🏗️ Fix project skeleton and align dependencies

[Miyamura80]

Summary

• Recreated missing skeleton code structure as empty placeholders to fix module resolution issues.
• Added __init__.py files to all source directories to satisfy Ruff's INP001 (implicit namespace package) rule and improve LSP reliability.
• Promoted pydantic, numpy, and requests to direct dependencies to fix deptry transitive dependency warnings.
• Configured deptry in pyproject.toml to ignore development/testing tools in CI checks.

[greptile-apps]

Greptile Overview

Greptile Summary

This PR fixes module resolution by adding __init__.py files to all source directories and aligns dependency management by promoting transitive dependencies to direct ones.

Key Changes:

• Added 54+ empty __init__.py files across src/, alembic/, and subdirectories to fix Ruff's INP001 rule violations
• Promoted pydantic>=2.10.0, numpy>=1.26.0, and requests>=2.31.0 from transitive to direct dependencies
• Configured deptry to ignore development/testing tools (pytest, vulture, pylint, etc.) in CI checks
• Added new src/utils/integration/telegram.py module for Telegram Bot API integration
• Reformatted long regex pattern in src/utils/logging_config.py

Issues Found:

• telegram.py references global_config.TELEGRAM_BOT_TOKEN and global_config.telegram.chat_ids which don't exist in common/global_config.py - this will cause runtime errors when instantiating the Telegram class
• Missing setup_logging() call in telegram.py per project logging standards

Confidence Score: 3/5

• This PR has critical runtime errors that must be fixed before merging
• The skeleton structure changes are safe, but the new telegram.py module references undefined config fields (TELEGRAM_BOT_TOKEN and telegram.chat_ids) that will cause AttributeError at runtime. Dependency changes are correct and lock file is properly updated.
• Pay close attention to src/utils/integration/telegram.py - requires config changes before this code can run

Important Files Changed

Filename	Overview
src/utils/integration/telegram.py	Added Telegram bot integration with message sending/deletion, but missing TELEGRAM_BOT_TOKEN in config and logging setup
pyproject.toml	Promoted pydantic, numpy, requests to direct dependencies and configured deptry ignore rules
src/utils/logging_config.py	Reformatted long regex pattern for better readability
uv.lock	Updated lock file to reflect new direct dependencies (pydantic, numpy, requests)

[greptile-apps]

_{3 files reviewed, 3 comments}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

TELEGRAM_BOT_TOKEN not defined in common/global_config.py. Add this field to the Config class or this will fail at runtime.

Prompt To Fix With AI

This is a comment left during a code review.
Path: src/utils/integration/telegram.py
Line: 15:15

Comment:
`TELEGRAM_BOT_TOKEN` not defined in `common/global_config.py`. Add this field to the `Config` class or this will fail at runtime.

How can I resolve this? If you propose a fix, please make it concise.

[greptile-apps]

global_config.telegram.chat_ids not defined in config structure. Add the telegram field with nested chat_ids to Config class or this will fail at runtime.

Prompt To Fix With AI

This is a comment left during a code review.
Path: src/utils/integration/telegram.py
Line: 84:84

Comment:
`global_config.telegram.chat_ids` not defined in config structure. Add the `telegram` field with nested `chat_ids` to `Config` class or this will fail at runtime.

How can I resolve this? If you propose a fix, please make it concise.

[greptile-apps]

Missing setup_logging() call. Per logging standards, import and call setup_logging() from src.utils.logging_config at module level.

Suggested change

	"""Telegram Bot integration for sending alerts and notifications."""
	import requests
	from loguru import logger as log
	from requests.exceptions import RequestException
	from common import global_config
	"""Telegram Bot integration for sending alerts and notifications."""
	import requests
	from loguru import logger as log
	from requests.exceptions import RequestException
	from common import global_config
	from src.utils.logging_config import setup_logging
	setup_logging()

Context Used: Context from dashboard - Standards for using logging in the project. (source)

_{Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!}

Prompt To Fix With AI

This is a comment left during a code review.
Path: src/utils/integration/telegram.py
Line: 1:7

Comment:
Missing `setup_logging()` call. Per logging standards, import and call `setup_logging()` from `src.utils.logging_config` at module level.

```suggestion
"""Telegram Bot integration for sending alerts and notifications."""

import requests
from loguru import logger as log
from requests.exceptions import RequestException

from common import global_config
from src.utils.logging_config import setup_logging

setup_logging()
```

**Context Used:** Context from `dashboard` - Standards for using logging in the project. ([source](https://app.greptile.com/review/custom-context?memory=ec5af2c7-d139-40b0-99e5-0f4bf1fee1d7))

<sub>Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!</sub>

How can I resolve this? If you propose a fix, please make it concise.