diff --git a/README.md b/README.md index c9f7621..1e69616 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,18 @@ ______________________________________________________________________ Run Stata's do-files with pytask. +## Table of Contents + +- [Installation](#installation) +- [Usage](#usage) + - [Dependencies and Products](#dependencies-and-products) + - [Accessing dependencies and products in the script](#accessing-dependencies-and-products-in-the-script) + - [YAML Configuration Files](#yaml-configuration-files) + - [Command Line Arguments](#command-line-arguments) + - [Repeating tasks with different scripts or inputs](#repeating-tasks-with-different-scripts-or-inputs) +- [Configuration](#configuration) +- [Changes](#changes) + ## Installation pytask-stata is available on [PyPI](https://pypi.org/project/pytask-stata) and @@ -99,9 +111,59 @@ def task_run_do_file(produces: Path = Path("auto.dta")): ### Accessing dependencies and products in the script Dependencies and products registered in the task function signature are used by pytask -to order tasks and track whether they are up-to-date. They are not automatically passed -to the Stata script. Use the `options` argument of the decorator to pass paths or other -values as command line arguments to your Stata executable. +to order tasks and track whether they are up-to-date. pytask-stata offers two modes to +pass these paths and other task data to the Stata script. + +1. Use the default YAML configuration file. This is the recommended mode if your Stata + installation can use the user-written `yaml` package. +1. Use the `options` argument of the decorator to pass command line arguments. This is + the compatibility mode for Stata installations where `yaml.ado` is not available or + not supported. + +Do not combine both interfaces. If `options` is supplied, pytask-stata assumes the +do-file receives all required values through command line arguments and does not create +a YAML configuration file. + +#### YAML Configuration Files + +By default, pytask-stata serializes all task keyword arguments and passes the path to +the generated YAML file as the first argument to the do-file. To read the file inside +Stata, install the user-written `yaml` package. + +```stata +ssc install yaml +``` + +Then read the configuration file in the Stata task. + +```python +from pathlib import Path + +from pytask import mark + + +@mark.stata(script=Path("script.do")) +def task_run_do_file( + depends_on: Path = Path("input.dta"), + produces: Path = Path("auto.dta"), +): + pass +``` + +```do +args config +yaml read using "`config'", locals replace +local depends_on = r(yaml_depends_on) +local produces = r(yaml_produces) + +use "`depends_on'", clear +save "`produces'" +``` + +#### Command Line Arguments + +Use the `options` argument of the decorator to pass paths or other values as command +line arguments to your Stata executable. This mode does not require the `yaml` package. For example, pass paths for the dependency and product with @@ -119,13 +181,13 @@ def task_run_do_file( pass ``` -And in your `script.do`, you can intercept the value with +And in your `script.do`, you can intercept the values with ```do * Intercept command line arguments and save them to macros. args depends_on produces -sysuse auto, clear +use "`depends_on'", clear save "`produces'" ``` @@ -133,8 +195,8 @@ The relative path inside the do-file works only because pytask-stata switches th current working directory to the directory of the task module before the task is executed. -To make the task independent from the current working directory, pass the full path as -an command line argument. Here is an example. +To make the task independent from the current working directory, pass the full path as a +command line argument. Here is an example. ```python # Absolute path to the build directory. diff --git a/docs/yaml.md b/docs/yaml.md new file mode 100644 index 0000000..594ad1e --- /dev/null +++ b/docs/yaml.md @@ -0,0 +1,36 @@ +# YAML Data Passed to Stata + +pytask-stata serializes task keyword arguments with PyYAML and passes the path to the +generated YAML file as the first command line argument to the do-file. Inside Stata, +read the file with the user-written `yaml` package. + +```stata +args config +yaml read using "`config'", locals replace +``` + +The `yaml` package stores parsed YAML in a Stata dataset with `key`, `value`, `level`, +`parent`, and `type` columns. With `locals`, scalar leaves are also available as +`r(yaml_)` macros. Nested keys are flattened with underscores. + +## Supported Types + +| Python value | YAML shape | Stata representation | Access pattern | +| -------------------------------- | ----------------------------- | -------------------------------------------------------------------- | ----------------------------------------- | +| Non-empty `str` | `name: hello` | `type=string`, `value=hello` | `r(yaml_name)` | +| `int` | `count: 42` | `type=numeric`, `value=42` | `r(yaml_count)` | +| `float` | `ratio: 3.14` | `type=numeric`, `value=3.14` | `r(yaml_ratio)` | +| `bool` | `enabled: true` | `type=boolean`, `value=1` or `0` | `r(yaml_enabled)` | +| `None` | `missing: null` | `type=null`, empty value | validate as `null`; no useful macro value | +| `pathlib.Path` | `path: build/out.dta` | `type=string`, POSIX-style path | `r(yaml_path)` | +| Flat `list` / `tuple` of scalars | `items:` plus `- value` lines | parent row plus `items_1`, `items_2`, ... rows with `type=list_item` | use flattened keys such as `items_1` | +| Nested `dict` with scalar leaves | nested mapping | flattened keys such as `config_child` | `yaml get config, attributes(child)` | + +## Recommended Limits + +Keep the YAML bridge to configuration-like data: scalar values, paths, flat scalar +lists, and nested dictionaries with scalar leaves. + +Avoid empty strings, lists of dictionaries, sets, bytes, decimals, and arbitrary Python +objects. PyYAML may emit YAML tags such as `!!set` or `!!binary`, or fail with a +`RepresenterError`; those forms are not useful as a stable Stata interface. diff --git a/justfile b/justfile index 483e4e3..d4dee13 100644 --- a/justfile +++ b/justfile @@ -12,7 +12,7 @@ test-ci: # Run type checking typing: - uv run --group typing --group test --isolated ty check + uv run --group typing --group test --group test-mock-stata --isolated ty check # Run linting and formatting lint: diff --git a/packages/stata_mock/src/stata_mock/cli.py b/packages/stata_mock/src/stata_mock/cli.py index 43370a6..2269cda 100644 --- a/packages/stata_mock/src/stata_mock/cli.py +++ b/packages/stata_mock/src/stata_mock/cli.py @@ -4,7 +4,10 @@ import re import sys +from dataclasses import dataclass +from dataclasses import field from pathlib import Path +from typing import Any INVALID_SYNTAX = 198 UNKNOWN_COMMAND = 199 @@ -44,38 +47,95 @@ def _parse_invocation(args: list[str]) -> tuple[Path, list[str], Path] | None: def _run_script(script: Path, options: list[str]) -> tuple[list[str], int | None]: lines = [f"running mock Stata for {script.name}"] - macros: dict[str, str] = {} + state = RuntimeState() - for raw_line in script.read_text().splitlines(): + for raw_line in _iter_stata_lines(script): line = raw_line.strip() if not line or line.startswith("*"): continue - line = _expand_local_macros(line, macros) + line = _expand_macros(line, state) lines.append(f". {line}") - error_code = _execute_line(line, macros, options) + error_code = _execute_line(line, state, options) if error_code is not None: return lines, error_code return lines, None -def _execute_line(line: str, macros: dict[str, str], options: list[str]) -> int | None: +def _iter_stata_lines(script: Path) -> list[str]: + lines: list[str] = [] + continued = "" + for raw_line in script.read_text().splitlines(): + stripped = raw_line.rstrip() + if stripped.endswith("///"): + continued += stripped.removesuffix("///").rstrip() + " " + continue + lines.append(continued + raw_line if continued else raw_line) + continued = "" + if continued: + lines.append(continued) + return lines + + +@dataclass +class YamlEntry: + """A flattened YAML key/value record.""" + + key: str + value: str + level: int + parent: str + type: str + + +@dataclass +class RuntimeState: + """Mutable state for a mock Stata do-file run.""" + + macros: dict[str, str] = field(default_factory=dict) + returns: dict[str, str] = field(default_factory=dict) + yaml_entries: dict[str, YamlEntry] = field(default_factory=dict) + + +def _execute_line(line: str, state: RuntimeState, options: list[str]) -> int | None: command, _, rest = line.partition(" ") command = command.lower() rest = rest.strip() if command == "args": - macros.update(dict(zip(rest.split(), options, strict=False))) + state.macros.update(dict(zip(rest.split(), options, strict=False))) + error_code = None + elif command == "local": + error_code = _set_local_macro(rest, state) elif command == "sysuse": - return None + error_code = None elif command == "save": - return _save_dataset(rest) + error_code = _save_dataset(rest) + elif command == "yaml": + error_code = _execute_yaml(rest, state) elif command in {"error", "exit"}: - return int(rest.split()[0]) + error_code = int(rest.split()[0]) else: - return UNKNOWN_COMMAND + error_code = UNKNOWN_COMMAND + + return error_code + +def _set_local_macro(rest: str, state: RuntimeState) -> int | None: + name, separator, value = rest.partition("=") + name = name.strip() + if not name: + return INVALID_SYNTAX + if separator: + value = value.strip() + if match := re.fullmatch(r"r\(([^)]+)\)", value): + state.macros[name] = state.returns.get(match.group(1), "") + else: + state.macros[name] = value.strip("\"'") + else: + value_parts = rest.split(maxsplit=1) + state.macros[value_parts[0]] = value_parts[1] if len(value_parts) > 1 else "" return None @@ -94,8 +154,345 @@ def _save_dataset(rest: str) -> int | None: return None -def _expand_local_macros(line: str, macros: dict[str, str]) -> str: - return re.sub(r"`([^']+)'", lambda match: macros.get(match.group(1), ""), line) +def _execute_yaml(rest: str, state: RuntimeState) -> int | None: + match = re.match(r"(?P\w+)(?P.