style: black

.pre-commit-config.yaml

@@ -1,8 +1,32 @@
 repos:
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.2.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
+    -   id: check-json
+    -   id: check-toml
+    -   id: pretty-format-json
+
+-   repo: https://gitlab.com/smop/pre-commit-hooks
+    rev: v1.0.0
+    hooks:
+    -   id: check-poetry
+
+-   repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.4.0
+    hooks:
+    -   id: lintr
+        args: [--warn_only, --key=value]
+    -   id: roxygenize
+    -   id: no-print-statement
+    -   id: no-debug-statement
+    -   id: deps-in-desc
+    -   id: use-tidy-description
+    -   id: parsable-R

README.md

@@ -10,6 +10,7 @@
 [![PyPI - Downloads](https://img.shields.io/pypi/dm/nbiatoolkit.svg?label=pypi%20downloads)](https://pypi.org/project/nbiatoolkit/)
 ![GitHub repo size](https://img.shields.io/github/repo-size/jjjermiah/nbia-toolkit)
 [![Docker Pulls](https://img.shields.io/docker/pulls/jjjermiah/nbiatoolkit)](https://hub.docker.com/r/jjjermiah/nbiatoolkit)
+[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit)](https://github.com/pre-commit/pre-commit)
 
 
 

docs/conf.py

@@ -10,9 +10,9 @@
 sys.path.insert(0, os.path.abspath("../src"))
 # -- Project information -----------------------------------------------------
 
-project = u"nbiatoolkit"
-copyright = u"2023, Jermiah Joseph"
-author = u"Jermiah Joseph"
+project = "nbiatoolkit"
+copyright = "2023, Jermiah Joseph"
+author = "Jermiah Joseph"
 
 # -- General configuration ---------------------------------------------------
 

src/nbiatoolkit/auth.py

@@ -5,9 +5,7 @@
 from cryptography.fernet import Fernet
 
 
-def encrypt_credentials(
-    key: bytes, username: str, password: str
-) -> Tuple[str, str]:
+def encrypt_credentials(key: bytes, username: str, password: str) -> Tuple[str, str]:
     """
     Encrypts the given username and password using the provided key.
 
@@ -141,7 +139,9 @@ def __init__(
         self.username, self.password = encrypt_credentials(
             key=self.fernet_key, username=username, password=password
         )
-        self.username, self.password = encrypt_credentials(key=self._fernet_key, username=username, password=password)
+        self.username, self.password = encrypt_credentials(
+            key=self._fernet_key, username=username, password=password
+        )
 
         if isinstance(base_url, NBIA_ENDPOINTS):
             self.base_url = base_url.value
@@ -154,7 +154,6 @@ def __init__(
         self.refresh_token = ""  # Fix: Assign an empty string instead of None
         self.scope = None
 
-
     @property
     def fernet_key(self) -> bytes:
         return self._fernet_key

src/nbiatoolkit/dicomsort/dicomsort.py

@@ -115,22 +115,25 @@ def sortDICOMFiles(
         return all(result)
 
 
-
 def _get_dicom_files(sourceDir) -> "list[str]":
-        dicom_file_paths = []
-        # Iterate over all files in the source directory
-        for root, dirs, files in os.walk(sourceDir):
-            for f in files:
-                dicom_file_paths.append(os.path.join(root, f)) if f.endswith(
-                    ".dcm"
-                ) else None
-        return dicom_file_paths
+    dicom_file_paths = []
+    # Iterate over all files in the source directory
+    for root, dirs, files in os.walk(sourceDir):
+        for f in files:
+            dicom_file_paths.append(os.path.join(root, f)) if f.endswith(
+                ".dcm"
+            ) else None
+    return dicom_file_paths
+
 
 # parallel function to read in each file using dcmread only
 
+
 def _read_in_dicom_file(filePath: str) -> Optional[pydicom.FileDataset]:
     try:
-        dataset: pydicom.FileDataset = pydicom.dcmread(filePath, stop_before_pixels=True)
+        dataset: pydicom.FileDataset = pydicom.dcmread(
+            filePath, stop_before_pixels=True
+        )
         return dataset
     except InvalidDicomError as e:
         print(f"Error reading file {filePath}: {e}")
@@ -139,6 +142,7 @@ def _read_in_dicom_file(filePath: str) -> Optional[pydicom.FileDataset]:
         print(f"Error reading file {filePath}: is ``None`` or of an unsupported type.")
         return None
 
