pybiolib 1.2.517__py3-none-any.whl → 1.2.558__py3-none-any.whl

biolib/_internal/types/resource_version.py

@@ -1,7 +1,13 @@
-from .typing import Literal, TypedDict
+from .typing import Literal, NotRequired, TypedDict
 
 
-class ResourceVersionDetailedDict(TypedDict):
+class ResourceVersionDict(TypedDict):
+    uuid: str
     semantic_version: str
     state: Literal['published', 'unpublished']
-    uuid: str
+    created_at: str
+    git_branch_name: NotRequired[str]
+
+
+class ResourceVersionDetailedDict(ResourceVersionDict):
+    pass

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

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()

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.dist-info → pybiolib-1.2.558.dist-info}/METADATA

@@ -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-1.2.517.dist-info → pybiolib-1.2.558.dist-info}/RECORD

@@ -21,15 +21,15 @@ biolib/_internal/types/data_record.py,sha256=9r_vdhVs60YTnzU4XQFXfDrfS2P2MqD3BH2
 biolib/_internal/types/experiment.py,sha256=D94iBdn2nS92lRW-TOs1a2WKXJD5ZtmzL4ypggKX2ys,176
 biolib/_internal/types/file_node.py,sha256=T6BIqo662f3nwMBRqtBHYsg6YuuUaKpiokHcVjv9_ME,283
 biolib/_internal/types/resource.py,sha256=uUI9Rt5ehkXv9NEDW9zsaPXiTXxnj811rSUW3g_joJw,437
-biolib/_internal/types/resource_version.py,sha256=sLxViYXloDDUhTDFgjegiQCj097OM1Ih1-uqlC_4ULA,174
-biolib/_internal/types/typing.py,sha256=D4EKKEe7kDx0K6lJi-H_XLtk-8w6nu2fdqn9bvzI-Xo,288
+biolib/_internal/types/resource_version.py,sha256=cU0YFHqxO-wX_Y6CoeK0Iei61gFwVoyR_kPOSTQ4mCs,304
+biolib/_internal/types/typing.py,sha256=qrsk8hHcGEbDpU1QQFzHAKnhQxkMe7uJ6pxHeAnfv1Y,414
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/_internal/utils/multinode.py,sha256=-J3PEAK3NaOwCn--5T7vWHkA3yu5w9QhmuhkQcH-2wY,8229
 biolib/_runtime/runtime.py,sha256=bZQ0m39R9jOBVAtlyvzDnOobKueOAQUCwMUZjDQnO7E,4439
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=EN3lDbbgWxw3aPDe8W5XIU6WkMfOHW7Dmsz-R6QqxAw,4176
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=U7PzLxDjYc73ZVcL1f-hKgwdroLqyvE0TiDa5xK0kzM,9621
+biolib/app/app.py,sha256=-Ed4wV3RSMIq7DgQqCHkzkooyr2RRzoUuOAtJRl3E5E,9622
 biolib/app/search_apps.py,sha256=K4a41f5XIWth2BWI7OffASgIsD0ko8elCax8YL2igaY,1470
 biolib/biolib_api_client/__init__.py,sha256=E5EMa19wJoblwSdQPYrxc_BtIeRsAuO0L_jQweWw-Yk,182
 biolib/biolib_api_client/api_client.py,sha256=ohvbWbpresxLHFGPkvXACfmiTYsBk8RBx5XsBbLYg_M,7546
@@ -101,7 +101,7 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=pBtnOHz0kKoFxlIGf08o8ZCEOze-CljwfOsTdhvCTCk,8646
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=edKfRiojv6f4sLzz1YfJupwvHL2zuh7L_2v_3a4gSCI,21456
+biolib/jobs/job.py,sha256=vmALUOA9APqz0qTjmlisT6ChZHUwOaTlX-1VLhWJSrA,23176
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -119,8 +119,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.517.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.517.dist-info/METADATA,sha256=bpM1eL9PbbUFvNoIdj58Y69eDD9yY8GSOf7G62_EghU,1570
-pybiolib-1.2.517.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-pybiolib-1.2.517.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.517.dist-info/RECORD,,
+pybiolib-1.2.558.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.558.dist-info/METADATA,sha256=QO2zAOtRMRujoLhdT7UcWJqp3xx5lssaGVTbpcH2R-M,1570
+pybiolib-1.2.558.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+pybiolib-1.2.558.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.558.dist-info/RECORD,,