pybiolib 1.2.883__py3-none-any.whl → 1.2.1890__py3-none-any.whl

biolib/cli/auth.py

@@ -3,7 +3,7 @@ import sys
 
 import click
 
-from biolib import api, biolib_errors
+from biolib import api
 from biolib.biolib_api_client.api_client import BiolibApiClient
 from biolib.biolib_logging import logger, logger_no_user_data
 from biolib.user import sign_in, sign_out
@@ -35,23 +35,11 @@ def logout() -> None:
 def whoami() -> None:
     client = BiolibApiClient.get()
     if client.is_signed_in:
-        user_uuid = None
-        if client.access_token is None:
-            print('Unable to fetch user credentials. Please try logging out and logging in again.')
-            exit(1)
-        try:
-            user_uuid = client.decode_jwt_without_checking_signature(jwt=client.access_token)['payload']['public_id']
-        except biolib_errors.BioLibError as error:
-            print(
-                f'Unable to reference user public_id in access token:\n {error.message}',
-                file=sys.stderr,
-            )
-            exit(1)
-        response = api.client.get(path=f'/user/{user_uuid}/')
+        response = api.client.get(path='/users/me/')
         user_dict = response.json()
         email = user_dict['email']
-        intrinsic_account = [account for account in user_dict['accounts'] if account['role'] == 'intrinsic'][0]
-        display_name = intrinsic_account['display_name']
+        display_name = user_dict['account']['display_name']
+
         print(f'Name: {display_name}\nEmail: {email}\nLogged into: {client.base_url}')
     else:
         print('Not logged in', file=sys.stderr)

biolib/cli/data_record.py

@@ -1,9 +1,11 @@
 import json
 import logging
 import os
+import sys
 from typing import Dict, List
 
 import click
+import rich.progress
 
 from biolib._data_record.data_record import DataRecord
 from biolib.biolib_api_client import BiolibApiClient
@@ -80,3 +82,83 @@ def describe(uri: str, output_as_json: bool) -> None:
             size_string = str(file_info['size_bytes'])
             leading_space_string = ' ' * (10 - len(size_string))
             print(f"{leading_space_string}{size_string}    {file_info['path']}")
+
+
+@data_record.command(help='Delete a Data Record')
+@click.argument('uri', required=True)
+def delete(uri: str) -> None:
+    record = DataRecord.get_by_uri(uri=uri)
+
+    print(f'You are about to delete the data record: {record.uri}')
+    print('This action cannot be undone.')
+
+    confirmation = input(f'To confirm deletion, please type the data record name "{record.name}": ')
+    if confirmation != record.name:
+        print('Data record name does not match. Deletion cancelled.')
+        return
+
+    record.delete()
+    print(f'Data record {record.uri} has been deleted.')
+
+
+def _clone_data_record_with_progress(
+    source_record: DataRecord,
+    dest_record: DataRecord,
+) -> None:
+    # pylint: disable=protected-access
+    total_size_in_bytes = source_record._get_zip_size_bytes()
+    # pylint: enable=protected-access
+
+    if total_size_in_bytes == 0:
+        logger.info('Source data record has no data to clone')
+        return
+
+    if sys.stdout.isatty():
+        with rich.progress.Progress(
+            rich.progress.TextColumn('[bold blue]{task.description}'),
+            rich.progress.BarColumn(),
+            rich.progress.TaskProgressColumn(),
+            rich.progress.TimeRemainingColumn(),
+            rich.progress.TransferSpeedColumn(),
+        ) as progress:
+            task_id = progress.add_task('Cloning data record', total=total_size_in_bytes)
+
+            def on_progress(bytes_uploaded: int, _total_bytes: int) -> None:
+                progress.update(task_id, completed=bytes_uploaded)
+
+            DataRecord.clone(source=source_record, destination=dest_record, on_progress=on_progress)
+    else:
+        logger.info(f'Cloning ~{round(total_size_in_bytes / 10**6)}mb of data')
+        DataRecord.clone(source=source_record, destination=dest_record)
+
+
+def _get_or_create_destination_record(destination_uri: str) -> Optional[DataRecord]:
+    try:
+        return DataRecord.get_by_uri(uri=destination_uri)
+    except Exception:
+        print(f'Destination data record "{destination_uri}" does not exist.')
+        confirmation = input('Would you like to create it? [y/N]: ')
+        if confirmation.lower() != 'y':
+            print('Clone cancelled.')
+            return None
+
+        return DataRecord.create(destination=destination_uri)
+
+
+@data_record.command(help='Clone a Data Record to another location')
+@click.argument('source_uri', required=True)
+@click.argument('destination_uri', required=True)
+def clone(source_uri: str, destination_uri: str) -> None:
+    BiolibApiClient.assert_is_signed_in(authenticated_action_description='clone a Data Record')
+
+    logger.info(f'Fetching source data record: {source_uri}')
+    source_record = DataRecord.get_by_uri(uri=source_uri)
+
+    logger.info(f'Checking destination data record: {destination_uri}')
+    dest_record = _get_or_create_destination_record(destination_uri)
+    if dest_record is None:
+        return
+
+    logger.info(f'Cloning from {source_record.uri} to {dest_record.uri}...')
+    _clone_data_record_with_progress(source_record=source_record, dest_record=dest_record)
+    logger.info('Clone completed successfully.')

