diff --git a/lab/model/__init__.py b/.github/workflows/ci.yml similarity index 100% rename from lab/model/__init__.py rename to .github/workflows/ci.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..6bae77b --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,62 @@ +name: CI + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + lint: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Install just + uses: taiki-e/install-action@just + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + cache-dependency-glob: "uv.lock" + + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: "3.12" + + - name: Install dependencies + run: uv sync --all-extras --dev + + - name: Lint + run: just lint + + test: + runs-on: ubuntu-latest + strategy: + matrix: + python-version: ["3.9", "3.10", "3.11", "3.12"] + + steps: + - uses: actions/checkout@v4 + + - name: Install just + uses: taiki-e/install-action@just + + - name: Install uv + uses: astral-sh/setup-uv@v4 + with: + enable-cache: true + cache-dependency-glob: "uv.lock" + + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + + - name: Install dependencies + run: uv sync --all-extras --dev + + - name: Test + run: just test diff --git a/Justfile b/Justfile new file mode 100644 index 0000000..6daa8ed --- /dev/null +++ b/Justfile @@ -0,0 +1,23 @@ +default: + @just --list + +test: + @uv run pytest + +test-s: + @uv run pytest -s + +ruff: + uv run ruff format lab + +pyright: + uv run pyright lab + +lint: + just ruff + just pyright + +lint-file file: + - ruff {{file}} + - pyright {{file}} + diff --git a/README.md b/README.md index 7abf2b0..75fcc9d 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,7 @@ # lab A CLI tool for managing computational science + +## Usage + +Running `lab run .` will search for a `Labfile` in the directory, and then run the experiments defined there. `lab` +will automatically resolve dependencies between experiments and run them in the right order. diff --git a/lab/cli/cli.py b/lab/cli/cli.py index e287bce..1610dd9 100644 --- a/lab/cli/cli.py +++ b/lab/cli/cli.py @@ -1,12 +1,19 @@ -import typer +import click +from dishka.integrations.click import setup_dishka +from lab.cli.commands.plan import plan -from lab.cli.commands import exp, run +from lab.cli.commands.run import run +from lab.di import DI -app = typer.Typer() +def start(): + @click.group() + @click.pass_context + def main(context: click.Context): + di = DI() + setup_dishka(container=di.container, context=context, auto_inject=True) -def main(): - exp.attach(app, name="exp") - run.attach(app, name="run") + main.command(name="plan")(plan) + main.command(name="run")(run) - app() + main() diff --git a/lab/cli/commands/exp.py b/lab/cli/commands/exp.py deleted file mode 100644 index 03eda46..0000000 --- a/lab/cli/commands/exp.py +++ /dev/null @@ -1,43 +0,0 @@ -import typer - - -def attach(app: typer.Typer, *, name: str): - exp_cmd = typer.Typer() - # - # # Create sub-apps for each registered experiment - # for name, exp in Experiment.get_registered_experiments().items(): - # exp_app = typer.Typer() - # exp_cmd.add_typer(exp_app, name=name) - # - # @exp_app.command("run") - # def run_experiment( - # exp=exp, # Capture experiment class in closure - # spec: str = typer.Argument(..., help="Specification file name"), - # vary: Optional[str] = typer.Option(None, help="Variation parameter"), - # k: int = typer.Option(1, "--K", "-K", help="Number of iterations"), - # ): - # """Run an experiment with the given specification""" - # vary_ = Vary.parse_str(vary) if vary else None - # spec_class = exp.spec() - # if not spec_class or not issubclass(spec_class, Spec): - # raise typer.BadParameter( - # f"Experiment {exp} does not have a valid Spec class" - # ) - # - # settings = Settings() - # namespaces = {Callable: func} - # - # specfile = ( - # settings.spec_root - # / "experiment" - # / exp.__name__.lower() - # / f"{spec}.yaml" - # ) - # experiment_spec = spec_class.parse_with_namespaces( - # yaml.safe_load(specfile.read_text()), namespaces - # ) - # experiment = experiment_spec.build() - # data = experiment(K=k, vary=vary_) - # data.plot() - - app.add_typer(exp_cmd, name=name) diff --git a/lab/cli/commands/plan.py b/lab/cli/commands/plan.py new file mode 100644 index 0000000..ded261e --- /dev/null +++ b/lab/cli/commands/plan.py @@ -0,0 +1,20 @@ +from pathlib import Path +from dishka import FromDishka +import rich +import click + +from lab.core.ui import UserInterface +from lab.project.service.labfile import LabfileService +from lab.project.service.plan import PlanService + + +@click.argument("path", type=click.Path(exists=True, path_type=Path)) +def plan(path: Path, ui: FromDishka[UserInterface]): + """Generate execution plan from Labfile""" + ui.print(f"Generating plan for [b]{path.resolve()}[/b]\n") + labfile_service = LabfileService() + plan_service = PlanService() + project = labfile_service.parse(path) + + plan = plan_service.create_execution_plan(project) + ui.print(str(plan)) diff --git a/lab/cli/commands/run.py b/lab/cli/commands/run.py index cd1b8b5..bfd7ee8 100644 --- a/lab/cli/commands/run.py +++ b/lab/cli/commands/run.py @@ -1,24 +1,53 @@ from pathlib import Path -from typing import Annotated -import rich -import typer +import logging +import click +from dishka import FromDishka -from lab.service.experiment import ExperimentService -from lab.service.labfile import LabfileService -from lab.service.pipeline import PipelineService +from lab.cli.utils import coro +from lab.core.logging import setup_logging +from lab.core.ui import UserInterface +from lab.project.service.labfile import LabfileService +from lab.project.service.plan import PlanService +from lab.runtime.runtime import Runtime +logger = logging.getLogger("lab") -def run(path: Annotated[Path, typer.Argument(help="Path to Labfile")]): - rich.print(f"Running [b]{path.resolve()}[/b]\n") - labfile_service = LabfileService() - project = labfile_service.parse(path) - experiment_service = ExperimentService() - pipeline_service = PipelineService(experiment_service=experiment_service) +@click.argument("path", type=click.Path(exists=True, path_type=Path)) +@coro +async def run( + path: Path, + ui: FromDishka[UserInterface], + runtime: FromDishka[Runtime], + labfile_service: FromDishka[LabfileService], + plan_service: FromDishka[PlanService], +): + """Run experiments defined in Labfile""" + setup_logging(Path("~/.local/lab/logs/lab.log")) - pipeline = pipeline_service.create_pipeline(project) - pipeline_service.run(pipeline) + try: + ui.display_start(str(path.resolve())) + # Load and parse project + logger.debug("Loading project", extra={"context": {"path": str(path)}}) + labfile_service = LabfileService() + project = labfile_service.parse(path) -def attach(app: typer.Typer, *, name: str): - app.command(name=name)(run) + # Create execution plan + plan_service = PlanService() + plan = plan_service.create_execution_plan(project) + + await runtime.start(plan) + + # # Execute experiments with progress display + # with ui.create_progress() as progress: + # task = progress.add_task( + # "Running experiments...", total=len(plan.ordered_experiments) + # ) + + ui.display_success() + + except Exception as e: + logger.exception("Execution failed") + ui.display_error(message="Execution failed", details=str(e)) + raise diff --git a/lab/cli/utils.py b/lab/cli/utils.py new file mode 100644 index 0000000..0a0a062 --- /dev/null +++ b/lab/cli/utils.py @@ -0,0 +1,11 @@ +import asyncio +from functools import wraps +from typing import Callable + + +def coro(f: Callable): + @wraps(f) + def wrapper(*args, **kwargs): + return asyncio.run(f(*args, **kwargs)) + + return wrapper diff --git a/lab/service/__init__.py b/lab/core/__init__.py similarity index 100% rename from lab/service/__init__.py rename to lab/core/__init__.py diff --git a/lab/core/database.py b/lab/core/database.py new file mode 100644 index 0000000..5bea814 --- /dev/null +++ b/lab/core/database.py @@ -0,0 +1,29 @@ +from typing import Optional +from sqlalchemy import create_engine, Engine +from sqlalchemy.pool import StaticPool + + +def make_db(database_url: Optional[str] = None) -> Engine: + """Create a database engine using SQLAlchemy. + + Args: + database_url: Optional database URL. Defaults to in-memory SQLite. + + Returns: + SQLAlchemy Engine instance + """ + if database_url is None: + database_url = "sqlite:///:memory:" + + connect_args = ( + {"check_same_thread": False} if database_url.startswith("sqlite") else {} + ) + + return create_engine( + database_url, + # For SQLite in-memory DB, use StaticPool to maintain a single connection + poolclass=StaticPool if database_url == "sqlite:///:memory:" else None, + connect_args=connect_args, + # Echo SQL for debugging + echo=False, + ) diff --git a/lab/core/logging.py b/lab/core/logging.py new file mode 100644 index 0000000..1e79aa9 --- /dev/null +++ b/lab/core/logging.py @@ -0,0 +1,54 @@ +import json +import logging.config +import os +import yaml +from datetime import datetime +from pathlib import Path +from typing import Optional + + +class JSONFormatter(logging.Formatter): + """JSON formatter for structured logging""" + + def format(self, record: logging.LogRecord) -> str: + log_obj = { + "timestamp": datetime.fromtimestamp(record.created).isoformat(), + "level": record.levelname, + "logger": record.name, + "message": record.getMessage(), + "context": getattr(record, "context", {}), + } + if record.exc_info: + log_obj["exception"] = self.formatException(record.exc_info) + return json.dumps(log_obj) + + +def load_logging_config(path: Path) -> dict: + config_template = path.read_text() + + config_str = config_template.replace( + "_LOG_FILE_", os.getenv("LOG_FILE", "/var/log/default.log") + ) + + return yaml.safe_load(config_str) + + +def setup_logging(log_file: Optional[Path] = None) -> None: + """Configure application logging from YAML file""" + if log_file: + # Ensure log directory exists + log_file = log_file.expanduser().resolve() + log_file.parent.mkdir(parents=True, exist_ok=True) + + # Set environment variable for template substitution + os.environ["LOG_FILE"] = str(log_file) + # Load config file + config_path = Path(__file__).parent / "logging.yaml" + config = load_logging_config(config_path) + + # Apply configuration + logging.config.dictConfig(config) + else: + # If no log file specified, use null handler + logger = logging.getLogger("lab") + logger.addHandler(logging.NullHandler()) diff --git a/lab/core/logging.yaml b/lab/core/logging.yaml new file mode 100644 index 0000000..ab984c1 --- /dev/null +++ b/lab/core/logging.yaml @@ -0,0 +1,41 @@ +version: 1 +disable_existing_loggers: false + +formatters: + json: + (): lab.core.logging.JSONFormatter + simple: + format: '%(asctime)s - %(name)s - %(levelname)s - %(message)s' + +handlers: + file: + class: logging.handlers.RotatingFileHandler + formatter: json + filename: _LOG_FILE_ + maxBytes: 10485760 # 10MB + backupCount: 5 + encoding: utf8 + + null_handler: + class: logging.NullHandler + +loggers: + lab: + level: DEBUG + handlers: [file] + propagate: false + + # Third party loggers + urllib3: + level: WARNING + handlers: [null_handler] + propagate: false + + asyncio: + level: WARNING + handlers: [null_handler] + propagate: false + +root: + level: WARNING + handlers: [null_handler] diff --git a/lab/core/messaging/__init__.py b/lab/core/messaging/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/core/messaging/bus.py b/lab/core/messaging/bus.py new file mode 100644 index 0000000..2c84e8f --- /dev/null +++ b/lab/core/messaging/bus.py @@ -0,0 +1,84 @@ +from abc import ABC, abstractmethod +import logging +from typing import Callable, Type + +from lab.core.messaging.message import Message, TMessage + + +class MessageBus(ABC): + """Interface for message bus implementations""" + + @abstractmethod + async def publish(self, message: Message) -> None: + """Publish a message to all registered handlers""" + pass + + @abstractmethod + def register_handler( + self, message_type: Type[TMessage], handler: Callable[[TMessage], None] + ) -> None: + """Register a handler for a specific message type""" + pass + + @abstractmethod + def subscribe( + self, message_type: Type[TMessage], subscriber: Callable[[TMessage], None] + ) -> None: + """Subscribe to notifications for a specific message type""" + pass + + +# In-memory implementation +class InMemoryMessageBus(MessageBus): + """Simple in-memory implementation of the message bus""" + + def __init__(self): + self._handlers: dict[Type[Message], list[Callable]] = {} + self._subscribers: dict[Type[Message], list[Callable]] = {} + self._logger = logging.getLogger(__name__) + + def register_handler( + self, message_type: Type[TMessage], handler: Callable[[TMessage], None] + ) -> None: + if message_type not in self._handlers: + self._handlers[message_type] = [] + self._handlers[message_type].append(handler) + self._logger.debug( + f"Registered handler {handler.__name__} for {message_type.__name__}" + ) + + def subscribe( + self, message_type: Type[TMessage], subscriber: Callable[[TMessage], None] + ) -> None: + if message_type not in self._subscribers: + self._subscribers[message_type] = [] + self._subscribers[message_type].append(subscriber) + self._logger.debug( + f"Added subscriber {subscriber.__name__} for {message_type.__name__}" + ) + + async def publish(self, message: Message) -> None: + message_type = type(message) + + # Call handlers + handlers = self._handlers.get(message_type, []) + for handler in handlers: + try: + await handler(message) + except Exception as e: + self._logger.error(f"Error in handler {handler.__name__}: {str(e)}") + + # Notify subscribers + subscribers = self._subscribers.get(message_type, []) + for subscriber in subscribers: + try: + await subscriber(message) + except Exception as e: + self._logger.error( + f"Error in subscriber {subscriber.__name__}: {str(e)}" + ) + + self._logger.debug( + f"Published {message_type.__name__} to " + f"{len(handlers)} handlers and {len(subscribers)} subscribers" + ) diff --git a/lab/core/messaging/message.py b/lab/core/messaging/message.py new file mode 100644 index 0000000..84fd637 --- /dev/null +++ b/lab/core/messaging/message.py @@ -0,0 +1,27 @@ +# Message type for type hints +from datetime import datetime +from enum import Enum +from typing import TypeVar +import uuid + +from pydantic import BaseModel, Field + + +TMessage = TypeVar("TMessage", bound="Message") + + +class MessagePriority(str, Enum): + LOW = "low" + NORMAL = "normal" + HIGH = "high" + + +class Message(BaseModel): + """Base message that all domain messages inherit from""" + + id: str = Field(default_factory=lambda: str(uuid.uuid4())) + timestamp: datetime = Field(default_factory=datetime.now) + priority: MessagePriority = MessagePriority.NORMAL + + class Config: + frozen = True diff --git a/lab/core/model.py b/lab/core/model.py new file mode 100644 index 0000000..b61bc52 --- /dev/null +++ b/lab/core/model.py @@ -0,0 +1,19 @@ +from datetime import datetime +from typing import Any, Generic, Protocol, TypeVar +from pydantic import BaseModel, Field + + +class Model(BaseModel): ... + + +class Event(Model): + timestamp: datetime = Field(default_factory=datetime.now) + kind: str + data: dict[str, Any] = Field(default_factory=dict) + + +E = TypeVar("E", bound=Event, contravariant=True) + + +class EventHandler(Protocol, Generic[E]): + def __call__(self, event: E) -> None: ... diff --git a/lab/core/provider.py b/lab/core/provider.