Merge branch 'main' into filter_mask

merge with main

.github/workflows/build.yml

@@ -55,7 +55,8 @@ jobs:
           editable: true
       - name: Run unit tests and generate coverage report
         run: |
-          coverage run --source=graphnet -m pytest tests/
+          coverage run --source=graphnet -m pytest tests/ --ignore=tests/examples
+          coverage run --source=graphnet -m pytest tests/examples/01_icetray
           coverage xml -o coverage.xml
       - name: Work around permission issue
         run: |
@@ -88,7 +89,8 @@ jobs:
       - name: Run unit tests and generate coverage report
         run: |
           set -o pipefail  # To propagate exit code from pytest
-          coverage run --source=graphnet -m pytest tests/ --ignore=tests/data/ --ignore=tests/deployment/
+          coverage run --source=graphnet -m pytest tests/ --ignore=tests/utilities --ignore=tests/data/ --ignore=tests/deployment/ --ignore=tests/examples/01_icetray/
+          coverage run --source=graphnet -m pytest tests/utilities
           coverage report -m
 
   build-macos:
@@ -108,5 +110,5 @@ jobs:
       - name: Run unit tests and generate coverage report
         run: |
           set -o pipefail  # To propagate exit code from pytest
-          coverage run --source=graphnet -m pytest tests/ --ignore=tests/data/ --ignore=tests/deployment/
+          coverage run --source=graphnet -m pytest tests/  --ignore=tests/data/ --ignore=tests/deployment/ --ignore=tests/examples/
           coverage report -m

configs/models/dynedge_PID_classification_example.yml

@@ -38,6 +38,7 @@ arguments:
   - ModelConfig:
       arguments:
         nb_outputs: 3 # number of classes
+        prediction_labels: ['noise', 'muon', 'neutrino']
         hidden_size: 128
         loss_function:
           ModelConfig:

examples/01_icetray/01_convert_i3_files.py

@@ -8,7 +8,6 @@
     I3FeatureExtractorIceCube86,
     I3RetroExtractor,
     I3TruthExtractor,
-    I3GenericExtractor,
 )
 from graphnet.data.dataconverter import DataConverter
 from graphnet.data.parquet import ParquetDataConverter
@@ -17,7 +16,17 @@
 from graphnet.utilities.imports import has_icecube_package
 from graphnet.utilities.logging import Logger
 
-from _common_icetray import ERROR_MESSAGE_MISSING_ICETRAY
+ERROR_MESSAGE_MISSING_ICETRAY = (
+    "This example requires IceTray to be installed, which doesn't seem to be "
+    "the case. Please install IceTray; run this example in the GraphNeT "
+    "Docker container which comes with IceTray installed; or run an example "
+    "script in one of the other folders:"
+    "\n * examples/02_data/"
+    "\n * examples/03_weights/"
+    "\n * examples/04_training/"
+    "\n * examples/05_pisa/"
+    "\nExiting."
+)
 
 CONVERTER_CLASS = {
     "sqlite": SQLiteDataConverter,
@@ -90,7 +99,7 @@ def main_icecube_upgrade(backend: str) -> None:
             "detector", choices=["icecube-86", "icecube-upgrade"]
         )
 
-        args = parser.parse_args()
+        args, unknown = parser.parse_known_args()
 
         # Run example script
         if args.detector == "icecube-86":

examples/01_icetray/02_compare_sqlite_and_parquet.py

@@ -16,7 +16,17 @@
 from graphnet.utilities.imports import has_icecube_package
 from graphnet.utilities.logging import Logger
 
-from _common_icetray import ERROR_MESSAGE_MISSING_ICETRAY
+ERROR_MESSAGE_MISSING_ICETRAY = (
+    "This example requires IceTray to be installed, which doesn't seem to be "
+    "the case. Please install IceTray; run this example in the GraphNeT "
+    "Docker container which comes with IceTray installed; or run an example "
+    "script in one of the other folders:"
+    "\n * examples/02_data/"
+    "\n * examples/03_weights/"
+    "\n * examples/04_training/"
+    "\n * examples/05_pisa/"
+    "\nExiting."
+)
 
 OUTPUT_DIR = f"{EXAMPLE_OUTPUT_DIR}/compare_sqlite_and_parquet"
 PULSEMAP = "SRTInIcePulses"
@@ -34,7 +44,7 @@ def convert_data() -> None:
             I3FeatureExtractorIceCube86(PULSEMAP),
         ],
         outdir=OUTPUT_DIR,
-        workers=10,
+        workers=1,
     )
 
