1.7 release (#2037)

* Bump dependencies: Python 3.7, Torch 1.10
* Update publishing script
* Consolidate unit test scripts

Co-authored-by: Max Balandat <[email protected]>

.conda/meta.yaml

@@ -13,11 +13,12 @@ build:
 
 requirements:
   host:
-    - python>=3.6
+    - python>=3.7
 
   run:
-    - pytorch>=1.9
-    - scikit-learn
+    - pytorch>=1.10
+    - numpy
+    - scikit-learn<=1.0.2  # newer versions require py3.8
     - scipy
 
 test:

.github/workflows/python-publish-pypi.yml → .github/workflows/deploy.yml

@@ -1,16 +1,19 @@
 # This workflow will upload a Python Package using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
 
-name: Upload Python Package to PyPI
+name: Upload Python Package to PyPI and Anaconda
 
 on:
   release:
     types: [created]
 
 jobs:
-  deploy:
-    runs-on: ubuntu-latest
+  run_test_suite:
+    uses: ./.github/workflows/run_test_suite.yml
 
+  deploy_pypi:
+    runs-on: ubuntu-latest
+    needs: run_test_suite
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
@@ -28,3 +31,15 @@ jobs:
       run: |
         python setup.py sdist bdist_wheel
         twine upload dist/*
+
+  deploy_conda:
+    runs-on: ubuntu-latest
+    needs: run_test_suite
+    steps:
+    - uses: actions/checkout@master
+    - name: publish-to-conda
+      uses: cornellius-gp/conda-package-publish-action@master
+      with:
+        subDir: '.'
+        AnacondaUsername: ${{ secrets.ANACONDA_PASSWORD }}
+        AnacondaPassword: ${{ secrets.ANACONDA_USERNAME }}

.github/workflows/run_test_suite.yml

@@ -0,0 +1,77 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Run Test Suite
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  workflow_call:
+
+jobs:
+  run_linter:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+    - name: Install dependencies
+      run: |
+        pip install flake8==4.0.1 flake8-print==4.0.0 pre-commit
+        pre-commit install
+        pre-commit run seed-isort-config || true
+    - name: Run linting
+      run: |
+        flake8
+    - name: Run pre-commit checks
+      # skipping flake8 here (run separatey above b/c pre-commit does not include flake8-print)
+      run: |
+        SKIP=flake8 pre-commit run --files test/**/*.py gpytorch/**/*.py
+
+  run_unit_tests:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        pytorch-version: ["master", "stable"]
+        pyro: ["with-pyro", "no-pyro"]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+    - name: Install dependencies
+      run: |
+        if [[ ${{ matrix.pytorch-version }} = "master" ]]; then
+          pip install --pre torch -f https://download.pytorch.org/whl/nightly/cpu/torch_nightly.html;
+        else
+          pip install torch==1.10+cpu -f https://download.pytorch.org/whl/torch_stable.html;
+        fi
+        if [[ ${{ matrix.pyro }} == "with-pyro" ]]; then
+          pip install "pyro-ppl<=1.8";
+        fi
+        pip install -r requirements.txt
+    - name: Run unit tests
+      run: |
+        python -m unittest discover
+
+  run_examples:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: "3.7"
+    - name: Install dependencies
+      run: |
+        pip install pytest nbval jupyter tqdm matplotlib torchvision scipy
+        python setup.py build develop
+        pip install "pyro-ppl<=1.8";
+    - name: Run example notebooks
+      run: |
+        grep -l smoke_test examples/**/*.ipynb | xargs grep -L 'smoke_test = False' | CI=true xargs pytest --nbval-lax --current-env

README.md

@@ -18,8 +18,8 @@ See our numerous [**examples and tutorials**](https://gpytorch.readthedocs.io/en
 ## Installation
 
 **Requirements**:
-- Python >= 3.6
-- PyTorch >= 1.9
+- Python >= 3.7
+- PyTorch >= 1.10
 
 Install GPyTorch using pip or conda:
 
@@ -96,4 +96,9 @@ GPyTorch is primarily maintained by:
 We would like to thank our other contributors including (but not limited to)  David Arbour, Eytan Bakshy, David Eriksson, Jared Frank, Sam Stanton, Bram Wallace, Ke Alexander Wang, Ruihan Wu.
 
 ## Acknowledgements
-Development of GPyTorch is supported by funding from the [Bill and Melinda Gates Foundation](https://www.gatesfoundation.org/), the [National Science Foundation](https://www.nsf.gov/), and [SAP](https://www.sap.com/index.html).
+Development of GPyTorch is supported by funding from
+the [Bill and Melinda Gates Foundation](https://www.gatesfoundation.org/),
+the [National Science Foundation](https://www.nsf.gov/),
+[SAP](https://www.sap.com/index.html),
+the [Simons Foundation](https://www.simonsfoundation.org),
+and the [Gatsby Charitable Trust](https://www.gatsby.org.uk).

docs/source/index.rst

@@ -31,6 +31,7 @@ GPyTorch's documentation
    kernels
    means
    marginal_log_likelihoods
+   metrics
    constraints
    distributions
    priors

docs/source/metrics.rst

@@ -0,0 +1,19 @@
+.. role:: hidden
+    :class: hidden-section
+
+gpytorch.metrics
+===================================
+
+.. automodule:: gpytorch.metrics
+.. currentmodule:: gpytorch.metrics
+
+See `the metrics tutorial`_ for usage instructions.
+
+.. automethod:: gpytorch.metrics.mean_absolute_error
+.. automethod:: gpytorch.metrics.mean_squared_error
+.. automethod:: gpytorch.metrics.mean_standardized_log_loss
+.. automethod:: gpytorch.metrics.negative_log_predictive_density
+.. automethod:: gpytorch.metrics.quantile_coverage_error
+
+.. _the metrics tutorial:
+    examples/00_Basic_Usage/Metrics.html

environment.yml

@@ -3,5 +3,6 @@ channels:
   - pytorch
 dependencies:
   - pytorch
-  - scikit-learn
+  - numpy
+  - scikit-learn<=1.0.2  # newer versions require py3.8
   - scipy

gpytorch/__init__.py

@@ -33,7 +33,7 @@
 from .mlls import ExactMarginalLogLikelihood
 from .module import Module
 
-__version__ = "1.6.0"
+__version__ = "1.7.0"
 
 __all__ = [
     # Submodules

requirements.txt

@@ -1,3 +1,4 @@
-torch>=1.9
-scikit-learn
+torch>=1.10
+numpy
+scikit-learn<=1.0.2  # newer versions require py3.8
 scipy

setup.py

@@ -25,8 +25,8 @@ def find_version(*file_paths):
 version = find_version("gpytorch", "__init__.py")
 
 
-torch_min = "1.9"
-install_requires = [">=".join(["torch", torch_min]), "scikit-learn", "scipy"]
+torch_min = "1.10"
+install_requires = [">=".join(["torch", torch_min])]
 # if recent dev version of PyTorch is installed, no need to install stable
 try:
     import torch
@@ -35,6 +35,7 @@ def find_version(*file_paths):
         install_requires = []
 except ImportError:
     pass
+install_requires += ["numpy", "scikit-learn<=1.0.2", "scipy"]
 
 
 # Run the setup