biolib/cli/index.py

@@ -0,0 +1,32 @@
+import json
+import logging
+import sys
+
+import click
+
+from biolib._index.index import Index
+from biolib.biolib_errors import BioLibError
+from biolib.biolib_logging import logger, logger_no_user_data
+
+
+@click.group(help='Manage Indexes')
+def index() -> None:
+    logger.configure(default_log_level=logging.INFO)
+    logger_no_user_data.configure(default_log_level=logging.INFO)
+
+
+@index.command(help='Create an Index')
+@click.argument('uri', required=True)
+@click.option('--config-path', required=True, type=click.Path(exists=True), help='Path to JSON config file')
+def create(uri: str, config_path: str) -> None:
+    try:
+        Index.create_from_config_file(uri=uri, config_path=config_path)
+    except json.JSONDecodeError as error:
+        print(f'Error: Invalid JSON in config file: {error}', file=sys.stderr)
+        sys.exit(1)
+    except BioLibError as error:
+        print(f'Error creating index: {error.message}', file=sys.stderr)
+        sys.exit(1)
+    except Exception as error:
+        print(f'Error reading config file: {error}', file=sys.stderr)
+        sys.exit(1)

biolib/cli/init.py

@@ -1,98 +1,420 @@
 import os
 import shutil
+import subprocess
 import sys
 
 import click
 
-from biolib import utils  # Import like this to let BASE_URL_IS_PUBLIC_BIOLIB be set correctly
+from biolib import (
+    biolib_errors,
+    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.add_gui_files import add_gui_files
+from biolib._internal.http_client import HttpClient, HttpError
+from biolib._internal.string_utils import normalize_for_docker_tag
 from biolib._internal.templates import templates
+from biolib._internal.utils import get_pip_command
+from biolib.api import client as api_client
+from biolib.biolib_api_client.api_client import BiolibApiClient
+from biolib.biolib_api_client.biolib_app_api import BiolibAppApi
+from biolib.biolib_logging import logger_no_user_data
+from biolib.typing_utils import Dict, List, Optional, Set
+from biolib.user.sign_in import sign_in
 from biolib.utils import BIOLIB_PACKAGE_VERSION
 
