pybiolib 1.2.814__tar.gz → 1.2.841__tar.gz

{pybiolib-1.2.814 → pybiolib-1.2.841}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.814
+Version: 1.2.841
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.814 → pybiolib-1.2.841}/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():

pybiolib-1.2.841/biolib/_internal/templates/__init__.py

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

pybiolib-1.2.841/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

pybiolib-1.2.841/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 }}

pybiolib-1.2.841/biolib/_internal/templates/init_template/Dockerfile

@@ -0,0 +1,10 @@
+FROM python:3.13.3-slim
+WORKDIR /home/biolib/
+
+COPY requirements.txt .
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY run.sh .
+COPY run.py .
+
+RUN mkdir output

pybiolib-1.2.841/biolib/_internal/templates/init_template/requirements.txt

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

pybiolib-1.2.841/biolib/_internal/templates/init_template/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)

pybiolib-1.2.841/biolib/_internal/templates/init_template/run.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+set -e
+python3 run.py "$@"

pybiolib-1.2.841/biolib/_internal/templates/templates.py

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

pybiolib-1.2.841/biolib/cli/init.py

@@ -0,0 +1,89 @@
+import os
+import shutil
+import sys
+
+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.templates import templates
+from biolib.utils import BIOLIB_PACKAGE_VERSION
+
+
+@click.command(help='Initialize a BioLib project', hidden=True)
+def init() -> None:
+    cwd = os.getcwd()
+
+    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:
+        # 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',
+                        )
+
+                        with open(destination_file, 'w') as f:
+                            f.write(new_content)
+                    except UnicodeDecodeError:
+                        shutil.copy2(source_file, destination_file)
+
+        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'# {app_name}\n')
+
+        add_copilot_prompts(force=False, style=include_copilot_style, silent=True)
+
+    except KeyboardInterrupt:
+        print('\nInit command cancelled.', file=sys.stderr)
+        exit(1)

{pybiolib-1.2.814 → pybiolib-1.2.841}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.814"
+version = "1.2.841"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"

pybiolib-1.2.814/biolib/cli/init.py

@@ -1,35 +0,0 @@
-import os
-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)
-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)
-
-    try:
-        project_name = input('Enter a name for your project: ')
-
-        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)
-
-        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-1.2.814/biolib/templates/__init__.py

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

pybiolib-1.2.814/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
-
-'''