pybiolib 1.2.911__py3-none-any.whl → 1.2.923__py3-none-any.whl

biolib/_internal/llm_instructions/.github/prompts/biolib_onboard_repo.prompt.md

@@ -0,0 +1,19 @@
+---
+mode: 'agent'
+tools: ['githubRepo', 'codebase']
+description: 'Handle onboarding and implementing code from a GitHub repository into a biolib application, with focus on creating easily editable and maintainable code structure.'
+---
+
+# Main task
+Your task is to help onboard and implement code from a GitHub repository into a biolib application. This involves understanding the repository structure, implementing the core functionality, and ensuring the code is easily editable for future iterations.
+Generally, you can do this by adding the repository into an src folder as a submodule, and reading the README.md file to understand how to run the code.
+You will then call the relevant functions or classes from the cloned repository in your biolib application
+
+## Key requirements:
+- Always ask the user for the GitHub repository if not already provided. Inform them that it needs to be in the format `author/repo_name`.
+- Use the #githubRepo tool to examine the repository structure, README, and key files to understand the project.
+- Focus on creating code that is easily editable and maintainable, as it's likely the implementation won't be perfect on the first attempt.
+- Structure the code in a modular way that allows for easy modifications and improvements.
+- Include clear comments for complex logic, but avoid over-commenting obvious code.
+- Follow the existing biolib application patterns and conventions.
+- Ensure all dependencies are properly specified in requirements.txt with versions locked down.

biolib/_internal/string_utils.py

@@ -0,0 +1,13 @@
+import re
+
+
+def normalize_for_docker_tag(name: str) -> str:
+    if not name:
+        return ''
+
+    normalized = re.sub(r'[^a-z0-9-]', '-', name.lower())
+
+    normalized = re.sub(r'-+', '-', normalized)
+    normalized = normalized.strip('-')
+
+    return normalized

biolib/cli/init.py

@@ -6,6 +6,7 @@ import click
 
 from biolib import utils  # Import like this to let BASE_URL_IS_PUBLIC_BIOLIB be set correctly
 from biolib._internal.add_copilot_prompts import add_copilot_prompts
+from biolib._internal.string_utils import normalize_for_docker_tag
 from biolib._internal.templates import templates
 from biolib.utils import BIOLIB_PACKAGE_VERSION
 
@@ -16,6 +17,7 @@ def init() -> None:
 
     app_uri = input('What URI do you want to create the application under? (leave blank to skip): ')
     app_name = app_uri.split('/')[-1] if app_uri else None
+    docker_tag = normalize_for_docker_tag(app_name) if app_name else None
     if not app_uri:
         print(
             'Remember to set the app URI in the .biolib/config.yml file later, '
@@ -79,7 +81,7 @@ def init() -> None:
                         new_content = new_content.replace('BIOLIB_REPLACE_APP_URI', replace_app_uri)
                         new_content = new_content.replace(
                             'BIOLIB_REPLACE_DOCKER_TAG',
-                            app_name if app_name else 'PUT_DOCKER_TAG_HERE',
+                            docker_tag if docker_tag else 'PUT_DOCKER_TAG_HERE',
                         )
 
                         with open(destination_file, 'w') as f:

{pybiolib-1.2.911.dist-info → pybiolib-1.2.923.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.911
+Version: 1.2.923
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.911.dist-info → pybiolib-1.2.923.dist-info}/RECORD

@@ -20,10 +20,12 @@ biolib/_internal/llm_instructions/.github/instructions/style-general.instruction
 biolib/_internal/llm_instructions/.github/instructions/style-python.instructions.md,sha256=xfypuPqMsz5ejobDoVI0HjmNqksl16aFuIol1nAhpHg,1034
 biolib/_internal/llm_instructions/.github/instructions/style-react-ts.instructions.md,sha256=GQoRL-bfPwwNIW4W0yN_guVIqFNVCG2_7adOCaxiz-w,755
 biolib/_internal/llm_instructions/.github/prompts/biolib_app_inputs.prompt.md,sha256=SMzXZImdID0yKjhE1fG54VrHdD8IVuwRxRKsMF-KjWs,697
+biolib/_internal/llm_instructions/.github/prompts/biolib_onboard_repo.prompt.md,sha256=BfCkVyafDHFBMu6qcvKlxpnXKJRHNDp5qR_fN4XB9pI,1515
 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=e0SnPh64X99ICUt5xPCIfbS3WHkUzMKLFFyaf6u2vqQ,18286
 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
 biolib/_internal/templates/init_template/.biolib/config.yml,sha256=y4ndTgbFvUE1UiGcIOqogT2Wm8jahGffeyU5rlCEltQ,427
 biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=sphjoiycV_oc4VbaA8wbUEokSMpnrdB6N-bYju_5Ibo,522
@@ -86,7 +88,7 @@ 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=_dhnKdlRMy2oSNRRsXdjFKVzayy2aiRQkeF948VCCkg,4438
+biolib/cli/init.py,sha256=OMYIltLJfF8q9VAvzDwNG0-1VixDkFGEN1ic2VhrW7c,4583
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
 biolib/cli/push.py,sha256=J8BswMYVeTacZBHbm4K4a2XbS_I8kvfgRZLoby2wi3I,1695
 biolib/cli/run.py,sha256=MCo0ZqW2pHBxOoCI3i5gAx5D0auW9fmxHqkAF4TRhms,2134
@@ -143,8 +145,8 @@ 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-1.2.911.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.911.dist-info/METADATA,sha256=3NtKERfyMQk905_gZB2Z6T_q14CsvhRfZMgs7Ac475k,1570
-pybiolib-1.2.911.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.911.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.911.dist-info/RECORD,,
+pybiolib-1.2.923.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.923.dist-info/METADATA,sha256=_6O5_T5lbKG9bEy2PBkthT5GWj6KyGyCGJMd337P_eI,1570
+pybiolib-1.2.923.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.923.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.923.dist-info/RECORD,,