pybiolib 1.2.347__py3-none-any.whl → 1.2.406__py3-none-any.whl

biolib/app/app.py

@@ -11,7 +11,7 @@ from biolib.biolib_api_client.app_types import App, AppVersion
 from biolib.biolib_api_client.biolib_app_api import BiolibAppApi
 from biolib.biolib_api_client.biolib_job_api import BiolibJobApi
 from biolib.biolib_binary_format import ModuleInput
-from biolib.biolib_errors import BioLibError
+from biolib.biolib_errors import BioLibError, JobResultNonZeroExitCodeError
 from biolib.biolib_logging import logger
 from biolib.compute_node.job_worker.job_worker import JobWorker
 from biolib.experiments.experiment import Experiment
@@ -59,10 +59,14 @@ class BioLibApp:
         machine_count: Optional[int] = None,
         experiment: Optional[str] = None,
         temporary_client_secrets: Optional[Dict[str, str]] = None,
+        check: bool = False,
     ) -> Job:
         if experiment_id and experiment:
             raise ValueError('Only one of experiment_id and experiment can be specified')
 
+        if check and not blocking:
+            raise ValueError('The argument "check" cannot be True when blocking is False')
+
         if not experiment_id:
             experiment_instance = Experiment(experiment) if experiment else Experiment.get_experiment_in_context()
             experiment_id = experiment_instance.uuid if experiment_instance else None
@@ -105,6 +109,11 @@ class BioLibApp:
             )
             job._stream_logs(enable_print=enable_print)  # pylint: disable=protected-access
 
+            if check:
+                exit_code = job.get_exit_code()
+                if exit_code != 0:
+                    raise JobResultNonZeroExitCodeError(exit_code)
+
         return job
 
     def exec(self, args=None, stdin=None, files=None, machine=''):

biolib/biolib_errors.py

@@ -43,3 +43,12 @@ class JobResultNotFound(JobResultError):
 
 class JobResultPermissionError(JobResultError):
     pass
+
+
+class JobResultNonZeroExitCodeError(JobResultError):
+    """Raised when an app returns a non-zero exit code and check=True."""
+    def __init__(self, exit_code: int, message: Optional[str] = None):
+        self.exit_code = exit_code
+        super().__init__(
+            message or f'App returned non-zero exit code: {exit_code}'
+        )

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -44,8 +44,10 @@ class DockerExecutor:
         self._send_system_exception = options['send_system_exception']
         self._send_stdout_and_stderr = options['send_stdout_and_stderr']
         self._random_docker_id = compute_node_utils.random_string(15)
-        self._reserved_system_ram = int(os.sysconf('SC_PAGE_SIZE') * os.sysconf('SC_PHYS_PAGES') * 0.06) + 500_000_000
-        logger_no_user_data.info(f"System RAM reserved: {self._reserved_system_ram}")
+        total_memory_in_bytes = int(os.sysconf('SC_PAGE_SIZE') * os.sysconf('SC_PHYS_PAGES'))
+        system_reserved_memory = int(total_memory_in_bytes * 0.1) + 500_000_000
+        self._available_memory_in_bytes = total_memory_in_bytes - system_reserved_memory
+        logger_no_user_data.info(f'Available memory for containers: {self._available_memory_in_bytes} bytes')
 
         if utils.IS_RUNNING_IN_CLOUD:
             self._compute_process_dir = os.getenv('BIOLIB_USER_DATA_PATH')
@@ -164,7 +166,6 @@ class DockerExecutor:
             may_contain_user_data=False,
         )
 
-
     def _execute_helper(self, module_input) -> None:
         job_uuid = self._options['job']['public_id']
         logger_no_user_data.debug(f'Initializing container for {job_uuid}.')
@@ -250,7 +251,6 @@ class DockerExecutor:
         logger_no_user_data.debug(f'Docker container exited with code {exit_code} for {job_uuid}')
         self._save_module_output_from_container(exit_code, self._metadata_for_save_output_on_cancel)
 
-
     def _save_module_output_from_container(self, exit_code: int, metadata: MetadataToSaveOutput) -> None:
         full_stdout = self._docker_api_client.logs(self._container.id, stdout=True, stderr=False)
         full_stderr = self._docker_api_client.logs(self._container.id, stdout=False, stderr=True)
@@ -267,7 +267,6 @@ class DockerExecutor:
             pre_start_diff=metadata['pre_start_diff'],
         )
 
