pybiolib 1.1.1971__py3-none-any.whl → 1.1.1974__py3-none-any.whl

biolib/jobs/job.py

@@ -56,7 +56,7 @@ class Job:
     @property
     def result(self) -> JobResult:
         if not self._result:
-            if self.get_status() == "completed":
+            if self.get_status() == 'completed':
                 self._result = JobResult(job_uuid=self._uuid, job_auth_token=self._auth_token)
             else:
                 raise BioLibError(f"Result is not available for {self._uuid}: status is {self._job_dict['state']}.")
@@ -65,17 +65,17 @@ class Job:
 
     @property
     def stdout(self) -> bytes:
-        logger.warning("The property .stdout is deprecated, please use .get_stdout()")
+        logger.warning('The property .stdout is deprecated, please use .get_stdout()')
         return self.result.get_stdout()
 
     @property
     def stderr(self) -> bytes:
-        logger.warning("The property .stderr is deprecated, please use .get_stderr()")
+        logger.warning('The property .stderr is deprecated, please use .get_stderr()')
         return self.result.get_stderr()
 
     @property
     def exitcode(self) -> int:
-        logger.warning("The property .exitcode is deprecated, please use .get_exit_code()")
+        logger.warning('The property .exitcode is deprecated, please use .get_exit_code()')
         return self.result.get_exit_code()
 
     def is_finished(self) -> bool:
@@ -109,8 +109,8 @@ class Job:
     def load_file_as_numpy(self, *args, **kwargs):
         try:
             import numpy  # type: ignore # pylint: disable=import-outside-toplevel,import-error
-        except:  # pylint: disable=raise-missing-from
-            raise Exception("Failed to import numpy, please make sure it is installed.")
+        except ImportError:  # pylint: disable=raise-missing-from
+            raise Exception('Failed to import numpy, please make sure it is installed.') from None
         file_handle = self.result.get_output_file(*args, **kwargs).get_file_handle()
         return numpy.load(file_handle, allow_pickle=False)  # type: ignore
 
@@ -198,7 +198,6 @@ class Job:
         except Exception as error:
             logger.error(f'Failed to cancel job {self._uuid} due to: {error}')
 
-
     def _get_cloud_job(self) -> CloudJobDict:
         self._refetch_job_dict(force_refetch=True)
         if self._job_dict['cloud_job'] is None:
@@ -290,7 +289,7 @@ class Job:
             status_json = self._get_job_status_from_compute_node(compute_node_url)
             if not status_json:
                 # this can happen if the job is finished but already removed from the compute node
-                logger.warning("WARN: We were unable to retrieve the full log of the job, please try again")
+                logger.warning('WARN: We were unable to retrieve the full log of the job, please try again')
                 break
             job_is_completed = status_json['is_completed']
             for status_update in status_json['status_updates']:
@@ -353,9 +352,9 @@ class Job:
                 return HttpClient.request(url=f'{compute_node_url}/v1/job/{self._uuid}/status/').json()
             except Exception:  # pylint: disable=broad-except
                 cloud_job = self._get_cloud_job()
-                logger.debug("Failed to get status from compute node, retrying...")
+                logger.debug('Failed to get status from compute node, retrying...')
                 if cloud_job['finished_at']:
-                    logger.debug("Job no longer exists on compute node, checking for error...")
+                    logger.debug('Job no longer exists on compute node, checking for error...')
                     if cloud_job['error_code'] != SystemExceptionCodes.COMPLETED_SUCCESSFULLY.value:
                         error_message = SystemExceptionCodeMap.get(
                             cloud_job['error_code'], f'Unknown error code {cloud_job["error_code"]}'

biolib/jobs/job_result.py

@@ -1,25 +1,24 @@
-from pathlib import Path
-from fnmatch import fnmatch
 import time
+from fnmatch import fnmatch
+from pathlib import Path
 
 from biolib.biolib_binary_format import ModuleOutputV2
-from biolib.biolib_binary_format.remote_stream_seeker import StreamSeeker
-from biolib.biolib_binary_format.utils import RemoteIndexableBuffer, LazyLoadedFile
 from biolib.biolib_binary_format.remote_endpoints import RemoteJobStorageResultEndpoint
+from biolib.biolib_binary_format.remote_stream_seeker import StreamSeeker
+from biolib.biolib_binary_format.utils import LazyLoadedFile, RemoteIndexableBuffer
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger
-from biolib.typing_utils import Optional, List, cast, Union, Callable
+from biolib.typing_utils import Callable, List, Optional, Union, cast
 
