pybiolib 1.2.1310__py3-none-any.whl → 1.2.1337__py3-none-any.whl

biolib/_session/session.py

@@ -5,17 +5,19 @@ from biolib.app import BioLibApp
 
 
 class Session:
-    def __init__(self, _init_dict: ApiClientInitDict) -> None:
+    def __init__(self, _init_dict: ApiClientInitDict, _experiment: Optional[str] = None) -> None:
         self._api = ApiClient(_init_dict=_init_dict)
+        self._experiment = _experiment
 
     @staticmethod
-    def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None) -> 'Session':
+    def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None, experiment: Optional[str] = None) -> 'Session':
         return Session(
             _init_dict=ApiClientInitDict(
                 refresh_token=refresh_token,
                 base_url=base_url or utils.load_base_url_from_env(),
                 client_type=client_type,
-            )
+            ),
+            _experiment=experiment,
         )
 
     def load(self, uri: str, suppress_version_warning: bool = False) -> BioLibApp:
@@ -39,4 +41,4 @@ class Session:
             >>> app = biolib.load('https://biolib.com/biolib/myapp/')
             >>> result = app.cli('--help')
         """
-        return BioLibApp(uri=uri, _api_client=self._api, suppress_version_warning=suppress_version_warning)
+        return BioLibApp(uri=uri, _api_client=self._api, suppress_version_warning=suppress_version_warning, _experiment=self._experiment)

biolib/app/app.py

@@ -25,8 +25,15 @@ from biolib._internal.file_utils import path_to_renamed_path
 
 
 class BioLibApp:
-    def __init__(self, uri: str, _api_client: Optional[ApiClient] = None, suppress_version_warning: bool = False):
+    def __init__(
+        self,
+        uri: str,
+        _api_client: Optional[ApiClient] = None,
+        suppress_version_warning: bool = False,
+        _experiment: Optional[str] = None,
+    ):
         self._api_client: Optional[ApiClient] = _api_client
+        self._experiment = _experiment
 
         app_response = BiolibAppApi.get_by_uri(uri=uri, api_client=self._api_client)
         self._app: App = app_response['app']
@@ -85,7 +92,12 @@ class BioLibApp:
             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_to_use = experiment if experiment is not None else self._experiment
+            experiment_instance: Optional[Experiment]
+            if experiment_to_use:
+                experiment_instance = Experiment(experiment_to_use)
+            else:
+                experiment_instance = Experiment.get_experiment_in_context()
             experiment_id = experiment_instance.uuid if experiment_instance else None
 
         module_input_serialized = self._get_serialized_module_input(args, stdin, files)

biolib/jobs/job.py

@@ -498,11 +498,17 @@ class Result:
             stdout_and_stderr_package = base64.b64decode(stdout_and_stderr_package_b64)
             stdout_and_stderr = StdoutAndStderr(stdout_and_stderr_package).deserialize()
 
-            sys.stdout.buffer.write(stdout_and_stderr)
-            if not IS_RUNNING_IN_NOTEBOOK:  # for some reason flushing in jupyter notebooks breaks \r handling
+            if IS_RUNNING_IN_NOTEBOOK:
+                sys.stdout.write(stdout_and_stderr.decode(encoding='utf-8', errors='replace'))
+            else:
+                sys.stdout.buffer.write(stdout_and_stderr)
+                # Note: we avoid flush() in notebook as that breaks \r handling
                 sys.stdout.buffer.flush()
         # flush after having processed all packages
-        sys.stdout.buffer.flush()
+        if IS_RUNNING_IN_NOTEBOOK:
+            sys.stdout.flush()
+        else:
+            sys.stdout.buffer.flush()
 
     def show(self) -> None:
         self._refetch_job_dict()
@@ -522,11 +528,19 @@ class Result:
             logger.info(f'--- The result {self.id} has already completed (no streaming will take place) ---')
             logger.info('--- The stdout log is printed below: ---')
             sys.stdout.flush()
-            sys.stdout.buffer.write(self.get_stdout())
-            sys.stdout.buffer.flush()
+            if IS_RUNNING_IN_NOTEBOOK:
+                sys.stdout.write(self.get_stdout().decode(encoding='utf-8', errors='replace'))
+                sys.stdout.flush()
+            else:
+                sys.stdout.buffer.write(self.get_stdout())
+                sys.stdout.buffer.flush()
             logger.info('--- The stderr log is printed below: ---')
-            sys.stderr.buffer.write(self.get_stderr())
-            sys.stderr.buffer.flush()
+            if IS_RUNNING_IN_NOTEBOOK:
+                sys.stderr.write(self.get_stderr().decode(encoding='utf-8', errors='replace'))
+                sys.stderr.flush()
+            else:
+                sys.stderr.buffer.write(self.get_stderr())
+                sys.stderr.buffer.flush()
             logger.info(f'--- The job {self.id} has already completed. Its output was printed above. ---')
             return
 

biolib/sdk/__init__.py

@@ -12,8 +12,18 @@ from biolib.app import BioLibApp as _BioLibApp
 Runtime = _Runtime
 