-
     def cleanup(self):
         # Don't clean up if already in the process of doing so, or done doing so
         if self._is_cleaning_up:
@@ -283,7 +282,7 @@ class DockerExecutor:
                 logger_no_user_data.debug(f'Container state {self._docker_container.status}')
                 self._save_module_output_from_container(
                     exit_code=self._docker_container.attrs['State']['ExitCode'],
-                    metadata=self._metadata_for_save_output_on_cancel
+                    metadata=self._metadata_for_save_output_on_cancel,
                 )
                 logger_no_user_data.debug('Saved results')
             except BaseException as error:
@@ -412,8 +411,15 @@ class DockerExecutor:
 
             if utils.IS_RUNNING_IN_CLOUD:
                 cloud_job = self._options['cloud_job']
-                create_container_args['mem_limit'] = (
-                    f'{cloud_job["reserved_memory_in_bytes"] - self._reserved_system_ram}b'
+                container_memory_limit_in_bytes = min(
+                    cloud_job['reserved_memory_in_bytes'], self._available_memory_in_bytes
+                )
+                create_container_args['mem_limit'] = f'{container_memory_limit_in_bytes}b'
+                logger_no_user_data.debug(
+                    'Setting container memory limit to '
+                    f'{container_memory_limit_in_bytes} bytes '
+                    f'(requested: {cloud_job["reserved_memory_in_bytes"]}, '
+                    f'available: {self._available_memory_in_bytes})'
                 )
                 create_container_args['nano_cpus'] = cloud_job['reserved_cpu_in_nano_shares']
                 create_container_args['pids_limit'] = 10_000

{pybiolib-1.2.347.dist-info → pybiolib-1.2.406.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.347
+Version: 1.2.406
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.347.dist-info → pybiolib-1.2.406.dist-info}/RECORD

@@ -29,7 +29,7 @@ biolib/_runtime/runtime.py,sha256=bZQ0m39R9jOBVAtlyvzDnOobKueOAQUCwMUZjDQnO7E,44
 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=mJafDLtnoX66egHF94NrUhmhzjpFzvRj2STh0RVGJCY,8862
+biolib/app/app.py,sha256=qhPa-nkIYwq1YUIZyRvs_gzNRJiRpHnOFxIvktDp6Jg,9222
 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
@@ -55,7 +55,7 @@ biolib/biolib_binary_format/system_status_update.py,sha256=aOELuQ0k-GtpaZTUxYd0G
 biolib/biolib_binary_format/utils.py,sha256=jq31QEShs7TSrSKZBr8jif-bJAwVzQrqVxmymL6crpU,5453
 biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghKm0wqQiljdo,1481
 biolib/biolib_download_container.py,sha256=8TmBV8iv3bCvkNlHa1SSsc4zl0wX_eaxhfnW5rvFIh8,1779
-biolib/biolib_errors.py,sha256=xtdo3ybqnc0jhd959kVmBczFdBczrFMr8cZyd4hjKLk,842
+biolib/biolib_errors.py,sha256=eyQolC4oGi350BDEMOd-gAHYVqo2L2lYgv6c4ZdXPjQ,1184
 biolib/biolib_logging.py,sha256=S2y6fk7jjxZQMN2BtKkHBb4JbVQQSSU97T7ep4P_QCE,2855
 biolib/cli/__init__.py,sha256=0v3c_J-U0k46c5ZWeQjLG_kTaKDJm81LBxQpDO2B_aI,1286
 biolib/cli/auth.py,sha256=rpWGmXs6Fz6CGrO9K8ibPRszOdXG78Vig_boKaVCD9A,2082
@@ -76,7 +76,7 @@ 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=NpDSgNWbnC0Qr6aFaQMEfhib3O9BMOPsia-YqeTMhpU,30966
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=UxWUSk15mM_H73q2k5_kBB1IWGYGphyXbyC-Bm0QneU,31550
 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=gw_T-oq0lty8Hg8WsTrqhtV-kyOF_l5nr9Xe8-kzetc,1657
@@ -118,8 +118,8 @@ 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-1.2.347.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.347.dist-info/METADATA,sha256=MMaf_ltA6Tg3gAgfrmO1W9bZeWMM3D6_fGQkgN1Ono8,1570
-pybiolib-1.2.347.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
-pybiolib-1.2.347.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.347.dist-info/RECORD,,
+pybiolib-1.2.406.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.406.dist-info/METADATA,sha256=RMsKTpxadkRTJtaOOCrJ8pg8vdwOyQGegrOWGX96SEs,1570
+pybiolib-1.2.406.dist-info/WHEEL,sha256=IYZQI976HJqqOpQU6PHkJ8fb3tMNBFjg-Cn-pwAbaFM,88
+pybiolib-1.2.406.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.406.dist-info/RECORD,,