pybiolib 1.2.1642__py3-none-any.whl → 1.2.1727__py3-none-any.whl

biolib/cli/init.py

@@ -10,18 +10,56 @@ from biolib import (
 )
 from biolib._internal.add_copilot_prompts import add_copilot_prompts
 from biolib._internal.add_gui_files import add_gui_files
-from biolib._internal.http_client import HttpError
+from biolib._internal.http_client import HttpClient, HttpError
 from biolib._internal.string_utils import normalize_for_docker_tag
 from biolib._internal.templates import templates
 from biolib.api import client as api_client
 from biolib.biolib_api_client.api_client import BiolibApiClient
 from biolib.biolib_api_client.biolib_app_api import BiolibAppApi
+from biolib.biolib_logging import logger_no_user_data
+from biolib.typing_utils import Optional
 from biolib.user.sign_in import sign_in
 from biolib.utils import BIOLIB_PACKAGE_VERSION
 
 
+def _get_latest_pypi_version() -> Optional[str]:
+    try:
+        response = HttpClient.request(
+            url='https://pypi.org/pypi/pybiolib/json',
+            timeout_in_seconds=5,
+            retries=1,
+        )
+        data = response.json()
+        version = data.get('info', {}).get('version')
+        if isinstance(version, str):
+            return version
+        return None
+    except Exception as error:
+        logger_no_user_data.debug(f'Failed to fetch latest version from PyPI: {error}')
+        return None
+
+
+def _is_current_version_outdated(current: str, latest: str) -> bool:
+    try:
+        current_parts = [int(x) for x in current.split('.')]
+        latest_parts = [int(x) for x in latest.split('.')]
+        return current_parts < latest_parts
+    except (ValueError, AttributeError):
+        return False
+
+
 @click.command(help='Initialize a BioLib project', hidden=True)
 def init() -> None:
+    latest_version = _get_latest_pypi_version()
+    if latest_version and _is_current_version_outdated(BIOLIB_PACKAGE_VERSION, latest_version):
+        print(f'A newer version of pybiolib is available: {latest_version} (current: {BIOLIB_PACKAGE_VERSION})')
+        print('To upgrade, run: pip install --upgrade pybiolib')
+        print()
+        continue_input = input('Do you want to continue with the current version? [y/N]: ')
+        if continue_input.lower() not in ['y', 'yes']:
+            print('Please upgrade pybiolib and run `biolib init` again.')
+            return
+
     cwd = os.getcwd()
 
     app_uri = input('What URI do you want to create the application under? (leave blank to skip): ')

biolib/cli/run.py

@@ -13,19 +13,23 @@ from biolib.typing_utils import Optional, Tuple
     help='Run an application on BioLib.',
 )
 @click.option('--experiment', type=str, required=False, help='Experiment name or URI to add the run to.')
-@click.option('--local', is_flag=True, required=False, help='Run the application locally.')
+@click.option('--local', is_flag=True, required=False, hidden=True)
 @click.option('--non-blocking', is_flag=True, required=False, help='Run the application non blocking.')
 @click.argument('uri', required=True)
 @click.argument('args', nargs=-1, type=click.UNPROCESSED)
 def run(experiment: Optional[str], local: bool, non_blocking: bool, uri: str, args: Tuple[str]) -> None:
+    if local:
+        print('Error: Running applications locally with --local is no longer supported.', file=sys.stderr)
+        sys.exit(1)
+
     if experiment:
         with Experiment(uri=experiment):
-            _run(local=local, non_blocking=non_blocking, uri=uri, args=args)
+            _run(non_blocking=non_blocking, uri=uri, args=args)
     else:
-        _run(local=local, non_blocking=non_blocking, uri=uri, args=args)
+        _run(non_blocking=non_blocking, uri=uri, args=args)
 
 
-def _run(local: bool, non_blocking: bool, uri: str, args: Tuple[str]) -> None:
+def _run(non_blocking: bool, uri: str, args: Tuple[str]) -> None:
     try:
         app = BioLibApp(uri=uri)
     except biolib_errors.BioLibError as error:
@@ -43,7 +47,6 @@ def _run(local: bool, non_blocking: bool, uri: str, args: Tuple[str]) -> None:
         args=list(args),
         stdin=_get_stdin(),
         files=None,
-        machine=('local' if local else ''),
         blocking=blocking,
     )
 

