ci: add lint, format-check, and security gates to CI pipeline

[zoeshawwang]

Add three new CI enforcement layers that were previously missing:

• ruff lint + format check job (was only in Makefile, never enforced in CI)
• pip-audit dependency vulnerability scanning job
• Expanded ruff rules: S (bandit/security), B (bugbear), UP (pyupgrade)

Fix all resulting lint violations across src/ and tests/:

• B904: add proper exception chains (raise from e)
• E501: wrap long lines in help strings and docstrings
• S110: annotate intentional try/except/pass with noqa + justification
• S101: replace assert with proper guard in invoke_cmd
• B007: prefix unused loop variable with underscore
• UP022: use capture_output instead of stdout/stderr=PIPE

Add matching Makefile targets (format-check, security) and pin pip-audit in dev dependencies for reproducible local runs.

Change-Id: I94d2355be83f4c44b144f217d2a0d0d5b74f5e2f
Co-developed-by: Claude noreply@anthropic.com

[Copilot]

Pull request overview

This PR adds CI enforcement for code quality and security checks (ruff lint/format + pip-audit) and updates the codebase to comply with the expanded Ruff rule set (security/bugbear/pyupgrade), primarily via exception chaining, safer typing, and formatting cleanups across src/ and tests/.

Changes:

• Add CI jobs for ruff check, ruff format --check, and pip-audit, plus matching Makefile targets.
• Expand Ruff lint rule selection to include S, B, and UP, with test-specific per-file ignores.
• Refactor Python code and tests to fix resulting lint violations (exception chaining, pyupgrade tweaks, long-line wrapping, typing modernizations).

