📌 Add myst-parser to environment.yml, lock env

microsoft · peterhessey · Aug 18, 2022 · Aug 5, 2022 · Aug 5, 2022 · Aug 8, 2022
commit 6e610b0ccb165b04c0044e63351179a4a19e3c9b
diff --git a/TestSubmodule/environment.yml b/TestSubmodule/environment.yml
@@ -53,10 +53,10 @@ dependencies:
  - pytorch-mutex=1.0=cuda
  - readline=8.1.2=h7f8727e_1
  - setuptools=61.2.0=py38h06a4308_0
- - sqlite=3.39.0=h5082296_0
+ - sqlite=3.39.2=h5082296_0
  - tk=8.6.12=h1ccaba5_0
  - torchvision=0.11.1=py38_cu113
- - typing_extensions=4.1.1=pyh06a4308_0
+ - typing_extensions=4.3.0=py38h06a4308_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - x264=1!157.20191217=h7b6447c_0
  - xz=5.2.5=h7f8727e_1
@@ -76,12 +76,12 @@ dependencies:
  - async-timeout==4.0.2
  - attrs==22.1.0
  - azure-common==1.1.28
- - azure-core==1.24.2
+ - azure-core==1.25.0
  - 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==1.3.1
+ - azure-mgmt-core==1.3.2
  - azure-mgmt-datafactory==1.1.0
  - azure-mgmt-keyvault==9.3.0
  - azure-mgmt-resource==12.1.0
@@ -118,24 +118,24 @@ dependencies:
  - commonmark==0.9.1
  - conda-merge==0.1.5
  - contextlib2==21.6.0
- - coverage==6.4.2
+ - coverage==6.4.3
  - cryptography==3.3.2
  - cycler==0.11.0
- - databricks-cli==0.17.0
+ - databricks-cli==0.17.1
  - dataclasses-json==0.5.2
- - debugpy==1.6.2
+ - debugpy==1.6.3
  - defusedxml==0.7.1
  - deprecated==1.2.13
  - distro==1.7.0
  - docker==4.3.1
- - docutils==0.17.1
+ - docutils==0.18.1
  - dotnetcore2==2.1.23
  - entrypoints==0.4
  - execnet==1.9.0
  - fastjsonschema==2.16.1
  - fastmri==0.2.0
  - flake8==3.8.3
- - flask==2.2.0
+ - flask==2.2.2
  - frozenlist==1.3.1
  - fsspec==2022.7.1
  - furo==2022.6.21
@@ -152,7 +152,7 @@ dependencies:
  - h5py==2.10.0
  - hi-ml==0.2.2
  - hi-ml-azure==0.2.2
- - humanize==4.2.3
+ - humanize==4.3.0
  - idna==3.3
  - imageio==2.15.0
  - imagesize==1.4.1
@@ -181,27 +181,32 @@ dependencies:
  - kiwisolver==1.4.4
  - lightning-bolts==0.4.0
  - llvmlite==0.34.0
+ - lxml==4.9.1
  - mako==1.2.1
  - markdown==3.4.1
+ - markdown-it-py==2.1.0
  - markupsafe==2.1.1
  - marshmallow==3.17.0
  - marshmallow-enum==1.5.1
  - matplotlib==3.3.0
  - mccabe==0.6.1
+ - mdit-py-plugins==0.3.0
+ - mdurl==0.1.2
  - mistune==0.8.4
  - mlflow==1.23.1
- - mlflow-skinny==1.27.0
+ - mlflow-skinny==1.28.0
  - monai==0.6.0
- - more-itertools==8.13.0
+ - more-itertools==8.14.0
  - msal==1.18.0
  - msal-extensions==0.3.1
  - msrest==0.7.1
  - msrestazure==0.6.4
  - multidict==6.0.2
  - mypy==0.910
  - mypy-extensions==0.4.3
+ - myst-parser==0.18.0
  - nbclient==0.6.6
- - nbconvert==6.5.0
+ - nbconvert==6.5.3
  - nbformat==5.4.0
  - ndg-httpsclient==0.5.1
  - nest-asyncio==1.5.5
@@ -250,12 +255,12 @@ dependencies:
  - pytest-xdist==1.34.0
  - python-dateutil==2.8.2
  - pytorch-lightning==1.5.5
- - pytz==2022.1
+ - pytz==2022.2.1
  - pywavelets==1.3.0
  - pyyaml==6.0
- - pyzmq==23.2.0
+ - pyzmq==23.2.1
  - qtconsole==5.3.1
- - qtpy==2.1.0