 
-@click.command(help='Initialize a BioLib project', hidden=True)
-def init() -> None:
+def _get_latest_pypi_version() -> Optional[str]:
+    try:
+        response = HttpClient.request(
+            url='https://pypi.org/pypi/pybiolib/json',
+            timeout_in_seconds=5,
+            retries=1,
+        )
+        data = response.json()
+        version = data.get('info', {}).get('version')
+        if isinstance(version, str):
+            return version
+        return None
+    except Exception as error:
+        logger_no_user_data.debug(f'Failed to fetch latest version from PyPI: {error}')
+        return None
+
+
+def _is_current_version_outdated(current: str, latest: str) -> bool:
+    try:
+        current_parts = [int(x) for x in current.split('.')]
+        latest_parts = [int(x) for x in latest.split('.')]
+        return current_parts < latest_parts
+    except (ValueError, AttributeError):
+        return False
+
+
+def _check_version_and_prompt_upgrade() -> bool:
+    latest_version = _get_latest_pypi_version()
+    if latest_version and _is_current_version_outdated(BIOLIB_PACKAGE_VERSION, latest_version):
+        print(f'A newer version of pybiolib is available: {latest_version} (current: {BIOLIB_PACKAGE_VERSION})')
+        pip_command = get_pip_command()
+        print(f'To upgrade, run: {pip_command} install --upgrade pybiolib')
+        print()
+        continue_input = input('Do you want to continue with the current version? [y/N]: ')
+        if continue_input.lower() not in ['y', 'yes']:
+            print('Please upgrade pybiolib and run `biolib init` again.')
+            return False
+    return True
+
+
+def _prompt_for_app_uri(prompt_text: str) -> Optional[str]:
+    app_uri = input(prompt_text)
+
+    if app_uri and not app_uri.startswith('@'):
+        try:
+            response = api_client.get('system/enterprise/config/', authenticate=False)
+            config = response.json()
+            prefix = config.get('resource_hostname_prefix')
+            if prefix:
+                app_uri = f'@{prefix}/{app_uri}'
+                print(f'Detected enterprise deployment, using URI: {app_uri}')
+        except HttpError as error:
+            if error.code not in [404, 501]:
+                print(f'Warning: Could not detect enterprise configuration: {error}')
+        except Exception as error:
+            print(f'Warning: Could not detect enterprise configuration: {error}')
+
+    return app_uri if app_uri else None
+
+
+def _validate_or_create_app(app_uri: str) -> bool:
+    try:
+        if BiolibApiClient.is_reauthentication_needed():
+            sign_in_input = input('You need to sign in to validate/create apps. Would you like to sign in? [y/N]: ')
+            if sign_in_input.lower() in ['y', 'yes']:
+                sign_in()
+            else:
+                print('Skipping app validation and creation. You can set the URI in .biolib/config.yml later.')
+                return False
+
+        BiolibAppApi.get_by_uri(app_uri)
+        print(f'App {app_uri} already exists.')
+    except biolib_errors.NotFound:
+        create_app_input = input(f'App {app_uri} does not exist. Would you like to create it? [y/N]: ')
+        if create_app_input.lower() in ['y', 'yes']:
+            try:
+                BiolibAppApi.create_app(app_uri)
+                print(f'Successfully created app {app_uri}')
+            except Exception as error:
+                print(f'Failed to create app {app_uri}: {str(error)}')
+                print('You can create the app manually later or set the URI in .biolib/config.yml')
+        else:
+            print('App creation skipped. You can create the app manually later or set the URI in .biolib/config.yml')
+    except Exception as error:
+        print(f'Failed to validate app {app_uri}: {str(error)}')
+        print('Continuing with initialization...')
+
+    return True
+
+
+def _find_conflicting_files(template_dir: str, cwd: str) -> List[str]:
+    conflicting_files: List[str] = []
+    for root, dirs, filenames in os.walk(template_dir):
+        dirs[:] = [d for d in dirs if '__pycache__' not in d]
+        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))
+    return conflicting_files
+
+
+def _prompt_for_overwrites(conflicting_files: List[str]) -> Set[str]:
+    files_to_overwrite: Set[str] = set()
+    if conflicting_files:
+        print('The following files already exist and would be overwritten:')
+        for conflicting_file in conflicting_files:
+            print(f'  {conflicting_file}')
+        print()
+
+        for conflicting_file in conflicting_files:
+            choice = input(f'Overwrite {conflicting_file}? [y/N]: ').lower().strip()
+            if choice in ['y', 'yes']:
+                files_to_overwrite.add(conflicting_file)
+    return files_to_overwrite
+
+
+def _copy_template_files(
+    template_dir: str,
+    cwd: str,
+    files_to_overwrite: Set[str],
+    replacements: Dict[str, str],
+) -> None:
+    for root, dirs, filenames in os.walk(template_dir):
+        dirs[:] = [d for d in dirs if '__pycache__' not in d]
+        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)
+            relative_file_path = os.path.relpath(destination_file, cwd)
+
+            if not os.path.exists(destination_file) or relative_file_path in files_to_overwrite:
+                try:
+                    with open(source_file) as f:
+                        content = f.read()
+
+                    new_content = content
