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Fix linting errors #132

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Merged
aboucaud merged 1 commit into from
May 13, 2026
Merged

Fix linting errors #132

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91 changes: 62 additions & 29 deletions src/lightcone/cli/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
The global config at ``~/.lightcone/config.yaml`` is auto-created with
defaults on first invocation if missing.
"""

from __future__ import annotations

import json
Expand All @@ -37,7 +38,15 @@

PERMISSION_TIERS: dict[str, dict[str, list[str]]] = {
"yolo": {
"allow": ["Bash(*)", "Edit", "Read", "Write", "WebSearch", "WebFetch", "mcp__*"],
"allow": [
"Bash(*)",
"Edit",
"Read",
"Write",
"WebSearch",
"WebFetch",
"mcp__*",
],
},
"recommended": {
"allow": ["Read", "Edit", "Write", "Bash(*)", "WebSearch", "WebFetch"],
Expand Down Expand Up @@ -123,11 +132,12 @@ def _project_root(start: Path | None = None) -> Path:
# =============================================================================
_LIGHTCONE = """
_______________________
| . _ |_ _|_ _ _ _ _
| . _ |_ _|_ _ _ _ _
|_|(_|| | | (_(_)| |(/_
_____|_________________
"""


@main.command()
@click.argument("directory", type=click.Path(path_type=Path), default=".")
@click.option("--no-git", is_flag=True, help="Skip git init")
Expand Down Expand Up @@ -181,9 +191,7 @@ def init(
try:
astra_init.callback(directory=directory, no_git=True) # type: ignore[misc]
except SystemExit as e:
raise click.ClickException(
f"astra init failed (exit code {e.code})."
) from e
raise click.ClickException(f"astra init failed (exit code {e.code}).") from e

# Point the spec at our project-local Containerfile. The astra
# boilerplate ships ``container: python:3.12-slim`` so the scaffold
Expand Down Expand Up @@ -233,25 +241,44 @@ def init(
if not no_venv:
if shutil.which("uv"):
with console.status("[dim]Creating virtual environment…[/dim]"):
subprocess.run(["uv", "venv", "--python", "3.12", ".venv"], cwd=directory, check=False, capture_output=True)
subprocess.run(
["uv", "venv", "--python", "3.12", ".venv"],
cwd=directory,
check=False,
capture_output=True,
)
with console.status("[dim]Installing lightcone-cli…[/dim]"):
subprocess.run(
["uv", "pip", "install", "--python", ".venv/bin/python", "lightcone-cli"],
[
"uv",
"pip",
"install",
"--python",
".venv/bin/python",
"lightcone-cli",
],
cwd=directory,
check=False,
capture_output=True,
)
else:
with console.status("[dim]Creating virtual environment…[/dim]"):
subprocess.run(["python", "-m", "venv", ".venv"], cwd=directory, check=False, capture_output=True)
subprocess.run(
["python", "-m", "venv", ".venv"],
cwd=directory,
check=False,
capture_output=True,
)
with console.status("[dim]Installing lightcone-cli…[/dim]"):
subprocess.run(
[".venv/bin/python", "-m", "pip", "install", "-q", "lightcone-cli"],
cwd=directory,
check=False,
capture_output=True,
)
console.print(f"[green]✓[/green] Virtual environment created in [cyan]{directory}/.venv[/cyan]")
console.print(
f"[green]✓[/green] Virtual environment created in [cyan]{directory}/.venv[/cyan]"
)

console.print(f"\n[green]Project initialized at[/green] {directory}")

Expand Down Expand Up @@ -439,9 +466,7 @@ def run(
rundirs = prepare_run_dirs(project)
ensure_snakemake_symlink(project, rundirs.snakemake_state)
if verbose:
console.print(
f"[dim]Scratch root:[/dim] {resolve_scratch_root(project)}"
)
console.print(f"[dim]Scratch root:[/dim] {resolve_scratch_root(project)}")

choice = load_runtime(project_path=project)
_ensure_images(project, runtime=choice.runtime)
Expand All @@ -457,12 +482,14 @@ def run(
# removes the container declarations.
if choice.runtime == "none" and not choice.explicit:
cfg_data = json.loads(cfg_path.read_text())
declared = sorted({
entry["container_image"]
for rule_entries in cfg_data.values()
for entry in rule_entries.values()
if entry.get("container_image")
})
declared = sorted(
{
entry["container_image"]
for rule_entries in cfg_data.values()
for entry in rule_entries.values()
if entry.get("container_image")
}
)
if declared:
console.print(
"[yellow]⚠ No container runtime found on PATH "
Expand Down Expand Up @@ -595,12 +622,18 @@ def _build_snakemake_cmd(
"""
cmd: list[str] = [
"snakemake",
"-s", str(snakefile_path),
"-d", str(project),
"--cores", n,
"--jobs", n,
"--executor", "dask",
"--rerun-triggers", *rerun_triggers.split(","),
"-s",
str(snakefile_path),
"-d",
str(project),
"--cores",
n,
"--jobs",
n,
"--executor",
"dask",
"--rerun-triggers",
*rerun_triggers.split(","),
]
if force:
# ``--force`` scopes to explicit targets; ``rule all`` itself
Expand Down Expand Up @@ -647,7 +680,9 @@ def _target_for(project: Path, output_id: str, universe: str) -> str:
)

_, to = matches[0]
target = resolve_output_path(project, to, universe) / to.output_id / MANIFEST_FILENAME
target = (
resolve_output_path(project, to, universe) / to.output_id / MANIFEST_FILENAME
)
return str(target.relative_to(project))


Expand Down Expand Up @@ -832,9 +867,7 @@ def _ensure_images(project: Path, *, runtime: str, force: bool = False) -> None:
# without depending on the runtime's registry resolution.
if image_exists_locally(spec_str, runtime=runtime) and not force:
continue
console.print(
f"[cyan]Pulling[/cyan] {spec_str} [dim](via {runtime})[/dim]"
)
console.print(f"[cyan]Pulling[/cyan] {spec_str} [dim](via {runtime})[/dim]")
try:
pull_image(spec_str, runtime=runtime)
except ContainerBuildError as e:
Expand Down Expand Up @@ -882,7 +915,7 @@ def export() -> None:
@click.option(
"--author",
default=None,
help="Author override, e.g. \"Name <email@host>\". Default: git config.",
help='Author override, e.g. "Name <email@host>". Default: git config.',
)
@click.option(
"--license",
Expand Down
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