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>

Author: 3 people

.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