+ - qtpy==2.2.0
  - querystring-parser==1.2.4
  - requests==2.28.1
  - requests-oauthlib==1.3.1
@@ -269,7 +274,7 @@ dependencies:
  - scikit-learn==0.23.2
  - scipy==1.5.2
  - seaborn==0.10.1
- - secretstorage==3.3.2
+ - secretstorage==3.3.3
  - send2trash==1.8.0
  - simpleitk==1.2.4
  - six==1.15.0
@@ -285,7 +290,7 @@ dependencies:
  - sphinxcontrib-jsmath==1.0.1
  - sphinxcontrib-qthelp==1.0.3
  - sphinxcontrib-serializinghtml==1.1.5
- - sqlalchemy==1.4.39
+ - sqlalchemy==1.4.40
  - sqlparse==0.4.2
  - stopit==1.1.2
  - stringcase==1.2.0
@@ -297,7 +302,7 @@ dependencies:
  - terminado==0.15.0
  - textwrap3==0.9.2
  - threadpoolctl==3.1.0
- - tifffile==2022.7.31
+ - tifffile==2022.8.12
  - tinycss2==1.1.1
  - toml==0.10.2
  - tomli==2.0.1
@@ -310,7 +315,7 @@ dependencies:
  - urllib3==1.26.7
  - webencodings==0.5.1
  - websocket-client==1.3.3
- - werkzeug==2.2.1
+ - werkzeug==2.2.2
  - widgetsnbextension==3.6.1
  - wrapt==1.14.1
  - yacs==0.1.8

diff --git a/docs/README.md b/docs/README.md
@@ -1,12 +1,6 @@
 # Building docs for InnerEye-DeepLearning
 
-1. First, make sure you have all the packages necessary for InnerEye.
-2. Install pip dependencies from docs/requirements.txt:
-
-```shell
-pip install -r requirements.txt
-```
-
-1. Run `make html` from the `docs` folder. This will create html files under docs/build/html.
-1. From the `docs/build/html` folder, run `python -m http.server 8080` to host the docs locally.
-1. From your browser, navigate to `http:https://localhost:8080` to view the documentation.
+1. First, make sure you have set up your conda environment as described in the [Quick Setup Guide](../README.md#quick-setup).
+2. Run `make html` from the `docs` folder. This will create html files under docs/build/html.
+3. From the `docs/build/html` folder, run `python -m http.server 8080` to host the docs locally.
+4. From your browser, navigate to `http:https://localhost:8080` to view the documentation.
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/environment.yml b/environment.yml
@@ -53,10 +53,10 @@ dependencies:
  - pytorch-mutex=1.0=cuda
  - readline=8.1.2=h7f8727e_1
  - setuptools=61.2.0=py38h06a4308_0
- - sqlite=3.39.0=h5082296_0
+ - sqlite=3.39.2=h5082296_0
  - tk=8.6.12=h1ccaba5_0
  - torchvision=0.11.1=py38_cu113
- - typing_extensions=4.1.1=pyh06a4308_0
+ - typing_extensions=4.3.0=py38h06a4308_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - x264=1!157.20191217=h7b6447c_0
  - xz=5.2.5=h7f8727e_1
@@ -76,12 +76,12 @@ dependencies:
  - async-timeout==4.0.2
  - attrs==22.1.0
  - azure-common==1.1.28
- - azure-core==1.24.2
+ - azure-core==1.25.0
  - 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==1.3.1
+ - azure-mgmt-core==1.3.2
  - azure-mgmt-datafactory==1.1.0
  - azure-mgmt-keyvault==9.3.0
  - azure-mgmt-resource==12.1.0
@@ -118,24 +118,24 @@ dependencies:
  - commonmark==0.9.1
  - conda-merge==0.1.5
  - contextlib2==21.6.0
- - coverage==6.4.2
+ - coverage==6.4.3
