pybiolib 1.2.876__py3-none-any.whl → 1.2.883__py3-none-any.whl

biolib/_internal/errors.py

@@ -0,0 +1,5 @@
+from biolib.biolib_errors import BioLibError
+
+
+class AuthenticationError(BioLibError):
+    """Raised when authentication is required but user is not signed in."""

biolib/_internal/push_application.py

@@ -1,5 +1,7 @@
 import os
 import re
+import sys
+import time
 from pathlib import Path
 
 import rich.progress
@@ -10,6 +12,7 @@ from biolib._internal.data_record.push_data import (
     push_data_path,
     validate_data_path_and_get_files_and_size_of_directory,
 )
+from biolib._internal.errors import AuthenticationError
 from biolib._internal.file_utils import get_files_and_size_of_directory, get_iterable_zip_stream
 from biolib._internal.types.push import PushResponseDict
 from biolib.biolib_api_client import BiolibApiClient
@@ -36,6 +39,13 @@ class DockerStatusUpdate(TypedDict, total=False):
 
 
 def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate], action: str) -> None:
+    if sys.stdout.isatty():
+        _process_docker_status_updates_with_progress_bar(status_updates, action)
+    else:
+        _process_docker_status_updates_with_logging(status_updates, action)
+
+
+def _process_docker_status_updates_with_progress_bar(status_updates: Iterable[DockerStatusUpdate], action: str) -> None:
     with rich.progress.Progress() as progress:
         layer_id_to_task_id = {}
         overall_task_id = progress.add_task(description=f'[bold blue]{action} Docker image', total=None)
@@ -97,6 +107,74 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
                 print(update)
 
 
+def _process_docker_status_updates_with_logging(status_updates: Iterable[DockerStatusUpdate], action: str) -> None:
+    layer_progress = {}
+    layer_status = {}
+    last_log_time = time.time()
+
+    logger.info(f'{action} Docker image...')
+
+    for update in status_updates:
+        current_time = time.time()
+
+        if 'progressDetail' in update and 'id' in update:
+            layer_id = update['id']
+            progress_detail = update['progressDetail']
+
+            if progress_detail and 'current' in progress_detail and 'total' in progress_detail:
+                current = progress_detail['current']
+                total = progress_detail['total']
+                percentage = (current / total * 100) if total > 0 else 0
+                layer_progress[layer_id] = percentage
+                layer_status[layer_id] = f'{action.lower()}'
+            elif update.get('status') == 'Layer already exists':
+                layer_progress[layer_id] = 100
+                layer_status[layer_id] = 'already exists'
+
+        elif 'status' in update and 'id' in update:
+            layer_id = update['id']
+            status = update['status']
+            layer_status[layer_id] = status.lower()
+
+            if status in ['Pushed', 'Uploaded'] or status == 'Layer already exists':
+                layer_progress[layer_id] = 100
+
+        elif 'status' in update and update['status']:
+            status = update['status']
+            if status not in ['Preparing', 'Pushing', 'Pushed', 'Waiting', 'Layer already exists']:
+                logger.info(f'{action} Docker image - {status}')
+
+        if current_time - last_log_time >= 10.0:
+            _log_progress_summary(action, layer_progress, layer_status)
+            last_log_time = current_time
+
+    _log_progress_summary(action, layer_progress, layer_status)
+    logger.info(f'{action} Docker image completed')
+
+
+def _log_progress_summary(action: str, layer_progress: dict, layer_status: dict) -> None:
+    if not layer_progress and not layer_status:
+        return
+
+    completed_layers = sum(1 for progress in layer_progress.values() if progress >= 100)
+    total_layers = len(layer_progress) if layer_progress else len(layer_status)
+
+    if total_layers > 0:
+        overall_percentage = completed_layers / total_layers * 100
+        logger.info(
+            f'{action} progress: {completed_layers}/{total_layers} layers completed ({overall_percentage:.1f}%)'
+        )
+
+    active_layers = [
+        layer_id
+        for layer_id, status in layer_status.items()
+        if status in ['preparing', 'waiting', 'pushing', 'uploading'] and layer_progress.get(layer_id, 0) < 100
+    ]
+
+    if active_layers:
+        logger.info(f'Active layers: {", ".join(active_layers[:5])}{"..." if len(active_layers) > 5 else ""}')
+
+
 def set_app_version_as_active(
     app_version_uuid: str,
 ):
@@ -127,13 +205,21 @@ def push_application(
 
     api_client = BiolibApiClient.get()
     if not api_client.is_signed_in:
-        # TODO: Create an exception class for expected errors like this that does not print stacktrace
-
-        raise Exception(
-            'You must be authenticated to push an application.\n'
-            'Please set the environment variable "BIOLIB_TOKEN=[your_deploy_token]"\n'
-            f'You can get a deploy key at: {api_client.base_url}/{app_uri_to_fetch}/settings/keys/'
-        ) from None
+        github_ref = os.getenv('GITHUB_REF')
+        if github_ref and not api_client.resource_deploy_key:
+            raise AuthenticationError(
+                'You must be authenticated to push an application.\n'
+                'Please set the environment variable "BIOLIB_TOKEN=[your_deploy_token]"\n'
+                f'You can get a deploy key at: {api_client.base_url}/{app_uri_to_fetch}/settings/keys/\n'
+                'Then add it to your GitHub repository at: '
+                'Settings -> Secrets and variables -> Actions -> Repository secrets'
+            )
+        else:
+            raise AuthenticationError(
+                'You must be authenticated to push an application.\n'
+                'Please set the environment variable "BIOLIB_TOKEN=[your_deploy_token]"\n'
+                f'You can get a deploy key at: {api_client.base_url}/{app_uri_to_fetch}/settings/keys/'
+            )
 
     # prepare zip file
     config_yml_path = app_path_absolute.joinpath('.biolib/config.yml')

biolib/cli/push.py

@@ -1,8 +1,10 @@
 import logging
+import sys
 from typing import Optional
 
 import click
 
+from biolib._internal.errors import AuthenticationError
 from biolib._internal.push_application import push_application
 from biolib.biolib_logging import logger, logger_no_user_data
 
@@ -34,11 +36,15 @@ def push(uri, path: str, copy_images_from_version: Optional[str], dev: bool, pre
     elif pre_release:
         set_as_active = False
         set_as_published = True
-    push_application(
-        app_path=path,
-        app_uri=uri,
-        app_version_to_copy_images_from=copy_images_from_version,
-        set_as_active=set_as_active,
-        set_as_published=set_as_published,
-        dry_run=dry_run,
-    )
+    try:
+        push_application(
+            app_path=path,
+            app_uri=uri,
+            app_version_to_copy_images_from=copy_images_from_version,
+            set_as_active=set_as_active,
+            set_as_published=set_as_published,
+            dry_run=dry_run,
+        )
+    except AuthenticationError as error:
+        print(error.message, file=sys.stderr)
+        exit(1)

{pybiolib-1.2.876.dist-info → pybiolib-1.2.883.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.876
+Version: 1.2.883
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.876.dist-info → pybiolib-1.2.883.dist-info}/RECORD

@@ -6,6 +6,7 @@ biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkm
 biolib/_internal/data_record/data_record.py,sha256=SD3-tKQY2RZv9ZSVNUhd2ISDYV64Fk1Sc642qyf_Vis,4618
 biolib/_internal/data_record/push_data.py,sha256=-L3a_7zZzDCXabBu3O4lWPMAMeBbeRPTrBlEM-_5SCI,2693
 biolib/_internal/data_record/remote_storage_endpoint.py,sha256=eCptuZ4DMAPnaNCVDvpWXwXGI6Jac9U1N5dqU8Cj95Q,1732
+biolib/_internal/errors.py,sha256=AokI6Dvaa22B__LTfSZUVdDsm0ye7lgBFv_aD9O_kbs,163
 biolib/_internal/file_utils.py,sha256=4jT6j7bB21c0JNn5BfnyWQib_zt0CVtJ_TiOFOStRcE,2604
 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
@@ -21,7 +22,7 @@ biolib/_internal/llm_instructions/.github/instructions/style-react-ts.instructio
 biolib/_internal/llm_instructions/.github/prompts/biolib_app_inputs.prompt.md,sha256=SMzXZImdID0yKjhE1fG54VrHdD8IVuwRxRKsMF-KjWs,697
 biolib/_internal/llm_instructions/.github/prompts/biolib_run_apps.prompt.md,sha256=-t1bmGr3zEFa6lKHaLcI98yq4Sg1TCMW8xbelNSHaOA,696
 biolib/_internal/llm_instructions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/_internal/push_application.py,sha256=snnd3aCPJeByEQTCajDi7Op5TH9-BXjJS9QCS8e6cjY,14347
+biolib/_internal/push_application.py,sha256=OwabiLPK8P_py3GavIzhYqcQL7hZ6XPKDrhSJUSxeRs,18023
 biolib/_internal/runtime.py,sha256=BiHl4klUHr36MCpqKaUso4idHeBZfPAahLYRQrabFqA,486
 biolib/_internal/templates/__init__.py,sha256=NVbhLUMC8HITzkLvP88Qu7FHaL-SvQord-DX3gh1Ykk,24
 biolib/_internal/templates/init_template/.biolib/config.yml,sha256=y4ndTgbFvUE1UiGcIOqogT2Wm8jahGffeyU5rlCEltQ,427
@@ -85,7 +86,7 @@ biolib/cli/data_record.py,sha256=t8DfJK2EZ_SNZ9drDA_N5Jqy8DNwf9f5SlFrIaOvtv0,350
 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
 biolib/cli/init.py,sha256=_dhnKdlRMy2oSNRRsXdjFKVzayy2aiRQkeF948VCCkg,4438
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
-biolib/cli/push.py,sha256=pSFEUQkQ69M__eR1nIT9ejW4V4_MtX3lb8ydEc1uKiM,1484
+biolib/cli/push.py,sha256=J8BswMYVeTacZBHbm4K4a2XbS_I8kvfgRZLoby2wi3I,1695
 biolib/cli/run.py,sha256=MCo0ZqW2pHBxOoCI3i5gAx5D0auW9fmxHqkAF4TRhms,2134
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
 biolib/cli/sdk.py,sha256=XisJwTft4QDB_99eGDlz-WBqqRwIqkVg7HyvxWtOG8w,471
@@ -140,8 +141,8 @@ 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=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.876.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.876.dist-info/METADATA,sha256=Vcom4VROgeB12DAZP7lZnWrX7hZ0wipD3drOcAn8RGs,1570
-pybiolib-1.2.876.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.876.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.876.dist-info/RECORD,,
+pybiolib-1.2.883.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.883.dist-info/METADATA,sha256=SpFwDiscPum6qx9WgKbEzFGSBnMntarbRXNVGXSW0I8,1570
+pybiolib-1.2.883.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.883.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.883.dist-info/RECORD,,