pybiolib 1.1.1998__py3-none-any.whl → 1.1.2004__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -356,6 +356,7 @@ class DockerExecutor:
                 cloud_job = self._options['cloud_job']
                 create_container_args['mem_limit'] = f'{cloud_job["reserved_memory_in_bytes"]}b'
                 create_container_args['nano_cpus'] = cloud_job['reserved_cpu_in_nano_shares']
+                create_container_args['pids_limit'] = 10_000
 
                 biolib_identity_user_email: Optional[str] = cloud_job.get('biolib_identity_user_email')
                 if biolib_identity_user_email:

biolib/jobs/job_result.py

@@ -34,7 +34,9 @@ class JobResult:
     def get_exit_code(self) -> int:
         return self._get_module_output().get_exit_code()
 
-    def save_files(self, output_dir: str, path_filter: Optional[PathFilter] = None) -> None:
+    def save_files(
+        self, output_dir: str, path_filter: Optional[PathFilter] = None, skip_file_if_exists: Optional[bool] = None
+    ) -> None:
         module_output = self._get_module_output()
         output_files = module_output.get_files()
         filtered_output_files = self._get_filtered_files(output_files, path_filter) if path_filter else output_files
@@ -60,7 +62,13 @@ class JobResult:
             # Remove leading slash of file_path
             destination_file_path = Path(output_dir) / Path(file.path.lstrip('/'))
             if destination_file_path.exists():
-                destination_file_path.rename(f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}')
+                if skip_file_if_exists:
+                    print(f'Skipping {destination_file_path} as a file with that name already exists locally.')
+                    continue
+                else:
+                    destination_file_path.rename(
+                        f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}'
+                    )
 
             dir_path = destination_file_path.parent
             if dir_path:

{pybiolib-1.1.1998.dist-info → pybiolib-1.1.2004.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1998
+Version: 1.1.2004
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1998.dist-info → pybiolib-1.1.2004.dist-info}/RECORD

@@ -63,7 +63,7 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=Lo7qgOm6uolNyH7QIuLqTY_6RLyPYeAlOk9HzC82U-s,27332
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=81ltJvSDpCPBgbffnSQF-fiRpk_94sWZWJRcP0IW_5k,27393
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/job_worker/executors/types.py,sha256=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
@@ -90,7 +90,7 @@ biolib/experiments/experiment.py,sha256=_ied3A3U6NFa6_ewEYn2TCozqeHvDxDqdRhMtZbF
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=aWKnf_2pYdr76gh3hxPiVs2iuXlpwZkKPTK81Pz4G2U,19072
-biolib/jobs/job_result.py,sha256=UGxE9MNLtwJiWmhw2UNjOQW7EZi7B-e2lL0PXYvsXeA,4925
+biolib/jobs/job_result.py,sha256=GAM99MOcHUgUvzL5r9BpdBKnTPfm6ipOh67HvNDO9TY,5236
 biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/lfs/__init__.py,sha256=Qv8vdYeK43JecT4SsE93ZYE2VmNiZENdNpW8P9-omxs,115
 biolib/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
@@ -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-1.1.1998.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1998.dist-info/METADATA,sha256=3V8P0UEv5bTpOlVUAfNJAS7GQPCu2v_l7mu1Xqvr_sc,1508
-pybiolib-1.1.1998.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1998.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1998.dist-info/RECORD,,
+pybiolib-1.1.2004.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2004.dist-info/METADATA,sha256=ulvo3XlgpOcN4qybIW2FgOo3oNBqcHeMb4uXUPI94WE,1508
+pybiolib-1.1.2004.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2004.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2004.dist-info/RECORD,,