reset

.flake8

@@ -2,4 +2,4 @@
 ignore = E226,E302,E41,W391, E701, W291, E722, W503, E128, E126, E127, E731, E401
 max-line-length = 160
 max-complexity = 25
-exclude = fastMRI/ test_outputs/
+exclude = fastMRI/ test_outputs/ hi-ml/

.github/workflows/linting_and_hello_world.yml

@@ -13,6 +13,7 @@ jobs:
       - uses: actions/checkout@v2
         with:
           lfs: true
+          submodules: true
 
       - name: flake8
         run: |
@@ -58,7 +59,8 @@ jobs:
       - uses: actions/checkout@v2
         with:
           lfs: true
-
+          submodules: true
+
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: InnerEye

.gitignore

@@ -131,6 +131,7 @@ dmypy.json
 
 # other
 .vscode/
+.devcontainer/
 
 /InnerEye/ML/src/aml_config
 *.exe
@@ -157,4 +158,11 @@ Tests/ML/test_outputs
 # This file contains the run recovery ID of the most recent job
 most_recent_run.txt
 # The default folder that contains downloaded Tensorboard files
-tensorboard_runs
+tensorboard_runs
+
+# InnerEye-DataQuality
+InnerEye-DataQuality/cifar-10-python.tar.gz
+InnerEye-DataQuality/name_stats_scoring.png
+InnerEye-DataQuality/cifar-10-batches-py
+InnerEye-DataQuality/logs
+InnerEye-DataQuality/data

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "fastMRI"]
 	path = fastMRI
 	url = https://github.com/facebookresearch/fastMRI
+[submodule "hi-ml"]
+	path = hi-ml
+	url = https://github.com/microsoft/hi-ml

.pre-commit-config.yaml

@@ -0,0 +1,35 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+# See https://github.com/pre-commit/pre-commit-hooks/blob/master/.pre-commit-config.yaml for an example with more hooks
+
+exclude: '^excluded_files_regex$'
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-yaml
+    - id: check-added-large-files
+    - id: check-ast
+    - id: check-merge-conflict
+    - id: debug-statements
+    - id: mixed-line-ending
+      args: [--fix=lf]
+
+-   repo: https://github.com/PyCQA/flake8
+    rev: 3.9.2
+    hooks:
+    -   id: flake8
+        additional_dependencies: [flake8-typing-imports==1.7.0]
+
+-   repo: https://github.com/pre-commit/mirrors-autopep8
+    rev: v1.5.7
+    hooks:
+    - id: autopep8
+
+-   repo: https://github.com/ambv/black
+    rev: 21.9b0
+    hooks:
+    - id: black
+      language_version: python3.7