pybiolib 1.2.701__py3-none-any.whl → 1.2.713__py3-none-any.whl

biolib/_internal/add_copilot_prompts.py

@@ -0,0 +1,43 @@
+import os
+import shutil
+import sys
+
+from biolib._internal import llm_instructions
+
+
+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"""
+        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')
+
+    conflicting_files = []
+
+    for root, _, files in os.walk(source_path):
+        relative_dir = os.path.relpath(root, source_path)
+        destination_dir = os.path.join(destination_path, relative_dir)
+        for file in files:
+            source_file = os.path.join(root, file)
+            destination_file = os.path.join(destination_dir, file)
+            if os.path.exists(destination_file) and not force:
+                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, current_working_directory))
+            else:
+                os.makedirs(destination_dir, exist_ok=True)
+                shutil.copy2(source_file, destination_file)
+
+    if conflicting_files:
+        print('The following files were not overwritten. Use --force to override them:', file=sys.stderr)
+        for conflicting_file in conflicting_files:
+            print(f'  {conflicting_file}', file=sys.stderr)
+        exit(1)
+
+    if not silent:
+        print(f'Prompt and instruction files added to {destination_path}/')

biolib/_internal/llm_instructions/.github/code-style.md

@@ -0,0 +1,9 @@
+Variable names are allowed to be verbose, and should be descriptive.
+
+Code comments should only be added for complex logic or unintuitive code that is not adequately explained by the function names themselves.
+
+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.
+
+Function definitions should be typed as specifically as possible.

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

@@ -1,10 +1,4 @@
-Variable names are allowed to be verbose, and should be descriptive.
-
-Code comments should only be added for complex logic or unintuitive code that is not adequately explained by the function names themselves.
-
-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.
+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.
 

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

biolib/_internal/types/resource_permission.py

@@ -0,0 +1,12 @@
+from .typing import TypedDict
+
+
+class ResourcePermissionDict(TypedDict):
+    uuid: str
+    action: str
+    resource_uuid: str
+    target_resource_uuid: str
+
+
+class ResourcePermissionDetailedDict(ResourcePermissionDict):
+    pass

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)

biolib/cli/sdk.py

@@ -1,10 +1,6 @@
-import os
-import shutil
-import sys
-
 import click
 
-from biolib._internal import llm_instructions
+from biolib._internal.add_copilot_prompts import add_copilot_prompts
 
 
 @click.group(name='sdk', help='Advanced commands for developers')
@@ -16,38 +12,5 @@ def sdk():
     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:
-    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)
-        exit(1)
-    source_path = os.path.join(os.path.dirname(llm_instructions.__file__), '.github')
-    destination_path = os.path.join(current_working_directory, '.github')
-
-    conflicting_files = []
-
-    for root, _, files in os.walk(source_path):
-        relative_dir = os.path.relpath(root, source_path)
-        destination_dir = os.path.join(destination_path, relative_dir)
-        for file in files:
-            source_file = os.path.join(root, file)
-            destination_file = os.path.join(destination_dir, file)
-            if os.path.exists(destination_file) and not force:
-                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, current_working_directory))
-            else:
-                os.makedirs(destination_dir, exist_ok=True)
-                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)
-        for conflicting_file in conflicting_files:
-            click.echo(f'  {conflicting_file}', file=sys.stderr)
-        exit(1)
-
-    click.echo(f'Prompt and instruction files added to {destination_path}/')
+def add_copilot_prompts_command(force: bool) -> None:
+    add_copilot_prompts(force)

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.dist-info → pybiolib-1.2.713.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.701
+Version: 1.2.713
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.701.dist-info → pybiolib-1.2.713.dist-info}/RECORD

