add logger tests (#23)

add logger config tests @heyufan1995 



### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] In-line docstrings updated.

---------

Signed-off-by: Wenqi Li <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/premerge-py-min.yml

@@ -46,11 +46,11 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
-        python -m pip install monai pyyaml
+        python -m pip install "monai[all]"
         python -m pip list
       shell: bash
     - name: Run quick tests (CPU ${{ runner.os }})
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
-        python tests/test_config.py
+        python -m unittest -v

data/README.md

@@ -20,7 +20,7 @@ The JSON file has the following structure:
     ],
     "training_transform": [
         # a set of monai transform configuration for dataset-specific loading
-    ]
+    ],
     "original_label_dict": {"1": "liver", ...},
     "label_dict": {"1": "liver", ...}
 }

scripts/infer.py

@@ -33,6 +33,7 @@
 from .utils.trans_utils import get_largest_connected_component_point
 
 rearrange, _ = optional_import("einops", name="rearrange")
+RankFilter, _ = optional_import("monai.utils", name="RankFilter")
 sys.path.insert(0, os.path.abspath(os.path.dirname(__file__)))
 CONFIG = {
     "version": 1,
@@ -45,7 +46,7 @@
             "propagate": False,
         }
     },
-    "filters": {"rank_filter": {"{}": "__main__.RankFilter"}},
+    "filters": {"rank_filter": {"{}": RankFilter}},
     "handlers": {
         "file": {
             "class": "logging.FileHandler",
@@ -352,7 +353,5 @@ def batch_infer_everything(self, datalist=str, basedir=str):
 
 
 if __name__ == "__main__":
-    from monai.utils import optional_import
-
     fire, _ = optional_import("fire")
     fire.Fire(InferClass)

scripts/train.py

@@ -35,7 +35,7 @@
 from monai.data import DataLoader, DistributedSampler, DistributedWeightedRandomSampler
 from monai.metrics import compute_dice
 from monai.networks.utils import copy_model_state
-from monai.utils import set_determinism
+from monai.utils import optional_import, set_determinism
 from torch.nn.parallel import DistributedDataParallel
 from torch.utils.data.sampler import RandomSampler, WeightedRandomSampler
 from torch.utils.tensorboard import SummaryWriter
@@ -62,6 +62,7 @@
 )
 
 nib.imageglobals.logger.setLevel(40)
+RankFilter, _ = optional_import("monai.utils", name="RankFilter")
 CONFIG = {
     "version": 1,
     "disable_existing_loggers": False,
@@ -83,7 +84,7 @@
             "propagate": False,
         },
     },
-    "filters": {"rank_filter": {"()": "__main__.RankFilter"}},
+    "filters": {"rank_filter": {"()": RankFilter}},
     "handlers": {
         "file": {
             "class": "logging.FileHandler",
@@ -1023,7 +1024,5 @@ def run(config_file: Optional[Union[str, Sequence[str]]] = None, **override):
 
 
 if __name__ == "__main__":
-    from monai.utils import optional_import
-
     fire, _ = optional_import("fire")
     fire.Fire()

tests/__init__.py

@@ -0,0 +1,10 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.

tests/test_logger.py

@@ -0,0 +1,33 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import logging
+import unittest
+
+from monai.apps.auto3dseg.auto_runner import logger
+
+
+class TestLogger(unittest.TestCase):
+    def test_vista3d_logger(self):
+        from scripts.train import CONFIG
+
+        logging.config.dictConfig(CONFIG)
+        logger.warning("check train logging format")
+
+    def test_vista3d_logger_infer(self):
+        from scripts.infer import CONFIG
+
+        logging.config.dictConfig(CONFIG)
+        logger.warning("check infer logging format")
+
+
+if __name__ == "__main__":
+    unittest.main()