pybiolib 1.1.1836__tar.gz → 1.1.1855__tar.gz

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1836
+Version: 1.1.1855
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/biolib/_internal/http_client.py

@@ -42,7 +42,7 @@ class HttpError(urllib.error.HTTPError):
 
 
 class HttpResponse:
-    def __init__(self, response):
+    def __init__(self, response) -> None:
         self.headers: Dict[str, str] = dict(response.headers)
         self.status_code: int = int(response.status)
         self.content: bytes = response.read()

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/biolib/compute_node/job_worker/cache_state.py

@@ -16,7 +16,7 @@ class DockerCacheStateError(CacheStateError):
 
 class LfsCacheState(CacheState):
 
-    def __init__(self):
+    def __init__(self) -> None:
         super().__init__()
 
         self._storage_path_for_write: str = self._get_storage_path_for_write()

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/biolib/compute_node/job_worker/executors/docker_executor.py

@@ -39,7 +39,7 @@ from biolib.typing_utils import List, Dict, Optional
 
 class DockerExecutor:
 
-    def __init__(self, options: LocalExecutorOptions):
+    def __init__(self, options: LocalExecutorOptions) -> None:
         self._options: LocalExecutorOptions = options
         self._is_cleaning_up = False
 

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/biolib/utils/cache_state.py

@@ -37,7 +37,7 @@ class CacheState(abc.ABC, Generic[StateType]):
     def _state_lock_path(self) -> str:
         return f'{self._state_path}.lock'
 
-    def __init__(self):
+    def __init__(self) -> None:
         self._state: Optional[StateType] = None
 
     def __enter__(self) -> StateType:

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/biolib/utils/seq_util.py

@@ -3,16 +3,21 @@ from io import BufferedIOBase
 from biolib.typing_utils import List, Optional, Dict, Union
 
 allowed_sequence_chars = set("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-_.")
+
+
 def find_invalid_sequence_characters(sequence):
     invalid_chars = [char for char in sequence if char not in allowed_sequence_chars]
     return invalid_chars
 
+
 class SeqUtilRecord:
-    def __init__(self,
-                 sequence: str,
-                 sequence_id: str,
-                 description: Optional['str'],
-                 properties: Optional[Dict[str, str]] = None):
+    def __init__(
+            self,
+            sequence: str,
+            sequence_id: str,
+            description: Optional['str'],
+            properties: Optional[Dict[str, str]] = None,
+    ):
         self.sequence = sequence
         self.id = sequence_id  # pylint: disable=invalid-name
         self.description = description
@@ -33,11 +38,11 @@ class SeqUtilRecord:
 class SeqUtil:
     @staticmethod
     def parse_fasta(
-        input_file: Union[str, BufferedIOBase] = None,
-        default_header: Optional[str] = None,
-        allow_any_sequence_characters: bool = False,
-        allow_empty_sequence: bool = False,
-        file_name: Optional[str] = None,
+            input_file: Union[str, BufferedIOBase, None] = None,
+            default_header: Optional[str] = None,
+            allow_any_sequence_characters: bool = False,
+            allow_empty_sequence: bool = False,
+            file_name: Optional[str] = None,
     ) -> List[SeqUtilRecord]:
         if input_file is None:
             if file_name:

{pybiolib-1.1.1836 → pybiolib-1.1.1855}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1836"
+version = "1.1.1855"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"
@@ -42,17 +42,19 @@ gunicorn = { version = ">=20.1.0", optional = true }
 compute-node = ["flask", "gunicorn"]
 
 [tool.poetry.dev-dependencies]
-mypy = "==0.971"
-pylint = "==2.13.9"
-pytest = "==7.0.1"
-pytest-timeout = "^2.1.0"
-types-click = "==7.1.8"
-types-Flask = "==1.1.1"
-types-PyYAML = "==5.4.3"
-types-termcolor = "==0.1.1"
-setuptools = "==59.6.0"
-jupyter = "^1.0.0"
+# For dev require 3.9 as minimum Python version
+jupyter = { version = "==1.0.0", python = ">=3.9" }
+mypy = { version = "==1.8.0", python = ">=3.9" }
+pandas = { version = "==2.2.1", python = ">=3.9" }
+pylint = { version = "==3.1.0", python = ">=3.9" }
+ruff = { version = "==0.3.1", python = ">=3.9" }
+pytest = { version = "==8.0.2", python = ">=3.9" }
+pytest-timeout = { version = "==2.2.0", python = ">=3.9" }
+setuptools = { version = "==69.1.1", python = ">=3.9" }
+types-click = { version = "==7.1.8", python = ">=3.9" }
+types-flask = { version = "==1.1.6", python = ">=3.9" }
+types-PyYAML = { version = "==6.0.12.12", python = ">=3.9" }
 
 [build-system]
-requires = ["poetry>=0.12"]
+requires = ["poetry>=1.8.0"]
 build-backend = "poetry.masonry.api"