biolib/compute_node/job_worker/job_worker.py

@@ -361,7 +361,7 @@ class JobWorker:
                 if remote_host_mappings:
                     remote_host_proxy = RemoteHostProxy(
                         remote_host_mappings=remote_host_mappings,
-                        job_id=job_id,
+                        job=job,
                         app_caller_network=None,
                     )
                     remote_host_proxy.start()
@@ -384,7 +384,7 @@ class JobWorker:
             try:
                 app_caller_proxy = RemoteHostProxy(
                     remote_host_mappings=[],
-                    job_id=job_id,
+                    job=job,
                     app_caller_network=self._internal_network,
                 )
                 app_caller_proxy.start()

biolib/compute_node/remote_host_proxy.py

@@ -1,4 +1,3 @@
-import base64
 import io
 import ipaddress
 import tarfile
@@ -10,7 +9,9 @@ from docker.models.networks import Network
 from docker.types import EndpointConfig
 
 from biolib import utils
+from biolib._internal.utils import base64_encode_string
 from biolib.biolib_api_client import BiolibApiClient, RemoteHost
+from biolib.biolib_api_client.job_types import CreatedJobDict
 from biolib.biolib_docker_client import BiolibDockerClient
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger_no_user_data
@@ -50,22 +51,26 @@ class RemoteHostProxy:
     def __init__(
         self,
         remote_host_mappings: List[RemoteHostMapping],
-        job_id: str,
+        job: CreatedJobDict,
         app_caller_network: Optional[Network] = None,
     ):
         self._remote_host_mappings = remote_host_mappings
         self._app_caller_network = app_caller_network
         self.is_app_caller_proxy = app_caller_network is not None
 
-        if not job_id:
-            raise Exception('RemoteHostProxy missing argument "job_id"')
+        if not job:
+            raise Exception('RemoteHostProxy missing argument "job"')
 
+        self._job = job
         suffix = '-AppCallerProxy' if app_caller_network else ''
-        self._name = f'biolib-remote-host-proxy-{job_id}{suffix}'
-        self._job_uuid = job_id
+        self._name = f'biolib-remote-host-proxy-{self._job_uuid}{suffix}'
         self._container: Optional[Container] = None
         self._docker = BiolibDockerClient().get_docker_client()
 
+    @property
+    def _job_uuid(self) -> str:
+        return self._job['uuid']
+
     def get_hostname_to_ip_mapping(self) -> Dict[str, str]:
         return {mapping.hostname: mapping.static_ip for mapping in self._remote_host_mappings}
 
@@ -174,8 +179,12 @@ class RemoteHostProxy:
             access_token = BiolibApiClient.get().access_token
             bearer_token = f'Bearer {access_token}' if access_token else ''
 
-            biolib_index_basic_auth = f'compute_node|admin:{compute_node_auth_token},{self._job_uuid}'
-            biolib_index_basic_auth_base64 = base64.b64encode(biolib_index_basic_auth.encode('utf-8')).decode('utf-8')
+            user_uuid = self._job['user_id']
+            if user_uuid:
+                biolib_index_basic_auth = f'biolib_user|{user_uuid.replace("-", "_")}:cloud-{compute_node_auth_token}'
+                biolib_index_auth_header_value = f'Basic {base64_encode_string(biolib_index_basic_auth)}'
+            else:
+                biolib_index_auth_header_value = ''
 
             nginx_config = f"""
 events {{
@@ -343,7 +352,7 @@ http {{
 
         location /api/proxy/index/ {{
             proxy_pass               https://$upstream_hostname$request_uri;
-            proxy_set_header         authorization "Basic {biolib_index_basic_auth_base64}";
+            proxy_set_header         authorization "{biolib_index_auth_header_value}";
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;
         }}
@@ -385,13 +394,6 @@ http {{
             proxy_ssl_server_name    on;
         }}
 
-        location /proxy/index/ {{
-            proxy_pass               https://$upstream_hostname$request_uri;
-            proxy_set_header         authorization "Basic {biolib_index_basic_auth_base64}";
-            proxy_set_header         cookie "";
-            proxy_ssl_server_name    on;
-        }}
-
         location / {{
             return 404 "Not found";
         }}

biolib/experiments/experiment.py

@@ -308,6 +308,19 @@ class Experiment:
             )
 
     def rename(self, destination: str) -> None:
+        r"""Rename this experiment to a new URI.
+
+        Args:
+            destination (str): The new URI for the experiment
+                (e.g., 'username/new-experiment-name').
+
+        Example::
+
+            >>> experiment = biolib.get_experiment(uri='username/my-experiment')
+            >>> experiment.rename('username/my-renamed-experiment')
+            >>> print(experiment.uri)
+            'username/my-renamed-experiment'
+        """
         self._api_client.patch(f'/resources/{self.uuid}/', data={'uri': destination})
         self._refetch()
 

