📌 Move sphinx deps to environment.yml + lock

.readthedocs.yaml

@@ -11,9 +11,5 @@ build:
 sphinx:
  configuration: docs/source/conf.py
 
-python:
- install:
- - requirements: docs/requirements.txt
-
 conda:
  environment: environment.yml

README.md

@@ -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)
 

TestSubmodule/environment.yml

@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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

create_and_lock_environment.sh

@@ -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)