Simplify code formatting tests (Project-MONAI#431)

* ENH: Update to new flake8 conformance tool

Allow for flake8 with newer pycodestyle and pyflakes versions

Forcing installation of flake8 3.7.9 was incompatiable with newer pycodestyle and pyflakes versions

ERROR: flake8 3.7.9 has requirement pycodestyle<2.6.0,>=2.5.0, but you'll have pycodestyle 2.6.0 which is incompatible.
ERROR: flake8 3.7.9 has requirement pyflakes<2.2.0,>=2.1.0, but you'll have pyflakes 2.2.0 which is incompatible.

* ENH: Add code format checking to test script

Use the test script to also perform code format
testing that must pass for CI to pass.

* Define common requirements-dev.txt for dev packages

Use a commond defintion file to define the devlopment
package dependancies.

* Update pythonapp.yml

Co-authored-by: Wenqi Li <wenqi.li@ucl.ac.uk>

Author: hjmjohnson

.github/workflows/pythonapp.yml

@@ -19,10 +19,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
-        pip install -r requirements.txt
+        pip install -r requirements-dev.txt
     - name: Lint with flake8
       run: |
-        pip install flake8==3.7.9 flake8-mypy flake8-bugbear flake8-comprehensions flake8-executable flake8-pyi mccabe pep8-naming
+        python -m pip install --upgrade pip wheel
+        pip install -r requirements-dev.txt
         flake8 --version
         python -c 'import monai; monai.config.print_config()'
         MYPYPATH=$(pwd)/monai flake8 $(pwd) --count --statistics
@@ -51,7 +52,7 @@ jobs:
     - name: Install the dependencies
       run: |
         python -m pip install torch==1.4
-        python -m pip install -r requirements.txt
+        python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run quick tests (CPU ${{ runner.os }})
       run: |
@@ -73,7 +74,7 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
         python -m pip install torch==1.4
-        python -m pip install -r requirements.txt
+        python -m pip install -r requirements-dev.txt
     - name: Run quick tests (GPU)
       run: |
         python -m pip list

.github/workflows/setupapp.yml

@@ -20,7 +20,7 @@ jobs:
         python -m pip install --upgrade pip wheel
         python -m pip uninstall -y torch torchvision
         python -m pip install torch==1.4
-        python -m pip install -r requirements.txt
+        python -m pip install -r requirements-dev.txt
         python -m pip list
     - name: Run unit tests report coverage
       run: |

CONTRIBUTING.md

@@ -126,12 +126,17 @@ To run a particular test, for example `tests/test_dice_loss.py`:
 python -m tests.test_dice_loss
 ```
 
+## Linting and code style testing
+
+```bash
+# Install the various static analysis tools for development
+pip install -r requirements-dev.txt
+```
+
 Before submitting a pull request, we recommend that all linting and unit tests
-should pass, by running the following commands locally:
+should pass, by running the following command locally:
 ```
-pip install flake8==3.7.9 flake8-mypy flake8-bugbear flake8-comprehensions flake8-executable flake8-pyi mccabe pycodestyle pyflakes
-flake8 . --count --statistics
-./runtests.sh --coverage
+./runtests.sh --codeformat --coverage
 ```
 
 _If it's not tested, it's broken_

monai/losses/focal_loss.py

@@ -64,7 +64,7 @@ def forward(self, input, target):
 
         if target.shape[1] != 1:
             raise ValueError(
-                f"target must have one channel, and should be a class index in the range [0, C-1] "
+                "target must have one channel, and should be a class index in the range [0, C-1] "
                 + f"where C is the number of classes inferred from 'input': C={i.shape[1]}."
             )
         # Change the shape of input and target to

requirements-dev.txt

@@ -0,0 +1,15 @@
+# Requirements for testing
+-r requirements.txt
+flake8>=3.8.1
+flake8-mypy
+flake8-bugbear
+flake8-comprehensions
+flake8-executable
+flake8-pyi
+mccabe
+pep8-naming
+pycodestyle
+pyflakes
+coverage
+parameterized
+black

requirements.txt

@@ -6,5 +6,3 @@ tensorboard
 pillow
 scipy
 scikit-image>=0.14.2
-coverage
-parameterized

runtests.sh

@@ -15,6 +15,7 @@ doQuickTests=false
 doNetTests=false
 doDryRun=false
 doZooTests=false
+doCodeFormat=false
 
 # testing command to run
 cmd="python3"
@@ -40,13 +41,61 @@ do
         --zoo)
             doZooTests=true
         ;;
+        --codeformat)
+            doCodeFormat=true
+
+        ;;
         *)
-            echo "runtests.sh [--coverage] [--quick] [--net] [--dryrun] [--zoo]"
+            echo "runtests.sh [--codeformat] [--coverage] [--quick] [--net] [--dryrun] [--zoo]"
             exit 1
         ;;
     esac
 done
 
+# report on code format
+if [ "$doCodeFormat" = 'true' ]
+then
+     # Ensure that the necessary packages for code format testing are installed
+     if [[ ! -f "$(which flake8)" ]] || [[ ! -f "$(which black)" ]]; then
+       pip install -r requirements-dev.txt
+     fi
+
+     set +e  # Disable exit on failure so that diagnostics can be given on failure
+     echo "----------------------------------"
+     echo "Verifying black formatting checks."
+     black --check "$(pwd)"
+     black_status=$?
+     echo "----------------------------------"
+     if [ ${black_status} -ne 0 ];
+     then
+       echo "----------------------------------"
+       echo "black code formatting test failed!"
+       echo "::: Run"
+       echo ":::        black \"$(pwd)\""
+       echo "::: to auto fixing formatting errors"
+       echo "----------------------------------"
+       exit ${black_status}
+     else
+       echo "*** black code format tests passed. ***"
+     fi
+
+     echo "-----------------------------------"
+     echo "Verifying flake8 formatting checks."
+     MYPYPATH="$(pwd)/monai" flake8 "$(pwd)" --count --statistics
+     flake8_status=$?
+     echo "-----------------------------------"
+     if [ ${flake8_status} -ne 0 ];
+     then
+       echo "----------------------------------"
+       echo "Formatting test failed!"
+       echo "Manually review and fix listed formatting errors"
+       exit ${flake8_status}
+     else
+       echo "*** flake8 code format tests passed. ***"
+     fi
+     set -e # Re-enable exit on failure
+fi
+
 # When running --quick, require doCoverage as well and set QUICKTEST environmental
 # variable to disable slow unit tests from running.
 if [ "$doQuickTests" = 'true' ]