biolib/utils/multipart_uploader.py

@@ -10,7 +10,7 @@ from biolib._internal.http_client import HttpClient
 from biolib.biolib_api_client import BiolibApiClient
 from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.typing_utils import TypedDict, List, Iterator, Tuple, Optional, Dict
+from biolib.typing_utils import Callable, Dict, Iterator, List, Optional, Tuple, TypedDict
 
 
 def get_chunk_iterator_from_bytes(byte_buffer: bytes, chunk_size_in_bytes: int = 50_000_000) -> Iterator[bytes]:
@@ -45,19 +45,20 @@ _UploadChunkReturnType = Tuple[_PartMetadata, int]
 
 
 class MultiPartUploader:
-
     def __init__(
-            self,
-            complete_upload_request: RequestOptions,
-            get_presigned_upload_url_request: RequestOptions,
-            start_multipart_upload_request: Optional[RequestOptions] = None,
-            use_process_pool: Optional[bool] = None,
+        self,
+        complete_upload_request: RequestOptions,
+        get_presigned_upload_url_request: RequestOptions,
+        start_multipart_upload_request: Optional[RequestOptions] = None,
+        use_process_pool: Optional[bool] = None,
+        on_progress: Optional[Callable[[int, int], None]] = None,
     ):
         self._complete_upload_request = complete_upload_request
         self._get_presigned_upload_url_request = get_presigned_upload_url_request
         self._start_multipart_upload_request = start_multipart_upload_request
         self._bytes_uploaded: int = 0
         self._use_process_pool = use_process_pool
+        self._on_progress = on_progress
 
     def upload(self, payload_iterator: Iterator[bytes], payload_size_in_bytes: int) -> None:
         parts: List[_PartMetadata] = []
@@ -85,21 +86,22 @@ class MultiPartUploader:
                 self._update_progress_bar_and_parts(
                     upload_chunk_response=upload_chunk_response,
                     parts=parts,
-                    payload_size_in_bytes=payload_size_in_bytes
+                    payload_size_in_bytes=payload_size_in_bytes,
                 )
         else:
             # use 16 cores, unless less is available
             pool_size = min(16, multiprocessing.cpu_count() - 1)
-            process_pool = multiprocessing.Pool(pool_size) if self._use_process_pool else \
-                multiprocessing.pool.ThreadPool(pool_size)
+            process_pool = (
+                multiprocessing.Pool(pool_size)
+                if self._use_process_pool
+                else multiprocessing.pool.ThreadPool(pool_size)
+            )
 
             try:
                 response: _UploadChunkReturnType
                 for response in process_pool.imap(self._upload_chunk, iterator_with_index):
                     self._update_progress_bar_and_parts(
-                        upload_chunk_response=response,
-                        parts=parts,
-                        payload_size_in_bytes=payload_size_in_bytes
+                        upload_chunk_response=response, parts=parts, payload_size_in_bytes=payload_size_in_bytes
                     )
             finally:
                 logger_no_user_data.debug('Multipart upload closing process pool...')
@@ -148,8 +150,9 @@ class MultiPartUploader:
                     if app_caller_proxy_job_storage_base_url:
                         # Done to hit App Caller Proxy when uploading result from inside an app
                         parsed_url = urlparse(presigned_upload_url)
-                        presigned_upload_url = \
+                        presigned_upload_url = (
                             f'{app_caller_proxy_job_storage_base_url}{parsed_url.path}?{parsed_url.query}'
+                        )
 
                     put_chunk_response = HttpClient.request(
                         url=presigned_upload_url,
@@ -169,10 +172,10 @@ class MultiPartUploader:
         raise BioLibError(f'Max retries hit, when uploading part {part_number}. Exiting...')
 
     def _update_progress_bar_and_parts(
-            self,
-            upload_chunk_response: _UploadChunkReturnType,
-            parts: List[_PartMetadata],
-            payload_size_in_bytes: int,
+        self,
+        upload_chunk_response: _UploadChunkReturnType,
+        parts: List[_PartMetadata],
+        payload_size_in_bytes: int,
     ) -> None:
         part_metadata, chunk_byte_length = upload_chunk_response
         part_number = part_metadata['PartNumber']
@@ -180,6 +183,9 @@ class MultiPartUploader:
         parts.append(part_metadata)
         self._bytes_uploaded += chunk_byte_length
 
