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📌 Move sphinx deps to environment.yml + lock
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@peterhessey
peterhessey committed Aug 3, 2022
1 parent 11ecd1f commit 5353ae3
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4 changes: 0 additions & 4 deletions .readthedocs.yaml
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Expand Up @@ -11,9 +11,5 @@ build:
sphinx:
configuration: docs/source/conf.py

python:
install:
- requirements: docs/requirements.txt

conda:
environment: environment.yml
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -56,7 +56,7 @@ that can route anonymized DICOM images to an inference service.
- The [InnerEye-Inference](https://github.com/microsoft/InnerEye-Inference) component offers a REST API that integrates
with the InnerEye-Gateway, to run inference on InnerEye-DeepLearning models.

Details can be found [here](docs/deploy_on_aml.md).
Details can be found [here](docs/source/docs/deploy_on_aml.md).

![docs/deployment.png](docs/source/docs/images/deployment.png)

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113 changes: 65 additions & 48 deletions TestSubmodule/environment.yml
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Expand Up @@ -10,8 +10,8 @@ dependencies:
- 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=py38h06a4308_0
- ca-certificates=2022.07.19=h06a4308_0
- certifi=2022.6.15=py38h06a4308_0
- cudatoolkit=11.3.1=h2bc3f7f_2
- ffmpeg=4.2.2=h20bf706_0
- freetype=2.11.0=h70c0345_0
Expand Down Expand Up @@ -42,18 +42,18 @@ dependencies:
- mkl-service=2.4.0=py38h7f8727e_0
- mkl_fft=1.3.1=py38hd3c417c_0
- mkl_random=1.2.2=py38h51133e4_0
- ncurses=6.3=h7f8727e_2
- ncurses=6.3=h5eee18b_3
- nettle=3.7.3=hbbd107a_1
- openh264=2.1.1=h4ff587b_0
- openssl=1.1.1o=h7f8727e_0
- openssl=1.1.1q=h7f8727e_0
- pip=20.1.1=py38_1
- python=3.8.3
- python-blosc=1.7.0=py38h7b6447c_0
- pytorch=1.10.0=py3.8_cuda11.3_cudnn8.2.0_0
- pytorch-mutex=1.0=cuda
- readline=8.1.2=h7f8727e_1
- setuptools=61.2.0=py38h06a4308_0
- sqlite=3.38.3=hc218d9a_0
- sqlite=3.39.0=h5082296_0
- tk=8.6.12=h1ccaba5_0
- torchvision=0.11.1=py38_cu113
- typing_extensions=4.1.1=pyh06a4308_0
Expand All @@ -63,19 +63,20 @@ dependencies:
- zlib=1.2.12=h7f8727e_2
- zstd=1.5.2=ha4553b6_0
- pip:
- absl-py==1.1.0
- absl-py==1.2.0
- adal==1.2.7
- aiohttp==3.8.1
- aiosignal==1.2.0
- alembic==1.8.0
- alabaster==0.7.12
- alembic==1.8.1
- ansiwrap==0.8.4
- applicationinsights==0.11.10
- argon2-cffi==21.3.0
- argon2-cffi-bindings==21.2.0
- async-timeout==4.0.2
- attrs==21.4.0
- attrs==22.1.0
- azure-common==1.1.28
- azure-core==1.24.1
- azure-core==1.24.2
- azure-graphrbac==0.61.1
- azure-identity==1.7.0
- azure-mgmt-authorization==0.61.0
Expand All @@ -102,39 +103,42 @@ dependencies:
- azureml-train-automl-client==1.36.0
- azureml-train-core==1.36.0
- azureml-train-restclients-hyperdrive==1.36.0
- babel==2.10.3
- backports-tempfile==1.0
- backports-weakref==1.0.post1
- beautifulsoup4==4.11.1
- black==22.3.0
- bleach==5.0.0
- black==22.6.0
- bleach==5.0.1
- cachetools==4.2.4
- cffi==1.15.0
- charset-normalizer==2.0.12
- cffi==1.15.1
- charset-normalizer==2.1.0
- click==8.1.3
- cloudpickle==1.6.0
- colorama==0.4.5
- commonmark==0.9.1
- conda-merge==0.1.5
- contextlib2==21.6.0
- coverage==6.4.1
- coverage==6.4.2
- cryptography==3.3.2
- cycler==0.11.0
- databricks-cli==0.17.0
- dataclasses-json==0.5.2
- debugpy==1.6.0
- debugpy==1.6.2
- defusedxml==0.7.1
- deprecated==1.2.13
- distro==1.7.0
- docker==4.3.1
- docutils==0.19
- dotnetcore2==2.1.23
- entrypoints==0.4
- execnet==1.9.0
- fastjsonschema==2.15.3
- fastjsonschema==2.16.1
- fastmri==0.2.0
- flake8==3.8.3
- flask==2.1.2
- frozenlist==1.3.0
- fsspec==2022.5.0
- flask==2.2.0
- frozenlist==1.3.1
- fsspec==2022.7.1
- furo==2022.6.21
- fusepy==3.0.1
- future==0.18.2
- gitdb==4.0.9
Expand All @@ -143,49 +147,50 @@ dependencies:
- google-auth-oauthlib==0.4.6
- gputil==1.4.0
- greenlet==1.1.2
- grpcio==1.46.3
- grpcio==1.47.0
- gunicorn==20.1.0
- h5py==2.10.0
- hi-ml==0.2.2
- hi-ml-azure==0.2.2
- humanize==4.2.0
- hi-ml-azure==0.2.4
