pyproject.toml

[project]
name = "exlabwizard"
version = "0.1.0"
description = "Desktop tool for standardized lab run/project directory creation, NAS sync, and LIMS integration"
readme = "README.md"
requires-python = ">=3.12"

# Runtime dependencies. Each entry cites the design-spec section that commits the dependency.
# Cross-OS conditionals use sys_platform markers; transitive backends (Cocoa on macOS, etc.) are pulled in by their parent packages.
dependencies = [
    # ---- Web framework + ASGI server (Backend §4.1, §4.2, §4.6) ----
    "fastapi>=0.110",
    "uvicorn[standard]>=0.27",
    "pydantic>=2.6",                       # API request/response models, config models
    "httpx>=0.27",                         # LIMS REST client + integration test client (Backend §7.2.5, §4.10.2)
    "packaging>=23",                       # semver comparison for the startup update notifier (§15.6, §15.8 item 3); also transitively present

    # ---- Native window + tray (Frontend §2; Backend §4.1, §4.3.2, §15) ----
    "nicegui>=1.4",                        # UI component library; mounts on FastAPI
    "pywebview>=5.0",                      # Native window for the NiceGUI surface
    "pystray>=0.19",                       # System-tray icon
    "plyer>=2.1",                          # Cross-platform OS notifications (§15.7.3)

    # ---- Template engine (Backend §5) ----
    "copier>=9.0",                         # _min_copier_version pinned by spec (§5.2)
    "jinja2>=3.1",                         # Used by Copier for .jinja-suffixed files
    "jinja2-ansible-filters>=1.3",         # Extra filters referenced in §5.6

    # ---- Cache file I/O + schema validation (HIGH-LEVERAGE; vectorization audit recommendation #1) ----
    "msgspec>=0.18",                       # Typed JSON Struct/encoder; replaces stdlib json on hot paths (§4.4.5, §11.3, §11.4); also handles plugin-host IPC envelopes (§6.3.2) and WebSocket frames (§4.6.2)

    # ---- Atomic file locking (vectorization recommendation #2; §4.4.5) ----
    "filelock>=3.13",                      # Cross-platform LOCK_EX/LOCK_SH; matches the spec's `with FileLock(...)` shape exactly

    # ---- Async SQLite (vectorization recommendation #3; §7.1.1, §7.2.4) ----
    "aiosqlite>=0.20",                     # Async-native access to lims_cache.db and sync_queue.db; removes the asyncio.to_thread roundtrip

    # ---- YAML I/O (config.yaml round-trip + read-only manifest reads; §6.1.2, §9, §10.7.1) ----
    "ruamel.yaml>=0.18",                   # Round-trip preserving comments + key order for config.yaml (Settings UI writes back via this)
    "pyyaml>=6.0",                         # Read-only path for copier.yml, manifest.yml, README front matter -- faster than ruamel for these

    # ---- Credential storage (Backend §7.4) ----
    "keyring>=24.0",                       # OS keyring (Keychain / Credential Manager / Secret Service)
    "cryptography>=42.0",                  # Fernet for encrypted-at-rest fallback when no keyring is available (§7.4.4)
    "argon2-cffi>=23.1",                   # Argon2id KDF for the master passphrase in the encrypted-at-rest fallback (§7.4.4)

    # ---- Markdown rendering (README preview, log viewer; Frontend §3.6.3, §3.6.5) ----
    "markdown-it-py>=3.0",                 # CommonMark-compliant; YAML-front-matter aware via the front_matter plugin

    # ---- Windows-only: plugin Job Object resource limits (Backend §6.3.3) ----
    "pywin32>=306; sys_platform == 'win32'",

    # ---- Linux-only: keyring's Secret Service backend (Backend §7.4); fallback path triggers when this fails to import ----
    "secretstorage>=3.3; sys_platform == 'linux'",
]

[project.urls]
Homepage = "https://github.com/exfab/ExLabWizard"
Repository = "https://github.com/exfab/ExLabWizard"
Documentation = "https://exfab.github.io/ExLabWizard/"

[project.optional-dependencies]
# Plugin-author libraries used in worked examples (Backend §6.6, §6.7).
# These are NOT bundled with the app; plugin authors install them in their plugin's own requirements.
# Listed here so that running `uv pip install -e .[plugin-examples]` picks them up for local plugin development.
plugin-examples = [
    "openpyxl>=3.1",                       # xlsx_field_filler worked example (§6.6)
    "python-docx>=1.1",                    # docx_variable_replacer illustrative plugin (§6.7)
]

# Testing (Backend §4.10).
test = [
    "pytest>=8.0",
    "pytest-asyncio>=0.23",
    "playwright>=1.40",                    # E2E browser automation against http://127.0.0.1:<port> (Backend §4.10.3)
    "pytest-cov>=4.1",                     # Coverage reporting; configured under [tool.coverage.run]
    "pytest-rerunfailures>=14",            # Opt-in retries for timing-sensitive flakes (@pytest.mark.flaky)
    # httpx is already in core deps -- used for AsyncClient(app=app) in integration tests too
]

# Build (Backend §15.1; PyInstaller --onedir with three entry points).
build = [
    "pyinstaller>=6.3",
]

# Lint / static analysis / pre-commit (Phase 1B tooling).
lint = [
    "ruff>=0.4",
    "mypy>=1.10",
    "pre-commit>=3.7",
]

# Documentation toolchain (Sphinx + pydata-sphinx-theme; see docs/conf.py).
docs = [
    "sphinx>=7.3",
    "pydata-sphinx-theme>=0.15",
    "sphinx-autodoc-typehints>=2.0",
    "sphinx-design>=0.6",
    "myst-parser>=3.0",
    "sphinx-copybutton>=0.5",
    "sphinxext-opengraph>=0.9",
]

# Dev convenience: install everything for local development with `uv pip install -e .[dev]`.
dev = [
    "exlabwizard[plugin-examples,test,build,lint,docs]",
]

[project.scripts]
# Three console entry points per Backend §15.3:
# - exlab-wizard       : CLI alias the operator double-clicks (Backend §15.3.3); spawns or focuses the tray.
# - exlab-wizard-tray  : Long-lived tray + server process (Backend §15.3.1); registered for autostart.
# - exlab-wizard-window: On-demand pywebview window subprocess (Backend §15.3.2); spawned by the tray.
exlab-wizard = "exlab_wizard.__main__:main"
exlab-wizard-tray = "exlab_wizard.tray.main:main"
exlab-wizard-window = "exlab_wizard.window.main:main"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/exlab_wizard"]

# ---------------------------------------------------------------------------
# Tool configuration (Phase 1B)
# ---------------------------------------------------------------------------

[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ruff.lint]
# Rule families:
#   E/W  : pycodestyle errors and warnings
#   F    : pyflakes
#   I    : import sorting (isort)
#   N    : pep8-naming
#   B    : flake8-bugbear
#   UP   : pyupgrade (modernize syntax for the py312 target)
#   ASYNC: flake8-async (catches blocking calls in async fns; matches Backend §4.4)
#   SIM  : flake8-simplify
#   TID  : flake8-tidy-imports
#   RUF  : ruff-specific rules
select = ["E", "F", "W", "I", "N", "B", "UP", "ASYNC", "SIM", "TID", "RUF"]
# E501 (line-too-long) is enforced via the formatter; we sometimes need long URLs in comments.
ignore = ["E501"]

[tool.ruff.lint.per-file-ignores]
# Tests can use bare asserts and looser naming. ASYNC240 is suppressed because
# pytest-asyncio test functions use synchronous pathlib operations against
# tmp_path; this is the established pytest idiom and not a concurrency hazard.
"tests/**/*.py" = ["N802", "N803", "N806", "ASYNC230", "ASYNC240"]

[tool.ruff.format]
quote-style = "double"

[tool.pytest.ini_options]
asyncio_mode = "auto"
testpaths = ["tests"]
python_files = ["test_*.py"]

[tool.coverage.run]
source = ["src/exlab_wizard"]
omit = [
    "src/exlab_wizard/_worker.py",
    "*/tests/*",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
    "raise NotImplementedError",
    "\\.\\.\\.",
]
show_missing = true

[tool.mypy]
python_version = "3.12"
strict = false
ignore_missing_imports = true
# Src-layout: keep mypy resolvable when the package is not editable-installed
# (e.g. fresh checkout without `pip install -e .`).
mypy_path = "src"