  - cryptography==3.3.2
  - cycler==0.11.0
- - databricks-cli==0.17.0
+ - databricks-cli==0.17.1
  - dataclasses-json==0.5.2
- - debugpy==1.6.2
+ - debugpy==1.6.3
  - defusedxml==0.7.1
  - deprecated==1.2.13
  - distro==1.7.0
  - docker==4.3.1
- - docutils==0.17.1
+ - docutils==0.18.1
  - dotnetcore2==2.1.23
  - entrypoints==0.4
  - execnet==1.9.0
  - fastjsonschema==2.16.1
  - fastmri==0.2.0
  - flake8==3.8.3
- - flask==2.2.0
+ - flask==2.2.2
  - frozenlist==1.3.1
  - fsspec==2022.7.1
  - furo==2022.6.21
@@ -152,7 +152,7 @@ dependencies:
  - h5py==2.10.0
  - hi-ml==0.2.2
  - hi-ml-azure==0.2.2
- - humanize==4.2.3
+ - humanize==4.3.0
  - idna==3.3
  - imageio==2.15.0
  - imagesize==1.4.1
@@ -181,27 +181,32 @@ dependencies:
  - kiwisolver==1.4.4
  - lightning-bolts==0.4.0
  - llvmlite==0.34.0
+ - lxml==4.9.1
  - mako==1.2.1
  - markdown==3.4.1
+ - markdown-it-py==2.1.0
  - markupsafe==2.1.1
  - marshmallow==3.17.0
  - marshmallow-enum==1.5.1
  - matplotlib==3.3.0
  - mccabe==0.6.1
+ - mdit-py-plugins==0.3.0
+ - mdurl==0.1.2
  - mistune==0.8.4
  - mlflow==1.23.1
- - mlflow-skinny==1.27.0
+ - mlflow-skinny==1.28.0
  - monai==0.6.0
- - more-itertools==8.13.0
+ - more-itertools==8.14.0
  - msal==1.18.0
  - msal-extensions==0.3.1
  - msrest==0.7.1
  - msrestazure==0.6.4
  - multidict==6.0.2
  - mypy==0.910
  - mypy-extensions==0.4.3
+ - myst-parser==0.18.0
  - nbclient==0.6.6
- - nbconvert==6.5.0
+ - nbconvert==6.5.3
  - nbformat==5.4.0
  - ndg-httpsclient==0.5.1
  - nest-asyncio==1.5.5
@@ -250,12 +255,12 @@ dependencies:
  - pytest-xdist==1.34.0
  - python-dateutil==2.8.2
  - pytorch-lightning==1.5.5
- - pytz==2022.1
+ - pytz==2022.2.1
  - pywavelets==1.3.0
  - pyyaml==6.0
- - pyzmq==23.2.0
+ - pyzmq==23.2.1
  - qtconsole==5.3.1
- - qtpy==2.1.0
+ - qtpy==2.2.0
  - querystring-parser==1.2.4
  - requests==2.28.1
  - requests-oauthlib==1.3.1
@@ -269,7 +274,7 @@ dependencies:
  - scikit-learn==0.23.2
  - scipy==1.5.2
  - seaborn==0.10.1
- - secretstorage==3.3.2
+ - secretstorage==3.3.3
  - send2trash==1.8.0
  - simpleitk==1.2.4
  - six==1.15.0
@@ -285,7 +290,7 @@ dependencies:
  - sphinxcontrib-jsmath==1.0.1
  - sphinxcontrib-qthelp==1.0.3
  - sphinxcontrib-serializinghtml==1.1.5
- - sqlalchemy==1.4.39
+ - sqlalchemy==1.4.40
  - sqlparse==0.4.2
  - stopit==1.1.2
  - stringcase==1.2.0
@@ -297,7 +302,7 @@ dependencies:
  - terminado==0.15.0
  - textwrap3==0.9.2
  - threadpoolctl==3.1.0
- - tifffile==2022.7.31
+ - tifffile==2022.8.12
  - tinycss2==1.1.1
  - toml==0.10.2
  - tomli==2.0.1
@@ -310,7 +315,7 @@ dependencies:
  - urllib3==1.26.7
  - webencodings==0.5.1
  - websocket-client==1.3.3
- - werkzeug==2.2.1
+ - werkzeug==2.2.2
  - widgetsnbextension==3.6.1
  - wrapt==1.14.1
  - yacs==0.1.8

diff --git a/primary_deps.yml b/primary_deps.yml
@@ -42,6 +42,7 @@ dependencies:
  - monai==0.6.0
  - mypy-extensions==0.4.3
  - mypy==0.910
+ - myst-parser==0.18.0
  - numba==0.51.2
  - numba==0.51.2
  - numpy==1.19.1