+        if self._on_progress is not None:
+            self._on_progress(self._bytes_uploaded, payload_size_in_bytes)
+
         approx_progress_percent = min(self._bytes_uploaded / (payload_size_in_bytes + 1) * 100, 100)
         approx_rounded_progress = round(approx_progress_percent, 2)
         logger_no_user_data.debug(

pybiolib-1.2.1727.dist-info/METADATA

@@ -0,0 +1,41 @@
+Metadata-Version: 2.4
+Name: pybiolib
+Version: 1.2.1727
+Summary: BioLib Python Client
+Project-URL: Homepage, https://github.com/biolib
+Author-email: biolib <hello@biolib.com>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: biolib
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.6.3
+Requires-Dist: appdirs>=1.4.3
+Requires-Dist: click>=8.0.0
+Requires-Dist: docker>=5.0.3
+Requires-Dist: importlib-metadata>=1.6.1
+Requires-Dist: pyyaml>=5.3.1
+Requires-Dist: rich>=12.4.4
+Requires-Dist: typing-extensions>=4.1.0; python_version < '3.11'
+Provides-Extra: compute-node
+Requires-Dist: flask>=2.0.1; extra == 'compute-node'
+Requires-Dist: gunicorn>=20.1.0; extra == 'compute-node'
+Description-Content-Type: text/markdown
+
+# PyBioLib
+
+PyBioLib is a Python package for running BioLib applications from Python scripts and the command line.
+
+### Python Example
+```python
+# pip3 install -U pybiolib
+import biolib
+samtools = biolib.load('samtools/samtools')
+print(samtools.cli(args='--help'))
+```
+
+### Command Line Example
+```bash
+pip3 install -U pybiolib
+biolib run samtools/samtools --help
+```