     # Run data converters.
@@ -85,7 +95,7 @@ def load_data() -> None:
 """
         )
 
-        args = parser.parse_args()
+        args, unknown = parser.parse_known_args()
 
         # Run example script(s)
         convert_data()

examples/01_icetray/03_i3_deployer_example.py

@@ -23,7 +23,17 @@
         I3InferenceModule,
     )
 
-from _common_icetray import ERROR_MESSAGE_MISSING_ICETRAY
+ERROR_MESSAGE_MISSING_ICETRAY = (
+    "This example requires IceTray to be installed, which doesn't seem to be "
+    "the case. Please install IceTray; run this example in the GraphNeT "
+    "Docker container which comes with IceTray installed; or run an example "
+    "script in one of the other folders:"
+    "\n * examples/02_data/"
+    "\n * examples/03_weights/"
+    "\n * examples/04_training/"
+    "\n * examples/05_pisa/"
+    "\nExiting."
+)
 
 # Constants
 features = FEATURES.UPGRADE
@@ -83,7 +93,7 @@ def main() -> None:
 """
         )
 
-        args = parser.parse_args()
+        args, unknown = parser.parse_known_args()
 
         # Run example script
         main()

examples/01_icetray/04_i3_module_in_native_icetray_example.py

@@ -26,7 +26,17 @@
         GraphNeTI3Module,
     )
 
-from _common_icetray import ERROR_MESSAGE_MISSING_ICETRAY
+ERROR_MESSAGE_MISSING_ICETRAY = (
+    "This example requires IceTray to be installed, which doesn't seem to be "
+    "the case. Please install IceTray; run this example in the GraphNeT "
+    "Docker container which comes with IceTray installed; or run an example "
+    "script in one of the other folders:"
+    "\n * examples/02_data/"
+    "\n * examples/03_weights/"
+    "\n * examples/04_training/"
+    "\n * examples/05_pisa/"
+    "\nExiting."
+)
 
 
 def apply_to_files(
@@ -116,7 +126,7 @@ def main() -> None:
 """
         )
 
-        args = parser.parse_args()
+        args, unknown = parser.parse_known_args()
 
         # Run example script
         main()

examples/02_data/01_read_dataset.py

@@ -113,8 +113,14 @@ def main(backend: str) -> None:
 """
     )
 
-    parser.add_argument("backend", choices=["sqlite", "parquet"])
+    parser.add_argument(
+        "backend",
+        choices=["sqlite", "parquet"],
+        default="sqlite",
+        const="sqlite",
+        nargs="?",
+    )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main(args.backend)

examples/02_data/02_plot_feature_distributions.py

@@ -66,6 +66,6 @@ def main() -> None:
 """
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main()

examples/02_data/03_convert_parquet_to_sqlite.py

@@ -57,6 +57,6 @@ def main(parquet_path: str, mc_truth_table: str) -> None:
         default="truth",
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main(args.parquet_path, args.mc_truth_table)

examples/02_data/04_ensemble_dataset.py

@@ -88,4 +88,5 @@ def main() -> None:
 Combine multiple Datasets using EnsembleDataset.
 """
     )
+    args, unknown = parser.parse_known_args()
     main()

examples/03_weights/01_fit_uniform_weights.py

@@ -37,6 +37,6 @@ def main() -> None:
 """
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main()

examples/03_weights/02_fit_bjoern_low_weights.py

@@ -45,6 +45,6 @@ def main() -> None:
 """
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main()

examples/04_training/01_train_dynedge.py

@@ -213,7 +213,7 @@ def main(
 
     parser.with_standard_arguments(
         "gpus",
-        ("max-epochs", 5),
+        ("max-epochs", 1),
         "early-stopping-patience",
         ("batch-size", 16),
         "num-workers",
@@ -225,7 +225,7 @@ def main(
         help="If True, Weights & Biases are used to track the experiment.",
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main(
         args.path,

examples/04_training/02_train_tito_model.py

@@ -182,7 +182,8 @@ def main(
 
     # Save model config and state dict - Version safe save method.
     model.save_state_dict(f"{path}/state_dict.pth")
-    model.save_config(f"{path}/model_config.yml")
+    # model.save_config(f"{path}/model_config.yml")
+    # Pending https://github.com/graphnet-team/graphnet/issues/606
 
