formatting?

src/prompt_systematic_review/pipeline.py

@@ -4,8 +4,6 @@
 import os
 
 
-
-
 """
 READ THIS
 https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions
@@ -14,34 +12,31 @@
 """
 
 
-
-
 class Pipeline:
-
-    def __init__(self, token=None,revision="main"):
+    def __init__(self, token=None, revision="main"):
         self.token = token
         self.root = f"hf://datasets/PromptSystematicReview/Prompt_Systematic_Review_Dataset@{revision}/"
         if token is not None:
             self.fs = HfFileSystem(token=token)
             login(token=token)
         else:
             self.fs = HfFileSystem()
-        self.revision=revision
+        self.revision = revision
 
     def is_logged_in(self):
         return self.token is not None
-    
+
     def get_revision(self):
         return self.revision
-    
-    def set_revision(self,revision):
+
+    def set_revision(self, revision):
         try:
             assert revision.isalnum()
-            self.revision=revision
+            self.revision = revision
             self.root = f"hf://datasets/PromptSystematicReview/Prompt_Systematic_Review_Dataset@{revision}/"
         except:
             raise ValueError("Revision must be alphanumeric")
-    
+
     def login(self, token):
         if self.token is not None:
             raise ValueError("Already Logged In")
@@ -51,22 +46,16 @@ def login(self, token):
             self.token = token
 
     def get_all_files(self):
-        return self.fs.ls(self.root, detail=False,revision=self.revision)
+        return self.fs.ls(self.root, detail=False, revision=self.revision)
 
     def get_all_data_files(self):
-        return self.fs.glob(self.root+"**.csv",revision=self.revision)
-    
+        return self.fs.glob(self.root + "**.csv", revision=self.revision)
+
     def read_from_file(self, fileName):
         return pd.read_csv(os.path.join(self.root, fileName))
 
-
     def write_to_file(self, fileName, dataFrame):
         if not self.is_logged_in():
             raise ValueError("Not Logged In")
         path = os.path.join(self.root, fileName)
         dataFrame.to_csv(path, index=False)
-
-
-
-
-

tests/test_paper.py

@@ -4,7 +4,6 @@
 from prompt_systematic_review.utils import process_paper_title
 
 
-
 def test_paper():
     paper1 = Paper(
         "How to write a paper",
@@ -32,7 +31,6 @@ def test_paper():
     assert paper1 != paper2 and paper2 != alsoPaper1
 
 
-
 def test_arxiv_source():
     # test that arXiv source returns papers properly
     arxiv_source = ArXivSource()
@@ -60,4 +58,3 @@ def test_arxiv_source():
     assert paper.keywords == [
         "foundational models in medical imaging: a comprehensive survey and future vision"
     ]
-

tests/test_pipeline.py

@@ -11,46 +11,54 @@
 def hashString(bytes):
     return str(hashlib.md5(bytes).hexdigest())
 
+
 @pytest.fixture
 def client():
-    return Pipeline(token=os.environ['HF_AUTH_TOKEN'],revision="test")
+    return Pipeline(token=os.environ["HF_AUTH_TOKEN"], revision="test")
+
 
 def test_login():
     testClient = Pipeline(revision="test")
     assert testClient.is_logged_in() == False
-    testClient.login(os.environ['HF_AUTH_TOKEN'])
+    testClient.login(os.environ["HF_AUTH_TOKEN"])
     assert testClient.is_logged_in() == True
 
+
 def test_get_all_files(client):
     assert len(client.get_all_files()) > 0
 
+
 def test_get_all_data_files(client):
     assert len(client.get_all_data_files()) > 0
     assert all([x.endswith(".csv") for x in client.get_all_data_files()])
 
+
 def test_read_from_file(client):
     assert len(client.read_from_file("test.csv")) > 0
     assert len(client.read_from_file("test.csv").columns) == 2
     assert client.read_from_file("test.csv")["Age"].mean() == 21
 
+
 def test_write_to_file(client):
     lenOfFiles = len(client.get_all_files())
     randString = random.randbytes(100) + str(time.time()).encode()
     randHash = hashString(randString)
-    csvDict = {"test":[1,3], "test2":[2,4]}
+    csvDict = {"test": [1, 3], "test2": [2, 4]}
     print(client.revision)
     client.write_to_file(f"{randHash[:10]}_test.csv", pd.DataFrame(csvDict))
     print(client.revision)
     time.sleep(1)
     # assert client.revision == "main"
-    df = client.read_from_file(f"{randHash[:10]}_test.csv") 
+    df = client.read_from_file(f"{randHash[:10]}_test.csv")
     assert df["test"].sum() == 4
     assert df["test2"].sum() == 6
-    #time.sleep(1)
-    print(client.root+f"{randHash[:10]}_test.csv")
-    delete_file(f"{randHash[:10]}_test.csv", "PromptSystematicReview/Prompt_Systematic_Review_Dataset", repo_type="dataset", revision="test")
-
-    assert len(client.get_all_files()) == lenOfFiles
+    # time.sleep(1)
+    print(client.root + f"{randHash[:10]}_test.csv")
+    delete_file(
+        f"{randHash[:10]}_test.csv",
+        "PromptSystematicReview/Prompt_Systematic_Review_Dataset",
+        repo_type="dataset",
+        revision="test",
+    )
 
-
-
+    assert len(client.get_all_files()) == lenOfFiles

tests/test_utils.py

@@ -2,6 +2,5 @@
 from prompt_systematic_review.utils import process_paper_title
 
 
-
 def test_process_paper_title():
     assert process_paper_title("Laws  of the\n Wildabeest") == "laws of the wildabeest"