{pybiolib-1.2.1642.dist-info → pybiolib-1.2.1727.dist-info}/RECORD

@@ -1,30 +1,38 @@
 biolib/__init__.py,sha256=-pz1Ipyj1KmB709yYpl2Y-iKOWXpLxcFzL48G8rr9cU,12146
-biolib/_data_record/data_record.py,sha256=DI3_0KOELoZruOd176SJLZU32RhCqoSrjHtm852-K34,12520
+biolib/biolib_download_container.py,sha256=8TmBV8iv3bCvkNlHa1SSsc4zl0wX_eaxhfnW5rvFIh8,1779
+biolib/biolib_errors.py,sha256=eyQolC4oGi350BDEMOd-gAHYVqo2L2lYgv6c4ZdXPjQ,1184
+biolib/biolib_logging.py,sha256=Y3qALGNYaTHdXP2aPFNWfxN71pk2Z3syMG6XrYcRZT8,2863
+biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biolib/tables.py,sha256=MmruV-nJLc3HbLVJBAiDuDCgS2-4oaUkpoCLLUNYbxQ,1173
+biolib/typing_utils.py,sha256=TMw723SPq8zy1VYsdgbq_LPsGtCm3VgFhzz6srt71u0,146
+biolib/_data_record/data_record.py,sha256=2MDs2KR_zA7hUjTDxzmih_ph0Iv6WAlEh4WBMoAGSvI,15441
 biolib/_index/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/_index/index.py,sha256=CXRWk_piVbZ1HDWm_QimBBXBai1ADVT282fbgQHlZ7c,1560
+biolib/_index/index.py,sha256=u89cQ-FpLAEPSPE-QN1X1Cevo_HemTcLX49hS87r5Zk,1560
 biolib/_index/types.py,sha256=iVn4R175FZgqHS6QJXssYUBpBHlkggepRA5-_qvrfuE,124
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/add_copilot_prompts.py,sha256=wcIdrceFcfKSoEjvM4uNzhKZ0I1-MCFkfNO4duqtGHA,1861
 biolib/_internal/add_gui_files.py,sha256=MrtvkIpe70tVVJYBBsMbRhjsxf55hFzlzn-ea2oinTc,2218
+biolib/_internal/errors.py,sha256=AokI6Dvaa22B__LTfSZUVdDsm0ye7lgBFv_aD9O_kbs,163
+biolib/_internal/file_utils.py,sha256=62yDRC_3hLKh0_Pbny7-syVduVSnc3H1Rv_D6zbGnS4,4518
+biolib/_internal/http_client.py,sha256=9-3HG6LnLwJfrwjCeFj5XigHVH8Dzz6Dpr58IjQJHDo,6221
+biolib/_internal/push_application.py,sha256=_CMCJZNLcRQ_hWje5_HvD8Re4l55NyTjniMglv3kjaw,21128
+biolib/_internal/runtime.py,sha256=SnunTYa1-056cvb_Z-JwYyUaz5Zoem8jm4RjY3V8zGw,554
+biolib/_internal/string_utils.py,sha256=N7J7oGu6_yA_z0pOiKqxEh__lRdiDLh6kigeDkQEZ5g,265
+biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
 biolib/_internal/data_record/data_record.py,sha256=vJbjkYj6kyncaNApN94uTJvve1C1XkYWHbWuiMFfzoU,4604
-biolib/_internal/data_record/push_data.py,sha256=kjl1J00lt-EoRFVMDV8jztMcq5uCH_Hh0XSkwxYc0q0,2683
+biolib/_internal/data_record/push_data.py,sha256=WAvZYLQHTA36kX4uvVu1p0UgiDpf0zNFK3blmfxdZ4Y,4369
 biolib/_internal/data_record/remote_storage_endpoint.py,sha256=qooTo6fdC3-x-ko9ipF7_fkg7hE3Fq06MWx4lwnAgAU,1760
-biolib/_internal/errors.py,sha256=AokI6Dvaa22B__LTfSZUVdDsm0ye7lgBFv_aD9O_kbs,163
-biolib/_internal/file_utils.py,sha256=62yDRC_3hLKh0_Pbny7-syVduVSnc3H1Rv_D6zbGnS4,4518
 biolib/_internal/fuse_mount/__init__.py,sha256=B_tM6RM2dBw-vbpoHJC4X3tOAaN1H2RDvqYJOw3xFwg,55
 biolib/_internal/fuse_mount/experiment_fuse_mount.py,sha256=08aUdEq_bvqLBft_gSLjOClKDy5sBnMts1RfJf7AP_U,7012
-biolib/_internal/http_client.py,sha256=9-3HG6LnLwJfrwjCeFj5XigHVH8Dzz6Dpr58IjQJHDo,6221
 biolib/_internal/index/__init__.py,sha256=O1m6QYmqc3DLy7hqAeYDJeGNEegdK9L10omDuNlUGhQ,38
 biolib/_internal/index/index.py,sha256=zuA-Vplkqmv89PiLrPki43CxdCrjEUiCiFEGsAEtlbs,764
 biolib/_internal/lfs/__init__.py,sha256=gSWo_xg61UniYgD7yNYxeT4I9uaXBCBSi3_nmZjnPpE,35
 biolib/_internal/lfs/cache.py,sha256=XMnUuB6vwyv8H_Ha6r6n-QruHUY_YrBj-l2xcXj57QI,2362
 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=_CMCJZNLcRQ_hWje5_HvD8Re4l55NyTjniMglv3kjaw,21128
-biolib/_internal/runtime.py,sha256=SnunTYa1-056cvb_Z-JwYyUaz5Zoem8jm4RjY3V8zGw,554
-biolib/_internal/string_utils.py,sha256=N7J7oGu6_yA_z0pOiKqxEh__lRdiDLh6kigeDkQEZ5g,265
 biolib/_internal/templates/__init__.py,sha256=NVbhLUMC8HITzkLvP88Qu7FHaL-SvQord-DX3gh1Ykk,24
+biolib/_internal/templates/templates.py,sha256=ni0euP0KD5NHkxJPIt__i2WvXxYIcC8qugQEoT9oIJQ,308
