pybiolib 1.1.2109__tar.gz → 1.1.2119__tar.gz

{pybiolib-1.1.2109 → pybiolib-1.1.2119}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2109
+Version: 1.1.2119
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

pybiolib-1.1.2119/biolib/_internal/types/__init__.py

@@ -0,0 +1 @@
+from .resources import *  # noqa: F403

pybiolib-1.1.2119/biolib/_internal/types/resources.py

@@ -0,0 +1,14 @@
+from .typing import Optional, TypedDict
+
+
+class ExperimentDict(TypedDict):
+    job_count: int
+    job_running_count: int
+
+
+class ResourceDict(TypedDict):
+    created_at: str
+    experiment: Optional[ExperimentDict]
+    name: str
+    uri: str
+    uuid: str

pybiolib-1.1.2119/biolib/_internal/types/typing.py

@@ -0,0 +1,7 @@
+import sys
+
+# import and expose everything from the typing module
+from typing import *  # noqa:F403 pylint: disable=wildcard-import, unused-wildcard-import
+
+if sys.version_info < (3, 8):  # noqa: UP036
+    from typing_extensions import Literal, TypedDict  # pylint: disable=unused-import

{pybiolib-1.1.2109 → pybiolib-1.1.2119}/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-1.1.2109 → pybiolib-1.1.2119}/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-1.1.2109 → pybiolib-1.1.2119}/biolib/experiments/experiment.py

@@ -1,6 +1,7 @@
 import time
 from collections import OrderedDict
 
+import biolib._internal.types as _types
 from biolib import api
 from biolib._internal.http_client import HttpError
 from biolib.biolib_errors import BioLibError, NotFound
@@ -23,8 +24,11 @@ class Experiment:
         }
     )
 
-    def __init__(self, uri: str):
-        self._experiment_dict: ExperimentDict = self._get_or_create_by_uri(uri)
+    def __init__(self, uri: str, _experiment_dict: Optional[ExperimentDict] = None):
+        if not _experiment_dict:
+            self._experiment_dict: ExperimentDict = self._get_or_create_by_uri(uri)
+        else:
+            self._experiment_dict = _experiment_dict
 
     def __enter__(self):
         Experiment._BIOLIB_EXPERIMENTS.append(self)
@@ -62,6 +66,21 @@ class Experiment:
             title='Experiments',
         ).print_table()
 
+    @staticmethod
+    def get_by_uri(uri: str) -> 'Experiment':
+        resource_dict: _types.ResourceDict = api.client.get('/resources/', params={'uri': uri}).json()
+        if not resource_dict['experiment']:
+            raise ValueError('Resource from URI is not an experiment')
+
+        legacy_experiment_dict = ExperimentDict(
+            created_at=resource_dict['created_at'],
+            job_count=resource_dict['experiment']['job_count'],
+            job_running_count=resource_dict['experiment']['job_running_count'],
+            name=resource_dict['name'],
+            uuid=resource_dict['uuid'],
+        )
+        return Experiment(uri=resource_dict['uri'], _experiment_dict=legacy_experiment_dict)
+
     def wait(self) -> None:
         self._refetch_experiment_dict()
         while self._experiment_dict['job_running_count'] > 0:

{pybiolib-1.1.2109 → pybiolib-1.1.2119}/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-1.1.2119/biolib/typing_utils.py

@@ -0,0 +1,2 @@
+# TODO: Deprecate and later remove this file
+from biolib._internal.types.typing import *  # pylint: disable=wildcard-import, unused-wildcard-import

{pybiolib-1.1.2109 → pybiolib-1.1.2119}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.2109"
+version = "1.1.2119"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"

pybiolib-1.1.2109/biolib/typing_utils.py

@@ -1,7 +0,0 @@
-import sys
-
-# import and expose everything from the typing module
-from typing import *  # pylint: disable=wildcard-import, unused-wildcard-import
-
-if sys.version_info < (3, 8):
-    from typing_extensions import TypedDict, Literal  # pylint: disable=unused-import