pybiolib 1.2.517__tar.gz → 1.2.558__tar.gz

{pybiolib-1.2.517 → pybiolib-1.2.558}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.517
+Version: 1.2.558
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib
@@ -26,7 +26,7 @@ Requires-Dist: gunicorn (>=20.1.0) ; extra == "compute-node"
 Requires-Dist: importlib-metadata (>=1.6.1)
 Requires-Dist: pyyaml (>=5.3.1)
 Requires-Dist: rich (>=12.4.4)
-Requires-Dist: typing_extensions (>=3.10.0) ; python_version < "3.8"
+Requires-Dist: typing-extensions (>=4.1.0) ; python_version < "3.11"
 Project-URL: Homepage, https://github.com/biolib
 Description-Content-Type: text/markdown
 

pybiolib-1.2.558/biolib/_internal/types/resource_version.py

@@ -0,0 +1,13 @@
+from .typing import Literal, NotRequired, TypedDict
+
+
+class ResourceVersionDict(TypedDict):
+    uuid: str
+    semantic_version: str
+    state: Literal['published', 'unpublished']
+    created_at: str
+    git_branch_name: NotRequired[str]
+
+
+class ResourceVersionDetailedDict(ResourceVersionDict):
+    pass

{pybiolib-1.2.517 → pybiolib-1.2.558}/biolib/_internal/types/typing.py

@@ -5,3 +5,6 @@ from typing import *  # noqa:F403 pylint: disable=wildcard-import, unused-wildca
 
 if sys.version_info < (3, 8):  # noqa: UP036
     from typing_extensions import Literal, TypedDict  # pylint: disable=unused-import
+
+if sys.version_info < (3, 11):  # noqa: UP036
+    from typing_extensions import NotRequired  # pylint: disable=unused-import

{pybiolib-1.2.517 → pybiolib-1.2.558}/biolib/app/app.py

@@ -108,7 +108,7 @@ class BioLibApp:
                 (utils.STREAM_STDOUT or stream_logs)
                 and (self._app_version.get('main_output_file') or self._app_version.get('stdout_render_type') == 'text')
             )
-            job._stream_logs(enable_print=enable_print) # pylint: disable=protected-access
+            job._stream_logs(enable_print=enable_print)  # pylint: disable=protected-access
 
             if check:
                 exit_code = job.get_exit_code()

{pybiolib-1.2.517 → pybiolib-1.2.558}/biolib/jobs/job.py

@@ -230,7 +230,35 @@ class Job:
         except Exception as error:
             raise BioLibError(f'Failed to rename job {self._uuid} due to: {error}') from error
 
-    def recompute(self, app_uri: Optional[str] = None, machine: Optional[str] = None, blocking: bool = True) -> 'Job':
+    def recompute(
+        self,
+        app_uri: Optional[str] = None,
+        machine: Optional[str] = None,
+        blocking: bool = True,
+        arguments: Optional[List[str]] = None,
+    ) -> 'Job':
+        """Recompute the job with the same input files but potentially different arguments.
+
+        Args:
+            app_uri (Optional[str], optional): The URI of the app to use for recomputation.
+                If None, uses the original app URI. Defaults to None.
+            machine (Optional[str], optional): The machine to run the job on.
+                If None, uses the original requested machine. Defaults to None.
+            blocking (bool, optional): Whether to block until the job completes.
+                If True, streams logs until completion. Defaults to True.
+            arguments (Optional[List[str]], optional): New arguments to use for the job.
+                If None, uses the original arguments. Defaults to None.
+
+        Returns:
+            Job: A new Job instance for the recomputed job.
+
+        Example::
+            >>> job = biolib.get_job("job_id")
+            >>> # Recompute with the same arguments
+            >>> new_job = job.recompute()
+            >>> # Recompute with different arguments
+            >>> new_job = job.recompute(arguments=["--new-arg", "value"])
+        """
         app_response = BiolibAppApi.get_by_uri(uri=app_uri or self._job_dict['app_uri'])
 
         job_storage_input = RemoteJobStorageEndpoint(
@@ -241,6 +269,16 @@ class Job:
         http_response = HttpClient.request(url=job_storage_input.get_remote_url())
         module_input_serialized = http_response.content
 
+        # If arguments are provided, deserialize the module input, update the arguments, and serialize it again
+        if arguments is not None:
+            module_input = ModuleInput(module_input_serialized)
+            module_input_dict = module_input.deserialize()
+
+            # Create a new ModuleInput with updated arguments
+            module_input_serialized = ModuleInput().serialize(
+                stdin=module_input_dict['stdin'], arguments=arguments, files=module_input_dict['files']
+            )
+
         original_requested_machine = (
             self._job_dict['requested_machine'] if self._job_dict['requested_machine'] else None
         )

{pybiolib-1.2.517 → pybiolib-1.2.558}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.517"
+version = "1.2.558"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"
@@ -32,7 +32,7 @@ importlib-metadata = ">=1.6.1"
 python = "^3.6.3"
 pyyaml = ">=5.3.1"
 rich = ">=12.4.4"
-typing_extensions = { version = ">=3.10.0", python = "<3.8" }
+typing-extensions = { version = ">=4.1.0", python = "<3.11" }
 
 # Optional dependencies included in the below `extras`
 flask = { version = ">=2.0.1", optional = true }

pybiolib-1.2.517/biolib/_internal/types/resource_version.py

@@ -1,7 +0,0 @@
-from .typing import Literal, TypedDict
-
-
-class ResourceVersionDetailedDict(TypedDict):
-    semantic_version: str
-    state: Literal['published', 'unpublished']
-    uuid: str