pybiolib 1.2.1180__py3-none-any.whl → 1.2.1228__py3-none-any.whl

biolib/_internal/push_application.py

@@ -1,4 +1,4 @@
-import copy
+import json
 import os
 import re
 import sys
@@ -239,15 +239,24 @@ def push_application(
     app_data_path: Optional[Path] = None
     try:
         with open(config_yml_path) as config_yml_file:
-            config = copy.deepcopy(yaml.safe_load(config_yml_file.read()))
-
-        app_data = config.get('app_data') or config.get('assets')
-        if app_data:
-            if config.get('app_data') and config.get('assets'):
+            try:
+                config = json.loads(json.dumps(yaml.safe_load(config_yml_file.read())))
+            except (TypeError, ValueError) as e:
                 raise BioLibError(
-                    'In .biolib/config.yml you cannot specify both "app_data" and "assets" fields. Please use only one.'
-                )
+                    f'The .biolib/config.yml file contains data types that are not supported '
+                    f'(must be JSON-serializable). Please ensure only standard JSON types '
+                    f'(str, int, float, bool, list, dict, null) are used. Original error: {e}'
+                ) from e
+
+        if 'assets' in config and 'app_data' not in config:
+            config['app_data'] = config.pop('assets')
+        elif 'assets' in config and 'app_data' in config:
+            raise BioLibError(
+                'In .biolib/config.yml you cannot specify both "app_data" and "assets" fields. Please use only one.'
+            )
 
+        app_data = config.get('app_data')
+        if app_data:
             field_name = 'app_data' if 'app_data' in config else 'assets'
             if not isinstance(app_data, str):
                 raise BioLibError(

biolib/experiments/experiment.py

@@ -1,5 +1,6 @@
 import time
 from collections import OrderedDict
+from pathlib import Path
 
 from biolib import api
 from biolib._internal.types.experiment import DeprecatedExperimentDict, ExperimentDict
@@ -8,6 +9,7 @@ from biolib._internal.utils import open_browser_window_from_notebook
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_errors import BioLibError
 from biolib.jobs.job import Job
+from biolib.jobs.job_result import PathFilter
 from biolib.jobs.types import JobsPaginatedResponse
 from biolib.tables import BioLibTable
 from biolib.typing_utils import Dict, List, Optional, Union
@@ -223,6 +225,80 @@ class Experiment:
         """
         return self.get_jobs(status=status)
 
+    def save_completed_results(
+        self,
+        output_dir: Optional[str] = None,
+        path_filter: Optional[PathFilter] = None,
+        skip_file_if_exists: bool = False,
+        overwrite: bool = False,
+    ) -> None:
+        r"""Save all completed results in this experiment to local folders.
+
+        Creates a folder structure with the experiment name as the root directory,
+        containing a subfolder for each completed result. Only results with
+        'completed' status will be saved.
+
+        Args:
+            output_dir (str, optional): Base directory where the experiment folder
+                will be created. If None, uses the current working directory.
+            path_filter (PathFilter, optional): Filter to select which files in the results to save.
+                Can be a glob pattern string or a callable function.
+            skip_file_if_exists (bool, optional): Whether to skip files that already exist
+                locally instead of raising an error. Defaults to False.
+            overwrite (bool, optional): Whether to overwrite existing files.
+                Defaults to False.
+
+        Example::
+
+            >>> # Save all completed results to current directory
+            >>> experiment.save_completed_results()
+            >>> # This creates: ./experiment_name/result_1/, ./experiment_name/result_2/, etc.
+
+            >>> # Save to specific directory
+            >>> experiment.save_completed_results(output_dir="/path/to/save")
+            >>> # This creates: /path/to/save/experiment_name/result_1/, etc.
+        """
+        base_dir = Path(output_dir) if output_dir else Path.cwd()
+
+        if base_dir == Path('/'):
+            raise BioLibError("Cannot save experiment results to root directory '/'")
+
+        experiment_folder = base_dir / self.name
+        experiment_folder.mkdir(parents=True, exist_ok=True)
+
+        completed_results: List[Job] = []
+        failed_results = False
+        print('Getting experiment status...')
+        for result in self.get_results():
+            if result.get_status() == 'completed':
+                completed_results.append(result)
+            elif result.get_status() != 'in_progress':
+                failed_results = True
+
+        if failed_results:
+            print(
+                'WARNING: Found failed or cancelled results in the experiment. '
+                'Please verify you have all your results, and consider removing the failed ones.'
+            )
+        if not completed_results:
+            print(f"No completed results found in experiment '{self.name}'")
+            return
+
+        print(f"Saving {len(completed_results)} completed results from experiment '{self.name}' to {experiment_folder}")
+
+        for result in completed_results:
+            result_name = result.get_name()
+            result_folder = experiment_folder / result_name
+
+            result_folder.mkdir(parents=True, exist_ok=True)
+
+            result.save_files(
+                output_dir=str(result_folder),
+                path_filter=path_filter,
+                skip_file_if_exists=skip_file_if_exists,
+                overwrite=overwrite,
+            )
+
     def rename(self, destination: str) -> None:
         api.client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
         self._refetch()

