doc}`Multi-Target Capabilities </userguide/objectives>`.
diff --git a/mypy.ini b/mypy.ini
@@ -11,7 +11,7 @@ exclude = (?x)(
           | baybe/deprecation.py
           | baybe/exceptions.py
           | baybe/scaler.py
-          | baybe/surrogate.py
+          | baybe/simulation.py
           )
 
 [mypy-gpytorch.*]

diff --git a/tests/test_deprecations.py b/tests/test_deprecations.py
@@ -5,7 +5,7 @@
 
 import pytest
 
-from baybe import BayBE, Campaign
+from baybe import Campaign
 from baybe.acquisition.base import AcquisitionFunction
 from baybe.exceptions import DeprecationError
 from baybe.objective import Objective as OldObjective
@@ -17,37 +17,16 @@
     FPSRecommender,
     RandomRecommender,
 )
-from baybe.searchspace import SearchSpace
 from baybe.strategies import (
     SequentialStrategy,
-    Strategy,
     StreamingSequentialStrategy,
     TwoPhaseStrategy,
 )
-from baybe.targets import Objective as ObjectiveFromTargets
 from baybe.targets.base import Target
 from baybe.targets.numerical import NumericalTarget
 from baybe.utils.interval import Interval
 
 
-def test_deprecated_baybe_class(parameters, objective):
-    """Using the deprecated ``BayBE`` class raises a warning."""
-    with pytest.warns(DeprecationWarning):
-        BayBE(SearchSpace.from_product(parameters), objective)
-
-
-def test_moved_objective(targets):
-    """Importing ``Objective`` from ``baybe.targets`` raises a warning."""
-    with pytest.warns(DeprecationWarning):
-        ObjectiveFromTargets(mode="SINGLE", targets=targets)
-
-
-def test_renamed_surrogate():
-    """Importing from ``baybe.surrogate`` raises a warning."""
-    with pytest.warns(DeprecationWarning):
-        from baybe.surrogate import GaussianProcessSurrogate  # noqa: F401
-
-
 def test_missing_recommender_type(config):
     """Specifying a recommender without a corresponding type raises a warning."""
     dict_ = json.loads(config)
@@ -65,7 +44,6 @@ def test_missing_recommender_type(config):
 @pytest.mark.parametrize(
     "test_objects",
     [
-        (Strategy, {}),
         (TwoPhaseStrategy, {}),
         (SequentialStrategy, {"recommenders": RECOMMENDERS}),
         (StreamingSequentialStrategy, {"recommenders": RECOMMENDERS}),