pybiolib 1.1.2097__tar.gz → 1.1.2112__tar.gz

{pybiolib-1.1.2097 → pybiolib-1.1.2112}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2097
+Version: 1.1.2112
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2097 → pybiolib-1.1.2112}/biolib/app/app.py

@@ -56,6 +56,7 @@ class BioLibApp:
         result_prefix: Optional[str] = None,
         timeout: Optional[int] = None,
         notify: bool = False,
+        machine_count: Optional[int] = None,
     ) -> Job:
         if not experiment_id:
             experiment = Experiment.get_experiment_in_context()
@@ -85,6 +86,7 @@ class BioLibApp:
             override_command=override_command,
             result_prefix=result_prefix,
             timeout=timeout,
+            requested_machine_count=machine_count,
         )
         if blocking:
             # TODO: Deprecate utils.STREAM_STDOUT and always stream logs by simply calling job.stream_logs()

{pybiolib-1.1.2097 → pybiolib-1.1.2112}/biolib/biolib_api_client/biolib_job_api.py

@@ -46,6 +46,7 @@ class BiolibJobApi:
             experiment_uuid: Optional[str] = None,
             timeout: Optional[int] = None,
             notify: bool = False,
+            requested_machine_count: Optional[int] = None,
     ):
         data = {
             'app_version_id': app_version_id,
@@ -73,6 +74,9 @@ class BiolibJobApi:
                 'requested_machine': machine
             })
 
+        if requested_machine_count:
+            data.update({'requested_machine_count': requested_machine_count})
+
         if experiment_uuid:
             data['experiment_uuid'] = experiment_uuid
 
@@ -156,6 +160,7 @@ class BiolibJobApi:
             caller_job_uuid: Optional[str] = None,
             requested_timeout_seconds: Optional[int] = None,
             notify: bool = False,
+            requested_machine_count: Optional[int] = None,
     ) -> Dict:
         job_dict: Dict = biolib.api.client.post(
             path='/jobs/create_job_with_data/',
@@ -171,6 +176,7 @@ class BiolibJobApi:
                 'client-version': BIOLIB_PACKAGE_VERSION,
                 'experiment-uuid': experiment_uuid,
                 'requested-machine': requested_machine,
+                'requested-machine-count': str(requested_machine_count) if requested_machine_count else None,
                 'result-name-prefix': result_name_prefix,
                 'requested-timeout-seconds': str(requested_timeout_seconds) if requested_timeout_seconds else None,
                 'notify': 'true' if notify else 'false',

{pybiolib-1.1.2097 → pybiolib-1.1.2112}/biolib/compute_node/job_worker/executors/docker_executor.py

@@ -270,6 +270,8 @@ class DockerExecutor:
     # TODO: type this method
     def _initialize_docker_container(self, module_input):
         try:
+            job_uuid = self._options['job']['public_id']
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container...')
             module = self._options['module']
             logger.debug(f"Initializing docker container with command: {module['command']}")
 
@@ -314,6 +316,7 @@ class DockerExecutor:
                     }
                 )
 
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Getting IPs for proxies...')
             for proxy in self._options['remote_host_proxies']:
                 proxy_ip = proxy.get_ip_address_on_network(internal_network)
                 if proxy.is_app_caller_proxy:
@@ -332,6 +335,7 @@ class DockerExecutor:
                 else:
                     extra_hosts[proxy.hostname] = proxy_ip
 
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Constructing container args...')
             create_container_args = {
                 'environment': environment_vars,
                 'extra_hosts': extra_hosts,
@@ -368,9 +372,10 @@ class DockerExecutor:
             if docker_runtime is not None:
                 create_container_args['runtime'] = docker_runtime
 
-            self._docker_container = BiolibDockerClient.get_docker_client().containers.create(**create_container_args)
-
-            logger_no_user_data.debug('Finished initializing docker container')
+            docker_client = BiolibDockerClient.get_docker_client()
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Creating container...')
+            self._docker_container = docker_client.containers.create(**create_container_args)
+            logger_no_user_data.debug(f'Job "{job_uuid}" finished initializing Docker container.')
         except Exception as exception:
             raise ComputeProcessException(
                 exception, SystemExceptionCodes.FAILED_TO_START_COMPUTE_CONTAINER.value, self._send_system_exception

{pybiolib-1.1.2097 → pybiolib-1.1.2112}/biolib/jobs/job.py

@@ -412,6 +412,7 @@ class Job:
         result_prefix: Optional[str] = None,
         timeout: Optional[int] = None,
         notify: bool = False,
+        requested_machine_count: Optional[int] = None,
     ) -> 'Job':
         if len(module_input_serialized) < 500_000:
             _job_dict = BiolibJobApi.create_job_with_data(
@@ -424,6 +425,7 @@ class Job:
                 requested_machine=machine,
                 requested_timeout_seconds=timeout,
                 result_name_prefix=result_prefix,
+                requested_machine_count=requested_machine_count,
             )
             return Job(cast(JobDict, _job_dict))
 
@@ -435,6 +437,7 @@ class Job:
             notify=notify,
             override_command=override_command,
             timeout=timeout,
+            requested_machine_count=requested_machine_count,
         )
         JobStorage.upload_module_input(job=job_dict, module_input_serialized=module_input_serialized)
         cloud_job = BiolibJobApi.create_cloud_job(job_id=job_dict['public_id'], result_name_prefix=result_prefix)

{pybiolib-1.1.2097 → pybiolib-1.1.2112}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.2097"
+version = "1.1.2112"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"