Reviewed changes

Copilot reviewed 55 out of 55 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
tests/unit/test_tool_cmd.py	Reformats unit tests and removes unused imports to satisfy Ruff rules.
tests/unit/test_super_agent_yaml.py	Minor formatting simplifications in YAML parsing tests.
tests/unit/test_super_agent_state.py	Test formatting and context-manager style updates.
tests/unit/test_super_agent_repl.py	Adds exception chaining for async iterator StopIteration handling; formatting cleanups.
tests/unit/test_super_agent_render.py	Formatting updates and minor string literal normalization for render tests.
tests/unit/test_super_agent_helpers.py	Formatting updates and adds blank lines to satisfy style rules.
tests/unit/test_skill_cmd.py	Reformats skill command unit tests; removes unused imports and wraps long lines.
tests/unit/test_sandbox_helpers.py	Updates multi-context-manager syntax and formatting.
tests/unit/test_output.py	Removes unused imports and reformats long expressions in output formatter tests.
tests/unit/test_model_helpers.py	Updates module docstring and formatting for lint compliance.
tests/unit/test_main.py	Minor whitespace/style cleanup.
tests/unit/test_error.py	Removes unused imports.
tests/unit/test_config.py	Refactors with blocks and list formatting for lint compliance.
tests/integration/test_tool_cmd.py	Reformats CLI integration tests for tool commands.
tests/integration/test_super_agent_run_cmd.py	Adds exception chaining and reformats integration tests for sa run.
tests/integration/test_super_agent_invoke_cmd.py	Adds exception chaining and reformats integration tests for sa invoke.
tests/integration/test_super_agent_crud_cmd.py	Reformats integration tests for super-agent CRUD.
tests/integration/test_super_agent_conv_cmd.py	Reformats conversation subcommand integration tests and patching helpers.
tests/integration/test_super_agent_chat_cmd.py	Adds exception chaining and reformats chat integration tests.
tests/integration/test_super_agent_apply_cmd.py	Reformats apply/render integration tests.
tests/integration/test_skill_cmd.py	Reformats skill integration tests and patching blocks.
tests/integration/test_sandbox_cmd.py	Reformats sandbox integration tests; fixes unused loop var naming.
tests/integration/test_model_cmd.py	Reformats model integration tests and SDK patch helpers.
tests/integration/test_main.py	Minor whitespace/style cleanup.
tests/integration/test_install_script.py	Uses capture_output=True for subprocess calls (pyupgrade).
tests/integration/test_config_cmd.py	Refactors with blocks to modern syntax and formatting.
tests/integration/test_cli_basic.py	Removes unused imports and refactors with blocks; formatting updates.
src/agentrun_cli/commands/tool_cmd.py	Typing modernization (PEP 604), exception-message wrapping, and formatting for ruff compliance.
src/agentrun_cli/commands/super_agent/run_cmd.py	Reformats click options and adds raise ... from e for usage errors.
src/agentrun_cli/commands/super_agent/invoke_cmd.py	Typing modernization, removes assert, and adds exception chaining for JSON/usage errors.
src/agentrun_cli/commands/super_agent/crud_cmd.py	Reformats click options and multi-arg functions; minor string wrapping.
src/agentrun_cli/commands/super_agent/conv_cmd.py	Minor formatting cleanup in serialization output.
src/agentrun_cli/commands/super_agent/chat_cmd.py	Reformats click options and adds exception chaining on usage errors.
src/agentrun_cli/commands/super_agent/apply_cmd.py	Adds exception chaining for YAML schema errors; refactors formatting in render/apply.
src/agentrun_cli/commands/super_agent/_helpers.py	Typing modernization for ctx config helper.
src/agentrun_cli/commands/skill_cmd.py	Typing modernization, file open cleanup, noqa justification for broad exception, and formatting.
src/agentrun_cli/commands/sandbox/template_cmd.py	Typing import cleanup and extensive click option formatting/wrapping.
src/agentrun_cli/commands/sandbox/process_cmd.py	Wraps long help text to satisfy line-length rules.
src/agentrun_cli/commands/sandbox/lifecycle_cmd.py	Wraps long option help and refactors formatting; minor import spacing.
src/agentrun_cli/commands/sandbox/exec_cmd.py	Wraps long option help and usage error messages; formatting updates.
src/agentrun_cli/commands/sandbox/browser_cmd.py	Wraps long option help and refactors output formatting blocks.
src/agentrun_cli/commands/sandbox/_helpers.py	Typing modernization and file open cleanup.
src/agentrun_cli/commands/model_cmd.py	Typing modernization, file open cleanup, and click option wrapping.
src/agentrun_cli/commands/config_cmd.py	Wraps long output strings to satisfy line-length rules.
src/agentrun_cli/_utils/super_agent_yaml.py	Typing modernization (PEP 604 / builtin generics) and minor formatting.
src/agentrun_cli/_utils/super_agent_state.py	Typing modernization and file open cleanup.
src/agentrun_cli/_utils/super_agent_repl.py	Switches to collections.abc.Callable, typing modernization, and minor formatting.
src/agentrun_cli/_utils/super_agent_render.py	Typing modernization, adds noqa justifications for broad exception swallowing, and formatting.
src/agentrun_cli/_utils/output.py	Typing modernization and import cleanup; minor signature refactors.
src/agentrun_cli/_utils/inner_client.py	Typing modernization for client factory.
src/agentrun_cli/_utils/error.py	Switches to collections.abc.Callable and removes unused whitespace/import patterns.
src/agentrun_cli/_utils/config.py	Typing modernization, import cleanup, and formatting refactors.
pyproject.toml	Adds pip-audit dev dependency, expands Ruff rule selection, and adds per-file ignores for tests.
Makefile	Adds format-check and security targets for local enforcement parity with CI.
.github/workflows/ci.yml	Adds new CI jobs for Ruff lint/format checking and pip-audit vulnerability scanning.

Comments suppressed due to low confidence (1)

pyproject.toml:57

• Same as above for the optional dev extras: pip-audit is added as ">=2.7.0" rather than being pinned. If you want reproducible audit behavior, use an exact pin (or bounded range) here as well so pip install .[dev] always pulls the expected version.

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0", "pytest-cov>=6.0.0",
    "pytest-asyncio>=1.2.0",
    "pyinstaller>=6.0.0",
    "ruff>=0.14.0",
    "mypy>=1.11.0",
    "types-PyYAML>=6.0",
    "pip-audit>=2.7.0",
]

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