Support TF 2.12 and numpy>=1.22 (#99)

Co-authored-by: ST John <st--@users.noreply.github.com>
Co-authored-by: Uri Granta <uri.granta@secondmind.ai>

.github/workflows/quality-check.yaml

@@ -22,7 +22,7 @@ jobs:
  strategy:
  matrix:
  python-version: ["3.7", "3.8", "3.9", "3.10"]
- tensorflow: ["~=2.5.0", "~=2.6.0", "~=2.7.0", "~=2.8.0", "~=2.9.0", "~=2.10.0", "~=2.11.0"]
+ tensorflow: ["~=2.5.0", "~=2.6.0", "~=2.7.0", "~=2.8.0", "~=2.9.0", "~=2.10.0", "~=2.11.0", "~=2.12.0"]
  include:
  - tensorflow: "~=2.5.0"
  keras: "~=2.6.0"
@@ -45,6 +45,9 @@ jobs:
  - tensorflow: "~=2.11.0"
  keras: "~=2.11.0"
  tensorflow-probability: "~=0.19.0"
+ - tensorflow: "~=2.12.0"
+ keras: "~=2.12.0"
+ tensorflow-probability: "~=0.19.0" # sic! no new tfp release
  exclude:
  # These older versions of TensorFlow don't work with Python 3.10:
  - python-version: "3.10"
@@ -53,12 +56,16 @@ jobs:
  tensorflow: "~=2.6.0"
  - python-version: "3.10"
  tensorflow: "~=2.7.0"
+ # These newer versions of TensorFlow don't work with Python 3.7:
+ - python-version: "3.7"
+ tensorflow: "~=2.12.0"
 
  name: Python-${{ matrix.python-version }} tensorflow${{ matrix.tensorflow }}
  env:
  VERSION_TF: ${{ matrix.tensorflow }}
  VERSION_KERAS: ${{ matrix.keras }}
  VERSION_TFP: ${{ matrix.tensorflow-probability }}
+ VERSION_PYTHON: ${{ matrix.python-version }}
  steps:
  - uses: actions/checkout@v3
  - uses: actions/setup-python@v4

Makefile

@@ -25,6 +25,13 @@ LINT_FILE_IGNORES = "$(LIB_NAME)/__init__.py:F401,F403 \
  $(LIB_NAME)/sampling/__init__.py:F401 \
  $(LIB_NAME)/utils/__init__.py:F401"
 
+# Python 3.7 uses a separate test requirements file
+ifeq ("$(VERSION_PYTHON)", "3.7")
+ TEST_REQUIREMENTS = "tests_requirements_37.txt"
+else
+ TEST_REQUIREMENTS = "tests_requirements.txt"
+endif
+
 
 help: ## Shows this help message
  # $(MAKEFILE_LIST) is set by make itself; the following parses the `target: ## help line` format and adds color highlighting
@@ -35,7 +42,7 @@ install: ## Install repo for developement
  @echo "\n=== pip install package with dev requirements =============="
  pip install --upgrade --upgrade-strategy eager \
  -r notebook_requirements.txt \
- -r tests_requirements.txt \
+ -r $(TEST_REQUIREMENTS) \
  tensorflow${VERSION_TF} \
  keras${VERSION_KERAS} \
  tensorflow-probability${VERSION_TFP} \

gpflux/helpers.py

@@ -22,7 +22,7 @@
 import inspect
 import warnings
 from dataclasses import fields
-from typing import List, Optional, Type, TypeVar, Union
+from typing import List, Optional, Type, TypeVar, Union, Any
 
 import numpy as np
 
@@ -261,7 +261,10 @@ def construct_gp_layer(
 T = TypeVar("T")
 
 
-def make_dataclass_from_class(dataclass: Type[T], instance: object, **updates: object) -> T:
+# HACK to get mypy to pass, should be (dataclass: Type[T], ...) -> T:
+# mypy said: gpflux/helpers.py:271: error: Argument 1 to "fields" has incompatible type "Type[T]";
+# expected "Union[DataclassInstance, Type[DataclassInstance]]" [arg-type]
+def make_dataclass_from_class(dataclass: Any, instance: object, **updates: object) -> Any:
  """
  Take a regular object ``instance`` with a superset of fields for a
  :class:`dataclasses.dataclass` (``@dataclass``-decorated class), and return an

gpflux/version.py

@@ -15,4 +15,4 @@
 #
 """Adds __version__"""
 
-__version__ = "0.4.1"
+__version__ = "0.4.2"

setup.py

@@ -9,9 +9,9 @@
  "gpflow>=2.6.3",
  "numpy",
  "scipy",
- "tensorflow>=2.5.0,<2.12.0; platform_system!='Darwin' or platform_machine!='arm64'",
+ "tensorflow>=2.5.0,<2.13.0; platform_system!='Darwin' or platform_machine!='arm64'",
  # NOTE: Support of Apple Silicon MacOS platforms is in an experimental mode
- "tensorflow-macos>=2.5.0,<2.12.0; platform_system=='Darwin' and platform_machine=='arm64'",
+ "tensorflow-macos>=2.5.0,<2.13.0; platform_system=='Darwin' and platform_machine=='arm64'",
  # NOTE: once we require tensorflow-probability>=0.12, we can remove our custom deepcopy handling
  "tensorflow-probability>=0.13.0,<0.20.0",
 ]

tests/gpflux/test_callbacks.py

@@ -136,7 +136,8 @@ def test_tensorboard_callback(tmp_path, model_and_loss, data, update_freq):
  "self_tracked_trackables[3].likelihood.variance",
  }
 
- if Version(tf.__version__) < Version("2.8"):
+ tf_version = Version(tf.__version__)
+ if tf_version < Version("2.8") or tf_version >= Version("2.12"):
  if update_freq == "batch":
  expected_tags |= {
  "batch_loss",

tests_requirements.txt

@@ -4,15 +4,15 @@ codecov
 click==8.0.4
 flake8==4.0.1
 isort==5.10.1
-mypy==0.921
+mypy
 pytest
 pytest-cov
 pytest-random-order
 pytest-mock
 
 # For mypy stubs:
 types-Deprecated
-numpy<1.22.0 # Newer versions of numpy are not compatible with Python 3.7.
+numpy
 
 tqdm
 

tests_requirements_37.txt

@@ -0,0 +1,27 @@
+# Test requirements specific to Python 3.7
+
+# Code quality tools:
+black==21.7b0
+codecov
+click==8.0.4
+flake8==4.0.1
+isort==5.10.1
+mypy
+pytest
+pytest-cov
+pytest-random-order
+pytest-mock
+
+# For mypy stubs:
+types-Deprecated
+numpy<1.22.0 # Newer versions of numpy are not compatible with Python 3.7.
+
+tqdm
+
+# Notebook tests:
+jupytext
+nbformat
+nbconvert
+jupyter_client
+ipykernel
+tornado