Merge branch 'dev' into codeql_issues

Author: ericspod

.github/workflows/weekly-preview.yml

@@ -10,6 +10,7 @@ on:
     branches:
       - dev
 
+
 env:
   PYTHON_VER: '3.10'
   PYTORCH_VER: '2.8.0'
@@ -66,10 +67,12 @@ jobs:
         cache: 'pip'
     - name: Install tools
       run: |
-        python -m pip install -U pip build
+        python -m pip install -U pip build twine
     - name: Build distribution
       run: |
         export HEAD_COMMIT_ID=$(git rev-parse HEAD)
+        # remove git clone dependencies, see https://github.com/Project-MONAI/MONAI/issues/5882
+        sed -i /git+/d pyproject.toml
         sed -i 's/name\ =\ "monai"$/name\ =\ "monai-weekly"/g' pyproject.toml
         echo "__commit_id__ = \"$HEAD_COMMIT_ID\"" >> monai/__init__.py
         git diff pyproject.toml monai/__init__.py
@@ -87,11 +90,12 @@ jobs:
         ls -lh dist
     - name: Test Installation
       run: |
+        twine check --strict dist/*
         pip install dist/*.whl
         pip list
         (cd "$(mktemp -d)" && python -c 'import monai; print(monai.__version__)')
     - name: Publish to PyPI
-      if: github.event_name == 'schedule'  # only publish on cron run
+      if: github.event_name == 'schedule' # only publish on cron run
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__

monai/utils/profiling.py

@@ -57,7 +57,7 @@ def torch_profiler_full(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-        with torch.autograd.profiler.profile() as prof:
+        with torch.autograd.profiler.profile(use_device="cuda") as prof:
             result = func(*args, **kwargs)
 
         print(prof, flush=True)
@@ -76,7 +76,7 @@ def torch_profiler_time_cpu_gpu(func):
 
     @wraps(func)
     def wrapper(*args, **kwargs):
-        with torch.autograd.profiler.profile() as prof:
+        with torch.autograd.profiler.profile(use_device="cuda") as prof:
             result = func(*args, **kwargs)
 
         cpu_time = prof.self_cpu_time_total

pyproject.toml

@@ -125,6 +125,7 @@ jsonschema = ["jsonschema"]
 lmdb = ["lmdb"]
 lpips = ["lpips==0.1.4"]
 matplotlib = ["matplotlib>=3.6.3"]
+# per #5882 this requirement must be on one line to get removed by sed in weekly-preview.yml
 metrics_reloaded = ["MetricsReloaded @ git+https://github.com/Project-MONAI/MetricsReloaded@monai-support"]
 mlflow = ["mlflow>=3.15.2"]
 nibabel = ["nibabel"]
@@ -147,6 +148,7 @@ pynrrd = ["pynrrd"]
 pynvml = ["nvidia-ml-py"]
 pyyaml = ["pyyaml"]
 requests = ["requests"]
+# per #5882 this requirement must be on one line to get removed by sed in weekly-preview.yml
 segment_anything = ["segment_anything @ git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588"]
 scipy = ["scipy>=1.12.0"]
 skimage = ["scikit-image>=0.19.0"]