pybiolib 1.1.2109__py3-none-any.whl → 1.1.2119__py3-none-any.whl

biolib/_internal/types/__init__.py

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

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

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

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()

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',

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:

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)

biolib/typing_utils.py

@@ -1,7 +1,2 @@
-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
+# TODO: Deprecate and later remove this file
+from biolib._internal.types.typing import *  # pylint: disable=wildcard-import, unused-wildcard-import

{pybiolib-1.1.2109.dist-info → pybiolib-1.1.2119.dist-info}/METADATA

@@ -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-1.1.2109.dist-info → pybiolib-1.1.2119.dist-info}/RECORD

@@ -16,19 +16,22 @@ biolib/_internal/libs/__init__.py,sha256=Jdf4tNPqe_oIIf6zYml6TiqhL_02Vyqwge6IELr
 biolib/_internal/libs/fusepy/__init__.py,sha256=AWDzNFS-XV_5yKb0Qx7kggIhPzq1nj_BZS5y2Nso08k,41944
 biolib/_internal/push_application.py,sha256=8P7eXvySn7CRp5XBDkO3xjTGixS8g7-jD-_iwzM_XDI,10020
 biolib/_internal/runtime.py,sha256=9pZ3s3L7LGxdqOgnHh1KK3Jjyn_9MjhQmKHI-6hMT3U,448
+biolib/_internal/types/__init__.py,sha256=h2I2aupN01HbhBelL-qQa8FLuXiH1tB3kKl8dPdhmnc,39
+biolib/_internal/types/resources.py,sha256=LlxuiesDDv3TvfEmz_BCCxH0V650bNHtS_LpBMA25T4,256
+biolib/_internal/types/typing.py,sha256=D4EKKEe7kDx0K6lJi-H_XLtk-8w6nu2fdqn9bvzI-Xo,288
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/_runtime/runtime.py,sha256=zy9HrE4X5hBqm8doUHkckyflquSBDSXV3REhT2MQGas,2767
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=9MD1qI52BnRC_QSydFGjyFquwFw0R9dkDfUrjUouuHQ,3490
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=8AvPYL1W2wxQ7t7BB2KeVU2WPrm3UL6vVuHPGs8g9L0,8388
+biolib/app/app.py,sha256=P2RwaDAskUHzlciuTJUroqUocRwoyOLT6YbgMyCRRDI,8484
 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=krlSRmmAwtdMMyN1XzQhh1gihB1ERSIVslWQ-dqI1yU,7188
 biolib/biolib_api_client/app_types.py,sha256=FxSr4UqfnMhLe34p8bm02wsC3g1Jz8iaing5tRKDOQI,2442
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
 biolib/biolib_api_client/biolib_app_api.py,sha256=DndlVxrNTes6DOaWyMINLGZQCRMWVvR7gwt5HVlyf5Y,4240
-biolib/biolib_api_client/biolib_job_api.py,sha256=IpFahcRzm7GNy8DJ-XHYe-x7r4Voba8o22IXw5puHn8,6782
+biolib/biolib_api_client/biolib_job_api.py,sha256=7bKfav3-12ewXkEUoLdCmbWdebW8148kxfGJW9SsXZI,7125
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
 biolib/biolib_api_client/job_types.py,sha256=Dl4NhU2xpgpXV-7YIoDf6WL63SLR5bni55OX8x5539M,1300
 biolib/biolib_api_client/lfs_types.py,sha256=joZWP6-sa5_Ug_6xIp5fHAgEo_bqLE3rbleQocZtDcg,339
@@ -91,10 +94,10 @@ biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2y
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=26tG73TADnOcXsAr7Iyf6smrLlCqB4x-vvmpUb8WqnA,11569
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=IMjnokTc9ZEKUjpsM_JnFolh9HsLbjXus_xKBb2ypJ8,7219
+biolib/experiments/experiment.py,sha256=o2gXMJVwK2SFljZ9RdTYFRH3jGKJmg3P39oERhEnZMQ,8126
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=npnARoP408SXD2UqyzFRJYdEJsP_gHoBh2xQkNegYqg,18884
+biolib/jobs/job.py,sha256=aJck0zl6QTE-70pkHY9tKDctchdJyA-YaCIozrlqGkA,19065
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
 biolib/runtime/__init__.py,sha256=Fg2ZIAmUegurLKagpBNfRgLcOwR2VZSmXQpb-ryRwI0,505
@@ -102,7 +105,7 @@ biolib/sdk/__init__.py,sha256=qJ_V_Edxolzi4VBQCrvem5lYIkJ0FVH3VZepSDuXjTc,1895
 biolib/tables.py,sha256=acH7VjwAbadLo8P84FSnKEZxCTVsF5rEg9VPuxElNs8,872
 biolib/templates/__init__.py,sha256=Yx62sSyDCDesRQDQgmbDsLpfgEh93fWE8r9u4g2azXk,36
 biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFveE,715
-biolib/typing_utils.py,sha256=krMhxB3SedVQA3HXIrC7DBXWpHKWN5JNmXGcSrrysOc,263
+biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
 biolib/user/sign_in.py,sha256=q-E2B3wLVwPU5plbITJXP4GDWWUzUcDpYu_y8BShNQ8,2039
 biolib/utils/__init__.py,sha256=fwjciJyJicvYyZcVTzfDBgD0SKY13DeXqvTeG4qZIy8,5548
@@ -111,8 +114,8 @@ 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-1.1.2109.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2109.dist-info/METADATA,sha256=Ib3gPLhMCJEEmlmAf7rgaOg4ZR2x1pQef1XCOCryito,1508
-pybiolib-1.1.2109.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2109.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2109.dist-info/RECORD,,
+pybiolib-1.1.2119.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2119.dist-info/METADATA,sha256=H_-CG3QcTCBRdKmXtXeAfdOOaCNQMNz7AQO3YdJHAGQ,1508
+pybiolib-1.1.2119.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2119.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2119.dist-info/RECORD,,