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Based on Python type hints." +optional = true +python-versions = ">=3.7" +files = [ + {file = "typer-0.12.5-py3-none-any.whl", hash = "sha256:62fe4e471711b147e3365034133904df3e235698399bc4de2b36c8579298d52b"}, + {file = "typer-0.12.5.tar.gz", hash = "sha256:f592f089bedcc8ec1b974125d64851029c3b1af145f04aca64d69410f0c9b722"}, +] + +[package.dependencies] +click = ">=8.0.0" +rich = ">=10.11.0" +shellingham = ">=1.3.0" +typing-extensions = ">=3.7.4.3" + +[[package]] +name = "types-pyyaml" +version = "6.0.12.20240917" +description = "Typing stubs for PyYAML" +optional = false +python-versions = ">=3.8" +files = [ + {file = "types-PyYAML-6.0.12.20240917.tar.gz", hash = "sha256:d1405a86f9576682234ef83bcb4e6fff7c9305c8b1fbad5e0bcd4f7dbdc9c587"}, + {file = "types_PyYAML-6.0.12.20240917-py3-none-any.whl", hash = "sha256:392b267f1c0fe6022952462bf5d6523f31e37f6cea49b14cee7ad634b6301570"}, +] + [[package]] name = "types-toml" version = "0.10.8.20240310" @@ -1899,13 +1966,13 @@ files = [ [[package]] name = "urllib3" -version = "2.2.2" +version = "2.2.3" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false python-versions = ">=3.8" files = [ - {file = "urllib3-2.2.2-py3-none-any.whl", hash = "sha256:a448b2f64d686155468037e1ace9f2d2199776e17f0a46610480d311f73e3472"}, - {file = "urllib3-2.2.2.tar.gz", hash = "sha256:dd505485549a7a552833da5e6063639d0d177c04f23bc3864e41e5dc5f612168"}, + {file = "urllib3-2.2.3-py3-none-any.whl", hash = "sha256:ca899ca043dcb1bafa3e262d73aa25c465bfb49e0bd9dd5d59f1d0acba2f8fac"}, + {file = "urllib3-2.2.3.tar.gz", hash = "sha256:e7d814a81dad81e6caf2ec9fdedb284ecc9c73076b62654547cc64ccdcae26e9"}, ] [package.extras] @@ -1982,13 +2049,13 @@ test = ["ase", "pytest", "pytest-cov", "qcelemental"] [[package]] name = "zipp" -version = "3.20.1" +version = "3.20.2" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"}, - {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"}, + {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, + {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, ] [package.extras] @@ -2000,12 +2067,14 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", type = ["pytest-mypy"] [extras] -all = ["geometric", "qcelemental", "qcengine", "tcpb", "xtb"] +all = ["geometric", "qcelemental", "qcengine", "tcpb", "typer", "xtb"] +cli = ["typer"] geometric = ["geometric"] qcengine = ["qcelemental", "qcengine"] +tcpb = ["tcpb"] xtb = ["xtb"] [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "13aedac08d290da2f1c1e99941a8f375dde111c3c72bccf4c28a992c3499a32b" +content-hash = "1b3aab4443d90e5792f6648de6a95617121e70789ee634f3e8753f01e38c1937" diff --git a/pyproject.toml b/pyproject.toml index 94cbb18..c39711a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,13 +19,15 @@ geometric = { version = "^1.0.1", optional = true } xtb = { version = "^22.1", optional = true } tcpb = { version = "^0.14.1", optional = true } tomli-w = "^1.0.0" -qcio = "^0.11.8" +qcio = {path = "../qcio", develop = true} qcparse = "^0.6.3" +typer = {version = "^0.12.5", optional = true} [tool.poetry.extras] qcengine = ["qcelemental", "qcengine"] geometric = ["geometric"] xtb = ["xtb"] +tcpb = ["tcpb"] cli = ["typer"] all = ["qcelemental", "qcengine", "geometric", "xtb", "tcpb", "typer"] @@ -41,6 +43,7 @@ qcelemental = "^0.26.0" qcengine = "^0.27.0" xtb = "^22.1" types-toml = "^0.10.8.20240310" +types-pyyaml = "^6.0.12.20240917" [tool.poetry.group.docs.dependencies] diff --git a/qcop/cli.py b/qcop/cli.py index 048a7b6..5f86769 100644 --- a/qcop/cli.py +++ b/qcop/cli.py @@ -1,50 +1,139 @@ +import json +import tempfile from pathlib import Path -from typing import Any, Optional +from typing import Annotated, Any, Optional import toml import typer -from pydantic import BaseModel -from qcio import ProgramInput +import yaml +from pydantic import ValidationError +from qcio import DualProgramInput, ProgramInput, Structure, utils +from rich import print as rprint + +from qcop import compute as qcop_compute app = typer.Typer() -# NOTE: This is not working. Just an initial idea from ChatGPT. -def create_empty_dict_from_model(model_class: Any) -> dict: - empty_model = {} - for field_name, field in model_class.model_fields.items(): - field_type = field.annotation.__class__ - if issubclass(field_type, BaseModel): - # If it's a nested model, recursively process it - empty_model[field_name] = create_empty_dict_from_model(field_type) - else: - # Set to None, an empty string, or a suitable default - empty_model[field_name] = "" - return empty_model +def _serialize_data(data: Any, filename: Path): + kwargs = {} + if filename.suffix == ".toml": + dump = toml.dump + elif filename.suffix == ".yaml" or filename.suffix == ".yml": + dump = yaml.dump + elif filename.suffix == ".json": + dump = json.dump + kwargs = {"indent": 2} + else: + raise ValueError(f"Unsupported file extension: {filename.suffix}") + with open(filename, "w") as f: + dump(data, f, **kwargs) + + +def _deserialize_data(filename: Path) -> Any: + if filename.suffix == ".toml": + load = toml.load + elif filename.suffix == ".yaml" or filename.suffix == ".yml": + load = yaml.load + elif filename.suffix == ".json": + load = json.load + else: + raise ValueError(f"Unsupported file extension: {filename.suffix}") + with open(filename, "r") as f: + return load(f) @app.command() -def new(filename: Optional[Path] = "input.toml", dual_program: bool = False): +def new( + filename: Path, + dual_program: Annotated[ + bool, typer.Option("--dual-program", "-dp", help="Create a DualProgramInput") + ] = False, + calctype: Annotated[ + str, typer.Option("--calctype", "-c", help="calctype for the input file") + ] = "energy", + no_structure: Annotated[ + bool, + typer.Option( + "--no-structure", "-ns", help="Exclude the structure from the input file" + ), + ] = False, +): """Create a new program input file.""" - count = 1 - while filename.exists(): - typer.echo(f"File already exists: {filename}") - filename = f"{filename.stem}_{count}{filename.suffix}" - count += 1 - typer.echo(f"Creating a new input file: {filename}") - model_dict = create_empty_dict_from_model(ProgramInput) - # Convert to TOML and write to file - import pdb + rprint(f"Creating a new input file: {filename}") + if not dual_program: + prog_inp = ProgramInput( + calctype=calctype, + structure=utils.water, + model={"method": "b3lyp", "basis": "6-31g"}, + keywords={"key1": "value1"}, + ) + else: + prog_inp = DualProgramInput( + calctype=calctype, + structure=utils.water, + subprogram="subprogram_name", + keywords={"key1": "value1"}, + subprogram_args={ + "model": {"method": "b3lyp", "basis": "6-31g"}, + "keywords": {"key1": "value1"}, + }, + ) - pdb.set_trace() - with open("empty_model.toml", "w") as file: - toml.dump(model_dict, file) + # Serialize data + serialized_data = prog_inp.model_dump(exclude_unset=True, exclude_none=True) + serialized_data["structure"].pop("connectivity") + if no_structure: + serialized_data.pop("structure") + + _serialize_data(serialized_data, filename) @app.command() -def two(): - pass +def compute( + input_filename: Path, + output_filename: Annotated[ + Path, + typer.Option("--output", "-o", help="Output filename"), + ], + program: Annotated[ + str, typer.Option("--program", "-p", help="Program name for the input file") + ], + structure: Optional[Path] = None, +): + """Compute the input file and save the results to the output_filename.""" + rprint(f"Computing {input_filename} and saving to {output_filename}") + + if structure is not None: + rprint(f"Using the structure file: {structure}") + struct = Structure.open(structure) + prog_inp_dict = _deserialize_data(input_filename) + prog_inp_dict["structure"] = struct.model_dump() + input_filename = Path( + tempfile.NamedTemporaryFile(delete=True, suffix=".toml").name + ) + _serialize_data(prog_inp_dict, input_filename) + + try: + prog_inp = ProgramInput.open(input_filename) + except ValidationError: + try: + prog_inp = DualProgramInput.open(input_filename) + except ValidationError: + rprint(f"Invalid input file: {input_filename}") + raise typer.Exit(1) + + prog_output = qcop_compute(program, prog_inp, print_stdout=True, raise_exc=False) + + if prog_output.success: + rprint("[bold green]Computation successful![/bold green]") + else: + rprint(prog_output.traceback) + rprint("[bold red]Computation failed![/bold red]") + + rprint(f"Saving the results to {output_filename}") + _serialize_data(prog_output.model_dump(), output_filename) if __name__ == "__main__":