revert changes unrelated to test restructuring

Author: garciadias

.gitignore

@@ -130,7 +130,6 @@ temp/
 .DS_Store
 
 # temporary testing data MedNIST
-tests/integration/testing_data/MedNIST*
 tests/testing_data/MedNIST*
 tests/testing_data/*Hippocampus*
 tests/testing_data/*.tiff

tests/bundle/test_bundle_ckpt_export.py

@@ -15,87 +15,89 @@
 import os
 import tempfile
 import unittest
-from pathlib import Path
 
 from parameterized import parameterized
 
 from monai.bundle import ConfigParser
 from monai.data import load_net_with_metadata
 from monai.networks import save_state
-from tests.util import command_line_tests, skip_if_windows
+from tests.utils import command_line_tests, skip_if_windows
 
 TEST_CASE_1 = ["", ""]
+
 TEST_CASE_2 = ["model", ""]
+
 TEST_CASE_3 = ["model", "True"]
 
 
 @skip_if_windows
 class TestCKPTExport(unittest.TestCase):
+
     def setUp(self):
         self.device = os.environ.get("CUDA_VISIBLE_DEVICES")
         if not self.device:
             os.environ["CUDA_VISIBLE_DEVICES"] = "0"  # default
-        module_path = Path(__file__).resolve().parents[1].as_posix()
-        self.meta_file = os.path.join(module_path, "testing_data", "metadata.json")
-        self.config_file = os.path.join(module_path, "testing_data", "inference.json")
-        self.tempdir_obj = tempfile.TemporaryDirectory()
-        tempdir = self.tempdir_obj.name
-        self.def_args = {"meta_file": "will be replaced by `meta_file` arg"}
-        self.def_args_file = os.path.join(tempdir, "def_args.yaml")
-
-        self.ckpt_file = os.path.join(tempdir, "model.pt")
-        self.ts_file = os.path.join(tempdir, "model.ts")
-
-        self.parser = ConfigParser()
-        self.parser.export_config_file(config=self.def_args, filepath=self.def_args_file)
-        self.parser.read_config(self.config_file)
-        self.net = self.parser.get_parsed_content("network_def")
-        self.cmd = ["coverage", "run", "-m", "monai.bundle", "ckpt_export", "network_def", "--filepath", self.ts_file]
-        self.cmd += [
-            "--meta_file",
-            self.meta_file,
-            "--config_file",
-            f"['{self.config_file}','{self.def_args_file}']",
-            "--ckpt_file",
-        ]
 
     def tearDown(self):
         if self.device is not None:
             os.environ["CUDA_VISIBLE_DEVICES"] = self.device
         else:
             del os.environ["CUDA_VISIBLE_DEVICES"]  # previously unset
-        self.tempdir_obj.cleanup()
 