 biolib/_internal/templates/copilot_template/.github/instructions/general-app-knowledge.instructions.md,sha256=-j8v0GRtDhHoqP2wcGUykiwU7HQ0DmkCNxw_01oKMdY,546
 biolib/_internal/templates/copilot_template/.github/instructions/style-general.instructions.md,sha256=tl2Ve1ZPlPBrH6CSrjIkiMA8xnM2tQIJs1cerKCyAkU,761
 biolib/_internal/templates/copilot_template/.github/instructions/style-python.instructions.md,sha256=xfypuPqMsz5ejobDoVI0HjmNqksl16aFuIol1nAhpHg,1034
@@ -36,7 +44,6 @@ biolib/_internal/templates/gui_template/.yarnrc.yml,sha256=Rz5t74b8A2OBIODAHQyLu
 biolib/_internal/templates/gui_template/App.tsx,sha256=VfaJO_mxbheRrfO1dU28G9Q4pGsGzeJpPREqtAT4fGE,1692
 biolib/_internal/templates/gui_template/Dockerfile,sha256=nGZQiL7coQBUnH1E2abK2PJ4XRjVS1QXn6HDX9UGpcE,479
 biolib/_internal/templates/gui_template/biolib-sdk.ts,sha256=zRN2h4ws7ZuidxYKaRPaurfTxNJN-hX0MdG6POvdxU0,1195
-biolib/_internal/templates/gui_template/dev-data/output.json,sha256=wKcJQtN7NGaCJkmEWyRjEbBtTLMHB6pOkqTgWsKmOh8,162
 biolib/_internal/templates/gui_template/index.css,sha256=WYds1xQY2of84ebHhRW9ummbw0Bg9N-EyfmBzJKigck,70
 biolib/_internal/templates/gui_template/index.html,sha256=EM5xzJ9CsJalgzL-jLNkAoP4tgosw0WYExcH5W6DOs8,403
 biolib/_internal/templates/gui_template/index.tsx,sha256=YrdrpcckwLo0kYIA-2egtzlo0OMWigGxnt7mNN4qmlU,234
@@ -44,22 +51,22 @@ biolib/_internal/templates/gui_template/package.json,sha256=4E8pDdnrYYjmKAL8NYFE
 biolib/_internal/templates/gui_template/tsconfig.json,sha256=T3DJIzeLQ2BL8HLfPHI-IvHtJhnMXdHOoRjkmQlJQAw,541
 biolib/_internal/templates/gui_template/vite-plugin-dev-data.ts,sha256=jLFSl7_DU9W3ScM6fm0aFSCzDhAtzhI9G6zr1exze84,1397
 biolib/_internal/templates/gui_template/vite.config.mts,sha256=5RjRfJHgqLOr-LRydBUnDPr5GrHQuRsviTMC60hvKxU,348
-biolib/_internal/templates/init_template/.biolib/config.yml,sha256=gxMVd1wjbsDvMv4byc8fKEdJFby4qgi6v38mO5qmhoY,453
-biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=3Os7FCptYHKK4ERI5_olM7s7V8KNIsVTBywfXI069sw,645
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 biolib/_internal/templates/init_template/.gitignore,sha256=dR_jhtT0boUspgk3S5PPUwuO0o8gKGIbdwu8IH638CY,20
 biolib/_internal/templates/init_template/Dockerfile,sha256=Cx3ktDxcpgAWAacIewm7mcI7lNEsmgAETvFtN7NA3Ms,199
 biolib/_internal/templates/init_template/requirements.txt,sha256=2GnBHsKg4tX5F06Z4YeLuId6jQO3-HGTITsaVBTDG0Y,42
 biolib/_internal/templates/init_template/run.py,sha256=oat-Vzcz4XZilrTtgy8CzfltBAa5v6iduGof4Tuulhg,402
 biolib/_internal/templates/init_template/run.sh,sha256=ncvInHCn_PgjXmvaa5oBU0vC3dgFJQ6k7fUJKJzpOh4,69
-biolib/_internal/templates/templates.py,sha256=ni0euP0KD5NHkxJPIt__i2WvXxYIcC8qugQEoT9oIJQ,308
-biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
-biolib/_internal/utils/__init__.py,sha256=xp1I-lVnu5owV1CW53jiPEZLKmqqHiPUDfauYDfJ7iQ,1540
+biolib/_internal/templates/init_template/.biolib/config.yml,sha256=gxMVd1wjbsDvMv4byc8fKEdJFby4qgi6v38mO5qmhoY,453
+biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=3Os7FCptYHKK4ERI5_olM7s7V8KNIsVTBywfXI069sw,645
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 biolib/_internal/utils/job_url.py,sha256=YpwqCP56BD15M8p2tuSY_Z3O9vWAkG2rJbQu2Z5zqq0,1265
 biolib/_internal/utils/multinode.py,sha256=N7kR49xD1PdkMVlxxzRiSYHfgi9MG-kLCwemcY1rojg,8323
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 biolib/_session/session.py,sha256=nP6ETTMUQygElrRIFq8zr9QqjHwmKMsvf6BpiRLUUW4,1821
 biolib/_shared/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biolib/_shared/types/account.py,sha256=_MY59S_8r3OqT630HzEoRnS6VnbbLm296wP2WrdpdjM,190
 biolib/_shared/types/account_member.py,sha256=aCcel1McoAsH83Mv1mqawK2Q-yt4OI0xrgPiKjg4Tqg,178
 biolib/_shared/types/app.py,sha256=Mz2QGD_jESX-K9JYnLWPo4YA__Q_1FQQTk9pvidCohU,118
