pybiolib 1.2.856__py3-none-any.whl → 1.2.871__py3-none-any.whl

biolib/_internal/push_application.py

@@ -38,6 +38,7 @@ class DockerStatusUpdate(TypedDict, total=False):
 def process_docker_status_updates(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)
 
         for update in status_updates:
             if 'progressDetail' in update and 'id' in update:
@@ -59,7 +60,39 @@ def process_docker_status_updates(status_updates: Iterable[DockerStatusUpdate],
                         task_id=layer_id_to_task_id[layer_id],
                         total=100,
                     )
+            elif 'status' in update and 'id' in update:
+                layer_id = update['id']
+                status = update['status']
 
+                if layer_id not in layer_id_to_task_id:
+                    layer_id_to_task_id[layer_id] = progress.add_task(description=f'[cyan]{action} layer {layer_id}')
+
+                if status in ['Preparing', 'Waiting']:
+                    progress.update(
+                        task_id=layer_id_to_task_id[layer_id], description=f'[yellow]{status} layer {layer_id}'
+                    )
+                elif status in ['Pushing', 'Uploading']:
+                    progress.update(
+                        task_id=layer_id_to_task_id[layer_id], description=f'[cyan]{status} layer {layer_id}'
+                    )
+                elif status in ['Pushed', 'Uploaded']:
+                    progress.update(
+                        task_id=layer_id_to_task_id[layer_id],
+                        description=f'[green]{status} layer {layer_id}',
+                        completed=100,
+                        total=100,
+                    )
+                elif status == 'Layer already exists':
+                    progress.update(
+                        task_id=layer_id_to_task_id[layer_id],
+                        description=f'[green]{status} - layer {layer_id}',
+                        completed=100,
+                        total=100,
+                    )
+            elif 'status' in update and update['status']:
+                status = update['status']
+                if status not in ['Preparing', 'Pushing', 'Pushed', 'Waiting', 'Layer already exists']:
+                    progress.update(task_id=overall_task_id, description=f'[bold blue]{action} Docker image - {status}')
             elif 'status' not in update and 'progressDetail' not in update:
                 print(update)
 

biolib/cli/init.py

@@ -26,6 +26,7 @@ def init() -> None:
 
     template_dir = templates.init_template()
     conflicting_files = []
+    files_to_overwrite = set()
 
     try:
         # First pass: check for conflicts
@@ -40,11 +41,17 @@ def init() -> None:
                     with open(source_file, 'rb') as fsrc, open(destination_file, 'rb') as fdest:
                         if fsrc.read() != fdest.read():
                             conflicting_files.append(os.path.relpath(destination_file, cwd))
+
         if conflicting_files:
-            print('The following files were not overwritten. Use --force to override them:', file=sys.stderr)
+            print('The following files already exist and would be overwritten:')
+            for conflicting_file in conflicting_files:
+                print(f'  {conflicting_file}')
+            print()
+
             for conflicting_file in conflicting_files:
-                print(f'  {conflicting_file}', file=sys.stderr)
-            exit(1)
+                choice = input(f'Overwrite {conflicting_file}? [y/N]: ').lower().strip()
+                if choice in ['y', 'yes']:
+                    files_to_overwrite.add(conflicting_file)
 
         replace_app_uri = app_uri if app_uri else 'PUT_APP_URI_HERE'
 
@@ -61,8 +68,9 @@ def init() -> None:
 
                 source_file = os.path.join(root, filename)
                 destination_file = os.path.join(destination_dir, filename)
+                relative_file_path = os.path.relpath(destination_file, cwd)
 
-                if not os.path.exists(destination_file):
+                if not os.path.exists(destination_file) or relative_file_path in files_to_overwrite:
                     try:
                         with open(source_file) as f:
                             content = f.read()

{pybiolib-1.2.856.dist-info → pybiolib-1.2.871.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.856
+Version: 1.2.871
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.856.dist-info → pybiolib-1.2.871.dist-info}/RECORD

@@ -21,7 +21,7 @@ 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=I7yHGcwK6udc2hVmOQIc1BcQBipAMibEjURMI6HgdXk,12502
+biolib/_internal/push_application.py,sha256=snnd3aCPJeByEQTCajDi7Op5TH9-BXjJS9QCS8e6cjY,14347
 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
@@ -83,7 +83,7 @@ biolib/cli/__init__.py,sha256=IHC2bEyA27pvgp-18SGfFVJOP456elanz7suDP8D084,1316
 biolib/cli/auth.py,sha256=rpWGmXs6Fz6CGrO9K8ibPRszOdXG78Vig_boKaVCD9A,2082
 biolib/cli/data_record.py,sha256=t8DfJK2EZ_SNZ9drDA_N5Jqy8DNwf9f5SlFrIaOvtv0,3501
 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
-biolib/cli/init.py,sha256=v6ebi969q4lMfBBjJEUbG50Z8J5vA1fkTYeVfm7iZ7Y,4083
+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/run.py,sha256=MCo0ZqW2pHBxOoCI3i5gAx5D0auW9fmxHqkAF4TRhms,2134
@@ -140,8 +140,8 @@ 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-1.2.856.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.856.dist-info/METADATA,sha256=8dJ2I-UmDG62OdLmb9QEm4g4DuF-Xu6AEIH1VaaGQrs,1570
-pybiolib-1.2.856.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.856.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.856.dist-info/RECORD,,
+pybiolib-1.2.871.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.871.dist-info/METADATA,sha256=zAOp7nhOZdgj0uu5QPYEqTPLsUfGUBDUekQxby2kgyU,1570
+pybiolib-1.2.871.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.871.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.871.dist-info/RECORD,,