- humanize==4.2.3
- idna==3.3
- imageio==2.15.0
- importlib-metadata==4.11.4
- importlib-resources==5.8.0
- imagesize==1.4.1
- importlib-metadata==4.12.0
- importlib-resources==5.9.0
- iniconfig==1.1.1
- innereye-dicom-rt==1.0.3
- ipykernel==6.15.0
- ipykernel==6.15.1
- ipython==7.31.1
- ipython-genutils==0.2.0
- ipywidgets==7.7.0
- ipywidgets==7.7.1
- isodate==0.6.1
- itsdangerous==2.1.2
- jeepney==0.8.0
- jinja2==3.0.2
- jmespath==0.10.0
- joblib==0.16.0
- jsonpickle==2.2.0
- jsonschema==4.6.0
- jsonschema==4.9.1
- jupyter==1.0.0
- jupyter-client==6.1.5
- jupyter-console==6.4.3
- jupyter-core==4.10.0
- jupyter-console==6.4.4
- jupyter-core==4.11.1
- jupyterlab-pygments==0.2.2
- jupyterlab-widgets==1.1.0
- kiwisolver==1.4.3
- jupyterlab-widgets==1.1.1
- kiwisolver==1.4.4
- lightning-bolts==0.4.0
- llvmlite==0.34.0
- mako==1.2.0
- markdown==3.3.7
- mako==1.2.1
- markdown==3.4.1
- markupsafe==2.1.1
- marshmallow==3.16.0
- marshmallow==3.17.0
- marshmallow-enum==1.5.1
- matplotlib==3.3.0
- mccabe==0.6.1
- mistune==0.8.4
- mlflow==1.23.1
- mlflow-skinny==1.26.1
- mlflow-skinny==1.27.0
- monai==0.6.0
- more-itertools==8.13.0
- msal==1.18.0
Expand All @@ -195,12 +200,12 @@ dependencies:
- multidict==6.0.2
- mypy==0.910
- mypy-extensions==0.4.3
- nbclient==0.6.4
- nbclient==0.6.6
- nbconvert==6.5.0
- nbformat==5.4.0
- ndg-httpsclient==0.5.1
- nest-asyncio==1.5.5
- networkx==2.8.4
- networkx==2.8.5
- nibabel==4.0.1
- notebook==6.4.12
- numba==0.51.2
Expand All @@ -215,11 +220,12 @@ dependencies:
- pathspec==0.9.0
- pexpect==4.8.0
- pillow==9.0.0
- pkgutil-resolve-name==1.3.10
- platformdirs==2.5.2
- pluggy==0.13.1
- portalocker==2.4.0
- portalocker==2.5.1
- prometheus-client==0.14.1
- prometheus-flask-exporter==0.20.2
- prometheus-flask-exporter==0.20.3
- protobuf==3.20.1
- psutil==5.7.2
- ptyprocess==0.7.0
Expand Down Expand Up @@ -251,11 +257,12 @@ dependencies:
- qtconsole==5.3.1
- qtpy==2.1.0
- querystring-parser==1.2.4
- requests==2.28.0
- recommonmark==0.7.1
- requests==2.28.1
- requests-oauthlib==1.3.1
- rich==10.13.0
- rpdb==0.1.6
- rsa==4.8
- rsa==4.9
- ruamel-yaml==0.16.12
- ruamel-yaml-clib==0.2.6
- runstats==1.8.0
Expand All @@ -268,8 +275,18 @@ dependencies:
- simpleitk==1.2.4
- six==1.15.0
- smmap==5.0.0
- snowballstemmer==2.2.0
- soupsieve==2.3.2.post1
- sqlalchemy==1.4.37
- sphinx==5.0.2
- sphinx-basic-ng==0.0.1a12
- sphinx-rtd-theme==1.0.0
- sphinxcontrib-applehelp==1.0.2
- sphinxcontrib-devhelp==1.0.2
- sphinxcontrib-htmlhelp==2.0.0
- sphinxcontrib-jsmath==1.0.1
- sphinxcontrib-qthelp==1.0.3
- sphinxcontrib-serializinghtml==1.1.5
- sqlalchemy==1.4.39
- sqlparse==0.4.2
- stopit==1.1.2
- stringcase==1.2.0
Expand All @@ -281,22 +298,22 @@ dependencies:
- terminado==0.15.0
- textwrap3==0.9.2
- threadpoolctl==3.1.0
- tifffile==2022.5.4
- tifffile==2022.7.31
- tinycss2==1.1.1
- toml==0.10.2
- tomli==2.0.1
- torchio==0.18.74
- torchmetrics==0.6.0
- tornado==6.1
- tornado==6.2
- tqdm==4.64.0
- typing-inspect==0.7.1
- umap-learn==0.5.2
- urllib3==1.26.7
- webencodings==0.5.1
- websocket-client==1.3.3
- werkzeug==2.1.2
- widgetsnbextension==3.6.0
- werkzeug==2.2.1
- widgetsnbextension==3.6.1
- wrapt==1.14.1
- yacs==0.1.8
- yarl==1.7.2
- zipp==3.8.0
- yarl==1.8.1
- zipp==3.8.1
4 changes: 2 additions & 2 deletions create_and_lock_environment.sh
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Expand Up @@ -15,11 +15,11 @@ env_name="${name_arr[1]}"

# clear old conda envs, create new one
export CONDA_ALWAYS_YES="true"
conda env remove --name ${env_name::-1}
conda env remove --name ${env_name}
conda env create --file primary_deps.yml

# export new environment to environment.yml
conda env export -n ${env_name::-1} | grep -v "prefix:" > environment.yml
conda env export -n ${env_name} | grep -v "prefix:" > environment.yml
unset CONDA_ALWAYS_YES

# remove python version hash (technically not locked, so still potential for problems here if python secondary deps change)
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4 changes: 0 additions & 4 deletions docs/requirements.txt
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