*)", rest) + if match is None: + return INVALID_SYNTAX + subcommand = match.group("subcommand") + remaining = match.group("remaining") + subcommand = {"check": "validate", "desc": "describe"}.get( + subcommand.lower(), + subcommand.lower(), + ) + remaining = remaining.strip() + + if subcommand == "read": + return _yaml_read(remaining, state) + if subcommand == "get": + return _yaml_get(remaining, state) + if subcommand == "validate": + return _yaml_validate(remaining, state) + if subcommand in {"describe", "list", "dir", "frames", "clear"}: + return None + return UNKNOWN_COMMAND + + +def _yaml_read(rest: str, state: RuntimeState) -> int | None: + match = re.match( + r'^using\s+("?)(?P.+?)\1(?:\s*,\s*(?P.*))?$', + rest, + ) + if match is None: + return INVALID_SYNTAX + + path = Path(match.group("filename")) + if not path.is_absolute(): + path = Path.cwd() / path + try: + data = _parse_yaml_subset(path.read_text()) + except (OSError, TypeError, ValueError): + return INVALID_SYNTAX + + entries = _flatten_yaml(data) + state.yaml_entries = {entry.key: entry for entry in entries} + options = _parse_options(match.group("options") or "") + prefix = options.get("prefix", "yaml_") + + state.returns.update( + { + "filename": path.as_posix(), + "n_keys": str(len(entries)), + "max_level": str(max((entry.level for entry in entries), default=0)), + "yaml_mode": "canonical", + "cache_hit": "0", + } + ) + if "locals" in options: + state.returns.update( + { + f"{prefix}{entry.key}": entry.value + for entry in entries + if entry.type != "parent" + } + ) + return None + + +def _yaml_get(rest: str, state: RuntimeState) -> int | None: + query, options = _split_command_options(rest) + query = query.strip() + if not query: + return INVALID_SYNTAX + + parent, _, key = query.partition(":") + if key: + search_key = f"{parent}_{key}" + result_name = key + else: + search_key = parent + result_name = parent.rsplit("_", maxsplit=1)[-1] + + entry = state.yaml_entries.get(search_key) + children = _get_yaml_child_attributes(search_key, state) + state.returns.update( + { + "key": key or parent, + "parent": parent if key else "", + "found": "1" if entry is not None or children else "0", + "n_attrs": str(len(children) or int(entry is not None)), + } + ) + if children: + attributes = str(options.get("attributes", "")).split() + allowed = set(attributes) if attributes else set(children) + state.returns.update( + {attr: value for attr, value in children.items() if attr in allowed} + ) + elif entry is not None: + state.returns[result_name] = entry.value + return None + + +def _get_yaml_child_attributes( + search_key: str, + state: RuntimeState, +) -> dict[str, str]: + prefix = f"{search_key}_" + attributes: dict[str, str] = {} + for key, entry in state.yaml_entries.items(): + if not key.startswith(prefix) or entry.type == "parent": + continue + attribute = key.removeprefix(prefix) + if "_" not in attribute: + attributes[attribute] = entry.value + return attributes + + +def _yaml_validate(rest: str, state: RuntimeState) -> int | None: + _, options = _split_command_options(rest) + valid = True + + required = str(options.get("required", "")).split() + for key in required: + valid = valid and key in state.yaml_entries + + for spec in str(options.get("types", "")).split(): + key, separator, expected_type = spec.partition(":") + if not separator: + return INVALID_SYNTAX + entry = state.yaml_entries.get(key) + valid = valid and entry is not None and entry.type == expected_type + + state.returns["valid"] = "1" if valid else "0" + return None if valid else INVALID_SYNTAX + + +def _parse_yaml_subset(text: str) -> dict[str, Any]: + if re.search(r"(^|\s)(---|\{|\}|\[[^\]]*\]|&\w+|\*\w+)", text): + msg = "Unsupported YAML syntax." + raise ValueError(msg) + + root: dict[str, Any] = {} + stack: list[tuple[int, dict[str, Any] | list[Any]]] = [(-1, root)] + + lines = text.splitlines() + for line_number, raw_line in enumerate(lines): + parsed_line = _parse_yaml_line(raw_line) + if parsed_line is None: + continue + + indent, stripped = parsed_line + if stripped.startswith("- "): + _parse_yaml_list_item(stripped, indent, stack) + continue + + _parse_yaml_mapping_item(stripped, indent, lines, line_number, stack) + + return root + + +def _parse_yaml_line(raw_line: str) -> tuple[int, str] | None: + if not raw_line.strip() or raw_line.lstrip().startswith("#"): + return None + + indent = len(raw_line) - len(raw_line.lstrip(" ")) + if indent % 2: + msg = "Only two-space indentation is supported." + raise ValueError(msg) + + return indent, raw_line.strip() + + +def _parse_yaml_list_item( + stripped: str, + indent: int, + stack: list[tuple[int, dict[str, Any] | list[Any]]], +) -> None: + while stack and indent < stack[-1][0]: + stack.pop() + parent = stack[-1][1] + if not isinstance(parent, list): + msg = "List item without list parent." + raise TypeError(msg) + + item = stripped.removeprefix("- ").strip() + if ":" in item: + msg = "List items must be scalar values." + raise ValueError(msg) + parent.append(_parse_yaml_scalar(item)) + + +def _parse_yaml_mapping_item( + stripped: str, + indent: int, + lines: list[str], + line_number: int, + stack: list[tuple[int, dict[str, Any] | list[Any]]], +) -> None: + key, separator, value = stripped.partition(":") + if not separator or not key or " " in key: + msg = "Invalid YAML mapping key." + raise ValueError(msg) + + while stack and indent <= stack[-1][0]: + stack.pop() + parent = stack[-1][1] + if not isinstance(parent, dict): + msg = "Mapping key inside list is not supported." + raise