@@ -67,23 +74,22 @@ biolib/_shared/types/data_record.py,sha256=9r_vdhVs60YTnzU4XQFXfDrfS2P2MqD3BH2xa
 biolib/_shared/types/experiment.py,sha256=7WERhHnkbO3qrPWZyJmu-KrKOGRXaX5xdLBUNHh17KE,714
 biolib/_shared/types/file_node.py,sha256=T6BIqo662f3nwMBRqtBHYsg6YuuUaKpiokHcVjv9_ME,283
 biolib/_shared/types/push.py,sha256=qSXCjdzOmHG7_QiwXaNSrVkESTMxnIKPvEut-9Mqt-g,108
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 biolib/_shared/types/resource_deploy_key.py,sha256=vwPKRHxjkrkEptBiJUovE4P0N4EuZr43_U0u_JP8Pag,204
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 biolib/_shared/types/result.py,sha256=MesSTBXCkaw8HydXgHf1OKGVLzsxhZ1KV5z4w-VI-0M,231
 biolib/_shared/types/typing.py,sha256=qrsk8hHcGEbDpU1QQFzHAKnhQxkMe7uJ6pxHeAnfv1Y,414
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 biolib/_shared/utils/__init__.py,sha256=3PaCkPREN3zgWszO65lHDdqwo958rD9OzCKGmUEP-Fc,216
 biolib/_shared/utils/resource_uri.py,sha256=-jZ9g8aenms0SInVrhvBHAgwy8MsaTNBLYFh4Dr1JOU,2909
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
-biolib/api/client.py,sha256=D42EV6E78BYzU6rBurGV2egLH3uO0C4R4dibsl6w6JM,7879
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 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
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 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
+biolib/biolib_api_client/api_client.py,sha256=JwH1_3rD0E_gs5x39TN_AajsC7o1wvQx3pAlGMzwANQ,6109
 biolib/biolib_api_client/app_types.py,sha256=P2MbwYZ0VsPUcbcX27lSvVlAYSbkz_IqWTcbxFyuu7I,2477
 biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36RSw,949
 biolib/biolib_api_client/biolib_app_api.py,sha256=slnJVuWtN_Et1PSnjN7mPmYWJvk0Rp-h0rvdrW1R9u8,6041
@@ -105,48 +111,45 @@ biolib/biolib_binary_format/system_exception.py,sha256=T3iL4_cSHAHim3RSDPS8Xyb1m
 biolib/biolib_binary_format/system_status_update.py,sha256=aOELuQ0k-GtpaZTUxYd0GFomP_OInmrK585y6fuQuKE,1191
 biolib/biolib_binary_format/utils.py,sha256=jq31QEShs7TSrSKZBr8jif-bJAwVzQrqVxmymL6crpU,5453
 biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghKm0wqQiljdo,1481
-biolib/biolib_download_container.py,sha256=8TmBV8iv3bCvkNlHa1SSsc4zl0wX_eaxhfnW5rvFIh8,1779
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 biolib/cli/__init__.py,sha256=A_AATNYLH7exu332OYds1PrqOAuK1sU5wDmYYY4tMvM,1352
 biolib/cli/auth.py,sha256=p9ZGY6ld2rnMbpsuRskvIQJNUHlSgYgcLTDsYGyUwyw,1407
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 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
 biolib/cli/index.py,sha256=UeE4lo4NYL7-3DGrJyv1OvbdKmTlKMwdArliHTmIzPY,1081
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 biolib/cli/lfs.py,sha256=mCwziiuzhsZW5UdpsVETDlVUvmO71gHKsV2D4wJ2qUY,4164
 biolib/cli/push.py,sha256=J8BswMYVeTacZBHbm4K4a2XbS_I8kvfgRZLoby2wi3I,1695
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 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
 biolib/cli/sdk.py,sha256=XisJwTft4QDB_99eGDlz-WBqqRwIqkVg7HyvxWtOG8w,471
 biolib/cli/start.py,sha256=BcjE4MRRLhBJULuSYQY0e7gMHudw7W-yFcz9klJ3xjo,2287
 biolib/compute_node/.gitignore,sha256=GZdZ4g7HftqfOfasFpBC5zV1YQAbht1a7EzcXD6f3zg,45
 biolib/compute_node/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 biolib/compute_node/cloud_utils/__init__.py,sha256=VZSScLqaz5tg_gpMvWgwkAu9Qf-vgW_QHRoDOaAmU44,67
 biolib/compute_node/cloud_utils/cloud_utils.py,sha256=_iaKelsmQLLwbDKVXZMXPFZayZPH9iHXc4NISFP9uzk,7462
 biolib/compute_node/job_worker/__init__.py,sha256=ipdPWaABKYrltxny15e2kK8PWdEE7VzXbkKK6wM_zDk,71
 biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSIiw4s90pNn83Netoo,4830
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
