File Tree: Fixed other tests to make full test suite functional

tests/chunk_parser_test.py

@@ -7,6 +7,10 @@ ex1 = "<think>reasoning goes here</think>response goes here"
 ex2 = "<think>reasoning goes here</thi"
 
 
+import pytest
+
+
+@pytest.mark.parametrize("example", [ex1, ex2])
 def test_example(example: str):
     res = models.ChatGenerationResult()
     for i in range(len(example)):
@@ -20,4 +24,3 @@ def test_example(example: str):
 if __name__ == "__main__":
     # test_example(ex1)
     test_example(ex2)
-    

tests/email_parser_test.py

@@ -3,10 +3,13 @@ import sys, os
 sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
 import asyncio
+import pytest
 from python.helpers.email_client import read_messages
 from python.helpers.dotenv import get_dotenv_value, load_dotenv
 
 
+@pytest.mark.skip(reason="This test is disabled as it has eternal dependencies and tests nothing automatically, please move it to a script or a manual test")
+@pytest.mark.asyncio
 async def test():
     load_dotenv()
     messages = await read_messages(

tests/test_fasta2a_client.py

@@ -8,6 +8,7 @@ sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
 
 
 import asyncio
+import pytest
 from python.helpers import settings
 
 
@@ -143,6 +144,7 @@ def validate_token_format():
         return False
 
 
+@pytest.mark.asyncio
 async def test_server_connectivity():
     """Test basic server connectivity."""
     try:

tests/test_file_tree_visualize.short.txt

@@ -1,341 +0,0 @@
-================================================================================
-Scenario: basic_breadth_first — Default breadth-first traversal with mixed folders/files
-================================================================================
---------------------------------------------------------------------------------
-Configuration: string • folders-first (name asc)
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-tmp/tests/file_tree/visualize/basic_breadth_first/
-├── alpha/
-│   ├── nested/
-│   │   └── inner.txt
-│   └── alpha_file.txt
-├── beta/
-│   └── beta_file.txt
-├── zeta/
-├── a.txt
-└── b.txt
---------------------------------------------------------------------------------
-Configuration: string • folders-first disabled
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : False
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-tmp/tests/file_tree/visualize/basic_breadth_first/
-├── a.txt
-├── b.txt
-├── alpha/
-│   ├── alpha_file.txt
-│   └── nested/
-│       └── inner.txt
-├── beta/
-│   └── beta_file.txt
-└── zeta/
---------------------------------------------------------------------------------
-Configuration: flat • folders-first
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : flat
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-level  type     name                   text
---------------------------------------------------------------------------------
-1      folder   alpha                 ├── alpha/
-2      folder   nested                │   ├── nested/
-3      file     inner.txt             │   │   └── inner.txt
-2      file     alpha_file.txt        │   └── alpha_file.txt
-1      folder   beta                  ├── beta/
-2      file     beta_file.txt         │   └── beta_file.txt
-1      folder   zeta                  ├── zeta/
-1      file     a.txt                 ├── a.txt
-1      file     b.txt                 └── b.txt
---------------------------------------------------------------------------------
-Configuration: nested • folders-first
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : nested
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-basic_breadth_first/
-├── alpha/  [folder]
-├── beta/  [folder]
-├── zeta/  [folder]
-├── a.txt  [file]
-└── b.txt  [file]
-
-================================================================================
-Scenario: sorting_variants — Demonstrate sorting by name and timestamp with folders/files
-================================================================================
---------------------------------------------------------------------------------
-Configuration: string • sort by name asc
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-tmp/tests/file_tree/visualize/sorting_variants/
-├── folder_alpha/
-├── folder_beta/
-├── file_first.txt
-├── file_second.txt
-└── file_third.txt
---------------------------------------------------------------------------------
-Configuration: string • sort by created desc
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : True
-  sort          : key=created, direction=desc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-tmp/tests/file_tree/visualize/sorting_variants/
-├── folder_alpha/
-├── folder_beta/
-├── file_third.txt
-├── file_first.txt
-└── file_second.txt
---------------------------------------------------------------------------------
-Configuration: flat • sort by modified asc
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : flat
-  folders_first : True
-  sort          : key=modified, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-level  type     name                   text
---------------------------------------------------------------------------------
-1      folder   folder_alpha          ├── folder_alpha/
-1      folder   folder_beta           ├── folder_beta/
-1      file     file_first.txt        ├── file_first.txt
-1      file     file_second.txt       ├── file_second.txt
-1      file     file_third.txt        └── file_third.txt
-
-================================================================================
-Scenario: ignore_and_limits — Ignore file semantics with max_folders/max_files summaries
-================================================================================
---------------------------------------------------------------------------------
-Configuration: string • folders-first with summaries
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : False
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 12
-  max_folders   : 1
-  max_files     : 2
-  ignore        : file:.treeignore
-
-tmp/tests/file_tree/visualize/ignore_and_limits/
-├── .treeignore
-├── guide.md
-├── # 2 more files
-├── archive/
-└── # 5 more folders
---------------------------------------------------------------------------------
-Configuration: nested • inspect truncated branches & comments
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : nested
-  folders_first : False
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 12
-  max_folders   : 1
-  max_files     : 2
-  ignore        : file:.treeignore
-
-ignore_and_limits/
-├── .treeignore  [file]
-├── guide.md  [file]
-├── # 2 more files  [comment]
-├── archive/  [folder]
-└── # 5 more folders  [comment]
-
-================================================================================
-Scenario: limits_exact_match — Per-directory limits exactly met (no summary comments)
-================================================================================
---------------------------------------------------------------------------------
-Configuration: string • exact matches (no summaries)
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : 2
-  max_files     : 2
-  ignore        : None
-
-tmp/tests/file_tree/visualize/limits_exact_match/
-└── pkg/
-    ├── dir1/
-    ├── dir2/
-    ├── a.py
-    └── b.py
---------------------------------------------------------------------------------
-Configuration: flat • exact matches (no summaries)
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : flat
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : 2
-  max_files     : 2
-  ignore        : None
-
-level  type     name                   text
---------------------------------------------------------------------------------
-1      folder   pkg                   └── pkg/
-2      folder   dir1                      ├── dir1/
-2      folder   dir2                      ├── dir2/
-2      file     a.py                      ├── a.py
-2      file     b.py                      └── b.py
-
-================================================================================
-Scenario: single_overflow — Single overflow entries promoted instead of summary comment
-================================================================================
---------------------------------------------------------------------------------
-Configuration: string • single folder overflow
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : 1
-  max_files     : None
-  ignore        : None
-
-tmp/tests/file_tree/visualize/single_overflow/
-└── pkg/
-    ├── dir_a/
-    ├── dir_b/
-    └── file_a.txt
---------------------------------------------------------------------------------
-Configuration: string • single file overflow
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : False
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : None
-  max_files     : 1
-  ignore        : None
-
-tmp/tests/file_tree/visualize/single_overflow/
-└── pkg/
-    ├���─ file_a.txt
-    ├── dir_a/
-    └── dir_b/
---------------------------------------------------------------------------------
-Configuration: flat • folders-first
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : flat
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 0
-  max_folders   : 1
-  max_files     : None
-  ignore        : None
-
-level  type     name                   text
---------------------------------------------------------------------------------
-1      folder   pkg                   └── pkg/
-2      folder   dir_a                     ├── dir_a/
-2      folder   dir_b                     ├── dir_b/
-2      file     file_a.txt                └── file_a.txt
-
-================================================================================
-Scenario: global_max_lines — Global max_lines finishing current depth before truncation
-================================================================================
---------------------------------------------------------------------------------
-Configuration: string • max_lines=6
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : string
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 6
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-tmp/tests/file_tree/visualize/global_max_lines/
-├── layer1_a/
-│   └── layer2_a/
-│       └── layer3_a/
-├── layer1_b/
-│   └── layer2_b/
-│       └── layer3_b/
-└── root_file.txt
---------------------------------------------------------------------------------
-Configuration: nested • max_lines=6
---------------------------------------------------------------------------------
-Parameters:
-  output_mode   : nested
-  folders_first : True
-  sort          : key=name, direction=asc
-  max_depth     : 0
-  max_lines     : 6
-  max_folders   : None
-  max_files     : None
-  ignore        : None
-
-global_max_lines/
-├── layer1_a/  [folder]
-├── layer1_b/  [folder]
-└── root_file.txt  [file]
-