@@ -1,6 +1,7 @@
 biolib/__init__.py,sha256=RL-YmqW1WUKk2FGuEt-8kzzlK1QZKcEtzBUsifWUNQM,10626
 biolib/_data_record/data_record.py,sha256=zKvnh5T-dIVY46-kgVzMBoZ666ZhcTCFQnWvZT0D6RM,12026
 biolib/_internal/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+biolib/_internal/add_copilot_prompts.py,sha256=jhyAMhQZZTvRFxARCdGxlZwtLDczRxjZEDl9-xzWZ34,1852
 biolib/_internal/data_record/__init__.py,sha256=fGdME6JGRU_2VxpJbYpGXYndjN-feUkmKY4fuMyq3cg,76
 biolib/_internal/data_record/data_record.py,sha256=SD3-tKQY2RZv9ZSVNUhd2ISDYV64Fk1Sc642qyf_Vis,4618
 biolib/_internal/data_record/push_data.py,sha256=-L3a_7zZzDCXabBu3O4lWPMAMeBbeRPTrBlEM-_5SCI,2693
@@ -13,19 +14,21 @@ biolib/_internal/lfs/__init__.py,sha256=gSWo_xg61UniYgD7yNYxeT4I9uaXBCBSi3_nmZjn
 biolib/_internal/lfs/cache.py,sha256=pQS2np21rdJ6I3DpoOutnzPHpLOZgUIS8TMltUJk_k4,2226
 biolib/_internal/libs/__init__.py,sha256=Jdf4tNPqe_oIIf6zYml6TiqhL_02Vyqwge6IELrAFhw,98
 biolib/_internal/libs/fusepy/__init__.py,sha256=AWDzNFS-XV_5yKb0Qx7kggIhPzq1nj_BZS5y2Nso08k,41944
-biolib/_internal/llm_instructions/.github/copilot-instructions.md,sha256=OAaZIipjpTA7_9dVygvLejdJRz5Gu1jOlT8bMsZh71c,697
+biolib/_internal/llm_instructions/.github/code-style.md,sha256=ODwlSFrQqZoZuXg2GVHV_BoSrFigu6gbnhDd68XMxRY,452
+biolib/_internal/llm_instructions/.github/copilot-instructions.md,sha256=GCGYxfjenwKjy6srtNMPqwIZzgau5o6xYkcFJb4SwVk,337
 biolib/_internal/llm_instructions/.github/prompts/biolib_app_inputs.prompt.md,sha256=DcBUNaViuNfXoomj-IVUcIcBtJlXuIYOroUfDM_R6wU,3212
 biolib/_internal/llm_instructions/.github/prompts/biolib_run_apps.prompt.md,sha256=HYv-MgpQKIU7Hv90SvZ3tqXY6KWxYVnqamXDRyInOHM,7926
 biolib/_internal/llm_instructions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/push_application.py,sha256=Ffj3iZ0nma4KHTB-PKCeFvhCHHhAEhgKClxnfBUpL8U,12296
 biolib/_internal/runtime.py,sha256=BiHl4klUHr36MCpqKaUso4idHeBZfPAahLYRQrabFqA,486
 biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
-biolib/_internal/types/__init__.py,sha256=xLgOQJFh3GRtiqIJq7MaqHReZx4pp34_zcaFQ_JjuJ4,198
+biolib/_internal/types/__init__.py,sha256=WvtlSHh77QhYVTLeRpoPAzqvByLzbEPf_ZqYGHFlQug,247
 biolib/_internal/types/app.py,sha256=Mz2QGD_jESX-K9JYnLWPo4YA__Q_1FQQTk9pvidCohU,118
 biolib/_internal/types/data_record.py,sha256=9r_vdhVs60YTnzU4XQFXfDrfS2P2MqD3BH2xa7lk6ck,852
 biolib/_internal/types/experiment.py,sha256=D94iBdn2nS92lRW-TOs1a2WKXJD5ZtmzL4ypggKX2ys,176
 biolib/_internal/types/file_node.py,sha256=T6BIqo662f3nwMBRqtBHYsg6YuuUaKpiokHcVjv9_ME,283
 biolib/_internal/types/resource.py,sha256=uUI9Rt5ehkXv9NEDW9zsaPXiTXxnj811rSUW3g_joJw,437
+biolib/_internal/types/resource_permission.py,sha256=jrWMOKVb5rROW-3ujFMExCGD54VVlvWl_gnipM99whk,229
 biolib/_internal/types/resource_version.py,sha256=cU0YFHqxO-wX_Y6CoeK0Iei61gFwVoyR_kPOSTQ4mCs,304
 biolib/_internal/types/typing.py,sha256=qrsk8hHcGEbDpU1QQFzHAKnhQxkMe7uJ6pxHeAnfv1Y,414
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
@@ -67,12 +70,12 @@ 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=GBMSrRAgNISqyqyisF2cYrKioTXJqFgkwASgA8VLnXc,936
+biolib/cli/init.py,sha256=PZLzQYbT7u78J1qSCcs-frVfWHohkrZHxLGRSmMdRg4,1061
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
 biolib/cli/push.py,sha256=RxB4RHpjtL27Fpq7WRGojJ53R9jUuE1Cq9_NmHFzNsM,1306
 biolib/cli/run.py,sha256=MCo0ZqW2pHBxOoCI3i5gAx5D0auW9fmxHqkAF4TRhms,2134
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
-biolib/cli/sdk.py,sha256=YTeriA-jC5XuEbhMMQ4DlOZXM2y0vN5YsKDNoAeZao8,2140
+biolib/cli/sdk.py,sha256=XisJwTft4QDB_99eGDlz-WBqqRwIqkVg7HyvxWtOG8w,471
 biolib/cli/start.py,sha256=rg8VVY8rboFhf1iQo3zE3WA5oh_R1VWWfYJEO1gMReY,1737
 biolib/compute_node/.gitignore,sha256=GZdZ4g7HftqfOfasFpBC5zV1YQAbht1a7EzcXD6f3zg,45
 biolib/compute_node/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -95,7 +98,7 @@ biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5K
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=7tm5Yk9coqJ9VbEdnO86tSXI0iM0omwIyKENxdxiVXk,8575
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
-biolib/compute_node/remote_host_proxy.py,sha256=1EZnB0WWG359Yy22xBoqRqGEmmlA12rpiG5u8B2381M,16533
+biolib/compute_node/remote_host_proxy.py,sha256=4rNR4iCmtwo5Wej-B1BcoZboNANCHEd0N_G5Uh1u9zI,16525
 biolib/compute_node/socker_listener_thread.py,sha256=T5_UikA3MB9bD5W_dckYLPTgixh72vKUlgbBvj9dbM0,1601
 biolib/compute_node/socket_sender_thread.py,sha256=YgamPHeUm2GjMFGx8qk-99WlZhEs-kAb3q_2O6qByig,971
 biolib/compute_node/utils.py,sha256=fWtFIcGatek1NaVOT9Vaey6UFp8GKLYGLAVu8jgOwi8,4861
@@ -126,8 +129,8 @@ 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-1.2.701.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.701.dist-info/METADATA,sha256=r4sy2tMZgB6dLiUiCnJAPjL-cuw09JWJvayRQIAMsE8,1570
-pybiolib-1.2.701.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-pybiolib-1.2.701.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.701.dist-info/RECORD,,
+pybiolib-1.2.713.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.713.dist-info/METADATA,sha256=NH_lLqax0t2OlS4_4IH9Z1a4XAcRQJi60muJwu_Tb7M,1570
+pybiolib-1.2.713.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+pybiolib-1.2.713.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.713.dist-info/RECORD,,