12317947314

Committed 13 Dec 2024 02:57PM UTC coverage: 44.571% (-50.6%) from 95.218%

Build # 12317947314

Build Type

Pull #334

github

Committed by

web-flow

Commit Message

Merge 17e42dc36 into 6d3310fb7

Pull Request Pull Request #334: Test mac on self-hosted runner

Run Details

234 of 525 relevant lines covered (44.57%)

1.78 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

35.29

/janus_core/cli/preprocess.py

# noqa: I002, FA102
"""Set up MLIP preprocessing commandline interface."""

# Issues with future annotations and typer
# c.f. https://github.com/maxb2/typer-config/issues/295
# from __future__ import annotations

from pathlib import Path
from typing import Annotated

from typer import Option, Typer

app = Typer()


@app.command()
def preprocess(
    mlip_config: Annotated[
        Path, Option(help="Configuration file to pass to MLIP CLI.")
    ],
    log: Annotated[Path, Option(help="Path to save logs to.")] = Path(
        "preprocess-log.yml"
    ),
    tracker: Annotated[
        bool, Option(help="Whether to save carbon emissions of calculation")
    ] = True,
    summary: Annotated[
        Path,
        Option(
            help=(
                "Path to save summary of inputs, start/end time, and carbon emissions."
            )
        ),
    ] = Path("preprocess-summary.yml"),
):
    """
    Convert training data to hdf5 by passing a configuration file to the MLIP's CLI.

    Parameters
    ----------
    mlip_config : Path
        Configuration file to pass to MLIP CLI.
    log : Optional[Path]
        Path to write logs to. Default is Path("preprocess-log.yml").
    tracker : bool
        Whether to save carbon emissions of calculation in log file and summary.
        Default is True.
    summary : Optional[Path]
        Path to save summary of inputs, start/end time, and carbon emissions. Default
        is Path("preprocess-summary.yml").
    """
    from janus_core.cli.utils import carbon_summary, end_summary, start_summary
    from janus_core.training.preprocess import preprocess as run_preprocess

    inputs = {"mlip_config": str(mlip_config)}

    # Save summary information before preprocessing begins
    start_summary(command="preprocess", summary=summary, inputs=inputs)

    log_kwargs = {"filemode": "w"}
    if log:
        log_kwargs["filename"] = log

    # Run preprocessing
    run_preprocess(
        mlip_config, attach_logger=True, log_kwargs=log_kwargs, track_carbon=tracker
    )

    # Save carbon summary
    if tracker:
        carbon_summary(summary=summary, log=log)

    # Save time after preprocessing has finished
    end_summary(summary)

1	# noqa: I002, FA102
2	"""Set up MLIP preprocessing commandline interface."""
3
4	# Issues with future annotations and typer
5	# c.f. https://github.com/maxb2/typer-config/issues/295
6	# from __future__ import annotations
7
8	from pathlib import Path	4✔
9	from typing import Annotated	4✔
10
11	from typer import Option, Typer	4✔
12
13	app = Typer()	4✔
14
15
16	@app.command()	4✔
17	def preprocess(	4✔
18	mlip_config: Annotated[
19	Path, Option(help="Configuration file to pass to MLIP CLI.")
20	],
21	log: Annotated[Path, Option(help="Path to save logs to.")] = Path(
22	"preprocess-log.yml"
23	),
24	tracker: Annotated[
25	bool, Option(help="Whether to save carbon emissions of calculation")
26	] = True,
27	summary: Annotated[
28	Path,
29	Option(
30	help=(
31	"Path to save summary of inputs, start/end time, and carbon emissions."
32	)
33	),
34	] = Path("preprocess-summary.yml"),
35	):
36	"""
37	Convert training data to hdf5 by passing a configuration file to the MLIP's CLI.
38
39	Parameters
40	----------
41	mlip_config : Path
42	Configuration file to pass to MLIP CLI.
43	log : Optional[Path]
44	Path to write logs to. Default is Path("preprocess-log.yml").
45	tracker : bool
46	Whether to save carbon emissions of calculation in log file and summary.
47	Default is True.
48	summary : Optional[Path]
49	Path to save summary of inputs, start/end time, and carbon emissions. Default
50	is Path("preprocess-summary.yml").
51	"""
52	from janus_core.cli.utils import carbon_summary, end_summary, start_summary	×
53	from janus_core.training.preprocess import preprocess as run_preprocess	×
54
55	inputs = {"mlip_config": str(mlip_config)}	×
56
57	# Save summary information before preprocessing begins
58	start_summary(command="preprocess", summary=summary, inputs=inputs)	×
59
60	log_kwargs = {"filemode": "w"}	×
61	if log:	×
62	log_kwargs["filename"] = log	×
63
64	# Run preprocessing
65	run_preprocess(	×
66	mlip_config, attach_logger=True, log_kwargs=log_kwargs, track_carbon=tracker
67	)
68
69	# Save carbon summary
70	if tracker:	×
71	carbon_summary(summary=summary, log=log)	×
72
73	# Save time after preprocessing has finished
74	end_summary(summary)	×

stfc / janus-core / 12317947314

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous