ENH: Add Environment Locking

.github/workflows/linting_and_hello_world.yml

@@ -67,7 +67,7 @@ jobs:
         with:
           activate-environment: InnerEye
           auto-activate-base: false
-          environment-file: environment.yml
+          environment-file: environment_win.yml
           python-version: 3.7
         if: always()
 

InnerEye/Azure/azure_util.py

@@ -234,6 +234,7 @@ def get_all_environment_files(project_root: Path) -> List[Path]:
     files = [innereye_yaml]
     if innereye_yaml != project_yaml:
         files.append(project_yaml)
+
     return files
 
 

InnerEye/ML/runner.py

@@ -306,6 +306,7 @@ def after_submission_hook(azure_run: Run) -> None:
                 # be necessary if the innereye package is installed. It is necessary when working with an outer project
                 # and InnerEye as a git submodule and submitting jobs from the local machine.
                 # In case of version conflicts, the package version in the outer project is given priority.
+                logging.info(f"Attempting to merge the following conda files: {source_config.conda_dependencies_files}")
                 merge_conda_files(source_config.conda_dependencies_files, temp_conda)
 
             # Calls like `self.azure_config.get_workspace()` will fail if we have no AzureML credentials set up, and so

TestSubmodule/environment.yml

@@ -1,7 +1,311 @@
-name: TestSubmodule
+# WARNING - DO NOT EDIT THIS FILE MANUALLY
+# Please refer to the environment documentation for instructions on how to create a new version of this file: https://github.com/microsoft/InnerEye-DeepLearning/blob/main/docs/environment.md
+name: InnerEye
 channels:
-  - defaults
   - pytorch
+  - defaults
 dependencies:
-  - pip=20.1.1
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=5.1=1_gnu
+  - blas=1.0=mkl
+  - blosc=1.21.0=h4ff587b_1
+  - bzip2=1.0.8=h7b6447c_0
+  - ca-certificates=2022.4.26=h06a4308_0
+  - certifi=2022.5.18.1=py37h06a4308_0
+  - cudatoolkit=11.3.1=h2bc3f7f_2
+  - ffmpeg=4.2.2=h20bf706_0
+  - freetype=2.11.0=h70c0345_0
+  - giflib=5.2.1=h7b6447c_0
+  - gmp=6.2.1=h2531618_2
+  - gnutls=3.6.15=he1e5248_0
+  - intel-openmp=2021.4.0=h06a4308_3561
+  - jpeg=9e=h7f8727e_0
+  - lame=3.100=h7b6447c_0
+  - lcms2=2.12=h3be6417_0
+  - libedit=3.1.20210910=h7f8727e_0
+  - libffi=3.2.1=hf484d3e_1007
+  - libgcc-ng=11.2.0=h1234567_0
+  - libgomp=11.2.0=h1234567_0
+  - libidn2=2.3.2=h7f8727e_0
+  - libopus=1.3.1=h7b6447c_0
+  - libpng=1.6.37=hbc83047_0
+  - libstdcxx-ng=11.2.0=h1234567_0
+  - libtasn1=4.16.0=h27cfd23_0
+  - libtiff=4.2.0=h2818925_1
+  - libunistring=0.9.10=h27cfd23_0
+  - libuv=1.40.0=h7b6447c_0
+  - libvpx=1.7.0=h439df22_0
+  - libwebp=1.2.2=h55f646e_0
+  - libwebp-base=1.2.2=h7f8727e_0
+  - lz4-c=1.9.3=h295c915_1
+  - mkl=2021.4.0=h06a4308_640
+  - mkl-service=2.4.0=py37h7f8727e_0
+  - mkl_fft=1.3.1=py37hd3c417c_0
+  - mkl_random=1.2.2=py37h51133e4_0
+  - ncurses=6.3=h7f8727e_2
+  - nettle=3.7.3=hbbd107a_1
+  - openh264=2.1.1=h4ff587b_0
+  - openssl=1.1.1o=h7f8727e_0
+  - pip=20.1.1=py37_1
   - python=3.7.3
+  - python-blosc=1.7.0=py37h7b6447c_0
+  - pytorch=1.10.0=py3.7_cuda11.3_cudnn8.2.0_0
+  - pytorch-mutex=1.0=cuda
+  - readline=7.0=h7b6447c_5
+  - setuptools=61.2.0=py37h06a4308_0
+  - sqlite=3.33.0=h62c20be_0
+  - tk=8.6.11=h1ccaba5_1
+  - torchvision=0.11.1=py37_cu113
+  - typing_extensions=4.1.1=pyh06a4308_0
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - x264=1!157.20191217=h7b6447c_0
+  - xz=5.2.5=h7f8727e_1
+  - zlib=1.2.12=h7f8727e_2
+  - zstd=1.5.2=ha4553b6_0
+  - pip:
+    - absl-py==1.0.0
+    - adal==1.2.7
+    - aiohttp==3.8.1
+    - aiosignal==1.2.0
+    - alembic==1.7.7
+    - ansiwrap==0.8.4
+    - applicationinsights==0.11.10
+    - argon2-cffi==21.3.0
+    - argon2-cffi-bindings==21.2.0
+    - async-timeout==4.0.2
+    - asynctest==0.13.0
+    - attrs==21.4.0
+    - azure-common==1.1.28
+    - azure-core==1.24.0
+    - azure-graphrbac==0.61.1
+    - azure-identity==1.7.0
+    - azure-mgmt-authorization==0.61.0
+    - azure-mgmt-containerregistry==10.0.0
+    - azure-mgmt-core==1.3.0
+    - azure-mgmt-datafactory==1.1.0
+    - azure-mgmt-keyvault==9.3.0
+    - azure-mgmt-resource==12.1.0
+    - azure-mgmt-storage==11.2.0
+    - azure-storage-blob==12.6.0
+    - azureml-automl-core==1.36.1
+    - azureml-core==1.36.0.post2
+    - azureml-dataprep==2.24.4
+    - azureml-dataprep-native==38.0.0
+    - azureml-dataprep-rslex==2.0.3
+    - azureml-dataset-runtime==1.36.0
+    - azureml-mlflow==1.36.0
+    - azureml-pipeline==1.36.0
+    - azureml-pipeline-core==1.36.0
+    - azureml-pipeline-steps==1.36.0
+    - azureml-sdk==1.36.0
+    - azureml-telemetry==1.36.0
+    - azureml-tensorboard==1.36.0
+    - azureml-train-automl-client==1.36.0
+    - azureml-train-core==1.36.0
+    - azureml-train-restclients-hyperdrive==1.36.0
+    - backcall==0.2.0
+    - backports-tempfile==1.0
+    - backports-weakref==1.0.post1
+    - beautifulsoup4==4.11.1
+    - black==22.3.0
+    - bleach==5.0.0
+    - cachetools==4.2.4
+    - cffi==1.15.0
+    - charset-normalizer==2.0.12
+    - click==8.1.3
+    - cloudpickle==1.6.0
+    - colorama==0.4.4
+    - commonmark==0.9.1
+    - conda-merge==0.1.5
+    - contextlib2==21.6.0
+    - coverage==6.4
+    - cryptography==3.3.2
+    - cucim==21.10.1
+    - cycler==0.11.0
+    - databricks-cli==0.16.6
+    - dataclasses-json==0.5.2
+    - debugpy==1.6.0
+    - decorator==5.1.1
+    - defusedxml==0.7.1
+    - deprecated==1.2.13
+    - distro==1.7.0
+    - docker==4.3.1
+    - dotnetcore2==2.1.23
+    - entrypoints==0.4
+    - execnet==1.9.0
+    - fastjsonschema==2.15.3
+    - flake8==3.8.3
+    - flask==2.1.2
+    - frozenlist==1.3.0
+    - fsspec==2022.5.0
+    - fusepy==3.0.1
+    - future==0.18.2
+    - gitdb==4.0.9
+    - gitpython==3.1.7
+    - google-auth==1.35.0
+    - google-auth-oauthlib==0.4.6
+    - gputil==1.4.0
+    - greenlet==1.1.2
+    - grpcio==1.46.3
+    - gunicorn==20.1.0
+    - h5py==2.10.0
+    - humanize==4.1.0
+    - idna==3.3
+    - imageio==2.15.0
+    - importlib-metadata==4.11.4
+    - importlib-resources==5.7.1
+    - iniconfig==1.1.1
+    - innereye-dicom-rt==1.0.3
+    - ipykernel==6.13.0
+    - ipython==7.31.1
+    - ipython-genutils==0.2.0
+    - ipywidgets==7.7.0
+    - isodate==0.6.1
+    - itsdangerous==2.1.2
+    - jedi==0.18.1
+    - jeepney==0.8.0
+    - jinja2==3.1.2
+    - jmespath==0.10.0
+    - joblib==0.16.0
+    - jsonpickle==2.2.0
+    - jsonschema==4.5.1
+    - jupyter==1.0.0
+    - jupyter-client==6.1.5
+    - jupyter-console==6.4.3
+    - jupyter-core==4.10.0
+    - jupyterlab-pygments==0.2.2
+    - jupyterlab-widgets==1.1.0
