pybiolib 1.2.814__py3-none-any.whl → 1.2.838__py3-none-any.whl

biolib/_internal/add_copilot_prompts.py

@@ -5,7 +5,7 @@ import sys
 from biolib._internal import llm_instructions
 
 
-def add_copilot_prompts(force: bool, silent: bool = False) -> None:
+def add_copilot_prompts(force: bool, style: bool = True, 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):
@@ -19,12 +19,14 @@ Error: Current directory has not been initialized as a BioLib application.
 
     conflicting_files = []
 
-    for root, _, files in os.walk(source_path):
+    for root, _, filenames 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)
+        for filename in filenames:
+            if 'style' in filename and not style:
+                continue
+            source_file = os.path.join(root, filename)
+            destination_file = os.path.join(destination_dir, filename)
             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():

biolib/_internal/templates/__init__.py

@@ -0,0 +1 @@
+from . import templates

biolib/_internal/templates/init_template/.biolib/config.yml

@@ -0,0 +1,18 @@
+biolib_version: 2
+
+modules:
+    main:
+        image: 'local-docker://BIOLIB_REPLACE_DOCKER_TAG:latest'
+        command: "bash run.sh"
+        working_directory: /home/biolib/
+        input_files:
+            - COPY / /home/biolib/
+        output_files:
+            - COPY /home/biolib/output/ /
+
+arguments:
+    -
+        key: --input
+        description: 'Input protein sequences'
+        type: sequence
+        required: true

biolib/_internal/templates/init_template/.github/workflows/biolib.yml

@@ -0,0 +1,13 @@
+name: BioLib Build & Push
+on: push
+jobs:
+    build-and-push:
+        runs-on: biolib-github-runner
+        steps:
+          - uses: actions/checkout@v4
+          - name: Build
+            run: docker build -t BIOLIB_REPLACE_DOCKER_TAG:latest .
+          - name: Push
+            run: biolib push $([ "$GITHUB_REF_NAME" != "main" ] && echo -n "--dev") BIOLIB_REPLACE_APP_URI
+            env:
+              BIOLIB_TOKEN: ${{ secrets.BIOLIB_TOKEN }}

biolib/_internal/templates/init_template/Dockerfile

@@ -0,0 +1,11 @@
+FROM python:3.13.3-slim
+WORKDIR /home/biolib/
+
+COPY run.sh .
+
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY src .
+
+RUN mkdir output

biolib/_internal/templates/init_template/requirements.txt

@@ -0,0 +1 @@
+pybiolib==BIOLIB_REPLACE_PYBIOLIB_VERSION

biolib/_internal/templates/init_template/run.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+python3 src/run.py "$@"

biolib/_internal/templates/init_template/src/run.py

@@ -0,0 +1,21 @@
+import argparse
+
+from biolib.sdk import Runtime
+
+
+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()
+
+
+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)

biolib/_internal/templates/templates.py

@@ -0,0 +1,5 @@
+import os
+
+
+def init_template():
+    return os.path.join(os.path.dirname(__file__), 'init_template')

biolib/cli/init.py

@@ -1,34 +1,88 @@
 import os
+import shutil
 import sys
 
 import click
 
-from biolib import templates
+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.templates import templates
+from biolib.utils import BIOLIB_PACKAGE_VERSION
 
 
-@click.command(help='Initialize a project with a .biolib/config.yml file', hidden=True)
+@click.command(help='Initialize a BioLib project', hidden=True)
 def init() -> None:
     cwd = os.getcwd()
-    config_file_path = f'{cwd}/.biolib/config.yml'
-    readme_path = f'{cwd}/README.md'
 
-    if os.path.exists(config_file_path):
-        print(f'The file "{config_file_path}" already exists', file=sys.stderr)
-        exit(1)
+    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
+    if not app_uri:
+        print(
+            'Remember to set the app URI in the .biolib/config.yml file later, '
+            'and docker image name in the .biolib/config.yml and .github/workflows/biolib.yml files.'
+        )
+    copilot_input = input('Do you want to include Copilot style prompts? [y/N]: ')
+    include_copilot_style = copilot_input.lower() == 'y'
+
+    template_dir = templates.init_template()
+    conflicting_files = []
 
     try:
-        project_name = input('Enter a name for your project: ')
+        # First pass: check for conflicts
+        for root, _, filenames in os.walk(template_dir):
+            relative_dir = os.path.relpath(root, template_dir)
+            destination_dir = cwd if relative_dir == '.' else os.path.join(cwd, relative_dir)
+            for filename in filenames:
+                source_file = os.path.join(root, filename)
+                destination_file = os.path.join(destination_dir, filename)
+                if os.path.exists(destination_file):
+                    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, cwd))
+        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)
+
+        replace_app_uri = app_uri if app_uri else 'PUT_APP_URI_HERE'
+
+        # Second pass: copy files (only if no conflicts)
+        for root, _, filenames in os.walk(template_dir):
+            relative_dir = os.path.relpath(root, template_dir)
+            destination_dir = os.path.join(cwd, relative_dir)
+            os.makedirs(destination_dir, exist_ok=True)
+
+            for filename in filenames:
+                if utils.BASE_URL_IS_PUBLIC_BIOLIB and filename == 'biolib.yml':
+                    continue
+
+                source_file = os.path.join(root, filename)
+                destination_file = os.path.join(destination_dir, filename)
+
+                if not os.path.exists(destination_file):
+                    try:
+                        with open(source_file) as f:
+                            content = f.read()
+
+                        new_content = content.replace('BIOLIB_REPLACE_PYBIOLIB_VERSION', BIOLIB_PACKAGE_VERSION)
+                        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',
+                        )
 