biolib/jobs/job.py

@@ -256,7 +256,7 @@ class Result:
         self,
         output_dir: str,
         path_filter: Optional[PathFilter] = None,
-        skip_file_if_exists: Optional[bool] = None,
+        skip_file_if_exists: bool = False,
         overwrite: bool = False,
     ) -> None:
         self.result.save_files(

biolib/jobs/job_result.py

@@ -38,7 +38,7 @@ class JobResult:
         self,
         output_dir: str,
         path_filter: Optional[PathFilter] = None,
-        skip_file_if_exists: Optional[bool] = None,
+        skip_file_if_exists: bool = False,
         overwrite: bool = False,
     ) -> None:
         module_output = self._get_module_output()

{pybiolib-1.2.1180.dist-info → pybiolib-1.2.1228.dist-info}/METADATA

@@ -1,8 +1,9 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1180
+Version: 1.2.1228
 Summary: BioLib Python Client
 License: MIT
+License-File: LICENSE
 Keywords: biolib
 Author: biolib
 Author-email: hello@biolib.com
@@ -17,6 +18,7 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Provides-Extra: compute-node
 Requires-Dist: appdirs (>=1.4.3)
 Requires-Dist: click (>=8.0.0)

{pybiolib-1.2.1180.dist-info → pybiolib-1.2.1228.dist-info}/RECORD

@@ -16,7 +16,7 @@ biolib/_internal/lfs/__init__.py,sha256=gSWo_xg61UniYgD7yNYxeT4I9uaXBCBSi3_nmZjn
 biolib/_internal/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
 biolib/_internal/libs/__init__.py,sha256=Jdf4tNPqe_oIIf6zYml6TiqhL_02Vyqwge6IELrAFhw,98
 biolib/_internal/libs/fusepy/__init__.py,sha256=AWDzNFS-XV_5yKb0Qx7kggIhPzq1nj_BZS5y2Nso08k,41944
-biolib/_internal/push_application.py,sha256=rP835wYU6PpF8w149G7uNiKs-OauHbGbjQryGucmIt8,18684
+biolib/_internal/push_application.py,sha256=Ljv7cFeaWRlMdHwn93lhooD227_ZvG8oIRTWHdDdB2M,19177
 biolib/_internal/runtime.py,sha256=BiHl4klUHr36MCpqKaUso4idHeBZfPAahLYRQrabFqA,486
 biolib/_internal/string_utils.py,sha256=N7J7oGu6_yA_z0pOiKqxEh__lRdiDLh6kigeDkQEZ5g,265
 biolib/_internal/templates/__init__.py,sha256=NVbhLUMC8HITzkLvP88Qu7FHaL-SvQord-DX3gh1Ykk,24
@@ -139,10 +139,10 @@ 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=7uD9yQPhePYvP2HCJ27EeZ_h6psfIWFgqm1RHZxzobs,12483
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=gY1-d7FgVrcQO3YzOJ0mHS6j7z7rl5XzXEuk7dFi1gU,10460
+biolib/experiments/experiment.py,sha256=4g1xMYmfp5yzSOdwjf3pUUULF9QjqBJb4uQ25FHrFrk,13688
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=B9v-dq9li0v9gDfmyyZOnCk-kN0vYPYxoybHWQsCkPg,27403
-biolib/jobs/job_result.py,sha256=L__GA5dNSDFHoQpAG2xb-tNqp_p4fQl53bAmlcvAt6M,6074
+biolib/jobs/job.py,sha256=AsWSnhDHNMz5_7pSsAfUYZx-34zahTDXLzhstSvLFiI,27394
+biolib/jobs/job_result.py,sha256=3uE_oj567-yGLr4UEFAf9CsM5lcEcjK8XE8v-CJKz8Q,6065
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
@@ -157,8 +157,8 @@ 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-1.2.1180.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1180.dist-info/METADATA,sha256=uvyCdpVr94yTPMbWsufxJaRXVosq8oC_uF1pg4VyLTI,1571
-pybiolib-1.2.1180.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.1180.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1180.dist-info/RECORD,,
+pybiolib-1.2.1228.dist-info/METADATA,sha256=jD07Dls__RR6S-_Svx_bR-Ip4rVpbPtpLo2_lpIoycU,1644
+pybiolib-1.2.1228.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1228.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1228.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1228.dist-info/RECORD,,

{pybiolib-1.2.1180.dist-info → pybiolib-1.2.1228.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.1.3
+Generator: poetry-core 2.2.1
 Root-Is-Purelib: true
 Tag: py3-none-any