Backport PR #3024 on branch 1.2.x ((ci) (test) Updated CUDA test yaml…

… file) (#3025)

Backport PR #3024: (ci) (test) Updated CUDA test yaml file

Co-authored-by: Ori Kronfeld <[email protected]>

.github/workflows/test_linux_cuda.yml

@@ -1,6 +1,8 @@
 name: test (cuda)
 
 on:
+  push:
+    branches: [main, "[0-9]+.[0-9]+.x"] #this is new
   pull_request:
     branches: [main, "[0-9]+.[0-9]+.x"]
     types: [labeled, synchronize, opened]
@@ -31,6 +33,7 @@ jobs:
 
     container:
       image: ghcr.io/scverse/scvi-tools:py3.12-cu12-base
+      #image: ghcr.io/scverse/scvi-tools:py3.12-cu12-${{ env.BRANCH_NAME }}-base
       options: --user root --gpus all
 
     name: integration
@@ -40,11 +43,24 @@ jobs:
       PYTHON: ${{ matrix.python }}
 
     steps:
+      #- name: Get the current branch name
+      #  id: vars
+      #  run: echo "BRANCH_NAME=$(echo $GITHUB_REF | awk -F'/' '{print $3}')" >> $GITHUB_ENV
+
       - uses: actions/checkout@v4
 
-      - run: |
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+
+      - name: Install dependencies
+        run: |
           python -m pip install --upgrade pip wheel uv
           python -m uv pip install --system "scvi-tools[tests] @ ."
+          python -m pip install jax[cuda]
+          python -m pip install nvidia-nccl-cu12
 
       - name: Run pytest
         env:

src/scvi/external/poissonvi/_model.py

@@ -235,8 +235,11 @@ def get_accessibility_estimates(
 
     @torch.inference_mode()
     def get_region_factors(self):
-        """Return region-specific factors."""
-        region_factors = self.module.decoder.px_scale_decoder[-2].bias.numpy()
+        """Return region-specific factors. CPU/GPU dependent"""
+        if self.device.type == "cpu":
+            region_factors = self.module.decoder.px_scale_decoder[-2].bias.numpy()
+        else:
+            region_factors = self.module.decoder.px_scale_decoder[-2].bias.cpu().numpy()  # gpu
         if region_factors is None:
             raise RuntimeError("region factors were not included in this model")
         return region_factors

tests/model/test_pyro.py

@@ -6,6 +6,7 @@
 import numpy as np
 import pyro
 import pyro.distributions as dist
+import pytest
 import torch
 from pyro import clear_param_store
 from pyro.infer.autoguide import AutoNormal, init_to_mean
@@ -215,6 +216,7 @@ def test_pyro_bayesian_regression_low_level(
     ]
 
 
+@pytest.mark.optional
 def test_pyro_bayesian_regression(accelerator: str, devices: list | str | int, save_path: str):
     adata = synthetic_iid()
     adata_manager = _create_indices_adata_manager(adata)
@@ -277,6 +279,7 @@ def test_pyro_bayesian_regression(accelerator: str, devices: list | str | int, s
     np.testing.assert_array_equal(linear_median_new, linear_median)
 
 
+@pytest.mark.optional
 def test_pyro_bayesian_regression_jit(
     accelerator: str,
     devices: list | str | int,