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/core/repository.py b/lab/core/repository.py new file mode 100644 index 0000000..abf883f --- /dev/null +++ b/lab/core/repository.py @@ -0,0 +1,19 @@ +from abc import ABC, abstractmethod +from typing import Optional, TypeVar, Generic +from uuid import UUID + + +T = TypeVar("T") + + +class Repository(ABC, Generic[T]): + """Abstract base repository""" + + @abstractmethod + async def save(self, entity: T) -> None: ... + + @abstractmethod + async def get(self, id: UUID) -> Optional[T]: ... + + @abstractmethod + async def list(self, **filters) -> list[T]: ... diff --git a/lab/service/service.py b/lab/core/service.py similarity index 100% rename from lab/service/service.py rename to lab/core/service.py diff --git a/lab/core/ui.py b/lab/core/ui.py new file mode 100644 index 0000000..41adf72 --- /dev/null +++ b/lab/core/ui.py @@ -0,0 +1,89 @@ +from rich.console import Console +from rich.progress import Progress, SpinnerColumn, TextColumn +from rich.table import Table +from typing import Optional, Sequence + +from lab.core.messaging.bus import MessageBus +from lab.runtime.messages import ( + ExperimentRunComplete, + ExperimentRunFailed, + ExperimentRunStarted, +) + + +class UserInterface: + """Handles all user interaction and feedback""" + + def __init__(self, message_bus: MessageBus): + self.verbose = False # @todo: parameterise via injected config + self.console = Console() + self.error_console = Console(stderr=True) + self._message_bus = message_bus + + self._message_bus.subscribe( + ExperimentRunStarted, self.render_experiment_started + ) + self._message_bus.subscribe( + ExperimentRunComplete, self.render_experiment_complete + ) + self._message_bus.subscribe(ExperimentRunFailed, self.render_experiment_failed) + + def create_progress(self) -> Progress: + """Create a progress display for long-running operations""" + return Progress( + SpinnerColumn(), + TextColumn("[bold blue]{task.description}"), + console=self.console, + ) + + def print(self, msg: str): + self.console.print(msg) + + def display_start(self, path: str) -> None: + """Display initial startup message""" + self.console.print(f"[bold]Running experiments from[/] {path}") + + def display_error(self, message: str, details: Optional[str] = None) -> None: + """Display error message to user""" + self.error_console.print(f"[red bold]Error:[/] {message}") + if details and self.verbose: + self.error_console.print(f"[dim]{details}[/]") + + def display_success(self) -> None: + """Display success message""" + self.console.print("[green]✓[/] All experiments completed successfully") + + def render_experiment_started(self, message: ExperimentRunStarted) -> None: + """Display when an experiment starts""" + self.console.print( + f"[bold blue]►[/] Started experiment: {message.run.experiment.name}" + ) + + def render_experiment_complete(self, message: ExperimentRunComplete) -> None: + """Display when an experiment completes""" + self.console.print( + f"[bold green]✓[/] Completed experiment: {message.run.experiment.name}" + ) + + def render_experiment_failed(self, message: ExperimentRunFailed) -> None: + """Display when an experiment fails""" + self.console.print( + f"[bold red]✗[/] Failed experiment: {message.run.experiment.name}" + ) + self.console.print(f" Error: {message.reason}", style="red") + + def display_experiment_summary(self, results: Sequence[dict]) -> None: + """Display summary table of experiment results""" + table = Table(title="Experiment Results") + table.add_column("Name") + table.add_column("Status") + table.add_column("Duration") + + for result in results: + table.add_row( + result["name"], + f"[green]✓[/]" if result["status"] == "success" else "[red]✗[/]", + f"{result['duration']:.2f}s", + ) + + self.console.print(table) diff --git a/lab/di.py b/lab/di.py index e69de29..70b54a6 100644 --- a/lab/di.py +++ b/lab/di.py @@ -0,0 +1,72 @@ +from typing import Iterable +from dishka import Container, Provider, Scope, make_container, provide +from sqlalchemy import Engine, StaticPool, create_engine + +from lab.core.messaging.bus import InMemoryMessageBus, MessageBus +from lab.core.ui import UserInterface +from lab.project.service.labfile import LabfileService +from lab.project.service.plan import PlanService +from lab.runtime.persistence.memory import ( + InMemoryExperimentRunRepository, + InMemoryProjectRunRepository, +) +from lab.runtime.persistence.run import ExperimentRunRepository, ProjectRunRepository +from lab.runtime.runtime import Runtime +from lab.runtime.service.run import RunService + + +class EngineProvider(Provider): + @provide(scope=Scope.APP) + def new_connection(self) -> Iterable[Engine]: + database_url = "@todo" + in_memory = database_url is None + if in_memory: + database_url = "sqlite:///:memory:" + + connect_args = ( + {"check_same_thread": False} if database_url.startswith("sqlite") else {} + ) + + engine = create_engine( + database_url, + poolclass=StaticPool if in_memory else None, + connect_args=connect_args, + echo=False, + ) + yield engine + + +class DI: + def __init__(self) -> None: + self._container = make_container( + self.core(), self.repositories(), self.services(), EngineProvider() + ) + + @property + def container(self) -> Container: + return self._container + + def core(self) -> Provider: + provider = Provider(scope=Scope.APP) + provider.provide(UserInterface) + provider.provide(InMemoryMessageBus, provides=MessageBus) + + return provider + + def repositories(self) -> Provider: + provider = Provider(scope=Scope.APP) + provider.provide( + InMemoryExperimentRunRepository, provides=ExperimentRunRepository + ) + provider.provide(InMemoryProjectRunRepository, provides=ProjectRunRepository) + + return provider + + def services(self) -> Provider: + provider = Provider(scope=Scope.APP) + provider.provide(RunService) + provider.provide(PlanService) + provider.provide(LabfileService) + provider.provide(Runtime) + + return provider diff --git a/lab/infra/__init__.py b/lab/infra/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/instrument/__init__.py b/lab/instrument/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/instrument/model/__init__.py b/lab/instrument/model/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/instrument/model/instrument.py b/lab/instrument/model/instrument.py new file mode 100644 index 0000000..56ed663 --- /dev/null +++ b/lab/instrument/model/instrument.py @@ -0,0 +1,62 @@ +from datetime import datetime +from enum import Enum +from typing import Optional +from uuid import UUID + +from pydantic import Field + +from lab.core.model import Model + + +class InstrumentKind(str, Enum): + COMPUTE = "compute" # Generic compute resources + GPU = "gpu" # GPU compute resources + PHYSICAL = "physical" # Physical lab equipment + SENSOR = "sensor" # Measurement devices + + +class InstrumentStatus(str, Enum): + AVAILABLE = "available" + IN_USE = "in_use" + UNKNOWN = "unknown" + + +class InstrumentCapability(Model): + """A specific capability of an instrument""" + + name: str # e.g. "temperature_measurement", "pressure_control" + unit: str # e.g. "celsius", "pascal" + range: tuple[float, float] # e.g. (-50, 100) + precision: float # e.g. 0.1 + + +class Instrument(Model): + id: UUID + kind: InstrumentKind + capabilities: set[InstrumentCapability] + status: InstrumentStatus + + +class InstrumentRequirements(Model): + """Requirements for instruments needed by an experiment""" + + capabilities: set[InstrumentCapability] + + +class InstrumentClaim(Model): + """Active claim on an instrument during execution""" + + instrument: Instrument + kind: InstrumentKind + acquired_at: datetime = Field(default_factory=datetime.now) + released_at: Optional[datetime] = None + + +class InstrumentMetric(Model): + """Metrics about instrument state""" + + timestamp: datetime = Field(default_factory=datetime.now) + instrument: Instrument + metric_name: str # e.g. "temperature", "pressure" + value: float + unit: Optional[str] = None diff --git a/lab/instrument/persistence/__init__.py b/lab/instrument/persistence/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/instrument/service/__init__.py b/lab/instrument/service/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/model/model.py b/lab/model/model.py deleted file mode 100644 index 86ce5fc..0000000 --- a/lab/model/model.py +++ /dev/null @@ -1,5 +0,0 @@ -from pydantic import BaseModel, ConfigDict - - -class Model(BaseModel): - model_config = ConfigDict(frozen=True) diff --git a/lab/model/pipeline.py b/lab/model/pipeline.py deleted file mode 100644 index cdbe4c3..0000000 --- a/lab/model/pipeline.py +++ /dev/null @@ -1,10 +0,0 @@ -from lab.model.model import Model -from lab.model.project import Experiment - - -class Pipeline(Model): - experiments: list[Experiment] - - # def run(self): - # for exp in self.experiments: - # diff --git a/lab/model/provider.py b/lab/model/provider.py deleted file mode 100644 index 4704ac5..0000000 --- a/lab/model/provider.py +++ /dev/null @@ -1,4 +0,0 @@ -from lab.model.model import Model - - -class Provider(Model): ... diff --git a/lab/project/__init__.py b/lab/project/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/project/model/__init__.py b/lab/project/model/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/service/ir.py b/lab/project/model/ir.py similarity index 88% rename from lab/service/ir.py rename to lab/project/model/ir.py index e5f6825..b4c82bb 100644 --- a/lab/service/ir.py +++ b/lab/project/model/ir.py @@ -1,16 +1,17 @@ from abc import ABC, abstractmethod -from pathlib import Path from typing import Optional, TypeVar, Union, Any from labfile.parse.transform import ProcessNode from pydantic import BaseModel from uuid import uuid4 -from lab.model.project import Experiment, ValueReference from labfile.model.tree import ( ReferenceNode, LiteralValue as TreeLiteralValue, ) +from lab.project.model.project import Experiment, ValueReference +from lab.runtime.model.execution import ScriptExecution + LiteralValue = Union[int, float, str] @@ -90,14 +91,14 @@ def from_parameters(cls, parameters: list[Parameter]) -> "ParameterSet": class ExperimentDefinition(Definition): """Intermediate representation of an experiment""" - path: str + via: str parameters: ParameterSet @classmethod def from_tree(cls, node: ProcessNode) -> "ExperimentDefinition": return cls( name=node.name, - path=node.via, + via=node.via, parameters=ParameterSet.from_tree(node.parameters), ) @@ -109,8 +110,14 @@ def to_domain(self, symbols: SymbolTable) -> Experiment: for name, value in self.parameters.values.items() } + # @todo: make this general + execution_method = ScriptExecution(command="python", args=[self.via]) + return Experiment( - id=uuid4(), name=self.name, path=Path(self.path), parameters=parameters + id=uuid4(), + name=self.name, + execution_method=execution_method, + parameters=parameters, ) def _build_parameter(self, value: Reference, symbols: SymbolTable): diff --git a/lab/project/model/plan.py b/lab/project/model/plan.py new file mode 100644 index 0000000..910efc5 --- /dev/null +++ b/lab/project/model/plan.py @@ -0,0 +1,69 @@ +from uuid import UUID, uuid4 + +from pydantic import Field +from lab.core.model import Model +from lab.project.model.project import Experiment, Project, ValueReference +from lab.runtime.model.execution import ScriptExecution + + +class ExecutionPlan(Model): + id: UUID = Field(default_factory=uuid4) + project: Project + ordered_experiments: list[Experiment] + + def __str__(self) -> str: + """Format the execution plan in a clear, visually appealing way.""" + # Header with plan ID + lines = ["┌─ Execution Plan ─" + "─" * 50, f"│ ID: {self.id}", "│"] + + # Build dependency graph for visualization + dep_graph: dict[str, set[str]] = {} + for exp in self.ordered_experiments: + dep_graph[exp.name] = {d.name for d in exp.dependencies} + + # Format experiments section + lines.append("│ Experiments:") + for i, exp in enumerate(self.ordered_experiments, 1): + # Experiment header with number and name + exp_header = f"│ {i}. {exp.name}" + if exp.dependencies: + deps = ", ".join(d.name for d in exp.dependencies) + exp_header += f" (depends on: {deps})" + lines.append(exp_header) + + # Execution method + if isinstance(exp.execution_method, ScriptExecution): + cmd = f"{exp.execution_method.command} {' '.join(exp.execution_method.args)}" + lines.append(f"│ Run: {cmd}") + + # Parameters + if exp.parameters: + lines.append("│ Parameters:") + for name, value in exp.parameters.items(): + if isinstance(value, ValueReference): + val_str = f"@{value.owner.name}.{value.attribute}" + else: + val_str = str(value) + lines.append(f"│ • {name}: {val_str}") + + # ASCII dependency graph + if len(self.ordered_experiments) > 1: + lines.extend(["│", "│ Dependency Flow:", "│ " + "─" * 30]) + + def build_graph_lines() -> list[str]: + graph = [] + for i, exp in enumerate(self.ordered_experiments): + prefix = ( + "└──► " if i == len(self.ordered_experiments) - 1 else "├──► " + ) + graph.append(f"│ {prefix}{exp.name}") + if i < len(self.ordered_experiments) - 1: + graph.append("│ │") + return graph + + lines.extend(build_graph_lines()) + + # Footer + lines.append("└" + "─" * 60) + + return "\n".join(lines) diff --git a/lab/model/project.py b/lab/project/model/project.py similarity index 70% rename from lab/model/project.py rename to lab/project/model/project.py index 82d4f41..79ab1f6 100644 --- a/lab/model/project.py +++ b/lab/project/model/project.py @@ -1,9 +1,10 @@ -from pathlib import Path from uuid import UUID -from typing import Literal, Optional, TypeAlias, Union +from typing import Optional, TypeAlias, Union +from lab.core.model import Model +from lab.instrument.model.instrument import InstrumentRequirements +from lab.runtime.model.execution import ExecutionMethod -from lab.model.model import Model ParameterValue: TypeAlias = Union[str, float, int] Parameters: TypeAlias = dict[str, ParameterValue] @@ -14,25 +15,14 @@ class ValueReference(Model): attribute: str -GPU = Literal["H100"] - - -class Instrument(Model): ... - - -class Compute(Instrument): - gpu: Optional[GPU] - - class Experiment(Model): id: UUID name: str - path: Path + execution_method: ExecutionMethod # @todo: add local model parameters: dict[str, ParameterValue | ValueReference] - - # instruments: list[Instrument] + requirements: Optional[InstrumentRequirements] = None # @todo: implement def __hash__(self) -> int: return hash(self.id) @@ -53,4 +43,4 @@ def dependencies(self) -> set["Experiment"]: class Project(Model): - experiments: list[Experiment] + experiments: set[Experiment] diff --git a/lab/project/persistence/__init__.py b/lab/project/persistence/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/project/service/__init__.py b/lab/project/service/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/service/labfile.py b/lab/project/service/labfile.py similarity index 72% rename from lab/service/labfile.py rename to lab/project/service/labfile.py index f7ca8ac..5aa2320 100644 --- a/lab/service/labfile.py +++ b/lab/project/service/labfile.py @@ -2,12 +2,12 @@ from labfile import parse from labfile.model.tree import LabfileNode -from lab.model.project import Project -from lab.service.service import Service -from lab.service.ir import ExperimentDefinition, SymbolTable +from lab.project.model.ir import ExperimentDefinition, SymbolTable +from lab.project.model.project import Project -class LabfileService(Service): + +class LabfileService: def parse(self, path: Path) -> Project: ast = parse(path) project = self._labfile_from_tree(ast) @@ -22,6 +22,6 @@ def _labfile_from_tree(self, tree: LabfileNode) -> Project: symbols = SymbolTable(table={d.name: d for d in processes}) # Convert to domain objects - processes = [d.to_domain(symbols) for d in processes] + processes = {d.to_domain(symbols) for d in processes} return Project(experiments=processes) diff --git a/lab/project/service/plan.py b/lab/project/service/plan.py new file mode 100644 index 0000000..35c6ac7 --- /dev/null +++ b/lab/project/service/plan.py @@ -0,0 +1,47 @@ +import networkx as nx + +from lab.project.model.plan import ExecutionPlan +from lab.project.model.project import Experiment, Project + + +class PlanService: + def create_execution_plan(self, project: Project) -> ExecutionPlan: + """Creates a plan for executing experiments, including parallel execution groups""" + ordered = self._resolve_execution_order(project) + + # Group independent experiments that can run in parallel + # This is a simple implementation - could be more sophisticated + parallel_groups = [] + current_group = set() + + for exp in ordered: + if not any(dep in current_group for dep in exp.dependencies): + current_group.add(exp) + else: + if current_group: + parallel_groups.append(current_group) + current_group = {exp} + + if current_group: + parallel_groups.append(current_group) + + return ExecutionPlan(ordered_experiments=ordered, project=project) + + ### PRIVATE ####################### + + def _resolve_execution_order(self, project: Project) -> list[Experiment]: + """Determines the order experiments should be executed in based on dependencies""" + # Build dependency graph + graph = nx.DiGraph() + + for experiment in project.experiments: + graph.add_node(experiment) + for dep in experiment.dependencies: + graph.add_edge(dep, experiment) + + # Check for cycles + if not nx.is_directed_acyclic_graph(graph): + raise ValueError("Experiment dependencies contain cycles") + + # Return topologically sorted order + return list(nx.topological_sort(graph)) diff --git a/lab/runtime/__init__.py b/lab/runtime/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/runtime/messages.py b/lab/runtime/messages.py new file mode 100644 index 0000000..cf58eb7 --- /dev/null +++ b/lab/runtime/messages.py @@ -0,0 +1,28 @@ +from lab.core.messaging.message import Message +from lab.runtime.model.run import ExperimentRun, ProjectRun + + +class ExperimentRunStarted(Message): + run: ExperimentRun + + +class ExperimentRunComplete(Message): + run: ExperimentRun + + +class ExperimentRunFailed(Message): + run: ExperimentRun + reason: str + + +class ProjectRunStarted(Message): + run: ProjectRun + + +class ProjectRunComplete(Message): + run: ProjectRun + + +class ProjectRunFailed(Message): + run: ProjectRun + reason: str diff --git a/lab/runtime/model/__init__.py b/lab/runtime/model/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/runtime/model/execution.py b/lab/runtime/model/execution.py new file mode 100644 index 0000000..1004375 --- /dev/null +++ b/lab/runtime/model/execution.py @@ -0,0 +1,72 @@ +from abc import ABC, abstractmethod +from datetime import datetime +from pathlib import Path +from typing import Any, Callable + +from pydantic import Field + +from lab.core.model import Model + + +class ExecutionMetrics(Model): + """System-level metrics about the execution""" + + start_time: datetime + end_time: datetime + duration_seconds: float + memory_peak_bytes: int + cpu_time_seconds: float + io_read_bytes: int + io_write_bytes: int + + +class ExecutionContext(Model): + """Environment for a single experiment run""" + + working_dir: Path + env_vars: dict[str, str] = Field(default_factory=dict) + metrics: list[ExecutionMetrics] = Field(default_factory=list) + # resource_claims: list[ResourceClaim] = Field(default_factory=list) + + +class ExecutionMethod(Model, ABC): + """How an experiment should be executed""" + + # async def prepare(self) -> None: ... + @abstractmethod + async def run(self, context: ExecutionContext) -> None: ... + + # async def cleanup(self, cancelled: bool) -> None: ... + + +class ScriptExecution(ExecutionMethod): + """Execute a shell command""" + + command: str + args: list[str] + env: dict[str, str] = Field(default_factory=dict) + + async def run(self, context: ExecutionContext) -> None: + print("TODO: implement ScriptExecution.run") + + +class LocalFunctionExecution(ExecutionMethod): + """Execute a Python function""" + + func: Callable + kwargs: dict[str, Any] = Field(default_factory=dict) + is_async: bool + + async def run(self, context: ExecutionContext) -> None: + print("TODO: implement LocalFunctionExecution.run") + + +class APIExecution(ExecutionMethod): + """Execute via external API (e.g. lab equipment)""" + + endpoint: str + method: str + payload: dict[str, Any] = Field(default_factory=dict) + + async def run(self, context: ExecutionContext) -> None: + print("TODO: implement APIExecution.run") diff --git a/lab/runtime/model/run.py b/lab/runtime/model/run.py new file mode 100644 index 0000000..81908b3 --- /dev/null +++ b/lab/runtime/model/run.py @@ -0,0 +1,45 @@ +from datetime import datetime +from enum import Enum +from typing import Optional +from uuid import UUID, uuid4 + +from pydantic import Field + +from lab.core.model import Model +from lab.project.model.project import Experiment, Project +from lab.runtime.model.execution import ExecutionContext + + +class RunStatus(str, Enum): + PENDING = "pending" + RUNNING = "running" + COMPLETED = "completed" + FAILED = "failed" + CANCELLED = "cancelled" + + +class ExperimentRun(Model): + """Instance of a single experiment being executed""" + + id: UUID = Field(default_factory=uuid4) + experiment: Experiment + project_run: "ProjectRun" + context: ExecutionContext + status: RunStatus = RunStatus.PENDING + started_at: datetime = Field(default_factory=datetime.now) + completed_at: Optional[datetime] = None + error: Optional[str] = None # Changed from Exception for serialization + # metrics: list[ExecutionMetrics] = Field(default_factory=list) + # instrument_metrics: list[InstrumentMetric] = Field(default_factory=list) + + +class ProjectRun(Model): + """A running instance of a project""" + + id: UUID = Field(default_factory=uuid4) + project: Project + experiment_runs: list[ExperimentRun] = Field(default_factory=list) + status: RunStatus = RunStatus.PENDING + started_at: datetime = Field(default_factory=datetime.now) + completed_at: Optional[datetime] = None + error: Optional[str] = None # Changed from Exception for serialization diff --git a/lab/runtime/persistence/__init__.py b/lab/runtime/persistence/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/runtime/persistence/memory.py b/lab/runtime/persistence/memory.py new file mode 100644 index 0000000..ba0ae42 --- /dev/null +++ b/lab/runtime/persistence/memory.py @@ -0,0 +1,64 @@ +from datetime import datetime +from typing import Optional, Dict +from uuid import UUID + +from lab.runtime.model.run import ProjectRun, ExperimentRun, RunStatus +from lab.runtime.persistence.run import ProjectRunRepository, ExperimentRunRepository + + +class InMemoryProjectRunRepository(ProjectRunRepository): + """In-memory implementation of ProjectRunRepository""" + + def __init__(self): + self._storage: Dict[UUID, ProjectRun] = {} + + async def save(self, entity: ProjectRun): + self._storage[entity.id] = entity + + async def get(self, id: UUID) -> Optional[ProjectRun]: + return self._storage.get(id) + + async def list( + self, + status: Optional[RunStatus] = None, + since: Optional[datetime] = None, + **filters, + ) -> list[ProjectRun]: + results = list(self._storage.values()) + + if status: + results = [run for run in results if run.status == status] + + if since: + results = [run for run in results if run.started_at >= since] + + return results + + +class InMemoryExperimentRunRepository(ExperimentRunRepository): + """In-memory implementation of ExperimentRunRepository""" + + def __init__(self): + self._storage: Dict[UUID, ExperimentRun] = {} + + async def save(self, entity: ExperimentRun): + self._storage[entity.id] = entity + + async def get(self, id: UUID) -> Optional[ExperimentRun]: + return self._storage.get(id) + + async def list( + self, + status: Optional[RunStatus] = None, + since: Optional[datetime] = None, + **filters, + ) -> list[ExperimentRun]: + results = list(self._storage.values()) + + if status: + results = [run for run in results if run.status == status] + + if since: + results = [run for run in results if run.started_at >= since] + + return results diff --git a/lab/runtime/persistence/run.py b/lab/runtime/persistence/run.py new file mode 100644 index 0000000..20d1e3d --- /dev/null +++ b/lab/runtime/persistence/run.py @@ -0,0 +1,30 @@ +from abc import abstractmethod +from datetime import datetime +from typing import Optional + +from lab.core.repository import Repository +from lab.runtime.model.run import ProjectRun, ExperimentRun, RunStatus + + +class ProjectRunRepository(Repository[ProjectRun]): + """Repository interface for project runs""" + + @abstractmethod + async def list( + self, + status: Optional[RunStatus] = None, + since: Optional[datetime] = None, + **filters, + ) -> list[ProjectRun]: ... + + +class ExperimentRunRepository(Repository[ExperimentRun]): + """Repository interface for experiment runs""" + + @abstractmethod + async def list( + self, + status: Optional[RunStatus] = None, + since: Optional[datetime] = None, + **filters, + ) -> list[ExperimentRun]: ... diff --git a/lab/runtime/runtime.py b/lab/runtime/runtime.py new file mode 100644 index 0000000..74b8fc0 --- /dev/null +++ b/lab/runtime/runtime.py @@ -0,0 +1,81 @@ +from pathlib import Path +from lab.project.model.plan import ExecutionPlan +from lab.project.model.project import Experiment, Project +from lab.runtime.model.execution import ExecutionContext +from lab.runtime.model.run import ( + ExperimentRun, + ProjectRun, + RunStatus, +) +from lab.runtime.service.run import RunService + + +class Runtime: + def __init__(self, run_service: RunService): + self._run_service = run_service + + async def start(self, plan: ExecutionPlan) -> ProjectRun: + project_run = ProjectRun(status=RunStatus.RUNNING, project=plan.project) + await self._run_service.project_run_started(project_run) + + try: + for experiment in plan.ordered_experiments: + context = await self._create_execution_context(experiment) + experiment_run = ExperimentRun( + experiment=experiment, + context=context, + status=RunStatus.RUNNING, + project_run=project_run, + ) + await self._run_service.experiment_run_started(experiment_run, context) + + try: + await experiment.execution_method.run(context) + await self._run_service.experiment_run_completed(experiment_run) + except Exception as e: + await self._run_service.experiment_run_failed( + experiment_run, str(e) + ) + + # Let orchestrator decide how to handle failure + # @todo: design error handling for the runtime... + if not self._should_continue(experiment, plan.project, e): + break + + await self._run_service.project_run_completed(project_run) + return project_run + except Exception as e: + await self._run_service.project_run_failed(project_run, str(e)) + raise + + def _should_continue( + self, failed_experiment: Experiment, project: Project, _: Exception + ) -> bool: + """ + Determines how to proceed when an experiment fails. + Returns True if execution should continue, False if it should stop. + """ + # Get experiments that depend on the failed one + dependent_experiments = { + exp for exp in project.experiments if failed_experiment in exp.dependencies + } + + # If other experiments depend on this one, we should stop + if dependent_experiments: + return False + + # If no dependencies, we can continue with other experiments + return True + + async def _create_execution_context( + self, experiment: Experiment + ) -> ExecutionContext: + # Create context with experiment-specific configuration + context = ExecutionContext( + working_dir=Path(f"experiments/{experiment.id}"), + env_vars={ + "EXPERIMENT_ID": str(experiment.id), + "EXPERIMENT_NAME": experiment.name, + }, + ) + return context diff --git a/lab/runtime/service/__init__.py b/lab/runtime/service/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/runtime/service/run.py b/lab/runtime/service/run.py new file mode 100644 index 0000000..2867311 --- /dev/null +++ b/lab/runtime/service/run.py @@ -0,0 +1,107 @@ +import logging +from typing import Optional, Union, Mapping +from datetime import datetime +from uuid import UUID + +from lab.core.messaging.bus import MessageBus +from lab.core.messaging.message import Message +from lab.runtime.messages import ( + ExperimentRunComplete, + ExperimentRunFailed, + ExperimentRunStarted, + ProjectRunComplete, + ProjectRunFailed, + ProjectRunStarted, +) +from lab.runtime.model.execution import ExecutionContext +from lab.runtime.model.run import ( + ExperimentRun, + ProjectRun, + RunStatus, +) +from lab.runtime.persistence.run import ExperimentRunRepository, ProjectRunRepository + +logger = logging.getLogger(__name__) + + +class RunService: + """Service for managing experiment runs""" + + def __init__( + self, + project_run_repo: ProjectRunRepository, + experiment_run_repo: ExperimentRunRepository, + message_bus: MessageBus, + ): + self._project_run_repo = project_run_repo + self._experiment_run_repo = experiment_run_repo + self._message_bus = message_bus + + async def project_run_started(self, run: ProjectRun) -> None: + """Start tracking a new pipeline run""" + await self._project_run_repo.save(run) + await self._emit(ProjectRunStarted(run=run)) + + async def experiment_run_started( + self, + run: ExperimentRun, + context: ExecutionContext, + ) -> ExperimentRun: + """Start tracking a new experiment run""" + run.project_run.experiment_runs.append(run) + # @todo(rory): do we have to save both, or will sqlalchemy do it recursively? + await self._project_run_repo.save(run.project_run) + await self._experiment_run_repo.save(run) + await self._emit(ExperimentRunStarted(run=run)) + return run + + async def experiment_run_completed( + self, + run: ExperimentRun, + ) -> None: + """Mark experiment as completed with results""" + run.status = RunStatus.COMPLETED + run.completed_at = datetime.now() + # run.metrics = metrics + # run.experiment_data = data + await self._experiment_run_repo.save(run) + await self._emit(ExperimentRunComplete(run=run)) + + async def experiment_run_failed(self, run: ExperimentRun, error: str) -> None: + """Mark experiment as failed""" + run.status = RunStatus.FAILED + run.completed_at = datetime.now() + run.error = error + await self._experiment_run_repo.save(run) + await self._emit(ExperimentRunFailed(run=run, reason=error)) + + async def project_run_failed(self, run: ProjectRun, error: str) -> None: + """Mark experiment as failed""" + run.status = RunStatus.FAILED + run.completed_at = datetime.now() + run.error = error + await self._project_run_repo.save(run) + await self._emit(ProjectRunFailed(run=run, reason=error)) + + async def project_run_completed(self, project_run: ProjectRun) -> None: + """Mark pipeline as completed""" + project_run.status = RunStatus.COMPLETED + project_run.completed_at = datetime.now() + await self._project_run_repo.save(project_run) + await self._emit(ProjectRunComplete(run=project_run)) + + # Query methods + async def get_project_run(self, id: UUID) -> Optional[ProjectRun]: + return await self._project_run_repo.get(id) + + async def get_experiment_run(self, id: UUID) -> Optional[ExperimentRun]: + return await self._experiment_run_repo.get(id) + + async def list_project_runs( + self, status: Optional[RunStatus] = None, since: Optional[datetime] = None + ) -> list[ProjectRun]: + return await self._project_run_repo.list(status, since) + + async def _emit(self, message: Message) -> None: + """Emit event to subscribers of that event type""" + await self._message_bus.publish(message) diff --git a/lab/sdk/__init__.py b/lab/sdk/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/lab/service/experiment.py b/lab/service/experiment.py deleted file mode 100644 index 4ab55b1..0000000 --- a/lab/service/experiment.py +++ /dev/null @@ -1,17 +0,0 @@ -import rich -from lab.model.pipeline import Pipeline -from lab.model.project import Experiment - - -class ExperimentService: - def run(self, experiment: Experiment): - """Run an experiment - - Either - acquire an instance of the relevant experiment class - run a script - """ - rich.print(f"Running [b]{experiment.name}[/b]...") - rich.print("...done.") - - def dependencies(self): ... diff --git a/lab/service/pipeline.py b/lab/service/pipeline.py deleted file mode 100644 index a45566c..0000000 --- a/lab/service/pipeline.py +++ /dev/null @@ -1,113 +0,0 @@ -from typing import Sequence, Set, Dict, List -from collections import defaultdict -from uuid import UUID -from lab.model.pipeline import Pipeline -from lab.model.project import Experiment, Project -from lab.service.experiment import ExperimentService - - -class PipelineService: - """Service for managing and executing pipelines of experiments.""" - - def __init__(self, experiment_service: ExperimentService) -> None: - self._experiment_service = experiment_service - - ### PUBLIC ############## - - def create_pipeline(self, labfile: Project) -> Pipeline: - """Create a Pipeline from a Labfile, with experimentes ordered by dependencies. - - Args: - labfile: The input Labfile containing experimentes, providers, and datasets - - Returns: - A Pipeline with ordered experiments ready for execution - - Raises: - ValueError: If circular dependencies are detected between experimentes - """ - ordered_experiments = self._order_experiments(labfile.experiments) - - # Create experiments from ordered experimentes - return Pipeline( - experiments=ordered_experiments, - ) - - def run(self, pipeline: Pipeline) -> None: - """Execute all experiments in the pipeline in dependency order. - - Args: - pipeline: The pipeline to execute - """ - for exp in pipeline.experiments: - self._experiment_service.run(exp) - - ### PRIVATE ############# - - def _validate_no_cycles( - self, - experiment: Experiment, - visited: Set[UUID], - path: Set[UUID], - graph: Dict[UUID, Set[Experiment]], - experiments: Sequence[Experiment], - ) -> None: - """Detect cycles in the experiment dependency graph using DFS. - - Raises ValueError if a cycle is found. - """ - path.add(experiment.id) - visited.add(experiment.id) - - for dependency in graph[experiment.id]: - if dependency.id in path: - cycle = " -> ".join( - next(exp.name for exp in experiments if exp.id == exp_id) - for exp_id in path - ) - raise ValueError( - f"Circular dependency detected: {cycle} -> {dependency.name}" - ) - if dependency.id not in visited: - self._validate_no_cycles(dependency, visited, path, graph, experiments) - - path.remove(experiment.id) - - def _order_experiments( - self, experimentes: Sequence[Experiment] - ) -> List[Experiment]: - """Order experimentes based on their dependencies using topological sort. - - Raises ValueError if circular dependencies are detected. - """ - # Build dependency graph - graph: Dict[UUID, Set[Experiment]] = defaultdict(set) - for experiment in experimentes: - graph[experiment.id].update(experiment.dependencies) - - # Validate no cycles exist - visited: Set[UUID] = set() - for experiment in experimentes: - if experiment.id not in visited: - self._validate_no_cycles( - experiment, visited, set(), graph, experimentes - ) - - # Perform topological sort - ordered: List[Experiment] = [] - visited = set() - - def visit(experiment: Experiment) -> None: - if experiment.id in visited: - return - visited.add(experiment.id) - - for dependency in graph[experiment.id]: - visit(dependency) - - ordered.append(experiment) - - for experiment in experimentes: - visit(experiment) - - return ordered diff --git a/lab/settings.py b/lab/settings.py index 8c3d8f0..2f98407 100644 --- a/lab/settings.py +++ b/lab/settings.py @@ -3,5 +3,5 @@ class Settings(BaseSettings): - root: Path = Path(__file__).parent.parent + root: Path = Path(__file__).parent.parent # @bug: this won't work when installed spec_root: Path = root / "spec" diff --git a/lab/types.py b/lab/types.py deleted file mode 100644 index 9d7f9ba..0000000 --- a/lab/types.py +++ /dev/null @@ -1,17 +0,0 @@ -from __future__ import annotations -from types import ModuleType -from typing import TYPE_CHECKING, Callable, Optional, Type - -from torch import Tensor - -from lab.model.network.dendrites import Dendrite - -if TYPE_CHECKING: - from lab.model.network.population import CellParameters, PopulationState - - -Namespaces = dict[Type | Callable, ModuleType] -StepFunction = Callable[ - [list[Dendrite], list[Dendrite], "CellParameters", Optional["PopulationState"]], - "PopulationState", -] diff --git a/pyproject.toml b/pyproject.toml index 14fa3bc..696c0f6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,22 +16,23 @@ dependencies = [ "pyyaml>=6.0.2", "termplotlib>=0.3.9", "matplotlib>=3.9.2", - "typer>=0.12.5", - "labfile @ git+https://github.com/flywheelhq/labfile@dev", + "labfile @ git+https://github.com/flywhl/labfile@main", "wireup>=0.12.0", + "sqlalchemy>=2.0.36", + "dishka>=1.4.2", + "click>=8.1.8", ] readme = "README.md" -requires-python = ">= 3.8" +requires-python = ">= 3.10" [build-system] requires = ["hatchling"] build-backend = "hatchling.build" [project.scripts] -lab = "lab.cli.cli:main" +lab = "lab.cli.cli:start" -[tool.rye] -managed = true +[tool.uv] dev-dependencies = [ "coverage>=7.6.7", "pre-commit>=4.0.1", @@ -44,6 +45,3 @@ dev-dependencies = [ [tool.hatch.metadata] allow-direct-references = true - -[tool.hatch.build.targets.wheel] -packages = ["lab"] diff --git a/requirements-dev.lock b/requirements-dev.lock deleted file mode 100644 index 54ccffa..0000000 --- a/requirements-dev.lock +++ /dev/null @@ -1,149 +0,0 @@ -# generated by rye -# use `rye lock` or `rye sync` to update this lockfile -# -# last locked with the following flags: -# pre: false -# features: [] -# all-features: false -# with-sources: false -# generate-hashes: false -# universal: false - --e file:. -annotated-types==0.7.0 - # via pydantic -black==24.10.0 -cachetools==5.5.0 - # via tox -cfgv==3.4.0 - # via pre-commit -chardet==5.2.0 - # via tox -click==8.1.7 - # via black - # via typer -colorama==0.4.6 - # via tox -contourpy==1.3.0 - # via matplotlib -coverage==7.6.7 -cycler==0.12.1 - # via matplotlib -distlib==0.3.9 - # via virtualenv -filelock==3.16.1 - # via torch - # via tox - # via virtualenv -fonttools==4.54.1 - # via matplotlib -fsspec==2024.10.0 - # via torch -identify==2.6.1 - # via pre-commit -iniconfig==2.0.0 - # via pytest -jinja2==3.1.4 - # via torch -kiwisolver==1.4.7 - # via matplotlib -labfile @ git+https://github.com/flywheelhq/labfile@7253dc2bf222c0d36752016ecfcfb0d4fcf0cb6c - # via lab -lark==1.2.2 - # via lab - # via labfile -markdown-it-py==3.0.0 - # via rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.9.2 - # via lab -mdurl==0.1.2 - # via markdown-it-py -mpmath==1.3.0 - # via sympy -mypy-extensions==1.0.0 - # via black -networkx==3.4.2 - # via torch -nodeenv==1.9.1 - # via pre-commit - # via pyright -numpy==2.1.3 - # via contourpy - # via lab - # via matplotlib - # via termplotlib -packaging==24.1 - # via black - # via matplotlib - # via pyproject-api - # via pytest - # via tox -pathspec==0.12.1 - # via black -pillow==11.0.0 - # via matplotlib -platformdirs==4.3.6 - # via black - # via tox - # via virtualenv -pluggy==1.5.0 - # via pytest - # via tox -polars==1.12.0 - # via lab -pre-commit==4.0.1 -pydantic==2.9.2 - # via lab - # via labfile - # via pydantic-settings -pydantic-core==2.23.4 - # via pydantic -pydantic-settings==2.6.1 - # via lab - # via labfile -pygments==2.18.0 - # via rich -pyparsing==3.2.0 - # via matplotlib -pyproject-api==1.8.0 - # via tox -pyright==1.1.388 -pytest==8.3.3 - # via wireup -python-dateutil==2.9.0.post0 - # via matplotlib -python-dotenv==1.0.1 - # via pydantic-settings -pyyaml==6.0.2 - # via lab - # via pre-commit -rich==13.9.4 - # via lab - # via typer -ruff==0.7.2 -shellingham==1.5.4 - # via typer -six==1.16.0 - # via python-dateutil -sympy==1.13.1 - # via torch -termplotlib==0.3.9 - # via lab -torch==2.5.1 - # via lab -tox==4.23.2 -typer==0.12.5 - # via lab -typing-extensions==4.12.2 - # via pydantic - # via pydantic-core - # via pyright - # via torch - # via typer -virtualenv==20.27.1 - # via pre-commit - # via tox -wireup==0.12.0 - # via lab diff --git a/requirements.lock b/requirements.lock deleted file mode 100644 index 7464d86..0000000 --- a/requirements.lock +++ /dev/null @@ -1,106 +0,0 @@ -# generated by rye -# use `rye lock` or `rye sync` to update this lockfile -# -# last locked with the following flags: -# pre: false -# features: [] -# all-features: false -# with-sources: false -# generate-hashes: false -# universal: false - --e file:. -annotated-types==0.7.0 - # via pydantic -click==8.1.7 - # via typer -contourpy==1.3.0 - # via matplotlib -cycler==0.12.1 - # via matplotlib -filelock==3.16.1 - # via torch -fonttools==4.54.1 - # via matplotlib -fsspec==2024.10.0 - # via torch -iniconfig==2.0.0 - # via pytest -jinja2==3.1.4 - # via torch -kiwisolver==1.4.7 - # via matplotlib -labfile @ git+https://github.com/flywheelhq/labfile@7253dc2bf222c0d36752016ecfcfb0d4fcf0cb6c - # via lab -lark==1.2.2 - # via lab - # via labfile -markdown-it-py==3.0.0 - # via rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.9.2 - # via lab -mdurl==0.1.2 - # via markdown-it-py -mpmath==1.3.0 - # via sympy -networkx==3.4.2 - # via torch -numpy==2.1.3 - # via contourpy - # via lab - # via matplotlib - # via termplotlib -packaging==24.1 - # via matplotlib - # via pytest -pillow==11.0.0 - # via matplotlib -pluggy==1.5.0 - # via pytest -polars==1.12.0 - # via lab -pydantic==2.9.2 - # via lab - # via labfile - # via pydantic-settings -pydantic-core==2.23.4 - # via pydantic -pydantic-settings==2.6.1 - # via lab - # via labfile -pygments==2.18.0 - # via rich -pyparsing==3.2.0 - # via matplotlib -pytest==8.3.3 - # via wireup -python-dateutil==2.9.0.post0 - # via matplotlib -python-dotenv==1.0.1 - # via pydantic-settings -pyyaml==6.0.2 - # via lab -rich==13.9.4 - # via lab - # via typer -shellingham==1.5.4 - # via typer -six==1.16.0 - # via python-dateutil -sympy==1.13.1 - # via torch -termplotlib==0.3.9 - # via lab -torch==2.5.1 - # via lab -typer==0.12.5 - # via lab -typing-extensions==4.12.2 - # via pydantic - # via pydantic-core - # via torch - # via typer -wireup==0.12.0 - # via lab diff --git a/tests/Labfile.test b/tests/Labfile.test index b2814a0..158843b 100644 --- a/tests/Labfile.test +++ b/tests/Labfile.test @@ -1,6 +1,3 @@ -USE PROVIDER torch - - EXPERIMENT SimulateReach AS single_reach VIA exp2.py WITH diff --git a/tests/parser/test_parser.py b/tests/parser/test_parser.py deleted file mode 100644 index b551798..0000000 --- a/tests/parser/test_parser.py +++ /dev/null @@ -1,10 +0,0 @@ -from pathlib import Path - -from lab.service.labfile import LabfileService - - -def test_parse_should_generate_valid_tree(): - labfile = Path(__file__).parent.parent / "Labfile.test" - labfile_service = LabfileService() - project = labfile_service.parse(labfile) - print(project) diff --git a/tests/service/test_pipeline.py b/tests/service/test_pipeline.py deleted file mode 100644 index 5436627..0000000 --- a/tests/service/test_pipeline.py +++ /dev/null @@ -1,86 +0,0 @@ -from pathlib import Path -import pytest -from uuid import uuid4 - -from lab.model.project import Experiment, Project, ValueReference -from lab.service.experiment import ExperimentService -from lab.service.pipeline import PipelineService - - -@pytest.fixture -def experiment_service(): - return ExperimentService() - - -@pytest.fixture -def pipeline_service(experiment_service): - return PipelineService(experiment_service=experiment_service) - - -def test_orders_independent_experiments(pipeline_service): - """Test that independent experiments remain in original order""" - exp1 = Experiment(id=uuid4(), name="exp1", path=Path("exp1.py"), parameters={}) - exp2 = Experiment(id=uuid4(), name="exp2", path=Path("exp2.py"), parameters={}) - - project = Project(experiments=[exp1, exp2]) - pipeline = pipeline_service.create_pipeline(project) - - assert pipeline.experiments == [exp1, exp2] - - -def test_orders_dependent_experiments(pipeline_service): - """Test that dependent experiments are ordered correctly""" - exp1 = Experiment(id=uuid4(), name="exp1", path=Path("exp1.py"), parameters={}) - exp2 = Experiment( - id=uuid4(), - name="exp2", - path=Path("exp2.py"), - parameters={"input": ValueReference(owner=exp1, attribute="output")}, - ) - - # Even if exp2 comes first in project, it should be ordered after exp1 - project = Project(experiments=[exp2, exp1]) - pipeline = pipeline_service.create_pipeline(project) - - assert pipeline.experiments == [exp1, exp2] - - -def test_orders_chain_of_dependencies(pipeline_service): - """Test that a chain of dependencies is ordered correctly""" - exp1 = Experiment(id=uuid4(), name="exp1", path=Path("exp1.py"), parameters={}) - exp2 = Experiment( - id=uuid4(), - name="exp2", - path=Path("exp2.py"), - parameters={"input": ValueReference(owner=exp1, attribute="output")}, - ) - exp3 = Experiment( - id=uuid4(), - name="exp3", - path=Path("exp3.py"), - parameters={"input": ValueReference(owner=exp2, attribute="output")}, - ) - - # Even if experiments are in random order in project - project = Project(experiments=[exp2, exp3, exp1]) - pipeline = pipeline_service.create_pipeline(project) - - assert pipeline.experiments == [exp1, exp2, exp3] - - -def test_detects_circular_dependencies(pipeline_service): - """Test that circular dependencies raise ValueError""" - exp1 = Experiment(id=uuid4(), name="exp1", path=Path("exp1.py"), parameters={}) - exp2 = Experiment( - id=uuid4(), - name="exp2", - path=Path("exp2.py"), - parameters={"input": ValueReference(owner=exp1, attribute="output")}, - ) - # Create circular dependency by making exp1 depend on exp2 - exp1.parameters["input"] = ValueReference(owner=exp2, attribute="output") - - project = Project(experiments=[exp1, exp2]) - - with pytest.raises(ValueError, match="Circular dependency detected"): - pipeline_service.create_pipeline(project) diff --git a/tests/unit/project/service/plan_test.py b/tests/unit/project/service/plan_test.py new file mode 100644 index 0000000..fab74ed --- /dev/null +++ b/tests/unit/project/service/plan_test.py @@ -0,0 +1,94 @@ +from uuid import UUID, uuid4 +import pytest + +from lab.project.model.project import Experiment, Project, ValueReference +from lab.project.model.plan import ExecutionPlan +from lab.project.service.plan import PlanService +from lab.runtime.model.execution import ScriptExecution + + +@pytest.fixture +def plan_service(): + return PlanService() + + +def create_experiment(name: str) -> Experiment: + """Create a test experiment with the given name""" + return Experiment( + id=uuid4(), + name=name, + execution_method=ScriptExecution(command="echo", args=["test"]), + parameters={}, + ) + + +def test_creates_plan_for_empty_project(plan_service: PlanService) -> None: + """Should handle empty projects gracefully""" + project = Project(experiments=set()) + + plan = plan_service.create_execution_plan(project) + + assert isinstance(plan, ExecutionPlan) + assert plan.project == project + assert len(plan.ordered_experiments) == 0 + + +def test_creates_plan_for_independent_experiments(plan_service: PlanService) -> None: + """Should preserve experiments when there are no dependencies""" + exp1 = create_experiment("exp1") + exp2 = create_experiment("exp2") + project = Project(experiments={exp1, exp2}) + + plan = plan_service.create_execution_plan(project) + + assert set(plan.ordered_experiments) == {exp1, exp2} + + +def test_orders_dependent_experiments(plan_service: PlanService) -> None: + """Should order experiments based on dependencies""" + exp1 = create_experiment("exp1") + exp2 = create_experiment("exp2") + exp2.parameters["input"] = ValueReference(owner=exp1, attribute="output") + project = Project(experiments={exp1, exp2}) + + plan = plan_service.create_execution_plan(project) + + assert plan.ordered_experiments == [exp1, exp2] + + +def test_detects_dependency_cycles(plan_service: PlanService) -> None: + """Should raise ValueError when dependencies form a cycle""" + exp1 = create_experiment("exp1") + exp2 = create_experiment("exp2") + exp1.parameters["input1"] = ValueReference(owner=exp2, attribute="output") + exp2.parameters["input2"] = ValueReference(owner=exp1, attribute="output") + project = Project(experiments={exp1, exp2}) + + with pytest.raises(ValueError, match="contain cycles"): + plan_service.create_execution_plan(project) + + +def test_handles_complex_dependencies(plan_service: PlanService) -> None: + """Should correctly order experiments with complex dependencies""" + exp1 = create_experiment("exp1") + exp2 = create_experiment("exp2") + exp3 = create_experiment("exp3") + exp4 = create_experiment("exp4") + + # exp2 depends on exp1 + exp2.parameters["input"] = ValueReference(owner=exp1, attribute="output") + # exp3 depends on exp1 + exp3.parameters["input"] = ValueReference(owner=exp1, attribute="output") + # exp4 depends on exp2 and exp3 + exp4.parameters["input1"] = ValueReference(owner=exp2, attribute="output") + exp4.parameters["input2"] = ValueReference(owner=exp3, attribute="output") + + project = Project(experiments={exp1, exp2, exp3, exp4}) + + plan = plan_service.create_execution_plan(project) + + # exp1 must come first, exp4 must come last + assert 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