Add bundle root directory to Python search directories automatically (#…

…6910)

Fixes #6722 .

### Description
Add scripts directory to Python search directories automatically in the
`run` function in `ConfigWorkflow`.

### 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.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: KumoLiu <[email protected]>

monai/bundle/workflows.py

@@ -12,6 +12,7 @@
 from __future__ import annotations
 
 import os
+import sys
 import time
 import warnings
 from abc import ABC, abstractmethod
@@ -170,6 +171,7 @@ class ConfigWorkflow(BundleWorkflow):
     """
     Specification for the config-based bundle workflow.
     Standardized the `initialize`, `run`, `finalize` behavior in a config-based training, evaluation, or inference.
+    Before `run`, we add bundle root directory to Python search directories automatically.
     For more information: https://docs.monai.io/en/latest/mb_specification.html.
 
     Args:
@@ -224,23 +226,23 @@ def __init__(
         super().__init__(workflow_type=workflow_type)
         if config_file is not None:
             _config_files = ensure_tuple(config_file)
-            config_root_path = Path(_config_files[0]).parent
+            self.config_root_path = Path(_config_files[0]).parent
             for _config_file in _config_files:
                 _config_file = Path(_config_file)
-                if _config_file.parent != config_root_path:
+                if _config_file.parent != self.config_root_path:
                     warnings.warn(
-                        f"Not all config files are in {config_root_path}. If logging_file and meta_file are"
-                        f"not specified, {config_root_path} will be used as the default config root directory."
+                        f"Not all config files are in {self.config_root_path}. If logging_file and meta_file are"
+                        f"not specified, {self.config_root_path} will be used as the default config root directory."
                     )
                 if not _config_file.is_file():
                     raise FileNotFoundError(f"Cannot find the config file: {_config_file}.")
         else:
-            config_root_path = Path("configs")
+            self.config_root_path = Path("configs")
 
-        logging_file = str(config_root_path / "logging.conf") if logging_file is None else logging_file
+        logging_file = str(self.config_root_path / "logging.conf") if logging_file is None else logging_file
         if logging_file is not None:
             if not os.path.exists(logging_file):
-                if logging_file == str(config_root_path / "logging.conf"):
+                if logging_file == str(self.config_root_path / "logging.conf"):
                     warnings.warn(f"Default logging file in {logging_file} does not exist, skipping logging.")
                 else:
                     raise FileNotFoundError(f"Cannot find the logging config file: {logging_file}.")
@@ -250,7 +252,7 @@ def __init__(
 
         self.parser = ConfigParser()
         self.parser.read_config(f=config_file)
-        meta_file = str(config_root_path / "metadata.json") if meta_file is None else meta_file
+        meta_file = str(self.config_root_path / "metadata.json") if meta_file is None else meta_file
         if isinstance(meta_file, str) and not os.path.exists(meta_file):
             raise FileNotFoundError(f"Cannot find the metadata config file: {meta_file}.")
         else:
@@ -283,8 +285,13 @@ def initialize(self) -> Any:
     def run(self) -> Any:
         """
         Run the bundle workflow, it can be a training, evaluation or inference.
+        Before run, we add bundle root directory to Python search directories automatically.
 
         """
+        _bundle_root_path = (
+            self.config_root_path.parent if self.config_root_path.name == "configs" else self.config_root_path
+        )
+        sys.path.insert(1, str(_bundle_root_path))
         if self.run_id not in self.parser:
             raise ValueError(f"run ID '{self.run_id}' doesn't exist in the config file.")
         return self._run_expr(id=self.run_id)

tests/test_integration_bundle_run.py

@@ -14,6 +14,7 @@
 import json
 import os
 import shutil
+import subprocess
 import sys
 import tempfile
 import unittest
@@ -44,6 +45,14 @@ def run(self):
         return self.val
 
 
+class _Runnable43:
+    def __init__(self, func):
+        self.func = func
+
+    def run(self):
+        self.func()
+
+
 class TestBundleRun(unittest.TestCase):
     def setUp(self):
         self.data_dir = tempfile.mkdtemp()
@@ -77,6 +86,69 @@ def test_tiny(self):
         with self.assertRaises(RuntimeError):
             # test wrong run_id="run"
             command_line_tests(cmd + ["run", "run", "--config_file", config_file])
+        with self.assertRaises(RuntimeError):
+            # test missing meta file
+            command_line_tests(cmd + ["run", "training", "--config_file", config_file])
+
+    def test_scripts_fold(self):
+        # test scripts directory has been added to Python search directories automatically
+        config_file = os.path.join(self.data_dir, "tiny_config.json")
+        meta_file = os.path.join(self.data_dir, "tiny_meta.json")
+        scripts_dir = os.path.join(self.data_dir, "scripts")
+        script_file = os.path.join(scripts_dir, "test_scripts_fold.py")
+        init_file = os.path.join(scripts_dir, "__init__.py")
+
+        with open(config_file, "w") as f:
+            json.dump(
+                {
+                    "imports": ["$import scripts"],
+                    "trainer": {
+                        "_target_": "tests.test_integration_bundle_run._Runnable43",
+                        "func": "$scripts.tiny_test",
+                    },
+                    # keep this test case to cover the "runner_id" arg
+                    "training": "[email protected]()",
+                },
+                f,
+            )
+        with open(meta_file, "w") as f:
+            json.dump(
+                {"version": "0.1.0", "monai_version": "1.1.0", "pytorch_version": "1.13.1", "numpy_version": "1.22.2"},
+                f,
+            )
+
+        os.mkdir(scripts_dir)
+        script_file_lines = ["def tiny_test():\n", "    print('successfully added scripts fold!') \n"]
+        init_file_line = "from .test_scripts_fold import tiny_test\n"
+        with open(script_file, "w") as f:
+            f.writelines(script_file_lines)
+            f.close()
+        with open(init_file, "w") as f:
+            f.write(init_file_line)
+            f.close()
+
+        cmd = ["coverage", "run", "-m", "monai.bundle"]
+        # test both CLI entry "run" and "run_workflow"
+        expected_condition = "successfully added scripts fold!"
+        command_run = cmd + ["run", "training", "--config_file", config_file, "--meta_file", meta_file]
+        completed_process = subprocess.run(command_run, check=True, capture_output=True, text=True)
+        output = repr(completed_process.stdout).replace("\\n", "\n").replace("\\t", "\t")  # Get the captured output
+        print(output)
+
+        self.assertTrue(expected_condition in output)
+        command_run_workflow = cmd + [
+            "run_workflow",
+            "--run_id",
+            "training",
+            "--config_file",
+            config_file,
+            "--meta_file",
+            meta_file,
+        ]
+        completed_process = subprocess.run(command_run_workflow, check=True, capture_output=True, text=True)
+        output = repr(completed_process.stdout).replace("\\n", "\n").replace("\\t", "\t")  # Get the captured output
+        print(output)
+        self.assertTrue(expected_condition in output)
 
         with self.assertRaises(RuntimeError):
             # test missing meta file