Update CI Python version to 3.12. (#3429)

* Update CI Python version to 3.12.

* Try Python 3.11 as there is some problem with ruff.

* Go back to Python version 3.12 after fixing formatting to comply with latest versions of black and ruff.

* Try going back to Python 3.11.

* Fix to comply with PEP 612 (see microsoft/pyright#5844 (comment)).

* Fix typo

* Go back to previous runtime.py and ignore mypy PEP 612 check.

* Back to Python 3.12,

* Back to Python 3.11.

* Update Sphinx version to 0.5.0.

* Update Sphinx version to 8.2.3.

* Try removing Sphnix version in order solve dependency conflict.

* List all Python modules for CI debug.

* Try with Python 3.12 due to jaraco/path#231.

* Unpin setuptools version.

* Updated Sphinx version to 7.3.7.

* Fix Sphinx issue (works on local machine).

* Remove unused import.

* Try different Sphinx versions.

* Use Sphnix upgrade path.

* Convert random seed to int data type.

* Update levy-stable kstest.

* Mark easyguide/test_easyguide.py::test_serialize as an expected failure according to the bug mentioned at #3430.

Author: BenZickel

.github/workflows/ci.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python ${{ matrix.python-version }}
@@ -29,7 +29,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+        python -m pip install --upgrade pip wheel setuptools
         pip install ruff black mypy nbstripout nbformat
     - name: Lint
       run: |
@@ -39,7 +39,7 @@ jobs:
     needs: lint
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -51,12 +51,13 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build graphviz
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
           pip install .[test]
           pip install -r docs/requirements.txt
+          pip install --upgrade sphinx docutils sphinx-rtd-theme
           pip freeze
       - name: Build docs and run doctest
         run: |
@@ -67,7 +68,7 @@ jobs:
     needs: lint
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -79,7 +80,7 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build graphviz pandoc
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
@@ -101,7 +102,7 @@ jobs:
     needs: docs
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -113,7 +114,7 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
@@ -133,7 +134,7 @@ jobs:
     needs: [docs, tutorials-html]
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -147,7 +148,7 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
@@ -169,7 +170,7 @@ jobs:
     needs: docs
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -181,7 +182,7 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
@@ -201,7 +202,7 @@ jobs:
     needs: docs
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -213,7 +214,7 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
@@ -233,7 +234,7 @@ jobs:
     needs: docs
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -245,7 +246,7 @@ jobs:
           sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
           sudo apt-get update
           sudo apt-get install gcc-9 g++-9 ninja-build
-          python -m pip install --upgrade pip wheel 'setuptools!=58.5.*,<60'
+          python -m pip install --upgrade pip wheel setuptools
           # Keep track of pyro-api master branch
           pip install https://github.com/pyro-ppl/pyro-api/archive/master.zip
           pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cpu
@@ -267,7 +268,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.12]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}

docs/source/conf.py

@@ -4,8 +4,6 @@
 import os
 import sys
 
-import sphinx_rtd_theme
-
 # import pkg_resources
 
 # -*- coding: utf-8 -*-
@@ -82,7 +80,7 @@
 
 if "READTHEDOCS" not in os.environ:
     # if developing locally, use pyro.__version__ as version
-    from pyro import __version__  # noqaE402
+    from pyro import __version__  # noqa: E402
 
     version = __version__
 
@@ -122,7 +120,6 @@
 # a list of builtin themes.
 #
 html_theme = "sphinx_rtd_theme"
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

examples/contrib/epidemiology/sir.py

@@ -177,7 +177,7 @@ def evaluate(args, model, samples):
         mean = samples[key].mean().item()
         std = samples[key].std().item()
         logging.info(
-            "{}: truth = {:0.3g}, estimate = {:0.3g} \u00B1 {:0.3g}".format(
+            "{}: truth = {:0.3g}, estimate = {:0.3g} \u00b1 {:0.3g}".format(
                 key, getattr(args, name), mean, std
             )
         )

examples/sir_hmc.py

@@ -486,7 +486,7 @@ def evaluate(args, samples):
         mean = samples[key].mean().item()
         std = samples[key].std().item()
         logging.info(
-            "{}: truth = {:0.3g}, estimate = {:0.3g} \u00B1 {:0.3g}".format(
+            "{}: truth = {:0.3g}, estimate = {:0.3g} \u00b1 {:0.3g}".format(
                 key, getattr(args, name), mean, std
             )
         )

examples/sparse_regression.py

@@ -295,7 +295,7 @@ def main(args):
         with torch.no_grad():
             init_losses.append(loss_fn(model, guide, X, Y, hypers).item())
 
