pybiolib 1.2.918__py3-none-any.whl → 1.2.931__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/cli/run.py

@@ -48,7 +48,7 @@ def _run(local: bool, non_blocking: bool, uri: str, args: Tuple[str]) -> None:
     )
 
     if blocking:
-        job.save_files('biolib_results')
+        job.save_files('biolib_results', overwrite=True)
 
         # Write stdout and stderr if it has not been streamed (Markdown is not streamed)
         if app.version.get('stdout_render_type') == 'markdown' or not sys.stdout.isatty():

biolib/jobs/job.py

@@ -226,7 +226,7 @@ class Result:
 
         return self._cached_input_arguments
 
-    def save_input_files(self, output_dir: str) -> None:
+    def save_input_files(self, output_dir: str, overwrite: bool = False) -> None:
         logger.info('Downloading input files...')
         module_input = self._get_module_input()
 
@@ -236,7 +236,12 @@ class Result:
             # Remove leading slash of file_path
             destination_file_path = Path(output_dir) / Path(path.lstrip('/'))
             if destination_file_path.exists():
-                destination_file_path.rename(f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}')
+                if not overwrite:
+                    raise BioLibError(f'File {destination_file_path} already exists. Set overwrite=True to overwrite.')
+                else:
+                    destination_file_path.rename(
+                        f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}'
+                    )
 
             dir_path = destination_file_path.parent
             if dir_path:
@@ -252,11 +257,13 @@ class Result:
         output_dir: str,
         path_filter: Optional[PathFilter] = None,
         skip_file_if_exists: Optional[bool] = None,
+        overwrite: bool = False,
     ) -> None:
         self.result.save_files(
             output_dir=output_dir,
             path_filter=path_filter,
             skip_file_if_exists=skip_file_if_exists,
+            overwrite=overwrite,
         )
 
     def get_status(self) -> str:

biolib/jobs/job_result.py

@@ -39,6 +39,7 @@ class JobResult:
         output_dir: str,
         path_filter: Optional[PathFilter] = None,
         skip_file_if_exists: Optional[bool] = None,
+        overwrite: bool = False,
     ) -> None:
         module_output = self._get_module_output()
         output_files = module_output.get_files()
@@ -68,6 +69,8 @@ class JobResult:
                 if skip_file_if_exists:
                     print(f'Skipping {destination_file_path} as a file with that name already exists locally.')
                     continue
+                elif not overwrite:
+                    raise BioLibError(f'File {destination_file_path} already exists. Set overwrite=True to overwrite.')
                 else:
                     destination_file_path.rename(
                         f'{destination_file_path}.biolib-renamed.{time.strftime("%Y%m%d%H%M%S")}'

{pybiolib-1.2.918.dist-info → pybiolib-1.2.931.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.918
+Version: 1.2.931
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.918.dist-info → pybiolib-1.2.931.dist-info}/RECORD

@@ -20,6 +20,7 @@ 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
@@ -90,7 +91,7 @@ biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5L
 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
+biolib/cli/run.py,sha256=RAAXbIx8Bi-4fNkEoz2ODJ0fEtyS7VxD3dkc2fVZwjY,2150
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
 biolib/cli/sdk.py,sha256=XisJwTft4QDB_99eGDlz-WBqqRwIqkVg7HyvxWtOG8w,471
 biolib/cli/start.py,sha256=rg8VVY8rboFhf1iQo3zE3WA5oh_R1VWWfYJEO1gMReY,1737
@@ -128,8 +129,8 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=gY1-d7FgVrcQO3YzOJ0mHS6j7z7rl5XzXEuk7dFi1gU,10460
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=INQuNpEpe8rQPWBWeDFRjcAd-i4U6hF63FAsJ0BkJ_Y,27086
-biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
+biolib/jobs/job.py,sha256=B9v-dq9li0v9gDfmyyZOnCk-kN0vYPYxoybHWQsCkPg,27403
+biolib/jobs/job_result.py,sha256=L__GA5dNSDFHoQpAG2xb-tNqp_p4fQl53bAmlcvAt6M,6074
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
@@ -144,8 +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-1.2.918.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.918.dist-info/METADATA,sha256=yJbyNLvWIrWR9kEiDv3PISDRJzx1PT14sgtXnhwb968,1570
-pybiolib-1.2.918.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.918.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.918.dist-info/RECORD,,
+pybiolib-1.2.931.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.931.dist-info/METADATA,sha256=hYj-LjppTQ0jEsBW9R2ViJhTCZ8OCPDntrR6mYiIXEg,1570
+pybiolib-1.2.931.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.931.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.931.dist-info/RECORD,,