Updates onnx and protobuf version due to vulnerabilities (#602)

# Description

Updates onnx and protobuf versions as previous dependency versions had
security vulnerabilities.

To avoid onnx 1.16.1, we are updating onnx to 1.18.0
To avoid protobuf 3.20.3, we are updating protobuf to 6.31.1

Also included some minor updates to add one more flaky test annotation
for test failure, and adding random_state to GaussianProcessRegressor to
resolve another security risk for non-reproducible results.

## Type of change

<!-- As you go through the list, delete the ones that are not
applicable. -->

- Bug fix (non-breaking change which fixes an issue)

## Checklist

- [x] I have run the [`pre-commit` checks](https://pre-commit.com/) with
`./isaaclab.sh --format`
- [x] I have made corresponding changes to the documentation
- [x] My changes generate no new warnings
- [ ] I have added tests that prove my fix is effective or that my
feature works
- [ ] I have updated the changelog and the corresponding version in the
extension's `config/extension.toml` file
- [ ] I have added my name to the `CONTRIBUTORS.md` or my name already
exists there

<!--
As you go through the checklist above, you can mark something as done by
putting an x character in it

For example,
- [x] I have done this task
- [ ] I have not done this task
-->

.github/workflows/license-exceptions.json

@@ -365,5 +365,10 @@
     "package": "regex",
     "license": "UNKNOWN",
     "comment": "Apache 2.0"
+  },
+  {
+    "package": "anyio",
+    "license": "UNKNOWN",
+    "comment": "MIT"
   }
 ]

source/isaaclab/setup.py

@@ -21,7 +21,7 @@ INSTALL_REQUIRES = [
     # generic
     "numpy<2",
     "torch>=2.7",
-    "onnx==1.16.1",  # 1.16.2 throws access violation on Windows
+    "onnx>=1.18.0",  # 1.16.2 throws access violation on Windows
     "prettytable==3.3.0",
     "toml",
     # devices

source/isaaclab/test/sensors/test_multi_tiled_camera.py

@@ -260,6 +260,7 @@ def test_all_annotators_multi_tiled_camera(setup_camera):
         del camera
 
 
+@flaky(max_runs=3, min_passes=1)
 def test_different_resolution_multi_tiled_camera(setup_camera):
     """Test multiple tiled cameras with different resolutions."""
     camera_cfg, sim, dt = setup_camera

source/isaaclab_rl/setup.py

@@ -22,7 +22,7 @@ INSTALL_REQUIRES = [
     "numpy<2",
     "torch>=2.7",
     "torchvision>=0.14.1",  # ensure compatibility with torch 1.13.1
-    "protobuf>=3.20.2,!=5.26.0",
+    "protobuf>=4.25.8,!=5.26.0",
     # configuration management
     "hydra-core",
     # data collection

source/isaaclab_tasks/isaaclab_tasks/direct/automate/automate_algo_utils.py

@@ -138,7 +138,7 @@ def model_succ_w_gp(held_asset_pose, fixed_asset_pose, success):
 
     # Create and fit the Gaussian Process Classifier
     # gp = GaussianProcessClassifier(kernel=kernel, random_state=42)
-    gp = GaussianProcessRegressor()
+    gp = GaussianProcessRegressor(random_state=42)
     gp.fit(relative_position, y)
 
     return gp

source/isaaclab_tasks/setup.py

@@ -21,7 +21,7 @@ INSTALL_REQUIRES = [
     "numpy<2",
     "torch>=2.7",
     "torchvision>=0.14.1",  # ensure compatibility with torch 1.13.1
-    "protobuf>=3.20.2,!=5.26.0",
+    "protobuf>=4.25.8,!=5.26.0",
     # basic logger
     "tensorboard",
     # automate

tools/test_settings.py

@@ -28,6 +28,7 @@ PER_TEST_TIMEOUTS = {
     "test_generate_dataset.py": 500,  # This test runs annotation for 10 demos and generation until one succeeds
     "test_environments_training.py": 6000,
     "test_simulation_render_config.py": 500,
+    "test_operational_space.py": 500,
 }
 """A dictionary of tests and their timeouts in seconds.