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Merge pull request #374 from tovrstra/cli-allow-changes
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Add command-line option `--allow-changes` to `iodata-convert`
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@tovrstra
tovrstra authored Jul 14, 2024
2 parents 4dceda6 + 0a4d979 commit f8af4e8
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Showing 2 changed files with 108 additions and 45 deletions.
29 changes: 24 additions & 5 deletions iodata/__main__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
"""CLI for file conversion."""

import argparse
from typing import Optional

import numpy as np

Expand All @@ -31,7 +32,7 @@
__version__ = "0.0.0.post0"


__all__ = ()
__all__ = ("convert",)


DESCRIPTION = """\
Expand Down Expand Up @@ -83,6 +84,14 @@ def parse_args():
parser.add_argument(
"-o", "--outfmt", help="Select the output format, overrides automatic detection."
)
parser.add_argument(
"-c",
"--allow-changes",
default=False,
action="store_true",
help="Allow (not trivially reversible) conversion of the input data to make it compatible "
"with the output format. Warnings will be emitted for all changes made.",
)
parser.add_argument(
"-m",
"--many",
Expand All @@ -95,7 +104,14 @@ def parse_args():
return parser.parse_args()


def convert(infn, outfn, many, infmt, outfmt):
def convert(
infn: str,
outfn: str,
many: bool = False,
infmt: Optional[str] = None,
outfmt: Optional[str] = None,
allow_changes: bool = False,
):
"""Convert file from one format to another.
Parameters
Expand All @@ -110,12 +126,15 @@ def convert(infn, outfn, many, infmt, outfmt):
The input format.
outfmt
The output format.
allow_changes
Allow prepare_dump functions to modify the data
to make it compatible with the output format.
"""
if many:
dump_many(load_many(infn, fmt=infmt), outfn, fmt=outfmt)
dump_many(load_many(infn, fmt=infmt), outfn, allow_changes=allow_changes, fmt=outfmt)
else:
dump_one(load_one(infn, fmt=infmt), outfn, fmt=outfmt)
dump_one(load_one(infn, fmt=infmt), outfn, allow_changes=allow_changes, fmt=outfmt)


def main():
Expand All @@ -124,7 +143,7 @@ def main():
np.seterr(divide="raise", over="raise", invalid="raise")

args = parse_args()
convert(args.input, args.output, args.many, args.infmt, args.outfmt)
convert(args.input, args.output, args.many, args.infmt, args.outfmt, args.allow_changes)


if __name__ == "__main__":
Expand Down
124 changes: 84 additions & 40 deletions iodata/test/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,59 +18,118 @@
# --
"""Unit tests for iodata.__main__."""

import functools
import os
import subprocess
import sys
from functools import partial
from importlib.resources import as_file, files
from typing import Optional
from warnings import warn

import pytest
from numpy.testing import assert_allclose, assert_equal

from ..__main__ import convert
from ..__main__ import convert as convfn
from ..api import load_many, load_one
from ..utils import FileFormatError, PrepareDumpError, PrepareDumpWarning


def _convscript(
infn: str,
outfn: str,
many: bool = False,
infmt: Optional[str] = None,
outfmt: Optional[str] = None,
allow_changes: bool = False,
):
"""Simulate the convert function by calling iodata-convert in a subprocess."""
args = [sys.executable, "-m", "iodata.__main__", infn, outfn]
if many:
args.append("-m")
if infmt is not None:
args.append(f"--infmt={infmt}")
if outfmt is not None:
args.append(f"--outfmt={outfmt}")
if allow_changes:
args.append("-c")
cp = subprocess.run(args, capture_output=True, check=False, encoding="utf8")
if cp.returncode == 0:
if allow_changes and "PrepareDumpWarning" in cp.stderr:
warn(PrepareDumpWarning(cp.stderr), stacklevel=2)
else:
if "PrepareDumpError" in cp.stderr:
raise PrepareDumpError(cp.stderr)
if "FileFormatError" in cp.stderr:
raise FileFormatError(cp.stderr)
raise RuntimeError(f"Failure not processed.\n{cp.stderr}")


def _check_convert_one(myconvert, tmpdir):
outfn = os.path.join(tmpdir, "tmp.xyz")
with as_file(files("iodata.test.data").joinpath("hf_sto3g.fchk")) as infn:
myconvert(infn, outfn)
myconvert(infn, outfn, allow_changes=False)
iodata = load_one(outfn)
assert iodata.natom == 2
assert_equal(iodata.atnums, [9, 1])
assert_allclose(iodata.atcoords, [[0.0, 0.0, 0.190484394], [0.0, 0.0, -1.71435955]])


def test_convert_one_autofmt(tmpdir):
myconvert = functools.partial(convert, many=False, infmt=None, outfmt=None)
_check_convert_one(myconvert, tmpdir)
def _check_convert_one_changes(myconvert, tmpdir):
outfn = os.path.join(tmpdir, "tmp.mkl")
with as_file(files("iodata.test.data").joinpath("hf_sto3g.fchk")) as infn:
with pytest.raises(PrepareDumpError):
myconvert(infn, outfn, allow_changes=False)
assert not os.path.isfile(outfn)
with pytest.warns(PrepareDumpWarning):
myconvert(infn, outfn, allow_changes=True)
iodata = load_one(outfn)
assert iodata.natom == 2
assert_equal(iodata.atnums, [9, 1])
assert_allclose(iodata.atcoords, [[0.0, 0.0, 0.190484394], [0.0, 0.0, -1.71435955]])


def test_convert_one_manfmt(tmpdir):
myconvert = functools.partial(convert, many=False, infmt="fchk", outfmt="xyz")
@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_one_autofmt(tmpdir, convert):
myconvert = partial(convfn, many=False, infmt=None, outfmt=None)
_check_convert_one(myconvert, tmpdir)


def test_script_one_autofmt(tmpdir):
def myconvert(infn, outfn):
subprocess.run([sys.executable, "-m", "iodata.__main__", infn, outfn], check=True)
@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_one_autofmt_changes(tmpdir, convert):
myconvert = partial(convert, many=False, infmt=None, outfmt=None)
_check_convert_one_changes(myconvert, tmpdir)


@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_one_manfmt(tmpdir, convert):
myconvert = partial(convert, many=False, infmt="fchk", outfmt="xyz")
_check_convert_one(myconvert, tmpdir)


def test_script_one_manfmt(tmpdir):
def myconvert(infn, outfn):
subprocess.run(
[sys.executable, "-m", "iodata.__main__", infn, outfn, "-i", "fchk", "-o", "xyz"],
check=True,
)
@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_one_nonexisting_infmt(tmpdir, convert):
myconvert = partial(convert, many=False, infmt="blablabla", outfmt="xyz")
with pytest.raises(FileFormatError):
_check_convert_one(myconvert, tmpdir)


@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_one_nonexisting_outfmt(tmpdir, convert):
myconvert = partial(convert, many=False, infmt="fchk", outfmt="blablabla")
with pytest.raises(FileFormatError):
_check_convert_one(myconvert, tmpdir)

_check_convert_one(myconvert, tmpdir)

@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_one_manfmt_changes(tmpdir, convert):
myconvert = partial(convert, many=False, infmt="fchk", outfmt="molekel")
_check_convert_one_changes(myconvert, tmpdir)


def _check_convert_many(myconvert, tmpdir):
outfn = os.path.join(tmpdir, "tmp.xyz")
with as_file(files("iodata.test.data").joinpath("peroxide_relaxed_scan.fchk")) as infn:
myconvert(infn, outfn)
myconvert(infn, outfn, allow_changes=False)
trj = list(load_many(outfn))
assert len(trj) == 13
for iodata in trj:
Expand All @@ -80,28 +139,13 @@ def _check_convert_many(myconvert, tmpdir):
assert_allclose(trj[5].atcoords[0], [0.0, 1.32466211, 0.0], atol=1e-5)


def test_convert_many_autofmt(tmpdir):
myconvert = functools.partial(convert, many=True, infmt=None, outfmt=None)
@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_many_autofmt(tmpdir, convert):
myconvert = partial(convert, many=True, infmt=None, outfmt=None)
_check_convert_many(myconvert, tmpdir)


def test_convert_many_manfmt(tmpdir):
myconvert = functools.partial(convert, many=True, infmt="fchk", outfmt="xyz")
_check_convert_many(myconvert, tmpdir)


def test_script_many_autofmt(tmpdir):
def myconvert(infn, outfn):
subprocess.run([sys.executable, "-m", "iodata.__main__", infn, outfn, "-m"], check=True)

_check_convert_many(myconvert, tmpdir)


def test_script_many_manfmt(tmpdir):
def myconvert(infn, outfn):
subprocess.run(
[sys.executable, "-m", "iodata.__main__", infn, outfn, "-m", "-i", "fchk", "-o", "xyz"],
check=True,
)

@pytest.mark.parametrize("convert", [convfn, _convscript])
def test_convert_many_manfmt(tmpdir, convert):
myconvert = partial(convert, many=True, infmt="fchk", outfmt="xyz")
_check_convert_many(myconvert, tmpdir)

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