+    - kiwisolver==1.4.2
+    - lightning-bolts==0.4.0
+    - llvmlite==0.34.0
+    - mako==1.2.0
+    - markdown==3.3.7
+    - markupsafe==2.1.1
+    - marshmallow==3.16.0
+    - marshmallow-enum==1.5.1
+    - matplotlib==3.3.0
+    - matplotlib-inline==0.1.3
+    - mccabe==0.6.1
+    - mistune==0.8.4
+    - mlflow==1.23.1
+    - mlflow-skinny==1.26.1
+    - monai==0.6.0
+    - more-itertools==8.13.0
+    - msal==1.17.0
+    - msal-extensions==0.3.1
+    - msrest==0.6.21
+    - msrestazure==0.6.4
+    - multidict==6.0.2
+    - mypy==0.910
+    - mypy-extensions==0.4.3
+    - nbclient==0.6.3
+    - nbconvert==6.5.0
+    - nbformat==5.4.0
+    - ndg-httpsclient==0.5.1
+    - nest-asyncio==1.5.5
+    - networkx==2.6.3
+    - nibabel==3.2.2
+    - notebook==6.4.11
+    - numba==0.51.2
+    - numpy==1.19.1
+    - oauthlib==3.2.0
+    - opencv-python-headless==4.5.1.48
+    - packaging==21.3
+    - pandas==1.1.0
+    - pandocfilters==1.5.0
+    - papermill==2.2.2
+    - param==1.9.3
+    - parso==0.8.3
+    - pathspec==0.9.0
+    - pexpect==4.8.0
+    - pickleshare==0.7.5
+    - pillow==9.0.0
+    - platformdirs==2.5.2
+    - pluggy==0.13.1
+    - portalocker==2.4.0
+    - prometheus-client==0.14.1
+    - prometheus-flask-exporter==0.20.1
+    - prompt-toolkit==3.0.29
+    - protobuf==3.20.1
+    - psutil==5.7.2
+    - ptyprocess==0.7.0
+    - py==1.11.0
+    - pyarrow==3.0.0
+    - pyasn1==0.4.8
+    - pyasn1-modules==0.2.8
+    - pycodestyle==2.6.0
+    - pycparser==2.21
+    - pydeprecate==0.3.1
+    - pydicom==2.0.0
+    - pyflakes==2.2.0
+    - pygments==2.12.0
+    - pyjwt==1.7.1
+    - pynndescent==0.5.7
+    - pyopenssl==20.0.1
+    - pyparsing==3.0.9
+    - pyrsistent==0.18.1
+    - pytest==6.0.1
+    - pytest-cov==2.10.1
+    - pytest-forked==1.3.0
+    - pytest-xdist==1.34.0
+    - python-dateutil==2.8.2
+    - pytorch-lightning==1.5.5
+    - pytz==2022.1
+    - pywavelets==1.3.0
+    - pyyaml==6.0
+    - pyzmq==23.0.0
+    - qtconsole==5.3.0
+    - qtpy==2.1.0
+    - querystring-parser==1.2.4
+    - requests==2.27.1
+    - requests-oauthlib==1.3.1
+    - rich==10.13.0
+    - rpdb==0.1.6
+    - rsa==4.8
+    - ruamel-yaml==0.16.12
+    - ruamel-yaml-clib==0.2.6
+    - runstats==1.8.0
+    - scikit-image==0.17.2
+    - scikit-learn==0.23.2
+    - scipy==1.5.2
+    - seaborn==0.10.1
+    - secretstorage==3.3.2
+    - send2trash==1.8.0
+    - simpleitk==1.2.4
+    - six==1.15.0
+    - smmap==5.0.0
+    - soupsieve==2.3.2.post1
+    - sqlalchemy==1.4.36
+    - sqlparse==0.4.2
+    - stopit==1.1.2
+    - stringcase==1.2.0
+    - tabulate==0.8.7
+    - tenacity==8.0.1
+    - tensorboard==2.3.0
+    - tensorboard-plugin-wit==1.8.1
+    - tensorboardx==2.1
+    - terminado==0.15.0
+    - textwrap3==0.9.2
+    - threadpoolctl==3.1.0
+    - tifffile==2021.11.2
+    - tinycss2==1.1.1
+    - toml==0.10.2
+    - tomli==2.0.1
+    - torchio==0.18.74
+    - torchmetrics==0.6.0
+    - tornado==6.1
+    - tqdm==4.64.0
+    - traitlets==5.2.1.post0
+    - typed-ast==1.4.3
+    - typing-inspect==0.7.1
+    - umap-learn==0.5.2
+    - urllib3==1.26.7
+    - wcwidth==0.2.5
+    - webencodings==0.5.1
+    - websocket-client==1.3.2
+    - werkzeug==2.1.2
+    - widgetsnbextension==3.6.0
+    - wrapt==1.14.1
+    - yacs==0.1.8
+    - yarl==1.7.2
+    - zipp==3.8.0