 
 if __name__ == "__main__":
@@ -223,7 +224,7 @@ def main(
 
     parser.with_standard_arguments(
         "gpus",
-        ("max-epochs", 5),
+        ("max-epochs", 1),
         ("early-stopping-patience", 2),
         ("batch-size", 16),
         "num-workers",
@@ -235,7 +236,7 @@ def main(
         help="If True, Weights & Biases are used to track the experiment.",
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main(
         args.path,

examples/04_training/03_train_dynedge_from_config.py

@@ -138,7 +138,7 @@ def main(
         "dataset-config",
         "model-config",
         "gpus",
-        ("max-epochs", 5),
+        ("max-epochs", 1),
         "early-stopping-patience",
         ("batch-size", 16),
         "num-workers",
@@ -157,7 +157,7 @@ def main(
         help="If True, Weights & Biases are used to track the experiment.",
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main(
         args.dataset_config,

examples/04_training/04_train_multiclassifier_from_configs.py

@@ -175,7 +175,7 @@ def main(
             ),
         ),
         "gpus",
-        ("max-epochs", 5),
+        ("max-epochs", 1),
         "early-stopping-patience",
         ("batch-size", 16),
         "num-workers",
@@ -188,7 +188,7 @@ def main(
         default=None,
     )
 
-    args = parser.parse_args()
+    args, unknown = parser.parse_known_args()
 
     main(
         args.dataset_config,

src/graphnet/models/graphs/edges/edges.py

@@ -26,7 +26,7 @@ def forward(self, graph: Data) -> Data:
             graph: a graph with edges
         """
         if graph.edge_index is not None:
-            self.warnonce(
+            self.warning_once(
                 "GraphBuilder received graph with pre-existing "
                 "structure. Will overwrite."
             )

src/graphnet/models/graphs/graph_definition.py

@@ -148,7 +148,8 @@ def forward(  # type: ignore
         if self._edge_definition is not None:
             graph = self._edge_definition(graph)
         else:
-            self.warnonce(
+
+            self.warning_once(
                 """No EdgeDefinition provided. 
                 Graphs will not have edges defined!"""  # noqa
             )
@@ -305,10 +306,11 @@ def _add_features_individually(
             if feature not in ["x"]:  # reserved for node features.
                 graph[feature] = graph.x[:, index].detach()
             else:
-                self.warnonce(
-                    """Cannot assign graph['x']. This field is reserved 
-                    for node features. Please rename your input feature."""  # noqa
-                )
+                self.warning_once(
+                    """Cannot assign graph['x']. This field is reserved for
+                      node features. Please rename your input feature."""
+                )  # noqa
+
         return graph
 
     def _add_custom_labels(

tests/examples/01_icetray/test_icetray_examples.py

@@ -0,0 +1,17 @@
+"""Test for examples in 01_icetray."""
+import runpy
+import os
+import pytest
+from glob import glob
+
+from graphnet.constants import GRAPHNET_ROOT_DIR
+
+EXAMPLE_PATH = os.path.join(GRAPHNET_ROOT_DIR, "examples/01_icetray")
+
+examples = glob(EXAMPLE_PATH + "/*.py")
+
+
+@pytest.mark.parametrize("example", examples)
+def test_script_execution(example: str) -> None:
+    """Test function that executes example."""
+    runpy.run_path(os.path.join(EXAMPLE_PATH, example))

tests/examples/02_data/test_data_examples.py

@@ -0,0 +1,16 @@
+"""Tests for examples in 02_data."""
+import runpy
+import os
+import pytest
+from glob import glob
+
+from graphnet.constants import GRAPHNET_ROOT_DIR
+
+EXAMPLE_PATH = os.path.join(GRAPHNET_ROOT_DIR, "examples/02_data")
+examples = glob(EXAMPLE_PATH + "/*.py")
+
+
+@pytest.mark.parametrize("example", examples)
+def test_script_execution(example: str) -> None:
+    """Test function that executes example."""
+    runpy.run_path(os.path.join(EXAMPLE_PATH, example))

tests/examples/03_weights/test_weights_examples.py

@@ -0,0 +1,16 @@
+"""Test for examples in 03_weights."""
+import runpy
+import os
+from graphnet.constants import GRAPHNET_ROOT_DIR
+from glob import glob
+import pytest
+
+EXAMPLE_PATH = os.path.join(GRAPHNET_ROOT_DIR, "examples/03_weights")
+
+examples = glob(EXAMPLE_PATH + "/*.py")
+
+
+@pytest.mark.parametrize("example", examples)
+def test_script_execution(example: str) -> None:
+    """Test function that executes example."""
+    runpy.run_path(os.path.join(EXAMPLE_PATH, example))