Test with Python 3.9 and TF 2.5 (#490)

.github/workflows/develop-checks.yaml

@@ -27,7 +27,17 @@ jobs:
       with:
         python-version: 3.7
     - run: pip install tox
-    - run: tox -e alltests
+    - run: tox -e tests -- --runslow yes
+
+  alltests_latest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - run: pip install tox
+    - run: tox -e tests_latest -- --runslow yes
 
   fulldocs:
     runs-on: ubuntu-latest

.github/workflows/quality-checks.yaml

@@ -48,6 +48,16 @@ jobs:
     - run: pip install tox
     - run: tox -e tests
 
+  tests_latest:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - run: pip install tox
+    - run: tox -e tests_latest
+
   docs:
     runs-on: ubuntu-latest
     steps:

CONTRIBUTING.md

@@ -72,7 +72,7 @@ $ tox -e tests
 
 To save time, some slower tests are not run by default. Run these with:
 ```bash
-$ tox -e alltests
+$ tox -e tests -- --runslow yes
 ```
 
 #### Code formatting

docs/requirements.txt

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# ping sphinx to 3.5 for now to work around https://github.com/plotly/plotly.js/issues/4563
+# pin sphinx to 3.5 for now to work around https://github.com/plotly/plotly.js/issues/4563
 # setting mathjax_path in docs/confg.py to https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js?config=TeX-MML-AM_CHTML
 # SHOULD fix this, but it doesn't seem to quite
 sphinx~=3.5.4

generate_constraints.sh

@@ -41,5 +41,6 @@ generate_for_env common_build/taskipy false
 generate_for_env common_build/types false
 generate_for_env notebooks true
 generate_for_env tests true
+generate_for_env tests/latest true
 
 rm -rf $VENV_DIR

setup.py

@@ -39,10 +39,10 @@
     install_requires=[
         "absl-py",
         "gpflow==2.2.*",
-        "gpflux==0.2.3",
+        "gpflux>=0.2.3",
         "numpy",
         "tensorflow>=2.4",
-        "tensorflow-probability>=0.12,<0.14.0",
+        "tensorflow-probability>=0.12",
         "greenlet>=1.1.0",
     ],
 )

tests/latest/constraints.txt

@@ -0,0 +1,59 @@
+absl-py==0.15.0
+astunparse==1.6.3
+attrs==21.4.0
+cached-property==1.5.2
+cachetools==5.0.0
+certifi==2021.10.8
+charset-normalizer==2.0.11
+cloudpickle==2.0.0
+dataclasses==0.6
+decorator==5.1.1
+Deprecated==1.2.13
+dm-tree==0.1.6
+flatbuffers==1.12
+gast==0.4.0
+google-auth==2.6.0
+google-auth-oauthlib==0.4.6
+google-pasta==0.2.0
+gpflow==2.2.1
+gpflux==0.2.7
+greenlet==1.1.2
+grpcio==1.34.1
+h5py==3.1.0
+idna==3.3
+importlib-metadata==4.10.1
+iniconfig==1.1.1
+keras-nightly==2.5.0.dev2021032900
+Keras-Preprocessing==1.1.2
+Markdown==3.3.6
+multipledispatch==0.6.0
+numpy==1.19.5
+oauthlib==3.2.0
+opt-einsum==3.3.0
+packaging==21.3
+pluggy==1.0.0
+protobuf==3.19.4
+py==1.11.0
+pyasn1==0.4.8
+pyasn1-modules==0.2.8
+pyparsing==3.0.7
+pytest==6.2.5
+requests==2.27.1
+requests-oauthlib==1.3.1
+rsa==4.8
+scipy==1.7.3
+six==1.15.0
+tabulate==0.8.9
+tensorboard==2.8.0
+tensorboard-data-server==0.6.1
+tensorboard-plugin-wit==1.8.1
+tensorflow==2.5.3
+tensorflow-estimator==2.5.0
+tensorflow-probability==0.13.0
+termcolor==1.1.0
+toml==0.10.2
+typing-extensions==3.7.4.3
+urllib3==1.26.8
+Werkzeug==2.0.2
+wrapt==1.12.1
+zipp==3.7.0

tests/latest/requirements.txt

@@ -0,0 +1,16 @@
+# Copyright 2020 The Trieste Contributors
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+packaging
+pytest

tests/unit/models/gpflow/test_models.py

@@ -248,7 +248,11 @@ def test_gaussian_process_regression_correctly_counts_params_that_can_be_sampled
     prior_for_lengthscale: bool,
 ) -> None:
     x = tf.constant(np.arange(1, 5 * dim + 1).reshape(-1, dim), dtype=tf.float64)  # shape: [5, d]
-    model = GaussianProcessRegression(gpr_model(x, fnc_3x_plus_10(x)))
+    optimizer = Optimizer(
+        optimizer=gpflow.optimizers.Scipy(),
+        minimize_args={"options": dict(maxiter=10)},
+    )
+    model = GaussianProcessRegression(gpr_model(x, fnc_3x_plus_10(x)), optimizer=optimizer)
     model.model.kernel = gpflow.kernels.RBF(lengthscales=tf.ones([dim], dtype=tf.float64))
     model.model.likelihood.variance.assign(1.0)
     gpflow.set_trainable(model.model.likelihood, True)

tox.ini

@@ -24,29 +24,36 @@ extend-exclude = docs/notebooks/,.venv
 
 [testenv]
 basepython = python3.7
-deps = pip~=20.3
+deps = pip
 whitelist_externals = bash
 setenv =
     CUDA_VISIBLE_DEVICES =
 commands =
+    # type checking
     types: pip install -r common_build/types/requirements.txt -c common_build/types/constraints.txt
-    types: mypy
+    types: mypy {posargs}
+    # formatting
     format: pip install -r common_build/format/requirements.txt -c common_build/format/constraints.txt
     format: black --check .
     format: flake8 --count .
     format: isort --check .
     format: black -l 80 --include \.pct\.py$ --check notebooks
-    tests: pip install -U pip
+    # tests (run with "-- --runslow yes" to run all tests)
     tests: pip install . -r tests/requirements.txt -c tests/constraints.txt
-    tests: pytest
-    alltests: pip install -U pip
-    alltests: pip install . -r tests/requirements.txt -c tests/constraints.txt
-    alltests: pytest --runslow yes
-    docs: pip install -U pip
+    tests: pytest {posargs}
+    # docs build
     docs: pip install . -r notebooks/requirements.txt -c notebooks/constraints.txt
     docs: pip install -r docs/requirements.txt -c docs/constraints.txt
     docs: bash -c "cd docs; make html"
-    quickdocs: pip install -U pip
+    # quickdocs build
     quickdocs: pip install . -r notebooks/requirements.txt -c notebooks/constraints.txt
     quickdocs: pip install -r docs/requirements.txt -c docs/constraints.txt
     quickdocs: bash -c "cd docs; python notebooks/quickrun/quickrun.py; if make html; then python notebooks/quickrun/quickrun.py --revert; else python notebooks/quickrun/quickrun.py --revert; exit 1; fi"
+
+[testenv:tests_latest]
+basepython = python3.9
+commands =
+    # test but with python 3.9 and latest supported version of tensorflow
+    tests_latest: pip install . -r tests/latest/requirements.txt -c tests/latest/constraints.txt
+    tests_latest: pytest {posargs}
+