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 biolib/compute_node/job_worker/job_legacy_input_wait_timeout_thread.py,sha256=_cvEiZbOwfkv6fYmfrvdi_FVviIEYr_dSClQcOQaUWM,1198
 biolib/compute_node/job_worker/job_max_runtime_timer_thread.py,sha256=K_xgz7IhiIjpLlXRk8sqaMyLoApcidJkgu29sJX0gb8,1174
 biolib/compute_node/job_worker/job_storage.py,sha256=J6B5wkBo3cqmT1AV-qJnm2Lt9Qmcp3qn-1AabjO9m60,4686
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 biolib/compute_node/job_worker/large_file_system.py,sha256=Xe_LILVfTD9LXb-0HwLqGsp1fWiI-pU55BqgJ-6t8-0,10357
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/network_alloc.py,sha256=b2xNrqHaVRKCMcFyZepQAuNsBWCzHMDTPeacBdo029s,3586
 biolib/compute_node/job_worker/network_buffer.py,sha256=YIiYz_QZNK7O8SSFzLZf2i7drTk1ewd_gvjg9NgG5LQ,9051
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=Tho8GdYVS93Jb5cJjuN3O0qGQ0JIlxabiaGfTp1ksV0,8594
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
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 biolib/compute_node/webserver/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/webserver/compute_node_results_proxy.py,sha256=6gZ-jYZAuK0m4uiUkaSmP7n61ywPoQyCv3DzNOy-gQ0,7980
 biolib/compute_node/webserver/gunicorn_flask_application.py,sha256=jPfR_YvNBekLUXWo_vHFV-FIwlb8s8tacKmGHvh93qc,914
@@ -156,25 +159,22 @@ 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
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 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
 biolib/jobs/job.py,sha256=3rP__a_UJWdUzOngtmYekzTV1ttKugB1EyXP7SIN37A,31845
 biolib/jobs/job_result.py,sha256=pbCk2raBK9rbi2RlgQM7MmBqi9K52X4D9n8_1qXjLGU,7636
 biolib/jobs/types.py,sha256=rFs6bQWsNI-nb1Hu9QzOW2zFZ8bOVt7ax4UpGVASxVA,1034
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 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
 biolib/user/sign_in.py,sha256=e_JnykVxemq8eUBD5GmthjDV504CT1Dmn0EshrDCGB8,2085
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 biolib/utils/cache_state.py,sha256=GNFLTo2KcoP4ypDoVVCItmkIAuHtsa_41sSDaK5JFCo,3119
-biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
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 biolib/utils/seq_util.py,sha256=rImaghQGuIqTVWks6b9P2yKuN34uePUYPUFW_Wyoa4A,6737
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1642.dist-info/METADATA,sha256=wcifrjdK4MJ5EIZQYcDvUZogwhWZY0P0D8r0vG-0Acs,1644
-pybiolib-1.2.1642.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1642.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1642.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1642.dist-info/RECORD,,
+pybiolib-1.2.1727.dist-info/METADATA,sha256=0nt4eELWDyf5xP9bYrkyUqFqBlug0Tg3FvrDZxLzjyI,1155
+pybiolib-1.2.1727.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+pybiolib-1.2.1727.dist-info/entry_points.txt,sha256=YtPvuWP8ukZ3WwWH5_hQ6UGW6nDi54rcW2_bGQnbG7M,43
+pybiolib-1.2.1727.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1727.dist-info/RECORD,,

{pybiolib-1.2.1642.dist-info → pybiolib-1.2.1727.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pybiolib-1.2.1727.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+biolib = biolib:call_cli

biolib/_shared/types/resource_types.py

@@ -1,18 +0,0 @@
-from .app import AppSlimDict
-from .data_record import DataRecordSlimDict
-from .experiment import DeprecatedExperimentDict
-from .typing import Optional, TypedDict
-
-
-class ResourceDict(TypedDict):
-    uuid: str
-    uri: str
-    name: str
-    created_at: str
-    description: str
-
-
-class ResourceDetailedDict(ResourceDict):
-    app: Optional[AppSlimDict]
-    data_record: Optional[DataRecordSlimDict]
-    experiment: Optional[DeprecatedExperimentDict]