build: drop py3.8 and torch1.12; update deps. fix slow tests. (#1233)

* add tutorials test; fix slow tests, typing.

* build: drop python3.8 and torch 1.12, update deps.

- add movie writer to dev deps
- downgrade scipy to enable py3.9 support

.github/workflows/cd.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
 
     - name: Cache dependency
       id: cache-dependencies

.github/workflows/ci.yml

@@ -20,8 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8']
-        torch-version: ['1.11', '2.2']
+        python-version: ['3.9', '3.12']
 
     steps:
     - name: Checkout
@@ -40,15 +39,15 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ matrix.torch-version }}$
+        key: ${{ runner.os }}-pip-${{ matrix.python-version }}
         restore-keys: |
           ${{ runner.os }}-pip-${{ matrix.python-version }}-
           ${{ runner.os }}-pip-
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install torch==${{ matrix.torch-version }} --extra-index-url https://download.pytorch.org/whl/cpu
+        pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
         pip install -e .[dev]
 
     - name: Run the fast CPU tests with coverage

.github/workflows/lint.yml

@@ -22,7 +22,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - uses: pre-commit/[email protected]
         with:
           extra_args: --all-files --show-diff-on-failure
@@ -40,14 +40,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Cache dependency
         id: cache-dependencies
         uses: actions/cache@v4
         with:
           path: ~/.cache/pip
-          key: ubuntu-latest-pip-3.8
+          key: ubuntu-latest-pip-3.9
           restore-keys: |
             ubuntu-latest-pip-
 

pyproject.toml

@@ -24,7 +24,7 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Development Status :: 3 - Alpha",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 dynamic = ["version"]
 readme = "README.md"
 keywords = ["Bayesian inference", "simulation-based inference", "PyTorch"]
@@ -33,14 +33,14 @@ dependencies = [
     "joblib>=1.0.0",
     "jupyter",
     "matplotlib",
-    "numpy",
+    "numpy<2.0.0",
     "pillow",
     "pyknos>=0.16.0",
     "pyro-ppl>=1.3.1",
     "scikit-learn",
-    "scipy",
+    "scipy<1.13",
     "tensorboard",
-    "torch>=1.8.0",
+    "torch>=1.13.0",
     "tqdm",
     "pymc>=5.0.0",
     "zuko>=1.2.0",
@@ -61,6 +61,7 @@ doc = [
     "mike"
 ]
 dev = [
+    "ffmpeg",
     # Lint
     "pre-commit == 3.5.0",
     "pyyaml",
@@ -134,9 +135,9 @@ xfail_strict = true
 
 # Pyright configuration
 [tool.pyright]
-include = ["sbi", "tests"]
-exclude = ["**/__pycache__", "**/__node_modules__", ".git", "docs", "examples", "tutorials", "tests"]
-python_version = "3.8"
+include = ["sbi"]
+exclude = ["**/__pycache__", "**/__node_modules__", ".git", "docs", "tutorials", "tests"]
+python_version = "3.9"
 reportUnsupportedDunderAll = false
 reportGeneralTypeIssues = false
 reportInvalidTypeForm = false

sbi/analysis/plot.py

@@ -179,10 +179,10 @@ def plt_kde_2d(
     ax.imshow(
         Z,
         extent=(
-            limits_col[0],
-            limits_col[1],
-            limits_row[0],
-            limits_row[1],
+            limits_col[0].item(),
+            limits_col[1].item(),
+            limits_row[0].item(),
+            limits_row[1].item(),
         ),
         **offdiag_kwargs["mpl_kwargs"],
     )
@@ -350,7 +350,7 @@ def get_offdiag_funcs(
 def _format_subplot(
     ax: Axes,
     current: str,
-    limits: Union[List, torch.Tensor],
+    limits: Union[List[List[float]], torch.Tensor],
     ticks: Optional[Union[List, torch.Tensor]],
     labels_dim: List[str],
     fig_kwargs: Dict,
@@ -384,6 +384,9 @@ def _format_subplot(
     ):
         ax.set_facecolor(fig_kwargs["fig_bg_colors"][current])
     # Limits
+    if isinstance(limits, Tensor):
+        assert limits.dim() == 2, "Limits should be a 2D tensor."
+        limits = limits.tolist()
     if current == "diag":
         eps = fig_kwargs["x_lim_add_eps"]
         ax.set_xlim((limits[col][0] - eps, limits[col][1] + eps))

tests/sbc_test.py

@@ -109,7 +109,7 @@ def test_consistent_sbc_results(density_estimator, cov_method):
     def simulator(theta):
         return linear_gaussian(theta, likelihood_shift, likelihood_cov)
 
-    num_simulations = 2000
+    num_simulations = 4000
     num_posterior_samples = 1000
     num_sbc_runs = 100
 

tests/tutorials_test.py

@@ -0,0 +1,39 @@
+import os
+
+import nbformat
+import pytest
+from nbclient.exceptions import CellExecutionError
+from nbconvert.preprocessors import ExecutePreprocessor
+
+
+def list_notebooks(directory: str) -> list:
+    """Return sorted list of all notebooks in a directory."""
+    notebooks = [
+        os.path.join(directory, f)
+        for f in os.listdir(directory)
+        if f.endswith("distributions.ipynb")
+    ]
+    return sorted(notebooks)
+
+
+@pytest.mark.slow
+@pytest.mark.parametrize("notebook_path", list_notebooks("tutorials/"))
+def test_tutorials(notebook_path):
+    """Test that all notebooks in the tutorials directory can be executed."""
+    with open(notebook_path) as f:
+        nb = nbformat.read(f, as_version=4)
+        ep = ExecutePreprocessor(timeout=600, kernel_name='python3')
+        print(f"Executing notebook {notebook_path}")
+        try:
+            ep.preprocess(nb, {'metadata': {'path': os.path.dirname(notebook_path)}})
+        except CellExecutionError as e:
+            # Conditional_distributions tutorial requires movie writer that is failing
+            # in GitHub CI.
+            if "Requested MovieWriter" in str(e):
+                print("Skipping error in movie writer.")
+            else:
+                raise CellExecutionError from e
+        except Exception as e:
+            raise AssertionError(
+                f"Error executing the notebook {notebook_path}: {e}"
+            ) from e