pybiolib 1.2.701__tar.gz → 1.2.716__tar.gz

{pybiolib-1.2.701 → pybiolib-1.2.716}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.701
+Version: 1.2.716
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

pybiolib-1.2.701/biolib/cli/sdk.py → pybiolib-1.2.716/biolib/_internal/add_copilot_prompts.py

@@ -2,28 +2,17 @@ import os
 import shutil
 import sys
 
-import click
-
 from biolib._internal import llm_instructions
 
 
-@click.group(name='sdk', help='Advanced commands for developers')
-def sdk():
-    pass
-
-
-@sdk.command(
-    name='add-copilot-prompts', help='Add BioLib-specific GitHub Copilot prompts and instructions to your repository'
-)
-@click.option('--force', is_flag=True, help='Force overwrite existing files.')
-def add_copilot_prompts(force: bool) -> None:
+def add_copilot_prompts(force: bool, silent: bool = False) -> None:
     current_working_directory = os.getcwd()
     config_file_path = f'{current_working_directory}/.biolib/config.yml'
     if not os.path.exists(config_file_path):
         err_string = """
 Error: Current directory has not been initialized as a BioLib application.
-       Please run the "biolib init" command first"""
-        click.echo(err_string, file=sys.stderr)
+       Please run the \"biolib init\" command first"""
+        print(err_string, file=sys.stderr)
         exit(1)
     source_path = os.path.join(os.path.dirname(llm_instructions.__file__), '.github')
     destination_path = os.path.join(current_working_directory, '.github')
@@ -45,9 +34,10 @@ Error: Current directory has not been initialized as a BioLib application.
                 shutil.copy2(source_file, destination_file)
 
     if conflicting_files:
-        click.echo('The following files were not overwritten. Use --force to override them:', file=sys.stderr)
+        print('The following files were not overwritten. Use --force to override them:', file=sys.stderr)
         for conflicting_file in conflicting_files:
-            click.echo(f'  {conflicting_file}', file=sys.stderr)
+            print(f'  {conflicting_file}', file=sys.stderr)
         exit(1)
 
-    click.echo(f'Prompt and instruction files added to {destination_path}/')
+    if not silent:
+        print(f'Prompt and instruction files added to {destination_path}/')

pybiolib-1.2.701/biolib/_internal/llm_instructions/.github/copilot-instructions.md → pybiolib-1.2.716/biolib/_internal/llm_instructions/.github/code-style.md

@@ -4,8 +4,6 @@ Code comments should only be added for complex logic or unintuitive code that is
 
 Unit tests are not necessary. Tests should instead be written as simple examples demonstrating the functionality of relevant functions.
 
-Always use 4 spaces for indentation when writing code.
+Always use 4 spaces for indentation.
 
-When running BioLib Apps, use [this file](prompts/biolib_run_apps.prompt.md) as context to understand how that works.
-
-When working with BioLib App inputs, use [this file](prompts/biolib_app_inputs.prompt.md) as context to understand how the different files should be connected and formatted.
+Function definitions should be typed as specifically as possible.

pybiolib-1.2.716/biolib/_internal/llm_instructions/.github/copilot-instructions.md

@@ -0,0 +1,5 @@
+Use yarn instead of npm whenever relevant.
+
+When running BioLib Apps, use [this file](prompts/biolib_run_apps.prompt.md) as context to understand how that works.
+
+When working with BioLib App inputs, use [this file](prompts/biolib_app_inputs.prompt.md) as context to understand how the different files should be connected and formatted.

{pybiolib-1.2.701 → pybiolib-1.2.716}/biolib/_internal/types/__init__.py

@@ -2,4 +2,5 @@ from .app import *  # noqa: F403
 from .data_record import *  # noqa: F403
 from .experiment import *  # noqa: F403
 from .resource import *  # noqa: F403
+from .resource_permission import *  # noqa: F403
 from .resource_version import *  # noqa: F403

pybiolib-1.2.716/biolib/_internal/types/resource_permission.py

@@ -0,0 +1,13 @@
+from .typing import TypedDict
+
+
+class ResourcePermissionDict(TypedDict):
+    uuid: str
+    created_at: str
+    action: str
+    resource_uuid: str
+    target_resource_uuid: str
+
+
+class ResourcePermissionDetailedDict(ResourcePermissionDict):
+    pass

{pybiolib-1.2.701 → pybiolib-1.2.716}/biolib/cli/init.py

@@ -4,6 +4,7 @@ import sys
 import click
 
 from biolib import templates
+from biolib._internal.add_copilot_prompts import add_copilot_prompts
 
 
 @click.command(help='Initialize a project with a .biolib/config.yml file', hidden=True)
@@ -26,6 +27,9 @@ def init() -> None:
         if not os.path.exists(readme_path):
             with open(readme_path, 'w') as readme_file:
                 readme_file.write(f'# {project_name}\n')
+
+        add_copilot_prompts(force=False, silent=True)
+
     except KeyboardInterrupt:
         print('\nInit command cancelled.', file=sys.stderr)
         exit(1)

pybiolib-1.2.716/biolib/cli/sdk.py

@@ -0,0 +1,16 @@
+import click
+
+from biolib._internal.add_copilot_prompts import add_copilot_prompts
+
+
+@click.group(name='sdk', help='Advanced commands for developers')
+def sdk():
+    pass
+
+
+@sdk.command(
+    name='add-copilot-prompts', help='Add BioLib-specific GitHub Copilot prompts and instructions to your repository'
+)
+@click.option('--force', is_flag=True, help='Force overwrite existing files.')
+def add_copilot_prompts_command(force: bool) -> None:
+    add_copilot_prompts(force)

{pybiolib-1.2.701 → pybiolib-1.2.716}/biolib/compute_node/remote_host_proxy.py

@@ -227,7 +227,7 @@ http {{
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;
         }}
-        
+
         location ~* "^/api/jobs/(?<job_id>[a-z0-9-]{{36}})/main_result/$" {{
             proxy_pass                  https://$upstream_hostname/api/jobs/$job_id/main_result/;
             proxy_set_header            authorization "";

{pybiolib-1.2.701 → pybiolib-1.2.716}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.701"
+version = "1.2.716"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"