+
 # sourceDir = "/Users/bhklab/Documents/GitHub/NBIA-toolkit/NBIA-Download"
 # files = _get_dicom_files(sourceDir=sourceDir)
 # dcm_list = []

src/nbiatoolkit/nbia.py

@@ -402,8 +402,9 @@ def getDICOMTags(
         self,
         SeriesInstanceUID: str,
     ) -> Union[list[dict], None]:
-        assert SeriesInstanceUID is not None and isinstance(SeriesInstanceUID, str), \
-            "SeriesInstanceUID must be a string"
+        assert SeriesInstanceUID is not None and isinstance(
+            SeriesInstanceUID, str
+        ), "SeriesInstanceUID must be a string"
 
         PARAMS = self.parsePARAMS({"SeriesUID": SeriesInstanceUID})
 
@@ -415,7 +416,6 @@ def getDICOMTags(
 
         return response
 
-
     def downloadSeries(
         self,
         SeriesInstanceUID: Union[str, list],

src/nbiatoolkit/utils/nbia_endpoints.py

@@ -29,8 +29,6 @@ class NBIA_ENDPOINTS(Enum):
     DOWNLOAD_SERIES = "v2/getImageWithMD5Hash"
     GET_DICOM_TAGS = "getDicomTags"
 
-
-
     # curl -H "Authorization:Bearer YOUR_ACCESS_TOKEN" -k "https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeriesMetaData"
     # curl -H "Authorization:Bearer YOUR_ACCESS_TOKEN" -k "https://services.cancerimagingarchive.net/nbia-api/services/v2/getSeriesSize"
 

tests/test_auth.py

@@ -8,10 +8,12 @@
 import time
 import requests
 
+
 @pytest.fixture
 def oauth() -> OAuth2:
     return OAuth2()
 
+
 def test_oauth2(oauth: OAuth2) -> None:
     assert oauth.client_id == "NBIA"
     assert oauth.username != "nbia_guest"
@@ -23,18 +25,21 @@ def test_oauth2(oauth: OAuth2) -> None:
     assert oauth.refresh_expiry is not None
     assert oauth.scope is not None
 
+
 def test_is_token_expired(oauth: OAuth2) -> None:
     assert oauth.is_token_expired() == False
     oauth.expiry_time = time.time() - 100
     assert oauth.is_token_expired() == True
 
+
 def test_refresh_token_or_request_new(oauth: OAuth2) -> None:
     oauth.refresh_token_or_request_new()
     assert oauth.access_token is not None
     assert oauth.refresh_token is not None
     assert oauth.refresh_expiry is not None
     assert oauth.expiry_time is not None
 
+
 def test_refresh_after_expiry(oauth: OAuth2) -> None:
     access_token_before = oauth.access_token
 
@@ -48,6 +53,7 @@ def test_refresh_after_expiry(oauth: OAuth2) -> None:
     assert oauth.expiry_time is not None
     assert oauth.is_token_expired() == False
 
+
 def test_failed_refresh(oauth: OAuth2) -> None:
     oauth.refresh_token = ""
     with pytest.raises(AssertionError):
@@ -58,6 +64,7 @@ def test_failed_refresh(oauth: OAuth2) -> None:
     with pytest.raises(requests.exceptions.HTTPError):
         oauth._refresh_access_token()
 
+
 def test_request_new_access_token(oauth: OAuth2) -> None:
     oauth.refresh_token = ""
     oauth.request_new_access_token()
@@ -67,6 +74,7 @@ def test_request_new_access_token(oauth: OAuth2) -> None:
     assert oauth.expiry_time is not None
     assert oauth.is_token_expired() == False
 
+
 def test_logout(oauth: OAuth2) -> None:
     oauth.logout()
     assert oauth.access_token is None