⚰️ Remove references to old submodules

InnerEye/Common/fixed_paths.py

@@ -6,7 +6,7 @@
 import os
 import sys
 from pathlib import Path
-from typing import List, Optional, Tuple
+from typing import Optional
 
 from InnerEye.Common.type_annotations import PathOrString
 
@@ -104,15 +104,6 @@ def get_environment_yaml_file() -> Path:
  return env
 
 
-def get_hi_ml_submodule_relative_paths() -> List[Tuple[Path, str]]:
- """
- Returns the paths relative to the repository root where the submodules for hi-ml and hi-ml-azure are expected.
- It returns a list with a tuple (folder name, expected subfolder in that folder)
- """
- return [(Path("hi-ml") / "hi-ml-azure" / "src", "health_azure"),
- (Path("hi-ml") / "hi-ml" / "src", "health_ml")]
-
-
 def add_submodules_to_path() -> None:
  """
  This function adds all submodules that the code uses to sys.path and to the environment variables. This is
@@ -123,9 +114,7 @@ def add_submodules_to_path() -> None:
  up in sys.path.
  """
  innereye_root = repository_root_directory()
- folders_to_add = [(innereye_root, "InnerEye"),
- (innereye_root / "fastMRI", "fastmri")]
- folders_to_add.extend([(innereye_root / p, folder) for p, folder in get_hi_ml_submodule_relative_paths()])
+ folders_to_add = [(innereye_root, "InnerEye")]
  for (folder, subfolder_that_must_exist) in folders_to_add:
  if (folder / subfolder_that_must_exist).is_dir():
  folder_str = str(folder)

InnerEye/ML/run_ml.py

@@ -654,11 +654,7 @@ def copy_file(source: Path, destination_file: str) -> None:
  # we can identify it by going up the folder structure off a known file (repository_root does exactly that)
  repository_root = fixed_paths.repository_root_directory()
  copy_folder(repository_root / INNEREYE_PACKAGE_NAME)
- # If hi-ml is used as a submodule, copy that too
- for relative_path, _ in fixed_paths.get_hi_ml_submodule_relative_paths():
- full_submodule_path = repository_root / relative_path
- if full_submodule_path.is_dir():
- copy_folder(full_submodule_path, relative_path)
+
  # Extra code directory is expected to be relative to the project root folder.
  if self.azure_config.extra_code_directory:
  extra_code_folder = self.project_root / self.azure_config.extra_code_directory

TestsOutsidePackage/test_register_model.py

@@ -52,8 +52,6 @@ def test_copy_child_paths_to_folder(is_ensemble: bool,
  project_root = Path(__file__).parent.parent
  ml_runner = MLRunner(model_config=fake_model, azure_config=azure_config, project_root=project_root)
  model_folder = test_output_dirs.root_dir / "final"
- hi_ml_submodules = [p for p, _ in fixed_paths.get_hi_ml_submodule_relative_paths()]
- has_submodule = any(folder.is_dir() for folder in hi_ml_submodules)
  ml_runner.copy_child_paths_to_folder(model_folder=model_folder, checkpoint_paths=checkpoints_absolute)
  expected_files = [
  fixed_paths.ENVIRONMENT_YAML_FILE_NAME,
@@ -63,9 +61,7 @@ def test_copy_child_paths_to_folder(is_ensemble: bool,
  "InnerEye/Common/fixed_paths.py",
  "InnerEye/Common/common_util.py",
  ]
- if has_submodule:
- expected_files.extend(["hi-ml/hi-ml/src/health_ml/__init__.py",
- "hi-ml/hi-ml-azure/src/health_azure/__init__.py"])
+
  for r in checkpoints_relative:
  expected_files.append(f"{CHECKPOINT_FOLDER}/{r}")
  for expected_file in expected_files: