pybiolib 1.2.883__py3-none-any.whl → 1.2.897__py3-none-any.whl

biolib/_internal/push_application.py

@@ -196,7 +196,10 @@ def push_application(
     parsed_uri = parse_app_uri(app_uri)
     app_name = parsed_uri['app_name']
 
-    app_uri_to_fetch = f"@{parsed_uri['resource_name_prefix']}/{parsed_uri['account_handle_normalized']}/{app_name}"
+    app_uri_prefix = (
+        f"@{parsed_uri['resource_name_prefix']}/" if parsed_uri['resource_name_prefix'] != 'biolib.com' else ''
+    )
+    app_uri_to_fetch = f"{app_uri_prefix}{parsed_uri['account_handle_normalized']}/{app_name}"
 
     version = parsed_uri['version']
     semantic_version = f"{version['major']}.{version['minor']}.{version['patch']}" if version else None
@@ -205,14 +208,14 @@ def push_application(
 
     api_client = BiolibApiClient.get()
     if not api_client.is_signed_in:
-        github_ref = os.getenv('GITHUB_REF')
-        if github_ref and not api_client.resource_deploy_key:
+        github_repository = os.getenv('GITHUB_REPOSITORY')
+        if github_repository and not api_client.resource_deploy_key:
+            github_secrets_url = f'https://github.com/{github_repository}/settings/secrets/actions/new'
             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'
+                f'Then add it to your GitHub repository at: {github_secrets_url}'
             )
         else:
             raise AuthenticationError(

biolib/_internal/templates/init_template/run.py

@@ -2,20 +2,11 @@ import argparse
 
 from biolib.sdk import Runtime
 
+parser = argparse.ArgumentParser(description='Process some biological sequences.')
+parser.add_argument('--input', type=str, required=True, help='Input protein sequences')
+args = parser.parse_args()
 
-def parse_args():
-    parser = argparse.ArgumentParser(description='Process some biological sequences.')
-    parser.add_argument('--input', type=str, required=True, help='Input protein sequences')
-    return parser.parse_args()
+# update the BioLib result name based on the provided file
+Runtime.set_result_name_from_file(args.input)
 
-
-def main(args):
-    sequence = args.input
-    # Add your processing logic here
-    print(f'Received sequence: {sequence}')
-
-
-if __name__ == '__main__':
-    args = parse_args()
-    Runtime.set_result_name_prefix_from_fasta(args.input)
-    main(args)
+print(f'Processing input file {args.input}...')

{pybiolib-1.2.883.dist-info → pybiolib-1.2.897.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.883
+Version: 1.2.897
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.883.dist-info → pybiolib-1.2.897.dist-info}/RECORD

@@ -22,7 +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=OwabiLPK8P_py3GavIzhYqcQL7hZ6XPKDrhSJUSxeRs,18023
+biolib/_internal/push_application.py,sha256=2XbQM2BWIuXX_zKIPPlbsEhtIoF_wBgbn2PtVnwqjUA,18203
 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
@@ -30,7 +30,7 @@ biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=sph
 biolib/_internal/templates/init_template/.gitignore,sha256=dR_jhtT0boUspgk3S5PPUwuO0o8gKGIbdwu8IH638CY,20
 biolib/_internal/templates/init_template/Dockerfile,sha256=Wv2r9aiazkL1wOf_BT1f5Kx_-txfrqSkYTtWI8HGdL8,169
 biolib/_internal/templates/init_template/requirements.txt,sha256=2GnBHsKg4tX5F06Z4YeLuId6jQO3-HGTITsaVBTDG0Y,42
-biolib/_internal/templates/init_template/run.py,sha256=GS2qGGmFGIthdxdSxZbGktwZc8x3Q2IVLubpp7hEROw,529
+biolib/_internal/templates/init_template/run.py,sha256=oat-Vzcz4XZilrTtgy8CzfltBAa5v6iduGof4Tuulhg,402
 biolib/_internal/templates/init_template/run.sh,sha256=CF25MYW8vNcZee6_Lydg0o5JDWG0YbrSvFHhMJ5I6x0,39
 biolib/_internal/templates/templates.py,sha256=-o0VdRMwPhnzL4VlCe3BZYl1aI9HLKtOmNjs6gu9fIQ,101
 biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
@@ -141,8 +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-1.2.883.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,,
+pybiolib-1.2.897.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.897.dist-info/METADATA,sha256=1uDEFqNE52A_jRETKr_IfRWhJbqDhXO6gsXHSeEWa8U,1570
+pybiolib-1.2.897.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.897.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.897.dist-info/RECORD,,