+                    for old_value, new_value in replacements.items():
+                        new_content = new_content.replace(old_value, new_value)
+
+                    with open(destination_file, 'w') as f:
+                        f.write(new_content)
+                except UnicodeDecodeError:
+                    shutil.copy2(source_file, destination_file)
+
+
+def _create_readme_if_needed(cwd: str, app_name: Optional[str]) -> None:
+    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')
+
+
+def _copy_gitignore(cwd: str) -> None:
+    gitignore_template_dir = templates.gitignore_template()
+    source_file = os.path.join(gitignore_template_dir, '.gitignore')
+    destination_file = os.path.join(cwd, '.gitignore')
+    if not os.path.exists(destination_file):
+        shutil.copy2(source_file, destination_file)
+
+
+def _copy_github_workflow(cwd: str, replacements: Dict[str, str]) -> None:
+    workflow_template_dir = templates.github_workflow_template()
+    source_file = os.path.join(workflow_template_dir, '.github', 'workflows', 'biolib.yml')
+    destination_dir = os.path.join(cwd, '.github', 'workflows')
+    destination_file = os.path.join(destination_dir, 'biolib.yml')
+
+    if not os.path.exists(destination_file):
+        os.makedirs(destination_dir, exist_ok=True)
+        with open(source_file) as f:
+            content = f.read()
+        for old_value, new_value in replacements.items():
+            content = content.replace(old_value, new_value)
+        with open(destination_file, 'w') as f:
+            f.write(content)
+
+
+def _prompt_and_run_yarn_install() -> None:
+    yarn_install_input = input('Do you want to run yarn install? [Y/n]: ')
+    if yarn_install_input.lower() not in ['n', 'no']:
+        print('Running yarn install...')
+        try:
+            subprocess.run(['yarn', 'install'], check=True)
+            print('yarn install completed successfully.')
+        except FileNotFoundError:
+            print(
+                'Error: yarn is not installed or not found in PATH. Please install yarn and run yarn install manually.'
+            )
+        except subprocess.CalledProcessError as error:
+            print(f'yarn install failed with exit code {error.returncode}. Please run yarn install manually.')
+        except Exception as error:
+            print(f'yarn install failed: {error}. Please run yarn install manually.')
+
+
+def _create_dashboard_dockerfile(cwd: str) -> None:
+    gui_template_dir = templates.gui_template()
+    gui_dockerfile = os.path.join(gui_template_dir, 'Dockerfile')
+    destination_file = os.path.join(cwd, 'Dockerfile')
+
+    if not os.path.exists(destination_file):
+        with open(gui_dockerfile) as f:
+            lines = f.readlines()
+
+        gui_builder_lines = []
+        for line in lines:
+            gui_builder_lines.append(line)
+            if line.strip() == 'RUN yarn build':
+                break
+
+        dist_export_stage = '\nFROM scratch AS dist_export\nCOPY --from=gui_builder /home/biolib/gui/dist /dist\n'
+        with open(destination_file, 'w') as f:
+            f.writelines(gui_builder_lines)
+            f.write(dist_export_stage)
+
+
+def _copy_gui_files_for_dashboard(cwd: str, app_name: str) -> None:
+    gui_template_dir = templates.gui_template()
+    gui_root_files = ['package.json', 'vite.config.mts', '.yarnrc.yml']
+
+    for root, _, filenames in os.walk(gui_template_dir):
+        relative_dir = os.path.relpath(root, gui_template_dir)
+
+        for filename in filenames:
+            if filename == 'Dockerfile':
+                continue
+
+            if filename in gui_root_files:
+                destination_dir = cwd
+            else:
+                if relative_dir == '.':
+                    destination_dir = os.path.join(cwd, 'gui')
+                else:
+                    destination_dir = os.path.join(cwd, 'gui', relative_dir)
+
+            source_file = os.path.join(root, filename)
+            destination_file = os.path.join(destination_dir, filename)
+
+            if not os.path.exists(destination_file):
+                os.makedirs(destination_dir, exist_ok=True)
+                try:
+                    with open(source_file) as f:
+                        content = f.read()
+                    new_content = content.replace('BIOLIB_REPLACE_APP_NAME', app_name)
+                    with open(destination_file, 'w') as f:
+                        f.write(new_content)
+                except UnicodeDecodeError:
+                    shutil.copy2(source_file, destination_file)
+
+
+def _init_dashboard() -> None:
+    if not _check_version_and_prompt_upgrade():
+        return
+
     cwd = os.getcwd()
+    app_uri = _prompt_for_app_uri('What URI do you want to create the dashboard under? (leave blank to skip): ')
+    app_name = app_uri.split('/')[-1] if app_uri else None
+
+    if app_uri:
+        if not _validate_or_create_app(app_uri):
+            return
+    else:
+        print(
+            'Remember to set the app URI in the .biolib/config.yml file later, '
+            'and update the .github/workflows/biolib.yml file.'
+        )
+
+    dashboard_template_dir = templates.dashboard_template()
+
+    try:
+        conflicting_files = _find_conflicting_files(dashboard_template_dir, cwd)
+        files_to_overwrite = _prompt_for_overwrites(conflicting_files)
+
+        replace_app_uri = app_uri if app_uri else 'PUT_APP_URI_HERE'
+        replace_app_name = app_name if app_name else 'biolib-dashboard'
 