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
     def test_export(self, key_in_ckpt, use_trace):
-        save_state(src=self.net if key_in_ckpt == "" else {key_in_ckpt: self.net}, path=self.ckpt_file)
-        full_cmd = self.cmd + [self.ckpt_file, "--key_in_ckpt", key_in_ckpt, "--args_file", self.def_args_file]
-        if use_trace == "True":
-            full_cmd += ["--use_trace", use_trace, "--input_shape", "[1, 1, 96, 96, 96]"]
-        command_line_tests(full_cmd)
-        self.assertTrue(os.path.exists(self.ts_file))
-
-        _, metadata, extra_files = load_net_with_metadata(
-            self.ts_file, more_extra_files=["inference.json", "def_args.json"]
-        )
-        self.assertIn("schema", metadata)
-        self.assertIn("meta_file", json.loads(extra_files["def_args.json"]))
-        self.assertIn("network_def", json.loads(extra_files["inference.json"]))
+        meta_file = os.path.join(os.path.dirname(__file__), "testing_data", "metadata.json")
+        config_file = os.path.join(os.path.dirname(__file__), "testing_data", "inference.json")
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg"}
+            def_args_file = os.path.join(tempdir, "def_args.yaml")
+
+            ckpt_file = os.path.join(tempdir, "model.pt")
+            ts_file = os.path.join(tempdir, "model.ts")
+
+            parser = ConfigParser()
+            parser.export_config_file(config=def_args, filepath=def_args_file)
+            parser.read_config(config_file)
+            net = parser.get_parsed_content("network_def")
+            save_state(src=net if key_in_ckpt == "" else {key_in_ckpt: net}, path=ckpt_file)
+
+            cmd = ["coverage", "run", "-m", "monai.bundle", "ckpt_export", "network_def", "--filepath", ts_file]
+            cmd += ["--meta_file", meta_file, "--config_file", f"['{config_file}','{def_args_file}']", "--ckpt_file"]
+            cmd += [ckpt_file, "--key_in_ckpt", key_in_ckpt, "--args_file", def_args_file]
+            if use_trace == "True":
+                cmd += ["--use_trace", use_trace, "--input_shape", "[1, 1, 96, 96, 96]"]
+            command_line_tests(cmd)
+            self.assertTrue(os.path.exists(ts_file))
+
+            _, metadata, extra_files = load_net_with_metadata(
+                ts_file, more_extra_files=["inference.json", "def_args.json"]
+            )
+            self.assertIn("schema", metadata)
+            self.assertIn("meta_file", json.loads(extra_files["def_args.json"]))
+            self.assertIn("network_def", json.loads(extra_files["inference.json"]))
 
     @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
     def test_default_value(self, key_in_ckpt, use_trace):
-        ckpt_file = os.path.join(self.tempdir_obj.name, "models/model.pt")
-        ts_file = os.path.join(self.tempdir_obj.name, "models/model.ts")
-
-        save_state(src=self.net if key_in_ckpt == "" else {key_in_ckpt: self.net}, path=ckpt_file)
-
-        # check with default value
-        cmd = ["coverage", "run", "-m", "monai.bundle", "ckpt_export", "--key_in_ckpt", key_in_ckpt]
-        cmd += ["--config_file", self.config_file, "--bundle_root", self.tempdir_obj.name]
-        if use_trace == "True":
-            cmd += ["--use_trace", use_trace, "--input_shape", "[1, 1, 96, 96, 96]"]
-        command_line_tests(cmd)
-        self.assertTrue(os.path.exists(ts_file))
+        config_file = os.path.join(os.path.dirname(__file__), "testing_data", "inference.json")
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg"}
+            def_args_file = os.path.join(tempdir, "def_args.yaml")
+            ckpt_file = os.path.join(tempdir, "models/model.pt")
+            ts_file = os.path.join(tempdir, "models/model.ts")
+
+            parser = ConfigParser()
+            parser.export_config_file(config=def_args, filepath=def_args_file)
+            parser.read_config(config_file)
+            net = parser.get_parsed_content("network_def")
+            save_state(src=net if key_in_ckpt == "" else {key_in_ckpt: net}, path=ckpt_file)
+
+            # check with default value
+            cmd = ["coverage", "run", "-m", "monai.bundle", "ckpt_export", "--key_in_ckpt", key_in_ckpt]
+            cmd += ["--config_file", config_file, "--bundle_root", tempdir]
+            if use_trace == "True":
+                cmd += ["--use_trace", use_trace, "--input_shape", "[1, 1, 96, 96, 96]"]
+            command_line_tests(cmd)
+            self.assertTrue(os.path.exists(ts_file))
 
 
 if __name__ == "__main__":

tests/integration/test_integration_classification_2d.py

@@ -212,7 +212,7 @@ def setUp(self):
             image_classes.extend([i] * len(image_files[i]))
 
         # split train, val, test
-        valid_frac, test_frac = 0.01, 0.01
+        valid_frac, test_frac = 0.1, 0.1
         self.train_x, self.train_y = [], []
         self.val_x, self.val_y = [], []
         self.test_x, self.test_y = [], []