TypeError(msg) + + if value.strip(): + parent[key] = _parse_yaml_scalar(value.strip()) + return + + next_line = _find_next_content_line(lines, line_number) + next_stripped = next_line.strip() if next_line is not None else "" + next_container: dict[str, Any] | list[Any] = ( + [] if next_stripped.startswith("- ") else {} + ) + parent[key] = next_container + stack.append((indent, next_container)) + + +def _find_next_content_line(lines: list[str], line_number: int) -> str | None: + """Return the next non-empty, non-comment line after ``current_line``.""" + for line in lines[line_number + 1 :]: + if line.strip() and not line.lstrip().startswith("#"): + return line + return None + + +def _parse_yaml_scalar(value: str) -> str | int | float | bool | None: + value = value.strip("\"'") + if value.lower() in {"true", "false"}: + return value.lower() == "true" + if value.lower() in {"null", "~"}: + return None + try: + return int(value) + except ValueError: + try: + return float(value) + except ValueError: + return value + + +def _flatten_yaml(data: dict[str, Any]) -> list[YamlEntry]: + entries: list[YamlEntry] = [] + + def recurse(value: Any, prefix: str, level: int, parent: str) -> None: + if isinstance(value, dict): + if prefix: + entries.append(YamlEntry(prefix, "", level, parent, "parent")) + for key, child in value.items(): + child_key = f"{prefix}_{key}" if prefix else key + recurse(child, child_key, level + 1, prefix) + return + if isinstance(value, list): + entries.append(YamlEntry(prefix, "", level, parent, "parent")) + for index, item in enumerate(value, start=1): + entries.append( + YamlEntry( + key=f"{prefix}_{index}", + value=_format_yaml_list_item(item), + level=level, + parent=prefix, + type="list_item", + ) + ) + return + + entries.append( + YamlEntry( + key=prefix, + value=_format_yaml_value(value), + level=level, + parent=parent, + type=_yaml_value_type(value), + ) + ) + + recurse(data, "", 0, "") + return entries + + +def _format_yaml_value(value: Any) -> str: + if isinstance(value, bool): + return "1" if value else "0" + if value is None: + return "" + return str(value) + + +def _format_yaml_list_item(value: Any) -> str: + if isinstance(value, bool): + return "true" if value else "false" + if value is None: + return "null" + return str(value) + + +def _yaml_value_type(value: Any) -> str: + if isinstance(value, bool): + return "boolean" + if isinstance(value, int | float): + return "numeric" + if value is None: + return "null" + return "string" + + +def _split_command_options(rest: str) -> tuple[str, dict[str, str | bool]]: + command, separator, options = rest.partition(",") + return command.strip(), _parse_options(options if separator else "") + + +def _parse_options(options: str) -> dict[str, str | bool]: + parsed: dict[str, str | bool] = {} + for option in _split_options(options): + if match := re.match(r"(?P\w+)\((?P.*)\)$", option): + parsed[_normalize_option_name(match.group("name"))] = match.group("value") + elif option: + parsed[_normalize_option_name(option)] = True + return parsed + + +def _split_options(options: str) -> list[str]: + return re.findall(r"\w+\([^)]*\)|\w+", options) + + +def _normalize_option_name(name: str) -> str: + return {"l": "locals", "s": "scalars", "q": "quiet"}.get(name, name) + + +def _expand_macros(line: str, state: RuntimeState) -> str: + def replace(match: re.Match[str]) -> str: + name = match.group(1) + if r_match := re.fullmatch(r"r\(([^)]+)\)", name): + return state.returns.get(r_match.group(1), "") + return state.macros.get(name, "") + + return re.sub(r"`([^']+)'", replace, line) def _parse_save_target(rest: str) -> str: diff --git a/pyproject.toml b/pyproject.toml index afb95b8..298e591 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ classifiers = [ "Programming Language :: Python :: 3 :: Only", ] requires-python = ">=3.10" -dependencies = ["click>=8.1.8,!=8.2.0", "pytask>=0.5.2"] +dependencies = ["click>=8.1.8,!=8.2.0", "pytask>=0.5.2", "pyyaml>=6.0.2"] dynamic = ["version"] [project.readme] diff --git a/src/pytask_stata/collect.py b/src/pytask_stata/collect.py index 04c4e13..45cfe97 100644 --- a/src/pytask_stata/collect.py +++ b/src/pytask_stata/collect.py @@ -24,6 +24,8 @@ from pytask import parse_products_from_task_function from pytask import remove_marks +from pytask_stata.serialization import SERIALIZERS +from pytask_stata.serialization import create_path_to_serialized from pytask_stata.shared import convert_task_id_to_name_of_log_file from pytask_stata.shared import stata @@ -32,12 +34,22 @@ def run_stata_script( _executable: str, _script: Path, _options: list[str], + _serialized: Path | None, _log_name: str, _cwd: Path, **_kwargs: Any, ) -> None: - """Run an R script.""" - cmd = [_executable, "-e", "do", _script.as_posix(), *_options, f"-{_log_name}"] + """Run a Stata do-file.""" + serialized_option = [] if _serialized is None else [_serialized.as_posix()] + cmd = [ + _executable, + "-e", + "do", + _script.as_posix(), + *_options, + *serialized_option, + f"-{_log_name}", + ] print("Executing " + " ".join(cmd) + ".") # noqa: T201 subprocess.run(cmd, cwd=_cwd, check=True) # noqa: S603 @@ -64,7 +76,8 @@ def pytask_collect_task( raise ValueError(msg) mark = _parse_stata_mark(mark=marks[0]) - script, options = stata(**marks[0].kwargs) + script = mark.kwargs["script"] + options = mark.kwargs["options"] or [] cast("Any", obj).pytask_meta.markers.append(mark) # Collect the nodes in @pytask.mark.julia and validate them. @@ -183,12 +196,73 @@ def pytask_collect_task( ) task.depends_on["_log_name"] = log_name_node + suffix = mark.kwargs["suffix"] + serialized = None if suffix is None else create_path_to_serialized(task, suffix) + task.depends_on["_serialized"] = _collect_serialized_node( + session=session, + path_nodes=path_nodes, + node_info=NodeInfo( + arg_name="_serialized", + path=(), + value=PythonNode(value=serialized), + task_path=path, + task_name=name, + ), + ) + return task return None +def _collect_serialized_node( + *, + session: Session, + path_nodes: Path, + node_info: NodeInfo, +) -> PythonNode: + """Collect the node for the serialized task configuration.""" + serialized_node = session.hook.pytask_collect_node( + session=session, + path=path_nodes, + node_info=node_info, + ) + return cast("PythonNode", serialized_node) + + def _parse_stata_mark(mark: Mark) -> Mark: """Parse a Stata mark.""" - script, options = stata(**mark.kwargs) - parsed_kwargs = {"script": script or None, "options": options or []} + script, options, serializer, suffix = stata(**mark.kwargs) + + if options is not None and (serializer is not None or suffix is not None): + msg = ( + "The @pytask.mark.stata interfaces cannot be mixed. Use either " + "'options' for command line arguments or 'serializer'/'suffix' for " + "serialized task arguments." + ) + raise ValueError(msg) + + if options is None and serializer is None: + serializer = "yaml" + + if isinstance(serializer, str) and serializer not in SERIALIZERS: + msg = ( + f"Serializer {serializer!r} is not known. Available serializers are " + f"{sorted(SERIALIZERS)}." + ) + raise ValueError(msg) + + proposed_suffix = ( + SERIALIZERS[serializer]["suffix"] + if isinstance(serializer, str) and serializer in SERIALIZERS and suffix is None + else suffix + ) + if serializer is not None and proposed_suffix is None: + msg = "Missing suffix for serialized Stata task." + raise ValueError(msg) + parsed_kwargs = { + "script": script or None, + "options": options, + "serializer": serializer, + "suffix": proposed_suffix, + } return Mark("stata", (), parsed_kwargs) diff --git a/src/pytask_stata/execute.py b/src/pytask_stata/execute.py index 07b4925..8ceaf22 100644 --- a/src/pytask_stata/execute.py +++ b/src/pytask_stata/execute.py @@ -4,16 +4,20 @@ import re from pathlib import Path +from typing import Any from typing import cast from pytask import PathNode +from pytask import PPathNode from pytask import PTask from pytask import PTaskWithPath from pytask import PythonNode from pytask import Session from pytask import has_mark from pytask import hookimpl +from pytask.tree_util import tree_map +from pytask_stata.serialization import serialize_keyword_arguments from pytask_stata.shared import STATA_COMMANDS @@ -29,6 +33,47 @@ def pytask_execute_task_setup(session: Session, task: PTask) -> None: ) raise RuntimeError(msg) + marks = list(task.markers) + stata_marks = [mark for mark in marks if mark.name == "stata"] + if stata_marks: + serializer = stata_marks[0].kwargs.get("serializer") + if serializer is None: + return + + serialized_node = task.depends_on["_serialized"] + if not isinstance(serialized_node, PythonNode) or not isinstance( + serialized_node.value, Path + ): + msg = ( + "Expected '_serialized' dependency to be a PythonNode " + "with a pathlib.Path value." + ) + raise TypeError(msg) + + path_to_serialized = serialized_node.value + path_to_serialized.parent.mkdir(parents=True, exist_ok=True) + kwargs = _collect_stata_keyword_arguments(task) + serialize_keyword_arguments(serializer, path_to_serialized, kwargs) + + +def _collect_stata_keyword_arguments(task: PTask) -> dict[str, Any]: + """Collect keyword arguments passed to the Stata config file.""" + kwargs: dict[str, Any] = { + **tree_map( + lambda node: ( + node.path.as_posix() if isinstance(node, PPathNode) else node.value + ), + task.depends_on, # ty: ignore[invalid-argument-type] + ), + **tree_map( + lambda node: ( + node.path.as_posix() if isinstance(node, PPathNode) else node.value + ), + task.produces, # ty: ignore[invalid-argument-type] + ), + } + return {key: value for key, value in kwargs.items() if not key.startswith("_")} + @hookimpl def pytask_execute_task_teardown(session: Session, task: PTask) -> None: diff --git a/src/pytask_stata/serialization.py b/src/pytask_stata/serialization.py new file mode 100644 index 0000000..245156c --- /dev/null +++ b/src/pytask_stata/serialization.py @@ -0,0 +1,80 @@ +"""Serialize task keyword arguments for Stata do-files.""" + +from __future__ import annotations + +import uuid +from collections.abc import Callable +from pathlib import Path +from typing import Any +from typing import TypedDict + +import yaml +from pytask import PTask +from pytask import PTaskWithPath + +__all__ = ["SERIALIZERS", "create_path_to_serialized", "serialize_keyword_arguments"] + +_HIDDEN_FOLDER = ".pytask/pytask-stata" + +SerializerFunc = Callable[..., str] + + +class SerializerEntry(TypedDict): + """Describe a serializer function and its output suffix.""" + + serializer: SerializerFunc + suffix: str + + +def _dump_yaml(kwargs: dict[str, Any]) -> str: + """Serialize task keyword arguments as YAML.""" + return yaml.safe_dump(kwargs, sort_keys=False) + + +SERIALIZERS: dict[str, SerializerEntry] = { + "yaml": {"serializer": _dump_yaml, "suffix": ".yaml"}, + "yml": {"serializer": _dump_yaml, "suffix": ".yml"}, +} + + +def create_path_to_serialized(task: PTask, suffix: str) -> Path: + """Create path to serialized task data.""" + return ( + (task.path.parent if isinstance(task, PTaskWithPath) else Path.cwd()) + .joinpath(_HIDDEN_FOLDER, str(uuid.uuid4())) + .with_suffix(suffix) + ) + + +def serialize_keyword_arguments( + serializer: str | SerializerFunc, + path_to_serialized: Path, + kwargs: dict[str, Any], +) -> None: + """Serialize keyword arguments.""" + if isinstance(serializer, str): + if serializer not in SERIALIZERS: + msg = f"Serializer {serializer!r} is not known." + raise ValueError(msg) + serializer_func = SERIALIZERS[serializer]["serializer"] + elif callable(serializer): + serializer_func = serializer + else: + msg = f"Serializer {serializer!r} is not known." + raise TypeError(msg) + + serialized = serializer_func(_normalize_for_stata(kwargs)) + path_to_serialized.write_text(serialized) + + +def _normalize_for_stata(value: Any) -> Any: + """Normalize values to objects supported by common config serializers.""" + if isinstance(value, Path): + return value.as_posix() + if isinstance(value, dict): + return {str(key): _normalize_for_stata(item) for key, item in value.items()} + if isinstance(value, list): + return [_normalize_for_stata(item) for item in value] + if isinstance(value, tuple): + return tuple(_normalize_for_stata(item) for item in value) + return value diff --git a/src/pytask_stata/shared.py b/src/pytask_stata/shared.py index bf8d1d3..8d09403 100644 --- a/src/pytask_stata/shared.py +++ b/src/pytask_stata/shared.py @@ -3,6 +3,7 @@ from __future__ import annotations import sys +from collections.abc import Callable from collections.abc import Iterable from collections.abc import Sequence from typing import TYPE_CHECKING @@ -44,21 +45,40 @@ STATA_COMMANDS = [] +_DEFAULT_OPTIONS = object() + + def stata( *, script: str | Path, - options: str | Iterable[str] | None = None, -) -> tuple[str | Path | None, str | Iterable[str] | None]: + options: str | Iterable[str] | None | object = _DEFAULT_OPTIONS, + serializer: str | Callable[..., str] | None = None, + suffix: str | None = None, +) -> tuple[ + str | Path | None, + list[str] | None, + str | Callable[..., str] | None, + str | None, +]: """Specify command line options for Stata. Parameters ---------- + script : str | Path + The path to the Stata do-file which is executed. options : str | Iterable[str] | None One or multiple command line options passed to Stata. + serializer : str | Callable[..., str] | None + A function to serialize data for the task. If ``None``, task data is not + serialized. + suffix : str | None + A suffix for the serialized file. If ``None``, infer it from known serializers. """ - options = [] if options is None else list(map(str, _to_list(options))) - return script, options + parsed_options = ( + None if options is _DEFAULT_OPTIONS else list(map(str, _to_list(options))) + ) + return script, parsed_options, serializer, suffix def convert_task_id_to_name_of_log_file(task: PTask) -> str: diff --git a/tests/test_collect.py b/tests/test_collect.py index 4a7ca3b..60e1ff7 100644 --- a/tests/test_collect.py +++ b/tests/test_collect.py @@ -16,13 +16,19 @@ (), {"script": "script.do", "options": "--option"}, does_not_raise(), - ("script.do", ["--option"]), + ("script.do", ["--option"], None, None), ), ( (), {"script": "script.do", "options": [1]}, does_not_raise(), - ("script.do", ["1"]), + ("script.do", ["1"], None, None), + ), + ( + (), + {"script": "script.do"}, + does_not_raise(), + ("script.do", None, None, None), ), ], ) @@ -38,7 +44,30 @@ def test_stata(args, kwargs, expectation, expected): ( Mark("stata", (), {"script": "script.do"}), does_not_raise(), + Mark( + "stata", + (), + { + "script": "script.do", + "options": None, + "serializer": "yaml", + "suffix": ".yaml", + }, + ), + ), + ( Mark("stata", (), {"script": "script.do", "options": []}), + does_not_raise(), + Mark( + "stata", + (), + { + "script": "script.do", + "options": [], + "serializer": None, + "suffix": None, + }, + ), ), ], ) @@ -50,3 +79,41 @@ def test_parse_stata_mark( with expectation: out = _parse_stata_mark(mark) assert out == expected + + +def test_parse_stata_mark_with_yaml(): + mark = Mark("stata", (), {"script": "script.do", "serializer": "yaml"}) + + out = _parse_stata_mark(mark) + + assert out == Mark( + "stata", + (), + { + "script": "script.do", + "options": None, + "serializer": "yaml", + "suffix": ".yaml", + }, + ) + + +def test_parse_stata_mark_raises_for_json(): + mark = Mark("stata", (), {"script": "script.do", "serializer": "json"}) + + with pytest.raises(ValueError, match="Serializer 'json' is not known"): + _parse_stata_mark(mark) + + +@pytest.mark.parametrize( + "kwargs", + [ + {"script": "script.do", "options": [], "serializer": "yaml"}, + {"script": "script.do", "options": [], "suffix": ".yaml"}, + ], +) +def test_parse_stata_mark_raises_for_mixed_interfaces(kwargs): + mark = Mark("stata", (), kwargs) + + with pytest.raises(ValueError, match="interfaces cannot be mixed"): + _parse_stata_mark(mark) diff --git a/tests/test_execute.py b/tests/test_execute.py index d622ad0..9f3a0f6 100644 --- a/tests/test_execute.py +++ b/tests/test_execute.py @@ -8,6 +8,7 @@ import pytest from pytask import ExitCode from pytask import Mark +from pytask import PythonNode from pytask import Session from pytask import Task from pytask import build @@ -40,6 +41,126 @@ def test_pytask_execute_task_setup_raise_error(stata, platform, expectation): pytask_execute_task_setup(session, task) +def test_pytask_execute_task_setup_serializes_keyword_arguments(tmp_path): + path_to_serialized = tmp_path / "config.txt" + product = tmp_path / "out.dta" + + def serializer(kwargs): + return f"produces={kwargs['produces']}" + + task = Task( + base_name="task_example", + path=tmp_path / "task_example.py", + function=lambda: None, + depends_on={ + "_serialized": PythonNode(value=path_to_serialized), + "_script": PythonNode(value=tmp_path / "script.do"), + "_options": PythonNode(value=[]), + "_log_name": PythonNode(value=""), + "produces": PythonNode(value=product), + }, + markers=[ + Mark( + "stata", + (), + { + "script": "script.do", + "serializer": serializer, + "suffix": ".txt", + }, + ) + ], + ) + session = Session(config={"stata": "stata", "platform": sys.platform}) + + pytask_execute_task_setup(session, task) + + assert path_to_serialized.read_text() == f"produces={product.as_posix()}" + + +@needs_stata +def test_run_do_file_with_yaml_config(runner, tmp_path): + task_source = """ + import pytask + from pathlib import Path + + @pytask.mark.stata(script="script.do") + def task_run_do_file(produces=Path("auto.dta")): + pass + """ + tmp_path.joinpath("task_example.py").write_text(textwrap.dedent(task_source)) + + do_file = """ + args config + yaml read using "`config'", locals replace + local produces = r(yaml_produces) + sysuse auto, clear + save "`produces'", replace + """ + tmp_path.joinpath("script.do").write_text(textwrap.dedent(do_file)) + + result = runner.invoke(cli, [tmp_path.as_posix()]) + + assert result.exit_code == ExitCode.OK + assert tmp_path.joinpath("auto.dta").exists() + + +@needs_stata +def test_run_do_file_with_supported_yaml_values(runner, tmp_path): + task_source = """ + from pathlib import Path + + import pytask + + + @pytask.task( + kwargs={ + "string_value": "hello", + "integer_value": 42, + "float_value": 3.14, + "bool_value": True, + "none_value": None, + "path_value": Path("input.txt"), + "list_numbers": [1, 2], + "tuple_strings": ("a", "b"), + "nested_mapping": { + "child_int": 1, + "child_bool": False, + "child_string": "value", + }, + } + ) + @pytask.mark.stata(script="script.do") + def task_run_do_file(produces=Path("supported.dta")): + pass + """ + tmp_path.joinpath("task_example.py").write_text(textwrap.dedent(task_source)) + tmp_path.joinpath("input.txt").write_text("input") + + do_file = """ + args config + yaml read using "`config'", locals replace + yaml validate, /// + required(string_value integer_value float_value bool_value none_value /// + path_value list_numbers list_numbers_1 list_numbers_2 /// + tuple_strings tuple_strings_1 tuple_strings_2 nested_mapping /// + nested_mapping_child_int nested_mapping_child_bool /// + nested_mapping_child_string produces) /// + types(integer_value:numeric float_value:numeric bool_value:boolean /// + none_value:null nested_mapping_child_bool:boolean) + yaml get nested_mapping, attributes(child_int child_bool child_string) quiet + local produces = r(yaml_produces) + sysuse auto, clear + save "`produces'", replace + """ + tmp_path.joinpath("script.do").write_text(textwrap.dedent(do_file)) + + result = runner.invoke(cli, [tmp_path.as_posix()]) + + assert result.exit_code == ExitCode.OK + assert tmp_path.joinpath("supported.dta").exists() + + @needs_stata def test_run_do_file(runner, tmp_path): task_source = """ diff --git a/tests/test_stata_mock.py b/tests/test_stata_mock.py new file mode 100644 index 0000000..57d56e2 --- /dev/null +++ b/tests/test_stata_mock.py @@ -0,0 +1,291 @@ +from __future__ import annotations + +import sys +import textwrap + +from stata_mock.cli import _flatten_yaml +from stata_mock.cli import _parse_yaml_subset +from stata_mock.cli import main + +NESTED_CHILD_LEVEL = 2 + + +def test_yaml_read_with_locals_exposes_r_macros_and_saves_product( + tmp_path, monkeypatch +): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text( + textwrap.dedent( + """ + produces: out.dta + database: + host: localhost + port: 5432 + debug: true + """ + ) + ) + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", locals replace + save "`r(yaml_produces)'" + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert (tmp_path / "out.dta").exists() + assert "end of mock do-file" in (tmp_path / "mock.log").read_text() + + +def test_yaml_subset_matches_stata_for_supported_scalar_and_nested_types(): + config = textwrap.dedent( + """ + string_value: hello + integer_value: 42 + float_value: 3.14 + bool_true: true + bool_false: false + none_value: null + path_value: build/output file.dta + list_numbers: + - 1 + - 2 + list_mixed: + - 1 + - two + - true + - null + nested_mapping: + child_int: 1 + child_bool: false + child_string: value + """ + ) + + entries = {entry.key: entry for entry in _flatten_yaml(_parse_yaml_subset(config))} + + assert entries["string_value"].value == "hello" + assert entries["string_value"].type == "string" + assert entries["integer_value"].value == "42" + assert entries["integer_value"].type == "numeric" + assert entries["float_value"].value == "3.14" + assert entries["float_value"].type == "numeric" + assert entries["bool_true"].value == "1" + assert entries["bool_true"].type == "boolean" + assert entries["bool_false"].value == "0" + assert entries["bool_false"].type == "boolean" + assert entries["none_value"].value == "" + assert entries["none_value"].type == "null" + assert entries["path_value"].value == "build/output file.dta" + assert entries["path_value"].type == "string" + + assert entries["list_numbers"].type == "parent" + assert entries["list_numbers_1"].value == "1" + assert entries["list_numbers_1"].parent == "list_numbers" + assert entries["list_numbers_1"].type == "list_item" + assert entries["list_mixed_3"].value == "true" + assert entries["list_mixed_3"].type == "list_item" + assert entries["list_mixed_4"].value == "null" + assert entries["list_mixed_4"].type == "list_item" + + assert entries["nested_mapping"].type == "parent" + assert entries["nested_mapping_child_int"].value == "1" + assert entries["nested_mapping_child_int"].level == NESTED_CHILD_LEVEL + assert entries["nested_mapping_child_int"].parent == "nested_mapping" + assert entries["nested_mapping_child_bool"].value == "0" + assert entries["nested_mapping_child_bool"].type == "boolean" + + +def test_yaml_read_supports_custom_prefix_for_r_macros(tmp_path, monkeypatch): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text("produces: prefixed.dta\n") + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", locals prefix(cfg_) replace + save "`r(cfg_produces)'" + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert (tmp_path / "prefixed.dta").exists() + + +def test_yaml_get_returns_attributes_for_nested_mapping(tmp_path, monkeypatch): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text( + textwrap.dedent( + """ + database: + host: localhost + port: 5432 + """ + ) + ) + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", replace + yaml get database:host, quiet + save "`r(host)'" + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert (tmp_path / "localhost.dta").exists() + + +def test_yaml_get_returns_child_attributes_for_parent_key(tmp_path, monkeypatch): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text( + textwrap.dedent( + """ + indicators: + CME_MRY0T4: + label: mortality + unit: deaths + dataflow: CME + """ + ) + ) + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", replace + yaml get indicators:CME_MRY0T4, attributes(label unit) quiet + save "`r(label)'" + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert (tmp_path / "mortality.dta").exists() + + +def test_yaml_validate_required_and_types_success(tmp_path, monkeypatch): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text( + textwrap.dedent( + """ + name: project + version: 1 + debug: false + """ + ) + ) + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", replace + yaml validate, required(name version debug) /// + types(version:numeric debug:boolean) + sysuse auto, clear + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert "end of mock do-file" in (tmp_path / "mock.log").read_text() + + +def test_yaml_validate_required_failure_returns_stata_syntax_error( + tmp_path, monkeypatch +): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text("name: project\n") + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", replace + yaml validate, required(name version) + sysuse auto, clear + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert "r(198)" in (tmp_path / "mock.log").read_text() + + +def test_yaml_read_rejects_unsupported_yaml_syntax(tmp_path, monkeypatch): + monkeypatch.chdir(tmp_path) + config = tmp_path / "config.yaml" + config.write_text("produces: &target out.dta\ncopy: *target\n") + script = tmp_path / "script.do" + script.write_text( + textwrap.dedent( + """ + args config + yaml read using "`config'", locals replace + save "`r(yaml_produces)'" + """ + ) + ) + + monkeypatch.setattr( + sys, + "argv", + ["Stata", "-e", "do", script.as_posix(), config.as_posix(), "-mock"], + ) + + assert main() == 0 + assert "r(198)" in (tmp_path / "mock.log").read_text() + assert not (tmp_path / "out.dta").exists() diff --git a/uv.lock b/uv.lock index c5c5fbf..b6f5ade 100644 --- a/uv.lock +++ b/uv.lock @@ -2,8 +2,8 @@ version = 1 revision = 3 requires-python = ">=3.10" resolution-markers = [ - "python_full_version >= '3.11'", - "python_full_version < '3.11'", + "python_full_version >= '3.13'", + "python_full_version < '3.13'", ] [manifest] @@ -14,11 +14,11 @@ members = [ [[package]] name = "attrs" -version = "25.3.0" +version = "26.1.0" source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/5a/b0/1367933a8532ee6ff8d63537de4f1177af4bff9f3e829baf7331f595bb24/attrs-25.3.0.tar.gz", hash = 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