Merge branch 'master' into reconfigure-checks

Author: hjmjohnson

.gitignore

@@ -123,3 +123,4 @@ temp/
 
 # temporary testing data MedNIST
 tests/testing_data/MedNIST*
+tests/testing_data/*Hippocampus*

runtests.sh

@@ -39,7 +39,7 @@ doCleanup=false
 NUM_PARALLEL=1
 
 function print_usage {
-    echo "runtests.sh [--codeformat] [--black] [--black-fix] [--isort] [--isort-fix] [--flake8] [--pytype] [--mypy]"
+    echo "runtests.sh [--codeformat] [--autofix] [--black] [--isort] [--flake8] [--pytype] [--mypy]"
     echo "            [--nounittests] [--coverage] [--quick] [--net] [--dryrun] [-j number] [--clean] [--help] [--version]"
     echo ""
     echo "MONAI unit testing utilities."
@@ -48,14 +48,13 @@ function print_usage {
     echo "./runtests.sh --codeformat --coverage     # run full tests (${green}recommended before making pull requests${noColor})."
     echo "./runtests.sh --codeformat --nounittests  # run coding style and static type checking."
     echo "./runtests.sh --quick                     # run minimal unit tests, for quick verification during code developments."
-    echo "./runtests.sh --black-fix                 # run automatic code formatting using \"black\"."
+    echo "./runtests.sh --autofix --nounittests     # run automatic code formatting using \"isort\" and \"black\"."
     echo "./runtests.sh --clean                     # clean up temporary files and run \"python setup.py develop --uninstall\"."
     echo ""
     echo "Code style check options:"
     echo "    --black           : perform \"black\" code format checks"
-    echo "    --black-fix       : format code using \"black\""
+    echo "    --autofix         : format code using \"isort\" and \"black\""
     echo "    --isort           : perform \"isort\" import sort checks"
-    echo "    --isort-fix       : sort imports using \"isort\""
     echo "    --flake8          : perform \"flake8\" code format checks"
     echo ""
     echo "Python type check options:"
@@ -102,14 +101,15 @@ function compile_cpp {
     fi
 }
 
-function clean_py() {
+function clean_py {
     # uninstall the development package
     echo "Uninstalling MONAI development files..."
     ${cmdPrefix}python setup.py -v develop --uninstall
 
-    # remove temporary files
-    echo "Removing temporary files..."
-    TO_CLEAN=${*:-'.'}
+    # remove temporary files (in the directory of this script)
+    TO_CLEAN="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+    echo "Removing temporary files in ${TO_CLEAN}"
+
     find ${TO_CLEAN} -type f -name "*.py[co]" -delete
     find ${TO_CLEAN} -type f -name ".coverage" -delete
     find ${TO_CLEAN} -type d -name "__pycache__" -delete
@@ -132,6 +132,11 @@ function print_error_msg() {
     echo ""
 }
 
+function print_style_fail_msg() {
+    echo "${red}Check failed!${noColor}"
+    echo "Please run auto style fixes: ${green}./runtests.sh --autofix --nounittests${noColor}"
+}
+
 if [ -z "$1" ]
 then
     print_error_msg "Too few arguments to $0"
@@ -168,17 +173,15 @@ do
         --black)
             doBlackFormat=true
         ;;
-        --black-fix)
+        --autofix)
+            doIsortFix=true
             doBlackFix=true
+            doIsortFormat=true
             doBlackFormat=true
         ;;
         --isort)
             doIsortFormat=true
         ;;
-        --isort-fix)
-            doIsortFix=true
-            doIsortFormat=true
-        ;;
         --flake8)
             doFlake8Format=true
         ;;
@@ -246,71 +249,72 @@ compile_cpp
 # unconditionally report on the state of monai
 print_version
 
-if [ $doBlackFormat = true ]
+
+if [ $doIsortFormat = true ]
 then
     set +e  # disable exit on failure so that diagnostics can be given on failure
-    if [ $doBlackFix = true ]
+    if [ $doIsortFix = true ]
     then
-        echo "${separator}${blue}black-fix${noColor}"
+        echo "${separator}${blue}isort-fix${noColor}"
     else
-        echo "${separator}${blue}black${noColor}"
+        echo "${separator}${blue}isort${noColor}"
     fi
 
     # ensure that the necessary packages for code format testing are installed
-    if [[ ! -f "$(which black)" ]]
+    if [[ ! -f "$(which isort)" ]]
     then
         install_deps
     fi
-    ${cmdPrefix}black --version
+    ${cmdPrefix}isort --version
 
-    if [ $doBlackFix = true ]
+    if [ $doIsortFix = true ]
     then
-        ${cmdPrefix}black "$(pwd)"
+        ${cmdPrefix}isort "$(pwd)"
     else
-        ${cmdPrefix}black --check "$(pwd)"
+        ${cmdPrefix}isort --check "$(pwd)"
     fi
 
-    black_status=$?
-    if [ ${black_status} -ne 0 ]
+    isort_status=$?
+    if [ ${isort_status} -ne 0 ]
     then
-        echo "${red}failed!${noColor}"
-        exit ${black_status}
+        print_style_fail_msg
+        exit ${isort_status}
     else
         echo "${green}passed!${noColor}"
     fi
     set -e # enable exit on failure
 fi
 
 
-if [ $doIsortFormat = true ]
+if [ $doBlackFormat = true ]
 then
     set +e  # disable exit on failure so that diagnostics can be given on failure
-    if [ $doIsortFix = true ]
+    if [ $doBlackFix = true ]
     then
-        echo "${separator}${blue}isort-fix${noColor}"
+        echo "${separator}${blue}black-fix${noColor}"
     else
-        echo "${separator}${blue}isort${noColor}"
+        echo "${separator}${blue}black${noColor}"
     fi
 
     # ensure that the necessary packages for code format testing are installed
-    if [[ ! -f "$(which isort)" ]]
+    if [[ ! -f "$(which black)" ]]
     then
         install_deps
     fi
-    ${cmdPrefix}isort --version
+    ${cmdPrefix}black --version
 
-    if [ $doIsortFix = true ]
+    if [ $doBlackFix = true ]
     then
-        ${cmdPrefix}isort "$(pwd)"
+        ${cmdPrefix}black "$(pwd)"
     else
-        ${cmdPrefix}isort --check "$(pwd)"
+        ${cmdPrefix}black --check "$(pwd)"
     fi
 
-    isort_status=$?
-    if [ ${isort_status} -ne 0 ]
+    black_status=$?
+    if [ ${black_status} -ne 0 ]
     then
-        echo "${red}failed!${noColor}"
-        exit ${isort_status}
+        print_style_fail_msg
+        exit ${black_status}
     else
         echo "${green}passed!${noColor}"
     fi
@@ -335,7 +339,7 @@ then
     flake8_status=$?
     if [ ${flake8_status} -ne 0 ]
     then
-        echo "${red}failed!${noColor}"
+        print_style_fail_msg
         exit ${flake8_status}
     else
         echo "${green}passed!${noColor}"