-        os.makedirs(f'{cwd}/.biolib', exist_ok=True)
-        with open(config_file_path, 'w') as config_file:
-            config_file.write(templates.example_app.CONFIG_YML)
+                        with open(destination_file, 'w') as f:
+                            f.write(new_content)
+                    except UnicodeDecodeError:
+                        shutil.copy2(source_file, destination_file)
 
-        if not os.path.exists(readme_path):
+        readme_path = os.path.join(cwd, 'README.md')
+        if not os.path.exists(readme_path) and app_name:
             with open(readme_path, 'w') as readme_file:
-                readme_file.write(f'# {project_name}\n')
+                readme_file.write(f'# {app_name}\n')
 
-        add_copilot_prompts(force=False, silent=True)
+        add_copilot_prompts(force=False, style=include_copilot_style, silent=True)
 
     except KeyboardInterrupt:
         print('\nInit command cancelled.', file=sys.stderr)

{pybiolib-1.2.814.dist-info → pybiolib-1.2.838.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.814
+Version: 1.2.838
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.814.dist-info → pybiolib-1.2.838.dist-info}/RECORD

@@ -1,7 +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/add_copilot_prompts.py,sha256=6gbqYsrTTUFTEEV62fp-UTDwZeJIjDfvywWgtW6AowQ,1967
 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
@@ -23,6 +23,14 @@ biolib/_internal/llm_instructions/.github/prompts/biolib_run_apps.prompt.md,sha2
 biolib/_internal/llm_instructions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/push_application.py,sha256=I7yHGcwK6udc2hVmOQIc1BcQBipAMibEjURMI6HgdXk,12502
 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
+biolib/_internal/templates/init_template/.github/workflows/biolib.yml,sha256=uJ1y06yVkL7H5SpW9XAX0Py4jQef6fgImQ-sZpTGHkc,447
+biolib/_internal/templates/init_template/Dockerfile,sha256=4X9Dpj72mfHcfbEXsr7KURKpHZ0z3vatIvvExOYR7SQ,167
+biolib/_internal/templates/init_template/requirements.txt,sha256=2GnBHsKg4tX5F06Z4YeLuId6jQO3-HGTITsaVBTDG0Y,42
+biolib/_internal/templates/init_template/run.sh,sha256=WvAn7Mr8EopkkBMngGbmqcoJmALSJkocoJ2SByvGBjk,36
+biolib/_internal/templates/init_template/src/run.py,sha256=GS2qGGmFGIthdxdSxZbGktwZc8x3Q2IVLubpp7hEROw,529
+biolib/_internal/templates/templates.py,sha256=-o0VdRMwPhnzL4VlCe3BZYl1aI9HLKtOmNjs6gu9fIQ,101
 biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
 biolib/_internal/types/__init__.py,sha256=WvtlSHh77QhYVTLeRpoPAzqvByLzbEPf_ZqYGHFlQug,247
 biolib/_internal/types/app.py,sha256=Mz2QGD_jESX-K9JYnLWPo4YA__Q_1FQQTk9pvidCohU,118
@@ -74,7 +82,7 @@ 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=PZLzQYbT7u78J1qSCcs-frVfWHohkrZHxLGRSmMdRg4,1061
+biolib/cli/init.py,sha256=VDarbLkkfhyEjlNc8UbjaF3y6J59DOn6ZUjY2MVmNJk,3945
 biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
 biolib/cli/push.py,sha256=pSFEUQkQ69M__eR1nIT9ejW4V4_MtX3lb8ydEc1uKiM,1484
 biolib/cli/run.py,sha256=MCo0ZqW2pHBxOoCI3i5gAx5D0auW9fmxHqkAF4TRhms,2134
@@ -122,8 +130,6 @@ biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
 biolib/sdk/__init__.py,sha256=Z1S5BgpvM87S2o1libtqkYN1CfYUhn_d4ChEJjwdFKM,2356
 biolib/tables.py,sha256=MmruV-nJLc3HbLVJBAiDuDCgS2-4oaUkpoCLLUNYbxQ,1173
-biolib/templates/__init__.py,sha256=Yx62sSyDCDesRQDQgmbDsLpfgEh93fWE8r9u4g2azXk,36
-biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFveE,715
 biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
 biolib/user/sign_in.py,sha256=e_JnykVxemq8eUBD5GmthjDV504CT1Dmn0EshrDCGB8,2085
@@ -133,8 +139,8 @@ 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-1.2.814.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.814.dist-info/METADATA,sha256=dkiANMd2NxMszfRSRvCAlAxPS-3Eas0SQAdzGs_8yOc,1570
-pybiolib-1.2.814.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-pybiolib-1.2.814.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.814.dist-info/RECORD,,
+pybiolib-1.2.838.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.838.dist-info/METADATA,sha256=_KI6b_KNTAPIdypWZLFOcEeCvK5wk7BfF-SzMq79AZI,1570
+pybiolib-1.2.838.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+pybiolib-1.2.838.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.838.dist-info/RECORD,,

biolib/templates/__init__.py

@@ -1 +0,0 @@
-import biolib.templates.example_app

biolib/templates/example_app.py

@@ -1,30 +0,0 @@
-CONFIG_YML = '''\
-biolib_version: 2
-
-modules:
-    main:
-        image: 'dockerhub://python:3.9-slim'
-        command: |
-            python3 -c "
-            import argparse
-            parser = argparse.ArgumentParser()
-            parser.add_argument('--name')
-            args = parser.parse_args()
-            print(f'Hello there, {args.name}!')
-            "
-        working_directory: /home/biolib/
-        input_files:
-            - COPY / /home/biolib/
-        output_files:
-            - COPY /home/biolib/ /
-
-arguments:
-    -
-        default_value: Charles Darwin
-        description: What is your name?
-        key: '--name'
-        key_value_separator: ' '
-        required: true
-        type: text
-
-'''