-    app_uri = input('What URI do you want to create the application under? (leave blank to skip): ')
+        replacements = {
+            'BIOLIB_REPLACE_APP_URI': replace_app_uri,
+            'BIOLIB_REPLACE_APP_NAME': replace_app_name,
+        }
+
+        _copy_template_files(dashboard_template_dir, cwd, files_to_overwrite, replacements)
+        _create_readme_if_needed(cwd, app_name)
+        _copy_gitignore(cwd)
+        _copy_github_workflow(
+            cwd,
+            {
+                'BIOLIB_REPLACE_APP_URI': replace_app_uri,
+                'BIOLIB_REPLACE_BUILD_COMMAND': 'docker build --target dist_export -o type=local,dest=. .',
+            },
+        )
+        _create_dashboard_dockerfile(cwd)
+        _copy_gui_files_for_dashboard(cwd, replace_app_name)
+        _prompt_and_run_yarn_install()
+
+        print('Dashboard template initialized successfully.')
+
+    except KeyboardInterrupt:
+        print('\nInit command cancelled.', file=sys.stderr)
+        exit(1)
+
+
+@click.command(help='Initialize a BioLib project', hidden=True)
+@click.argument('template_type', required=False, default=None)
+def init(template_type: Optional[str]) -> None:
+    if template_type == 'dashboard':
+        _init_dashboard()
+        return
+
+    if template_type is not None:
+        print(f"Unknown template type: '{template_type}'. Available templates: dashboard")
+        print('Run `biolib init` without arguments for the default Python application template.')
+        return
+
+    if not _check_version_and_prompt_upgrade():
+        return
+
+    cwd = os.getcwd()
+    app_uri = _prompt_for_app_uri('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:
+    docker_tag = normalize_for_docker_tag(app_name) if app_name else None
+
+    if app_uri:
+        if not _validate_or_create_app(app_uri):
+            return
+    else:
         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 = []
-    files_to_overwrite = set()
+    advanced_setup_input = input('Do you want to set up advanced features like Copilot and GUI? [y/N]: ')
+    advanced_setup = advanced_setup_input.lower() == 'y'
+    include_copilot = False
+    include_gui = False
+    if advanced_setup:
+        copilot_enabled_input = input('Do you want to include Copilot instructions and prompts? [y/N]: ')
+        include_copilot = copilot_enabled_input.lower() == 'y'
+        include_gui_input = input('Do you want to include GUI setup? [y/N]: ')
+        include_gui = include_gui_input.lower() == 'y'
+
+    init_template_dir = templates.init_template()
 