 
-def get_session(refresh_token: str, base_url: Optional[str] = None, client_type: Optional[str] = None) -> _Session:
-    return _Session.get_session(refresh_token=refresh_token, base_url=base_url, client_type=client_type)
+def get_session(
+    refresh_token: str,
+    base_url: Optional[str] = None,
+    client_type: Optional[str] = None,
+    experiment: Optional[str] = None,
+) -> _Session:
+    return _Session.get_session(
+        refresh_token=refresh_token,
+        base_url=base_url,
+        client_type=client_type,
+        experiment=experiment,
+    )
 
 
 def push_app_version(uri: str, path: str) -> _BioLibApp:

{pybiolib-1.2.1310.dist-info → pybiolib-1.2.1337.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1310
+Version: 1.2.1337
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1310.dist-info → pybiolib-1.2.1337.dist-info}/RECORD

@@ -63,11 +63,11 @@ biolib/_internal/utils/__init__.py,sha256=xp1I-lVnu5owV1CW53jiPEZLKmqqHiPUDfauYD
 biolib/_internal/utils/job_url.py,sha256=YpwqCP56BD15M8p2tuSY_Z3O9vWAkG2rJbQu2Z5zqq0,1265
 biolib/_internal/utils/multinode.py,sha256=N7kR49xD1PdkMVlxxzRiSYHfgi9MG-kLCwemcY1rojg,8323
 biolib/_runtime/runtime.py,sha256=9q6Wuo8SBcJIezyScAgq2MDfpT0Pg8lcfbBFmeCWiUE,5974
-biolib/_session/session.py,sha256=US1Y1jfFIAm86-Lq3C7nCXpZXUJXXBVBkND9djMNYxI,1649
+biolib/_session/session.py,sha256=Ymi9OQW_u_CfYA3JlBakPwRhNaKlb20P2G8SmtJhnzA,1824
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=2GpKE7QrPgyPdgJgrV7XnZByIJf1n26UCy3aoaHBs1M,7881
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
-biolib/app/app.py,sha256=Jc2PwNsZDKca9NxvasI_yrnb0q_S9PrJ94lva-y2Zpc,11882
+biolib/app/app.py,sha256=FjiqT7jCH0pSzKpG_v2Z9ysdUaPhhdPmW5gC-IbnAl0,12230
 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=IONzXeFCHl4wuct6fqOC_7NiTv_zFy6ys0hsAtvLzTA,7578
@@ -142,12 +142,12 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=4g1xMYmfp5yzSOdwjf3pUUULF9QjqBJb4uQ25FHrFrk,13688
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=-yF9JnHH0CEJIqp3qV9Dsv8AwBi_H1alqcKwhh3AORI,29075
+biolib/jobs/job.py,sha256=X7F_jCwAwtPcI1qu-oLamZNzt1IVSIeOPWlax1ztfAM,29674
 biolib/jobs/job_result.py,sha256=_xqQu9z9BqPQrU6tjqKPuKlQDt5W0Zw5xiQvzEBkDyE,5266
 biolib/jobs/types.py,sha256=rFs6bQWsNI-nb1Hu9QzOW2zFZ8bOVt7ax4UpGVASxVA,1034
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
-biolib/sdk/__init__.py,sha256=Z1S5BgpvM87S2o1libtqkYN1CfYUhn_d4ChEJjwdFKM,2356
+biolib/sdk/__init__.py,sha256=TATbgncVHIzxo_U1zpD1YrdngIIvJkT3S0o2qe3dcg4,2471
 biolib/tables.py,sha256=MmruV-nJLc3HbLVJBAiDuDCgS2-4oaUkpoCLLUNYbxQ,1173
 biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
@@ -158,8 +158,8 @@ 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=rImaghQGuIqTVWks6b9P2yKuN34uePUYPUFW_Wyoa4A,6737
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1310.dist-info/METADATA,sha256=LNNxEg6rvoh17x8AIKHxVEHRW5CsI2k_Ybi3VrT_o6o,1644
-pybiolib-1.2.1310.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1310.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1310.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1310.dist-info/RECORD,,
+pybiolib-1.2.1337.dist-info/METADATA,sha256=rH78s_I8v02Htgz31ys8-Ap2-E8JBXQD3rfcF86_KsA,1644
+pybiolib-1.2.1337.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1337.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1337.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1337.dist-info/RECORD,,