Move pip requirements to text file

InnerEye/Common/fixed_paths.py

@@ -41,6 +41,7 @@ def repository_parent_directory(path: Optional[PathOrString] = None) -> Path:
 INNEREYE_PACKAGE_NAME = "InnerEye"
 # Child paths to include in a registered model that live outside InnerEye/.
 ENVIRONMENT_YAML_FILE_NAME = "environment.yml"
+PIP_REQUIREMENTS_FILE_NAME = "requirements.txt"
 
 DEFAULT_AML_UPLOAD_DIR = "outputs"
 DEFAULT_RESULT_IMAGE_NAME = "segmentation.nii.gz"

requirements.txt

@@ -0,0 +1,62 @@
+azure-mgmt-resource==12.1.0
+azure-mgmt-datafactory==1.1.0
+azure-storage-blob==12.6.0
+azureml-mlflow==1.36.0
+azureml-sdk==1.36.0
+azureml-tensorboard==1.36.0
+conda-merge==0.1.5
+cryptography==3.3.2
+cucim==21.10.1; platform_system=="Linux"
+dataclasses-json==0.5.2
+docker==4.3.1
+flake8==3.8.3
+gitpython==3.1.7
+gputil==1.4.0
+h5py==2.10.0
+ipython==7.31.1
+imageio==2.15.0
+InnerEye-DICOM-RT==1.0.1
+joblib==0.16.0
+jupyter==1.0.0
+jupyter-client==6.1.5
+lightning-bolts==0.4.0
+matplotlib==3.3.0
+mlflow==1.23.1
+monai==0.6.0
+mypy==0.910
+mypy-extensions==0.4.3
+numba==0.51.2
+numpy==1.19.1
+numba==0.51.2
+opencv-python-headless==4.5.1.48
+pandas==1.1.0
+papermill==2.2.2
+param==1.9.3
+pillow==9.0.0
+psutil==5.7.2
+pydicom==2.0.0
+pyflakes==2.2.0
+PyJWT==1.7.1
+pytest==6.0.1
+pytest-cov==2.10.1
+pytest-forked==1.3.0
+pytest-xdist==1.34.0
+pytorch-lightning==1.5.5
+rich==10.13.0
+rpdb==0.1.6
+ruamel.yaml==0.16.12
+runstats==1.8.0
+scikit-image==0.17.2
+scikit-learn==0.23.2
+scipy==1.5.2
+seaborn==0.10.1
+simpleitk==1.2.4
+six==1.15.0
+stopit==1.1.2
+tabulate==0.8.7
+tensorboard==2.3.0
+tensorboardX==2.1
+torchio==0.18.74
+torchmetrics==0.6.0
+umap-learn==0.5.2
+yacs==0.1.8

setup.py

@@ -5,11 +5,9 @@
 import os
 import shutil
 from pathlib import Path
-from typing import List
+from typing import List, Optional
 
-import ruamel.yaml
 import setuptools
-from ruamel.yaml.comments import CommentedMap
 
 from InnerEye.Common import fixed_paths
 from InnerEye.Common.common_util import namespace_to_path
@@ -45,7 +43,7 @@ def _get_innereye_packages() -> List[str]:
  return [x for x in setuptools.find_namespace_packages(str(package_root)) if x.startswith(INNEREYE_PACKAGE_NAME)]
 
 
-def _get_source_packages(exclusions: List[str] = None) -> List[str]:
+def _get_source_packages(exclusions: Optional[List[str]] = None) -> List[str]:
  exclusions = [] if not exclusions else exclusions
  return [x for x in _get_innereye_packages() if not any([e in x for e in exclusions])]
 
@@ -92,15 +90,7 @@ def _get_child_package(root: str, child: str) -> str:
  and not os.path.exists(os.path.join(str(package_root), INNEREYE_PACKAGE_NAME, file)):
  raise FileNotFoundError(f"File {file} in package data does not exist")
 
-with open(package_root / fixed_paths.ENVIRONMENT_YAML_FILE_NAME, "r") as env_file:
- yaml_contents = ruamel.yaml.round_trip_load(env_file)
-env_dependencies = yaml_contents["dependencies"]
-pip_list = None
-for d in env_dependencies:
- if isinstance(d, CommentedMap) and "pip" in d:
- pip_list = list(d["pip"])
-if not pip_list:
- raise ValueError("Expected there is a 'pip' section in the environment file?")
+pip_list = (package_root / fixed_paths.PIP_REQUIREMENTS_FILE_NAME).read_text().splitlines()
 
 git_prefix = "git+"
 required_packages = []