     try:
-        # First pass: check for conflicts
-        for root, dirs, filenames in os.walk(template_dir):
-            dirs[:] = [d for d in dirs if '__pycache__' not in d]
-            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 already exist and would be overwritten:')
-            for conflicting_file in conflicting_files:
-                print(f'  {conflicting_file}')
-            print()
-
-            for conflicting_file in conflicting_files:
-                choice = input(f'Overwrite {conflicting_file}? [y/N]: ').lower().strip()
-                if choice in ['y', 'yes']:
-                    files_to_overwrite.add(conflicting_file)
+        conflicting_files = _find_conflicting_files(init_template_dir, cwd)
+        files_to_overwrite = _prompt_for_overwrites(conflicting_files)
 
         replace_app_uri = app_uri if app_uri else 'PUT_APP_URI_HERE'
+        replace_app_name = app_name if app_name else 'biolib-app'
+
+        gui_config = "main_output_file: '/result.html'\n" if include_gui else ''
+        gui_mv_command = 'mv result.html output/result.html\n' if include_gui else ''
+
+        replacements = {
+            'BIOLIB_REPLACE_PYBIOLIB_VERSION': BIOLIB_PACKAGE_VERSION,
+            'BIOLIB_REPLACE_APP_URI': replace_app_uri,
+            'BIOLIB_REPLACE_DOCKER_TAG': docker_tag if docker_tag else 'PUT_DOCKER_TAG_HERE',
+            'BIOLIB_REPLACE_APP_NAME': replace_app_name,
+            'BIOLIB_REPLACE_GUI_CONFIG\n': gui_config,
+            'BIOLIB_REPLACE_GUI_MV_COMMAND\n': gui_mv_command,
+        }
+
+        _copy_template_files(init_template_dir, cwd, files_to_overwrite, replacements)
+        _create_readme_if_needed(cwd, app_name)
+        _copy_gitignore(cwd)
+        build_tag = docker_tag if docker_tag else 'PUT_DOCKER_TAG_HERE'
+        _copy_github_workflow(
+            cwd,
+            {
+                'BIOLIB_REPLACE_APP_URI': replace_app_uri,
+                'BIOLIB_REPLACE_BUILD_COMMAND': f'docker build -t {build_tag}:latest .',
+            },
+        )
+
+        if include_copilot:
+            add_copilot_prompts(force=False, silent=True)
 
-        # Second pass: copy files (only if no conflicts)
-        for root, dirs, filenames in os.walk(template_dir):
-            dirs[:] = [d for d in dirs if '__pycache__' not in d]
-            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)
-                relative_file_path = os.path.relpath(destination_file, cwd)
-
-                if not os.path.exists(destination_file) or relative_file_path in files_to_overwrite:
-                    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)
+        if include_gui:
+            add_gui_files(force=False, silent=True)
+            _prompt_and_run_yarn_install()
 
     except KeyboardInterrupt:
         print('\nInit command cancelled.', file=sys.stderr)

biolib/cli/lfs.py

@@ -13,7 +13,7 @@ from biolib.biolib_logging import logger, logger_no_user_data
 from biolib.typing_utils import Optional
 
 
-@click.group(help='Manage Large File Systems')
+@click.group(help='Manage Large File Systems', hidden=True)
 def lfs() -> None:
     pass