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refactor: modularize monolithic __init__.py into command-specific submodules#2461

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darion-yaphet wants to merge 31 commits intogithub:mainfrom
darion-yaphet:refactor/init-module-split
Open

refactor: modularize monolithic __init__.py into command-specific submodules#2461
darion-yaphet wants to merge 31 commits intogithub:mainfrom
darion-yaphet:refactor/init-module-split

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Description

This PR addresses the technical debt in src/specify_cli/__init__.py by refactoring the monolithic entry point (previously >5,000 lines) into a clean, modular, and maintainable architecture.

Key architectural improvements:

  • Command Handler Extraction: Moved all major CLI command groups into dedicated modules under src/specify_cli/commands/ (init.py, integration.py, preset.py, extension.py, and workflow.py).
  • Service Modularization: Extracted shared utilities and core services into focused internal modules: _helpers.py, _fs.py, _ui.py, _git.py, _assets.py, _console.py, and _version.py.
  • Conflict Resolution: Resolved extensive merge conflicts in __init__.py caused by multiple overlapping refactoring branches, successfully bridging HEAD with the incoming modular command structures.
  • Entry Point Simplification: __init__.py now acts strictly as the typer application entry point, handling only app configuration and sub-command registration.

These changes are purely structural. The external CLI interface, command behaviors, and arguments remain fully backward compatible.

Testing

  • Tested locally with uv run specify --help
  • Ran existing tests with uv sync && uv run pytest
  • Tested with a sample project (if applicable)

AI Disclosure

  • I did not use AI assistance for this contribution
  • I did use AI assistance (describe below)

Code refactoring and complex merge conflict resolutions in src/specify_cli/__init__.py were accomplished via a pair-programming session with an AI coding assistant (Antigravity). The AI helped to safely extract thousands of lines of monolithic logic into the new modular file structure (commands/* and _* internal services), utilizing sed and structural parsing to ensure no command implementations were lost during the cross-branch merges.

darion-yaphet and others added 25 commits May 6, 2026 11:02
Move StepTracker, get_key, select_with_arrows, BannerGroup, show_banner,
BANNER, and TAGLINE from __init__.py into the new _ui.py module. Re-export
all symbols from __init__.py to preserve the public API.
Moves handle_vscode_settings, merge_json_files, save_init_options, and
load_init_options (plus INIT_OPTIONS_FILE constant) from __init__.py
into the new _fs.py module; re-exports them via __init__.py import.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Move the four _locate_* functions from __init__.py into a dedicated
AssetService class in _assets.py. Backward-compatible wrapper functions
remain in __init__.py delegating to a module-level singleton.
Move git operations into a pure GitService class with zero console output.
Backward-compatible wrappers in __init__.py retain Rich print calls.
Move version checking logic (get_installed_version, normalize_tag, is_newer,
fetch_latest_tag) into a dedicated VersionService class in _version.py; replace
the four original functions in __init__.py with thin backward-compatible wrappers.
Remove now-dead InvalidVersion/Version imports from __init__.py.
Moves run_command, check_tool, _install_shared_infra,
ensure_executable_scripts, ensure_constitution_from_template, and
_get_skills_dir (plus CLAUDE_LOCAL_PATH/CLAUDE_NPM_LOCAL_PATH) out of
__init__.py into a new _helpers.py module. Re-exports all symbols from
__init__.py for backward compatibility. Removes now-unused top-level
subprocess import. Updates test_check_tool.py patch targets to the
canonical _helpers namespace.
- Move `init` command (~630 lines) from `__init__.py` to `commands/init.py`
  using the `register(app)` pattern to avoid circular imports
- Move `AGENT_CONFIG`, `AI_ASSISTANT_ALIASES`, `AI_ASSISTANT_HELP`,
  `SCRIPT_TYPE_CHOICES`, `get_speckit_version`, `_parse_integration_options`
  to `_helpers.py`; re-export from `__init__.py` for backward compatibility
- Fix `_get_skills_dir` in `_helpers.py` to use module-local `AGENT_CONFIG`
  instead of circular `from specify_cli import AGENT_CONFIG`
- Use `sys.modules` lookup for `select_with_arrows` so existing test patches
  on `specify_cli.select_with_arrows` continue to work
- `__init__.py` reduced from 4501 → 3734 lines
- Remove dead import _get_skills_dir from _helpers
- Delete five one-line wrapper functions (_is_git_repo, _init_git_repo,
  _locate_bundled_extension/workflow/preset) and inline direct calls
  to _git_svc and _svc at all call sites
- Remove redundant inline `import shutil as _shutil`; use top-level shutil
- Promote BRANCH_NUMBERING_CHOICES to module-level _BRANCH_NUMBERING_CHOICES
- Add -> str return type annotation on _build_integration_equivalent
- Remove empty finally: pass block
Extracts integration_app, all @integration_app.command handlers, and
helper functions (_read_integration_json, _write_integration_json,
_remove_integration_json, _normalize_script_type, _resolve_script_type,
_update_init_options_for_integration) from __init__.py into the focused
commands/integration.py module. __init__.py re-exports the public
symbols via a clean import block.
Extracts all preset_app and preset_catalog_app command handlers out of
the monolithic __init__.py into src/specify_cli/commands/preset.py.
Updates test patch target for _locate_bundled_preset to the new module path.
Extracted all extension_app and catalog_app command handlers and private
helpers (_resolve_installed_extension, _resolve_catalog_extension,
_print_extension_info, _locate_bundled_extension) from __init__.py into
the new commands/extension.py module. Updated the single patched test
target from specify_cli._locate_bundled_extension to
specify_cli.commands.extension._locate_bundled_extension.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Extracted all workflow_app and workflow_catalog_app command handlers
from __init__.py into src/specify_cli/commands/workflow.py using the
sub-typer pattern consistent with preset.py and extension.py.

- Replaced 660 lines of inline handlers with a 3-line import + add_typer
- Added module-level constants _SPECIFY_DIR and _WORKFLOWS_SUBDIR
- All handlers carry -> None return type annotations
- Lazy inline imports used for WorkflowEngine, WorkflowRegistry, etc.
- No circular imports; __init__.py now ~340 lines (was 995)
Remove stdlib imports no longer used in the file body (zipfile, tempfile,
shutil, json, shlex, yaml, os), unused Rich imports (Text, Live), dead
_TOML_AGENTS constant, and slim down _ui/_helpers/_assets/_git/_version
imports to only what is actually needed. Retain urllib.request/urllib.error
and all backward-compat re-exports (select_with_arrows, _get_skills_dir,
AI_ASSISTANT_ALIASES, AI_ASSISTANT_HELP, _install_shared_infra,
_parse_integration_options, _fs helpers) that are patched or imported by
the test suite or by internal sibling modules.

All 1765 tests pass.
@darion-yaphet darion-yaphet requested a review from mnriem as a code owner May 6, 2026 03:44
Resolved 60+ linting issues across the source code and test suite to ensure consistency following the modularization refactor.

Key changes:
- Cleaned up unused imports (F401) and redundant variable assignments (F841) in src/specify_cli/ and tests/.
- Fixed ambiguous variable names (E741) by renaming 'l' to 'line' in list comprehensions within test files.
- Removed extraneous f-string prefixes (F541) from static strings.
- Standardized import ordering and resolved module-level import placement issues (E402) in src/specify_cli/__init__.py.
- Split multiple imports on single lines (E401) to comply with PEP 8.
- Restored essential service singletons (_svc, _git_svc, _ver_svc) in the main entry point required by wrapper functions.

All checks passed via .
Restored several key constants and functions to the package root in  that were removed during modularization. These exports are required by the existing test suite.

Resolved names:
- AI_ASSISTANT_ALIASES & AI_ASSISTANT_HELP (re-exported from ._helpers)
- save_init_options, merge_json_files, & handle_vscode_settings (re-exported from ._fs)

Fixed ImportErrors in:
- tests/test_agent_config_consistency.py
- tests/test_branch_numbering.py
- tests/test_merge.py

Verified that all 41 affected tests now pass.
… state schema

- Introduce integration.json schema v1 with default_integration,
  installed_integrations, and integration_settings fields; migrate
  legacy v0 format on first read
- Add 'integration install' multi-install support: allow multiple
  multi_install_safe integrations to coexist without --force
- Add 'integration use' command to switch default integration
  without uninstall/reinstall
- Update 'integration switch' to set default when target is already
  installed, or perform full uninstall/reinstall otherwise
- Update 'integration uninstall' to handle multi-install state and
  refresh templates for the new default on default removal
- Update 'integration upgrade' to skip template refresh when
  upgrading a non-default integration
- Add 'Multi-install Safe' column to 'integration list' table
- Enforce integration_state_schema version guard in list/install/etc.
- Export _refresh_shared_templates, _parse_integration_options,
  select_with_arrows, and urllib from __init__ for test monkeypatching
- Delegate _install_shared_infra to shared_infra.install_shared_infra
  to gain symlink-safe writes and atomic template updates
- Write integration.json in schema v1 format during 'init'
- Fix remove_catalog bool priority to fall back to yaml index
- Fix extension/workflow catalog list to use is_dir() instead of exists()
- Split long Rich console messages onto separate lines to prevent
  ANSI span wrapping in narrow terminal environments
- Remove unused urllib.error import; mark urllib.request with noqa F401
  (required for test monkeypatching of specify_cli.urllib.request.urlopen)
- Add noqa E402 to late imports that must follow function definitions
- Remove unused yaml import from integration.py
- Remove unused INTEGRATION_REGISTRY imports in uninstall/info/search
- Remove unused IntegrationCatalogError imports in info/search
- Remove unused default_key variable in integration_use
- Remove extraneous f-string prefixes on string literals without placeholders
Path objects on Windows use backslashes, causing test assertions that
check for forward-slash paths to fail. Call .as_posix() on every
relative_to() result before printing to ensure consistent POSIX-style
separators across platforms.
…indows

The previous fix used relative_to().as_posix(), which silently fails when
project_root and the resolved absolute path have different representations
(e.g. short vs. long paths, symlinks) on Windows.

Replace all user-facing path output with more robust alternatives:
- Catalog 'Config saved to' messages: hardcode the known POSIX-relative path
  string directly (.specify/preset-catalogs.yml etc.) instead of computing
  it from Path objects at runtime
- Catalog 'Config:' dim hints: same hardcoded approach
- Uninstall skipped-file listing: use os.path.relpath() + replace(os.sep, '/')
  which handles resolved vs. unresolved path mismatches on all platforms
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