-    pyro.set_rng_seed(np.argmin(init_losses))
+    pyro.set_rng_seed(int(np.argmin(init_losses)))
     pyro.clear_param_store()
     guide = AutoDelta(model, init_loc_fn=init_loc_fn)
 

examples/toy_mixture_model_discrete_enumeration.py

@@ -2,22 +2,22 @@
 # SPDX-License-Identifier: Apache-2.0
 
 """
- A toy mixture model to provide a simple example for implementing discrete enumeration.
-
- (A) -> [B] -> (C)
-
- A is an observed Bernoulli variable with Beta prior.
- B is a hidden variable which is a mixture of two Bernoulli distributions (with Beta priors),
- chosen by A being true or false.
- C is observed, and like B, is a mixture of two Bernoulli distributions (with Beta priors),
- chosen by B being true or false.
- There is a plate over the three variables for n independent observations of data.
-
- Because B is hidden and discrete we wish to marginalize it out of the model.
- This is done by:
-    1) marking the model method with `@pyro.infer.config_enumerate`
-    2) marking the B sample site in the model with `infer={"enumerate": "parallel"}`
-    3) passing `pyro.infer.SVI` the `pyro.infer.TraceEnum_ELBO` loss function
+A toy mixture model to provide a simple example for implementing discrete enumeration.
+
+(A) -> [B] -> (C)
+
+A is an observed Bernoulli variable with Beta prior.
+B is a hidden variable which is a mixture of two Bernoulli distributions (with Beta priors),
+chosen by A being true or false.
+C is observed, and like B, is a mixture of two Bernoulli distributions (with Beta priors),
+chosen by B being true or false.
+There is a plate over the three variables for n independent observations of data.
+
+Because B is hidden and discrete we wish to marginalize it out of the model.
+This is done by:
+   1) marking the model method with `@pyro.infer.config_enumerate`
+   2) marking the B sample site in the model with `infer={"enumerate": "parallel"}`
+   3) passing `pyro.infer.SVI` the `pyro.infer.TraceEnum_ELBO` loss function
 """
 
 import argparse

pyro/contrib/epidemiology/compartmental.py

@@ -100,7 +100,7 @@ def transition(self, params, state, t): ...
         model = MyModel(...)
         model.fit_svi(num_samples=100)  # or .fit_mcmc(...)
         R0 = model.samples["R0"]  # An example parameter.
-        print("R0 = {:0.3g} \u00B1 {:0.3g}".format(R0.mean(), R0.std()))
+        print("R0 = {:0.3g} \u00b1 {:0.3g}".format(R0.mean(), R0.std()))
 
         # Predict latent variables.
         samples = model.predict()

pyro/contrib/gp/models/sgpr.py

@@ -19,7 +19,7 @@ class SparseGPRegression(GPModel):
     the covariance matrix :math:`k(X, X)` will require a lot of computational steps to
     compute its inverse (for log likelihood and for prediction). By introducing an
     additional inducing-input parameter :math:`X_u`, we can reduce computational cost
-    by approximate :math:`k(X, X)` by a low-rank Nystr\u00F6m approximation :math:`Q`
+    by approximate :math:`k(X, X)` by a low-rank Nystr\u00f6m approximation :math:`Q`
     (see reference [1]), where
 
     .. math:: Q = k(X, X_u) k(X_u,X_u)^{-1} k(X_u, X).
@@ -72,7 +72,7 @@ class SparseGPRegression(GPModel):
     References:
 
     [1] `A Unifying View of Sparse Approximate Gaussian Process Regression`,
-    Joaquin Qui\u00F1onero-Candela, Carl E. Rasmussen
+    Joaquin Qui\u00f1onero-Candela, Carl E. Rasmussen
 
     [2] `Variational learning of inducing variables in sparse Gaussian processes`,
     Michalis Titsias

pyro/nn/module.py

@@ -824,7 +824,7 @@ def __getstate__(self) -> Dict[str, Any]:
 
 
 def pyro_method(
-    fn: Callable[Concatenate[_PyroModule, _P], _T]
+    fn: Callable[Concatenate[_PyroModule, _P], _T],
 ) -> Callable[Concatenate[_PyroModule, _P], _T]:
     """
     Decorator for top-level methods of a :class:`PyroModule` to enable pyro

pyro/poutine/block_messenger.py

@@ -84,7 +84,7 @@ def _make_default_hide_fn(
 
 
 def _negate_fn(
-    fn: Callable[["Message"], Optional[bool]]
+    fn: Callable[["Message"], Optional[bool]],
 ) -> Callable[["Message"], bool]:
     # typed version of lambda msg: not fn(msg)
     def negated_fn(msg: "Message") -> bool: