adds a basic clang formatter (Project-MONAI#1006)

* adds a basic clang formatter

Signed-off-by: Wenqi Li <[email protected]>

* fixes clang-format version

Signed-off-by: Wenqi Li <[email protected]>

* update to use monai native APIs

Signed-off-by: Wenqi Li <[email protected]>

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>

* run test utils using coverage

Signed-off-by: Wenqi Li <[email protected]>

* testing autoformat

Signed-off-by: Wenqi Li <[email protected]>

* [MONAI] python code formatting

Signed-off-by: monai-bot <[email protected]>

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>

* update based on comments

Signed-off-by: Wenqi Li <[email protected]>

Co-authored-by: monai-bot <[email protected]>
Co-authored-by: Nic Ma <[email protected]>

.clang-format

@@ -0,0 +1,88 @@
+---
+AccessModifierOffset: -1
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   false
+AlignTrailingComments: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: false
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ForEachMacros:   [ FOR_EACH_RANGE, FOR_EACH, ]
+IncludeCategories:
+  - Regex:           '^<.*\.h(pp)?>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 2000000
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...

.github/workflows/pythonapp.yml

@@ -175,6 +175,10 @@ jobs:
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
         ./runtests.sh --quick
+        if [ ${{ matrix.environment }} == "PT16+CUDA110" ]; then
+          # test the clang-format tool downloading once
+          coverage run -m tests.clang_format_utils
+        fi
         coverage xml
     - name: Upload coverage
       uses: codecov/codecov-action@v1

.gitignore

@@ -125,5 +125,8 @@ temp/
 tests/testing_data/MedNIST*
 tests/testing_data/*Hippocampus*
 
+# clang format tool
+.clang-format-bin/
+
 # VSCode
 .vscode/

docs/source/apps.rst

@@ -18,7 +18,7 @@ Applications
 `Utilities`
 -----------
 
-.. autofunction:: check_md5
+.. autofunction:: check_hash
 
 .. autofunction:: download_url
 

monai/apps/utils.py

@@ -24,56 +24,67 @@
 gdown, has_gdown = optional_import("gdown", "3.6")
 
 
-def check_md5(filepath: str, md5_value: Optional[str] = None) -> bool:
+def check_hash(filepath: str, val: Optional[str] = None, hash_type: str = "md5") -> bool:
     """
-    check MD5 signature of specified file.
+    Verify hash signature of specified file.
 
     Args:
-        filepath: path of source file to verify MD5.
-        md5_value: expected MD5 value of the file.
+        filepath: path of source file to verify hash value.
+        val: expected hash value of the file.
+        hash_type: 'md5' or 'sha1', defaults to 'md5'.
 
     """
-    if md5_value is not None:
-        md5 = hashlib.md5()
-        try:
-            with open(filepath, "rb") as f:
-                for chunk in iter(lambda: f.read(1024 * 1024), b""):
-                    md5.update(chunk)
-        except Exception as e:
-            print(f"Exception in check_md5: {e}")
-            return False
-        if md5_value != md5.hexdigest():
-            return False
+    if val is None:
+        print(f"Expected {hash_type} is None, skip {hash_type} check for file {filepath}.")
+        return True
+    if hash_type.lower() == "md5":
+        actual_hash = hashlib.md5()
+    elif hash_type.lower() == "sha1":
+        actual_hash = hashlib.sha1()
     else:
-        print(f"expected MD5 is None, skip MD5 check for file {filepath}.")
-
+        raise NotImplementedError(f"Unknown 'hash_type' {hash_type}.")
+    try:
+        with open(filepath, "rb") as f:
+            for chunk in iter(lambda: f.read(1024 * 1024), b""):
+                actual_hash.update(chunk)
+    except Exception as e:
+        print(f"Exception in check_hash: {e}")
+        return False
+    if val != actual_hash.hexdigest():
+        print("check_hash failed.")
+        return False
+
+    print(f"Verified '{os.path.basename(filepath)}', {hash_type}: {val}.")
     return True
 
 
-def download_url(url: str, filepath: str, md5_value: Optional[str] = None) -> None:
+def download_url(url: str, filepath: str, hash_val: Optional[str] = None, hash_type: str = "md5") -> None:
     """
-    Download file from specified URL link, support process bar and MD5 check.
+    Download file from specified URL link, support process bar and hash check.
 
     Args:
         url: source URL link to download file.
         filepath: target filepath to save the downloaded file.
-        md5_value: expected MD5 value to validate the downloaded file.
-            if None, skip MD5 validation.
+        hash_val: expected hash value to validate the downloaded file.
+            if None, skip hash validation.
+        hash_type: 'md5' or 'sha1', defaults to 'md5'.
 
     Raises:
-        RuntimeError: When the MD5 validation of the ``filepath`` existing file fails.
+        RuntimeError: When the hash validation of the ``filepath`` existing file fails.
         RuntimeError: When a network issue or denied permission prevents the
             file download from ``url`` to ``filepath``.
         URLError: See urllib.request.urlretrieve.
         HTTPError: See urllib.request.urlretrieve.
         ContentTooShortError: See urllib.request.urlretrieve.
         IOError: See urllib.request.urlretrieve.
-        RuntimeError: When the MD5 validation of the ``url`` downloaded file fails.
+        RuntimeError: When the hash validation of the ``url`` downloaded file fails.
 
     """
     if os.path.exists(filepath):
-        if not check_md5(filepath, md5_value):
-            raise RuntimeError(f"MD5 check of existing file failed: filepath={filepath}, expected MD5={md5_value}.")
+        if not check_hash(filepath, hash_val, hash_type):
+            raise RuntimeError(
+                f"{hash_type} check of existing file failed: filepath={filepath}, expected {hash_type}={hash_val}."
+            )
         print(f"file {filepath} exists, skip downloading.")
         return
 
@@ -110,8 +121,8 @@ def download_url(url: str, filepath: str, md5_value: Optional[str] = None) -> No
             logging.debug("IO Error - %s" % e)
         finally:
             if file_size == os.path.getsize(tmp_file_path):
-                if md5_value and not check_md5(tmp_file_path, md5_value):
-                    raise Exception("Error validating the file against its MD5 hash")
+                if hash_val and not check_hash(tmp_file_path, hash_val, hash_type):
+                    raise Exception(f"Error validating the file against its {hash_type} hash")
                 shutil.move(tmp_file_path, filepath)
             elif file_size == -1:
                 raise Exception("Error getting Content-Length from server: %s" % url)
@@ -128,34 +139,38 @@ def _process_hook(blocknum: int, blocksize: int, totalsize: int):
             print(f"download failed from {url} to {filepath}.")
             raise e
 
-    if not check_md5(filepath, md5_value):
+    if not check_hash(filepath, hash_val, hash_type):
         raise RuntimeError(
-            f"MD5 check of downloaded file failed: URL={url}, filepath={filepath}, expected MD5={md5_value}."
+            f"{hash_type} check of downloaded file failed: URL={url}, "
+            f"filepath={filepath}, expected {hash_type}={hash_val}."
         )
 
 
-def extractall(filepath: str, output_dir: str, md5_value: Optional[str] = None) -> None:
+def extractall(filepath: str, output_dir: str, hash_val: Optional[str] = None, hash_type: str = "md5") -> None:
     """
     Extract file to the output directory.
     Expected file types are: `zip`, `tar.gz` and `tar`.
 
     Args:
         filepath: the file path of compressed file.
         output_dir: target directory to save extracted files.
-        md5_value: expected MD5 value to validate the compressed file.
-            if None, skip MD5 validation.
+        hash_val: expected hash value to validate the compressed file.
+            if None, skip hash validation.
+        hash_type: 'md5' or 'sha1', defaults to 'md5'.
 
     Raises:
-        RuntimeError: When the MD5 validation of the ``filepath`` compressed file fails.
+        RuntimeError: When the hash validation of the ``filepath`` compressed file fails.
         ValueError: When the ``filepath`` file extension is not one of [zip", "tar.gz", "tar"].
 
     """
     target_file = os.path.join(output_dir, os.path.basename(filepath).split(".")[0])
     if os.path.exists(target_file):
         print(f"extracted file {target_file} exists, skip extracting.")
         return
-    if not check_md5(filepath, md5_value):
-        raise RuntimeError(f"MD5 check of compressed file failed: filepath={filepath}, expected MD5={md5_value}.")
+    if not check_hash(filepath, hash_val, hash_type):
+        raise RuntimeError(
+            f"{hash_type} check of compressed file failed: " f"filepath={filepath}, expected {hash_type}={hash_val}."
+        )
 
     if filepath.endswith("zip"):
         zip_file = zipfile.ZipFile(filepath)
@@ -169,7 +184,9 @@ def extractall(filepath: str, output_dir: str, md5_value: Optional[str] = None)
         raise ValueError('Unsupported file extension, available options are: ["zip", "tar.gz", "tar"].')
 
 
-def download_and_extract(url: str, filepath: str, output_dir: str, md5_value: Optional[str] = None) -> None:
+def download_and_extract(
+    url: str, filepath: str, output_dir: str, hash_val: Optional[str] = None, hash_type: str = "md5"
+) -> None:
     """
     Download file from URL and extract it to the output directory.
 
@@ -178,9 +195,10 @@ def download_and_extract(url: str, filepath: str, output_dir: str, md5_value: Op
         filepath: the file path of compressed file.
         output_dir: target directory to save extracted files.
             default is None to save in current directory.
-        md5_value: expected MD5 value to validate the downloaded file.
-            if None, skip MD5 validation.
+        hash_val: expected hash value to validate the downloaded file.
+            if None, skip hash validation.
+        hash_type: 'md5' or 'sha1', defaults to 'md5'.
 
     """
-    download_url(url=url, filepath=filepath, md5_value=md5_value)
-    extractall(filepath=filepath, output_dir=output_dir, md5_value=md5_value)
+    download_url(url=url, filepath=filepath, hash_val=hash_val, hash_type=hash_type)
+    extractall(filepath=filepath, output_dir=output_dir, hash_val=hash_val, hash_type=hash_type)

runexamples.sh

@@ -1,4 +1,16 @@
 #!/bin/bash
+
+# Copyright 2020 MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 set -e
 # script for running the examples