 PathFilter = Union[str, Callable[[str], bool]]
 
 
 class JobResult:
-
     def __init__(
-            self,
-            job_uuid: str,
-            job_auth_token: str,
-            module_output: Optional[ModuleOutputV2] = None,
+        self,
+        job_uuid: str,
+        job_auth_token: str,
+        module_output: Optional[ModuleOutputV2] = None,
     ):
         self._job_uuid: str = job_uuid
         self._job_auth_token: str = job_auth_token
@@ -75,10 +74,10 @@ class JobResult:
         files = self._get_module_output().get_files()
         filtered_files = self._get_filtered_files(files, path_filter=filename)
         if not filtered_files:
-            raise BioLibError(f"File {filename} not found in results.")
+            raise BioLibError(f'File {filename} not found in results.')
 
         if len(filtered_files) != 1:
-            raise BioLibError(f"Found multiple results for filename {filename}.")
+            raise BioLibError(f'Found multiple results for filename {filename}.')
 
         return filtered_files[0]
 
@@ -100,8 +99,8 @@ class JobResult:
         glob_filter = cast(str, path_filter)
 
         # since all file paths start with /, make sure filter does too
-        if not glob_filter.startswith("/"):
-            glob_filter = "/" + glob_filter
+        if not glob_filter.startswith('/'):
+            glob_filter = '/' + glob_filter
 
         def _filter_function(file: LazyLoadedFile) -> bool:
             return fnmatch(file.path, glob_filter)

biolib/jobs/types.py

@@ -1,4 +1,4 @@
-from biolib.typing_utils import TypedDict, Optional, Literal, List
+from biolib.typing_utils import List, Literal, Optional, TypedDict
 
 JobState = Literal['in_progress', 'completed', 'failed', 'cancelled']
 

{pybiolib-1.1.1971.dist-info → pybiolib-1.1.1974.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1971
+Version: 1.1.1974
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1971.dist-info → pybiolib-1.1.1974.dist-info}/RECORD

@@ -89,9 +89,9 @@ biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 biolib/experiments/experiment.py,sha256=kUQsH9AGAckPKT_nzaRuTh8Mb2pVUpxnuX9IstRTOEo,6351
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=WFcHYYOkvAhmYRUykWFbjhshiF_dy1-eiPIMCS1CIeo,16157
-biolib/jobs/job_result.py,sha256=8GasUmUXD8SjUYrE2N-HrDx7-AI6TEkFONH8H91t01Q,4913
-biolib/jobs/types.py,sha256=4OAvlhOKANzFMrZDd-mhXpEd8RaKcx8sPneZUoWhJ2U,970
+biolib/jobs/job.py,sha256=-H83m5BJs0l9Pe_lsExlcqH5gAHOVREeQBZs6umWdYc,16178
+biolib/jobs/job_result.py,sha256=bJm0q7L_11ekOJBiC6jIaeYo_zxDJKSB0TGsLI30BBo,4896
+biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/lfs/__init__.py,sha256=Qv8vdYeK43JecT4SsE93ZYE2VmNiZENdNpW8P9-omxs,115
 biolib/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
 biolib/lfs/utils.py,sha256=HSs7F2wXklYhhv5tabfaeC5noXJyxRjbGD5IhWOVdxs,5918
@@ -109,8 +109,8 @@ 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=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.1971.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1971.dist-info/METADATA,sha256=Ldnxyz9Y43LOU6soZJP8EulbEQuVLL1zVaz-bGEObK4,1508
-pybiolib-1.1.1971.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1971.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1971.dist-info/RECORD,,
+pybiolib-1.1.1974.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1974.dist-info/METADATA,sha256=pTLqiAvKtqfjL4SzRbwKtNUCKdpePX8CJzlm2S4naFI,1508
+pybiolib-1.1.1974.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.1974.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1974.dist-info/RECORD,,