26061440371

Committed 18 May 2026 09:26PM UTC coverage: 58.632% (+2.2%) from 56.443%

Build # 26061440371

Build Type

Pull #19

github

Committed by

MuellerSeb

Commit Message

Use explicit transfer molds for f2py handles

Pull Request Pull Request #19: F2py wrapper support

Coverage Stats

252 of 368 new or added lines in 4 files covered. (68.48%)

1 existing line in 1 file now uncovered.

1671 of 2850 relevant lines covered (58.63%)

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0.0

/src/nml_tools/cli.py

"""Command line interface for nml-tools."""

from __future__ import annotations

import logging
import math
import re
import sys
from pathlib import Path
from typing import Any

import click
import f90nml  # type: ignore
from click.exceptions import Exit

from ._version import __version__
from .codegen_f2py import (
    F2pyCTypeMap,
    build_f2py_namelist_spec,
    collect_f2py_kind_usage,
    generate_f2cmap,
    generate_f2py_wrappers,
    generate_python_wrappers,
    merge_f2py_kind_usage,
)
from .codegen_fortran import ConstantSpec, generate_fortran, generate_helper
from .codegen_markdown import generate_docs
from .codegen_template import generate_template
from .schema import load_schema
from .validate import validate_namelist

if sys.version_info >= (3, 11):
    import tomllib
else:  # pragma: no cover - python<3.11
    import tomli as tomllib

logger = logging.getLogger(__name__)
_FORTRAN_IDENTIFIER = re.compile(r"^[A-Za-z][A-Za-z0-9_]*$")
_CONTEXT_SETTINGS = {"help_option_names": ["-h", "--help"]}


def _configure_logging(verbose: int, quiet: int) -> None:
    base_level = logging.INFO
    level = base_level - (10 * verbose) + (10 * quiet)
    level = max(logging.DEBUG, min(logging.CRITICAL, level))
    logging.basicConfig(level=level, format="%(levelname)s: %(message)s")


def _load_config(path: Path) -> dict[str, Any]:
    with path.open("rb") as handle:
        data = tomllib.load(handle)
    if not isinstance(data, dict):
        raise click.ClickException("config must be a table")
    return data


def _load_config_checked(path: Path) -> dict[str, Any]:
    try:
        return _load_config(path)
    except FileNotFoundError as exc:
        raise click.ClickException(str(exc)) from exc
    except Exception as exc:  # pragma: no cover - tomllib may raise ValueError
        raise click.ClickException(f"failed to read config: {exc}") from exc


def _resolve_optional_path(
    value: Any,
    *,
    base_dir: Path,
    key: str,
) -> Path | None:
    if value is None:
        return None
    if not isinstance(value, str):
        raise click.ClickException(f"config '{key}' must be a string")
    return base_dir / value


def _load_helper_settings(
    config: dict[str, Any],
    base_dir: Path,
) -> tuple[Path | None, str, int, str | None]:
    default_buffer = 1024
    helper_raw = config.get("helper")
    if helper_raw is None:
        helper_path = _resolve_optional_path(
            config.get("helper_path"),
            base_dir=base_dir,
            key="helper_path",
        )
        helper_module_raw = config.get("helper_module", "nml_helper")
        if not isinstance(helper_module_raw, str):
            raise click.ClickException("config 'helper_module' must be a string")
        helper_module = helper_module_raw.strip()
        if not helper_module:
            raise click.ClickException("config 'helper_module' must be a non-empty string")
        return helper_path, helper_module, default_buffer, None

    if not isinstance(helper_raw, dict):
        raise click.ClickException("config 'helper' must be a table")
    if "helper_path" in config or "helper_module" in config:
        logger.warning("config uses [helper]; ignoring legacy helper_path/helper_module")
    helper_path = _resolve_optional_path(
        helper_raw.get("path"),
        base_dir=base_dir,
        key="helper.path",
    )
    helper_module_raw = helper_raw.get("module", "nml_helper")
    if not isinstance(helper_module_raw, str):
        raise click.ClickException("config 'helper.module' must be a string")
    helper_module = helper_module_raw.strip()
    if not helper_module:
        raise click.ClickException("config 'helper.module' must be a non-empty string")
    header_raw = helper_raw.get("header")
    if header_raw is None:
        header = None
    else:
        if not isinstance(header_raw, str):
            raise click.ClickException("config 'helper.header' must be a string")
        header = header_raw.rstrip()
        if not header:
            header = None
    buffer_raw = helper_raw.get("buffer", default_buffer)
    if isinstance(buffer_raw, bool) or not isinstance(buffer_raw, int):
        raise click.ClickException("config 'helper.buffer' must be an integer")
    if buffer_raw <= 0:
        raise click.ClickException("config 'helper.buffer' must be positive")
    return helper_path, helper_module, buffer_raw, header


def _load_kind_settings(config: dict[str, Any]) -> tuple[str, dict[str, str], set[str]]:
    kinds_raw = config.get("kinds")
    if not isinstance(kinds_raw, dict):
        raise click.ClickException("config must define a [kinds] table")
    module_raw = kinds_raw.get("module")
    if not isinstance(module_raw, str) or not module_raw.strip():
        raise click.ClickException("config 'kinds.module' must be a non-empty string")
    module = module_raw.strip()

    map_raw = kinds_raw.get("map", {})
    if map_raw is None:
        map_raw = {}
    if not isinstance(map_raw, dict):
        raise click.ClickException("config 'kinds.map' must be a table")
    kind_map: dict[str, str] = {}
    for alias, target in map_raw.items():
        if not isinstance(alias, str) or not isinstance(target, str):
            raise click.ClickException("config 'kinds.map' keys and values must be strings")
        kind_map[alias] = target

    real_raw = kinds_raw.get("real", [])
    integer_raw = kinds_raw.get("integer", [])
    if not isinstance(real_raw, list) or not all(isinstance(item, str) for item in real_raw):
        raise click.ClickException("config 'kinds.real' must be a list of strings")
    if not isinstance(integer_raw, list) or not all(isinstance(item, str) for item in integer_raw):
        raise click.ClickException("config 'kinds.integer' must be a list of strings")
    allowlist = set(real_raw) | set(integer_raw)

    return module, kind_map, allowlist


def _load_f2py_settings(
    config: dict[str, Any],
    base_dir: Path,
) -> tuple[Path | None, F2pyCTypeMap]:
    f2py_raw = config.get("f2py")
    if f2py_raw is None:
        return None, F2pyCTypeMap(real={}, integer={})
    if not isinstance(f2py_raw, dict):
        raise click.ClickException("config 'f2py' must be a table")
    if "python_package" in f2py_raw:
        raise click.ClickException(
            "config 'f2py.python_package' is no longer supported; "
            "place the f2py extension next to the generated Python wrapper"
        )

    f2cmap_path = _resolve_optional_path(
        f2py_raw.get("f2cmap_path"),
        base_dir=base_dir,
        key="f2py.f2cmap_path",
    )

    c_types_raw = f2py_raw.get("c_types", {})
    if c_types_raw is None:
        c_types_raw = {}
    if not isinstance(c_types_raw, dict):
        raise click.ClickException("config 'f2py.c_types' must be a table")

    real = _load_f2py_ctype_table(c_types_raw, "real")
    integer = _load_f2py_ctype_table(c_types_raw, "integer")
    return f2cmap_path, F2pyCTypeMap(real=real, integer=integer)


def _load_f2py_ctype_table(c_types: dict[str, Any], key: str) -> dict[str, str]:
    raw = c_types.get(key, {})
    if raw is None:
        raw = {}
    if not isinstance(raw, dict):
        raise click.ClickException(f"config 'f2py.c_types.{key}' must be a table")
    values: dict[str, str] = {}
    for kind, c_type in raw.items():
        if not isinstance(kind, str) or not kind.strip():
            raise click.ClickException(
                f"config 'f2py.c_types.{key}' keys must be non-empty strings"
            )
        if not isinstance(c_type, str) or not c_type.strip():
            raise click.ClickException(
                f"config 'f2py.c_types.{key}.{kind}' must be a non-empty string"
            )
        values[kind.strip()] = c_type.strip()
    return values


def _format_constant_literal(value: int | float) -> tuple[str, str]:
    if isinstance(value, bool):
        raise click.ClickException("config constants must not be boolean")
    if isinstance(value, int):
        return "integer", str(value)
    if isinstance(value, float):
        literal = repr(float(value))
        if literal.lower() == "nan":
            raise click.ClickException("config constants must not be NaN")
        if "." not in literal and "e" not in literal and "E" not in literal:
            literal = f"{literal}.0"
        return "real", literal
    raise click.ClickException("config constants must be integers or reals")


def _load_constants(config: dict[str, Any]) -> tuple[dict[str, int | float], list[ConstantSpec]]:
    constants_raw = config.get("constants", {})
    if constants_raw is None:
        constants_raw = {}
    if not isinstance(constants_raw, dict):
        raise click.ClickException("config 'constants' must be a table")

    constants: dict[str, int | float] = {}
    specs: list[ConstantSpec] = []
    for name_raw, entry in constants_raw.items():
        if not isinstance(name_raw, str):
            raise click.ClickException("config constants must use string keys")
        name = name_raw.strip()
        if not name:
            raise click.ClickException("config constants must have non-empty names")
        if not _FORTRAN_IDENTIFIER.match(name):
            raise click.ClickException(
                f"config constant '{name}' must be a valid Fortran identifier"
            )
        if not isinstance(entry, dict):
            raise click.ClickException(f"config constant '{name}' must be a table with 'value'")
        if "value" not in entry:
            raise click.ClickException(f"config constant '{name}' must define 'value'")
        value = entry.get("value")
        if not isinstance(value, (int, float)):
            raise click.ClickException("config constants must be integers or reals")
        type_spec, literal = _format_constant_literal(value)
        doc = entry.get("doc")
        if doc is not None:
            if not isinstance(doc, str):
                raise click.ClickException(f"config constant '{name}' doc must be a string")
            doc = " ".join(doc.splitlines()).strip() or None
        specs.append(
            ConstantSpec(
                name=name,
                type_spec=type_spec,
                value=literal,
                doc=doc,
            )
        )
        constants[name] = value
    return constants, specs


def _load_bool_field(section: dict[str, Any], key: str, *, label: str) -> bool:
    value = section.get(key, False)
    if isinstance(value, bool):
        return value
    raise click.ClickException(f"config '{label}' must be a boolean")


def _load_documentation_settings(
    config: dict[str, Any],
) -> tuple[str | None, bool, bool, str]:
    doc_raw = config.get("documentation")
    if doc_raw is None:
        return None, False, False, "numpy"
    if not isinstance(doc_raw, dict):
        raise click.ClickException("config 'documentation' must be a table")
    module_doc = None
    if "module" in doc_raw:
        module_raw = doc_raw.get("module")
        if not isinstance(module_raw, str):
            raise click.ClickException("config 'documentation.module' must be a string")
        module_doc = module_raw.strip() or None
    md_doxygen_id_from_name = _load_bool_field(
        doc_raw,
        "md_doxygen_id_from_name",
        label="documentation.md_doxygen_id_from_name",
    )
    md_add_toc_statement = _load_bool_field(
        doc_raw,
        "md_add_toc_statement",
        label="documentation.md_add_toc_statement",
    )
    py_style_raw = doc_raw.get("py-style", "numpy")
    if not isinstance(py_style_raw, str):
        raise click.ClickException("config 'documentation.py-style' must be a string")
    py_style = py_style_raw.strip().lower()
    if py_style not in {"numpy", "doxygen"}:
        raise click.ClickException(
            "config 'documentation.py-style' must be 'numpy' or 'doxygen'"
        )
    return module_doc, md_doxygen_id_from_name, md_add_toc_statement, py_style


def _parse_cli_constants(values: tuple[str, ...]) -> dict[str, int | float]:
    constants: dict[str, int | float] = {}
    for entry in values:
        if "=" not in entry:
            raise click.ClickException("constants must be provided as NAME=VALUE")
        raw_name, raw_value = entry.split("=", 1)
        name = raw_name.strip()
        if not name:
            raise click.ClickException("constants must use non-empty names")
        if not _FORTRAN_IDENTIFIER.match(name):
            raise click.ClickException(f"constant '{name}' must be a valid identifier")
        value_text = raw_value.strip()
        if not value_text:
            raise click.ClickException(f"constant '{name}' must define a value")
        if value_text.lower() in {"nan", "+nan", "-nan", "inf", "+inf", "-inf"}:
            raise click.ClickException(f"constant '{name}' must be finite")
        if re.fullmatch(r"[+-]?\d+", value_text):
            value: int | float = int(value_text)
        else:
            try:
                value = float(value_text)
            except ValueError as exc:
                raise click.ClickException(
                    f"constant '{name}' value '{value_text}' must be numeric"
                ) from exc
            if math.isinf(value) or math.isnan(value):
                raise click.ClickException(f"constant '{name}' must be finite")
        constants[name] = value
    return constants


def _iter_namelists(config: dict[str, Any], base_dir: Path) -> list[dict[str, Any]]:
    raw_entries = config.get("namelists")
    if raw_entries is None and "nml-files" in config:
        raise click.ClickException("config uses deprecated 'nml-files'; rename to 'namelists'")
    if not isinstance(raw_entries, list) or not raw_entries:
        raise click.ClickException("config must define non-empty 'namelists'")

    entries: list[dict[str, Path | None]] = []
    for entry in raw_entries:
        if not isinstance(entry, dict):
            raise click.ClickException("each namelists entry must be a table")
        schema_raw = entry.get("schema")
        if not isinstance(schema_raw, str):
            raise click.ClickException("namelists entry must define string 'schema'")
        schema_path = base_dir / schema_raw
        f2py_path = _resolve_optional_path(
            entry.get("f2py_path"),
            base_dir=base_dir,
            key="f2py_path",
        )
        py_path = _resolve_optional_path(
            entry.get("py_path"),
            base_dir=base_dir,
            key="py_path",
        )
        if py_path is not None and f2py_path is None:
            raise click.ClickException("namelists entry with 'py_path' must define 'f2py_path'")
        entries.append(
            {
                "schema": schema_path,
                "mod_path": _resolve_optional_path(
                    entry.get("mod_path"),
                    base_dir=base_dir,
                    key="mod_path",
                ),
                "doc_path": _resolve_optional_path(
                    entry.get("doc_path"),
                    base_dir=base_dir,
                    key="doc_path",
                ),
                "temp_path": _resolve_optional_path(
                    entry.get("temp_path"),
                    base_dir=base_dir,
                    key="temp_path",
                ),
                "f2py_path": f2py_path,
                "py_path": py_path,
            }
        )
    return entries


def _iter_templates(config: dict[str, Any], base_dir: Path) -> list[dict[str, Any]]:
    raw_entries = config.get("templates")
    if raw_entries is None:
        return []
    if not isinstance(raw_entries, list) or not raw_entries:
        raise click.ClickException("config 'templates' must be a non-empty list")

    entries: list[dict[str, Any]] = []
    for entry in raw_entries:
        if not isinstance(entry, dict):
            raise click.ClickException("each templates entry must be a table")
        output_raw = entry.get("output")
        if not isinstance(output_raw, str):
            raise click.ClickException("templates entry must define string 'output'")
        output_path = base_dir / output_raw

        schemas_raw = entry.get("schemas")
        if not isinstance(schemas_raw, list) or not schemas_raw:
            raise click.ClickException("templates entry must define non-empty 'schemas'")
        if not all(isinstance(item, str) for item in schemas_raw):
            raise click.ClickException("templates 'schemas' entries must be strings")
        schema_paths = [base_dir / item for item in schemas_raw]

        doc_mode = entry.get("doc_mode", "plain")
        if not isinstance(doc_mode, str):
            raise click.ClickException("templates 'doc_mode' must be a string")
        value_mode = entry.get("value_mode", "empty")
        if not isinstance(value_mode, str):
            raise click.ClickException("templates 'value_mode' must be a string")
        values_raw = entry.get("values", {})
        if values_raw is None:
            values_raw = {}
        if not isinstance(values_raw, dict):
            raise click.ClickException("templates 'values' must be a table")

        entries.append(
            {
                "output": output_path,
                "schemas": schema_paths,
                "doc_mode": doc_mode,
                "value_mode": value_mode,
                "values": values_raw,
            }
        )
    return entries


def _generate_f2py_outputs(
    loaded_entries: list[dict[str, Any]],
    *,
    helper_module: str,
    helper_buffer: int,
    kind_module: str,
    kind_map: dict[str, str],
    kind_allowlist: set[str],
    constants: dict[str, int | float],
    f2cmap_path: Path | None,
    f2py_c_types: F2pyCTypeMap,
    py_style: str,
    include_python: bool,
) -> None:
    f2py_groups: dict[Path, list[dict[str, Any]]] = {}
    py_groups: dict[Path, list[tuple[dict[str, Any], Path]]] = {}
    for loaded in loaded_entries:
        entry = loaded["entry"]
        schema = loaded["schema"]
        f2py_path = entry["f2py_path"]
        if f2py_path is None:
            continue
        f2py_groups.setdefault(f2py_path, []).append(schema)
        py_path = entry["py_path"]
        if include_python and py_path is not None:
            py_groups.setdefault(py_path, []).append((schema, f2py_path))

    for f2py_path, schemas in f2py_groups.items():
        try:
            logger.info("Generating f2py wrappers at %s", f2py_path)
            generate_f2py_wrappers(
                schemas,
                f2py_path,
                helper_module=helper_module,
                kind_module=kind_module,
                kind_map=kind_map,
                kind_allowlist=kind_allowlist,
                constants=constants,
                errmsg_len=helper_buffer,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc

    if f2cmap_path is not None:
        try:
            usage = merge_f2py_kind_usage(
                collect_f2py_kind_usage(schemas, constants=constants)
                for schemas in f2py_groups.values()
            )
            logger.info("Generating f2py kind map at %s", f2cmap_path)
            generate_f2cmap(f2cmap_path, usage, f2py_c_types)
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc

    if not include_python:
        return
    for py_path, entries in py_groups.items():
        try:
            logger.info("Generating Python f2py wrappers at %s", py_path)
            specs = [
                (
                    build_f2py_namelist_spec(
                        schema,
                        helper_module=helper_module,
                        kind_module=kind_module,
                        kind_map=kind_map,
                        kind_allowlist=kind_allowlist,
                        constants=constants,
                        errmsg_len=helper_buffer,
                    ),
                    f2py_path.stem,
                )
                for schema, f2py_path in entries
            ]
            generate_python_wrappers(
                specs,
                py_path,
                py_style=py_style,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc


@click.group(context_settings=_CONTEXT_SETTINGS)
@click.version_option(__version__, "-V", "--version", prog_name="nml-tools")
@click.option("--verbose", "-v", count=True, help="Increase verbosity (repeatable).")
@click.option("--quiet", "-q", count=True, help="Decrease verbosity (repeatable).")
def cli(verbose: int, quiet: int) -> None:
    """nml-tools command line interface."""
    _configure_logging(verbose, quiet)


@cli.command("generate", context_settings=_CONTEXT_SETTINGS)
@click.option(
    "--config",
    "config_path",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
    default="nml-config.toml",
    show_default=True,
)
def generate(config_path: Path) -> None:
    """Generate outputs from a configuration file."""
    logger.info("Loading config from %s", config_path)
    config = _load_config_checked(config_path)
    base_dir = config_path.parent
    logger.debug("Base directory: %s", base_dir)
    helper_path, helper_module, helper_buffer, helper_header = _load_helper_settings(
        config,
        base_dir,
    )
    (
        module_doc,
        md_doxygen_id_from_name,
        md_add_toc_statement,
        py_style,
    ) = _load_documentation_settings(config)
    constants, constant_specs = _load_constants(config)
    kind_module, kind_map, kind_allowlist = _load_kind_settings(config)
    f2cmap_path, f2py_c_types = _load_f2py_settings(config, base_dir)
    if helper_path is not None:
        try:
            logger.info("Generating helper module at %s", helper_path)
            generate_helper(
                helper_path,
                module_name=helper_module,
                len_buf=helper_buffer,
                constants=constant_specs,
                module_doc=module_doc,
                helper_header=helper_header,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc
    entries = _iter_namelists(config, base_dir)
    logger.info("Found %d schema entries", len(entries))
    loaded_entries: list[dict[str, Any]] = []
    for namelist_entry in entries:
        schema_path = namelist_entry["schema"]
        if schema_path is None:
            raise click.ClickException("namelists entry missing schema path")
        try:
            logger.info("Loading schema %s", schema_path)
            schema = load_schema(schema_path)
        except (FileNotFoundError, ValueError) as exc:
            raise click.ClickException(str(exc)) from exc
        loaded_entries.append({"entry": namelist_entry, "schema": schema})
        mod_path = namelist_entry["mod_path"]
        if mod_path is not None:
            try:
                logger.info("Generating Fortran module at %s", mod_path)
                generate_fortran(
                    schema,
                    mod_path,
                    helper_module=helper_module,
                    kind_module=kind_module,
                    kind_map=kind_map,
                    kind_allowlist=kind_allowlist,
                    constants=constants,
                    module_doc=module_doc,
                    f2py_handle_helpers=namelist_entry["f2py_path"] is not None,
                )
            except ValueError as exc:
                raise click.ClickException(str(exc)) from exc
        doc_path = namelist_entry["doc_path"]
        if doc_path is not None:
            try:
                logger.info("Generating Markdown docs at %s", doc_path)
                generate_docs(
                    schema,
                    doc_path,
                    constants=constants,
                    md_doxygen_id_from_name=md_doxygen_id_from_name,
                    md_add_toc_statement=md_add_toc_statement,
                )
            except ValueError as exc:
                raise click.ClickException(str(exc)) from exc

    _generate_f2py_outputs(
        loaded_entries,
        helper_module=helper_module,
        helper_buffer=helper_buffer,
        kind_module=kind_module,
        kind_map=kind_map,
        kind_allowlist=kind_allowlist,
        constants=constants,
        f2cmap_path=f2cmap_path,
        f2py_c_types=f2py_c_types,
        py_style=py_style,
        include_python=True,
    )

    template_entries = _iter_templates(config, base_dir)
    if template_entries:
        logger.info("Found %d template entries", len(template_entries))
    for template_entry in template_entries:
        try:
            schemas = []
            for schema_path in template_entry["schemas"]:
                logger.info("Loading schema %s", schema_path)
                schemas.append(load_schema(schema_path))
            logger.info("Generating template at %s", template_entry["output"])
            generate_template(
                schemas,
                template_entry["output"],
                doc_mode=template_entry["doc_mode"],
                value_mode=template_entry["value_mode"],
                constants=constants,
                kind_map=kind_map,
                kind_allowlist=kind_allowlist,
                values=template_entry["values"],
            )
        except (FileNotFoundError, ValueError) as exc:
            raise click.ClickException(str(exc)) from exc


@cli.command("gen-fortran", context_settings=_CONTEXT_SETTINGS)
@click.option(
    "--config",
    "config_path",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
    default="nml-config.toml",
    show_default=True,
)
def gen_fortran(config_path: Path) -> None:
    """Generate Fortran module(s)."""
    logger.info("Loading config from %s", config_path)
    config = _load_config_checked(config_path)
    base_dir = config_path.parent
    logger.debug("Base directory: %s", base_dir)
    helper_path, helper_module, helper_buffer, helper_header = _load_helper_settings(
        config,
        base_dir,
    )
    module_doc, _, _, py_style = _load_documentation_settings(config)
    constants, constant_specs = _load_constants(config)
    kind_module, kind_map, kind_allowlist = _load_kind_settings(config)
    f2cmap_path, f2py_c_types = _load_f2py_settings(config, base_dir)
    if helper_path is not None:
        try:
            logger.info("Generating helper module at %s", helper_path)
            generate_helper(
                helper_path,
                module_name=helper_module,
                len_buf=helper_buffer,
                constants=constant_specs,
                module_doc=module_doc,
                helper_header=helper_header,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc

    entries = _iter_namelists(config, base_dir)
    logger.info("Found %d schema entries", len(entries))
    loaded_entries: list[dict[str, Any]] = []
    for entry in entries:
        schema_path = entry["schema"]
        if schema_path is None:
            raise click.ClickException("namelists entry missing schema path")
        try:
            logger.info("Loading schema %s", schema_path)
            schema = load_schema(schema_path)
        except (FileNotFoundError, ValueError) as exc:
            raise click.ClickException(str(exc)) from exc
        loaded_entries.append({"entry": entry, "schema": schema})
        mod_path = entry["mod_path"]
        if mod_path is None:
            continue
        try:
            logger.info("Generating Fortran module at %s", mod_path)
            generate_fortran(
                schema,
                mod_path,
                helper_module=helper_module,
                kind_module=kind_module,
                kind_map=kind_map,
                kind_allowlist=kind_allowlist,
                constants=constants,
                module_doc=module_doc,
                f2py_handle_helpers=entry["f2py_path"] is not None,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc

    _generate_f2py_outputs(
        loaded_entries,
        helper_module=helper_module,
        helper_buffer=helper_buffer,
        kind_module=kind_module,
        kind_map=kind_map,
        kind_allowlist=kind_allowlist,
        constants=constants,
        f2cmap_path=f2cmap_path,
        f2py_c_types=f2py_c_types,
        py_style=py_style,
        include_python=False,
    )


@cli.command("validate", context_settings=_CONTEXT_SETTINGS)
@click.option(
    "--config",
    "config_path",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
    default=None,
)
@click.option(
    "--schema",
    "schema_paths",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
    multiple=True,
)
@click.option(
    "--input",
    "input_option",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
)
@click.option(
    "--constants",
    "constant_args",
    multiple=True,
    help="Additional constants as NAME=VALUE (repeatable).",
)
@click.argument(
    "input_path",
    required=False,
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
)
def validate(
    config_path: Path | None,
    schema_paths: tuple[Path, ...],
    input_option: Path | None,
    constant_args: tuple[str, ...],
    input_path: Path | None,
) -> None:
    """Validate a namelist file against schema definitions."""
    if input_option is not None and input_path is not None:
        raise click.ClickException("input path provided twice")
    input_path = input_option or input_path
    if input_path is None:
        raise click.ClickException("input path is required")
    constants = _parse_cli_constants(constant_args)
    schemas: list[dict[str, Any]] = []

    if schema_paths:
        if config_path is not None:
            logger.info("Loading config from %s", config_path)
            config = _load_config_checked(config_path)
            cfg_constants, _ = _load_constants(config)
            constants = {**cfg_constants, **constants}
        for schema_file in schema_paths:
            try:
                logger.info("Loading schema %s", schema_file)
                schemas.append(load_schema(schema_file))
            except (FileNotFoundError, ValueError) as exc:
                raise click.ClickException(str(exc)) from exc
        require_all = True
    else:
        if config_path is None:
            config_path = Path("nml-config.toml")
        logger.info("Loading config from %s", config_path)
        config = _load_config_checked(config_path)
        base_dir = config_path.parent
        cfg_constants, _ = _load_constants(config)
        constants = {**cfg_constants, **constants}
        entries = _iter_namelists(config, base_dir)
        logger.info("Found %d schema entries", len(entries))
        for entry in entries:
            schema_path = entry["schema"]
            if schema_path is None:
                raise click.ClickException("namelists entry missing schema path")
            try:
                logger.info("Loading schema %s", schema_path)
                schemas.append(load_schema(schema_path))
            except (FileNotFoundError, ValueError) as exc:
                raise click.ClickException(str(exc)) from exc
        require_all = False

    if not schemas:
        raise click.ClickException("no schemas provided for validation")

    try:
        logger.info("Reading namelist %s", input_path)
        namelist_file = f90nml.read(input_path)
    except Exception as exc:  # pragma: no cover - f90nml raises custom errors
        raise click.ClickException(f"failed to read namelist: {exc}") from exc

    file_entries: dict[str, tuple[str, Any]] = {}
    for name, values in namelist_file.items():
        if not isinstance(name, str):
            raise click.ClickException("namelist names must be strings")
        key = name.lower()
        if key in file_entries:
            raise click.ClickException(f"namelist '{name}' appears multiple times")
        file_entries[key] = (name, values)

    schema_entries: dict[str, dict[str, Any]] = {}
    for schema in schemas:
        namelist_name = schema.get("x-fortran-namelist")
        if not isinstance(namelist_name, str) or not namelist_name.strip():
            raise click.ClickException("schema must define non-empty 'x-fortran-namelist'")
        key = namelist_name.lower()
        if key in schema_entries:
            raise click.ClickException(f"duplicate schema for namelist '{namelist_name}'")
        schema_entries[key] = schema

    for key, (name, _) in file_entries.items():
        if key not in schema_entries:
            raise click.ClickException(f"input contains unknown namelist '{name}'")

    validated = 0
    for key, schema in schema_entries.items():
        if key not in file_entries:
            if require_all:
                raise click.ClickException(
                    f"input is missing namelist '{schema.get('x-fortran-namelist')}'"
                )
            continue
        try:
            validate_namelist(
                schema,
                file_entries[key][1],
                constants=constants,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc
        validated += 1
    logger.info("Validation completed (%d namelist%s).", validated, "" if validated == 1 else "s")


@cli.command("gen-markdown", context_settings=_CONTEXT_SETTINGS)
@click.option(
    "--config",
    "config_path",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
    default="nml-config.toml",
    show_default=True,
)
def gen_markdown(config_path: Path) -> None:
    """Generate Markdown docs."""
    logger.info("Loading config from %s", config_path)
    config = _load_config_checked(config_path)
    base_dir = config_path.parent
    constants, _ = _load_constants(config)
    _, md_doxygen_id_from_name, md_add_toc_statement, _ = _load_documentation_settings(
        config
    )
    entries = _iter_namelists(config, base_dir)
    logger.info("Found %d schema entries", len(entries))
    for entry in entries:
        schema_path = entry["schema"]
        if schema_path is None:
            raise click.ClickException("namelists entry missing schema path")
        try:
            logger.info("Loading schema %s", schema_path)
            schema = load_schema(schema_path)
        except (FileNotFoundError, ValueError) as exc:
            raise click.ClickException(str(exc)) from exc
        doc_path = entry["doc_path"]
        if doc_path is None:
            continue
        try:
            logger.info("Generating Markdown docs at %s", doc_path)
            generate_docs(
                schema,
                doc_path,
                constants=constants,
                md_doxygen_id_from_name=md_doxygen_id_from_name,
                md_add_toc_statement=md_add_toc_statement,
            )
        except ValueError as exc:
            raise click.ClickException(str(exc)) from exc


@cli.command("gen-template", context_settings=_CONTEXT_SETTINGS)
@click.option(
    "--config",
    "config_path",
    type=click.Path(exists=True, dir_okay=False, path_type=Path),
    default="nml-config.toml",
    show_default=True,
)
def gen_template(config_path: Path) -> None:
    """Generate template namelist(s)."""
    logger.info("Loading config from %s", config_path)
    config = _load_config_checked(config_path)
    base_dir = config_path.parent
    constants, _ = _load_constants(config)
    _, kind_map, kind_allowlist = _load_kind_settings(config)
    templates = _iter_templates(config, base_dir)
    if not templates:
        raise click.ClickException("config must define non-empty 'templates'")
    logger.info("Found %d template entries", len(templates))
    for entry in templates:
        try:
            schemas = []
            for schema_path in entry["schemas"]:
                logger.info("Loading schema %s", schema_path)
                schemas.append(load_schema(schema_path))
            logger.info("Generating template at %s", entry["output"])
            generate_template(
                schemas,
                entry["output"],
                doc_mode=entry["doc_mode"],
                value_mode=entry["value_mode"],
                constants=constants,
                kind_map=kind_map,
                kind_allowlist=kind_allowlist,
                values=entry["values"],
            )
        except (FileNotFoundError, ValueError) as exc:
            raise click.ClickException(str(exc)) from exc


def main(argv: list[str] | None = None) -> int:
    """Entry point for the CLI."""
    try:
        cli.main(args=argv, prog_name="nml-tools", standalone_mode=False)
    except Exit as exc:
        return exc.exit_code
    except click.ClickException as exc:
        exc.show()
        return 1
    return 0


if __name__ == "__main__":  # pragma: no cover - CLI entry point
    raise SystemExit(main())

MuellerSeb / nml-tools / 26061440371

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