Enable all ruff lints

pyproject.toml

@@ -68,10 +68,13 @@ src = ["src"]
 target-version = "py311"
 
 [tool.ruff.lint]
-select = ["ANN", "E", "F", "I"]
+select = ["ALL"]
 ignore = [
   "ANN101",  # self should not be annotated.
-  "ANN102"  # cls should not be annotated.
+  "ANN102",  # cls should not be annotated.
+  "COM812",  # missing trailing comma in Python 3.5+
+  "ISC001",  # implicitly concatenated strings on a single line.
+  "T201"  # print
 ]
 fixable = ["ALL"]
 unfixable = []

src/ecpac/cli.py

@@ -1,5 +1,6 @@
+"""Cli utilities."""
+
 import pathlib as pl
-from typing import Optional
 
 import click
 
@@ -20,14 +21,14 @@ def check_exist_dir(path: pl.Path, label: str = "") -> bool:
     return False
 
 
-def option_or_prompt(opt: Optional[str], prompt: str, default: Optional[str] = None) -> str:
+def option_or_prompt(opt: str | None, prompt: str, *, default: str | None = None) -> str:
     """Prompt the user for input if the option is not provided."""
     if opt is not None:
         return opt
     return click.prompt(prompt, default=default, type=str)
 
 
-def option_or_confirm(opt: Optional[bool], prompt: str, default: Optional[bool] = False) -> bool:
+def option_or_confirm(opt: bool | None, prompt: str, *, default: bool | None = False) -> bool:
     """Prompt the user for input (confirmation boolean) if the option is not provided."""
     if opt is not None:
         return opt

src/ecpac/consts.py

@@ -1,3 +1,5 @@
+"""Constants."""
+
 import os
 import pathlib as pl
 

src/ecpac/icons.py

@@ -1,3 +1,5 @@
+"""Unicode emojis used as icons."""
+
 ICON_CHECK = "\U00002705"  # Check Mark
 ICON_CROSS = "\U0000274C"  # Cross Mark
 ICON_FOLDER = "\U0001F4C1"  # File Folder

src/ecpac/main.py

@@ -1,3 +1,5 @@
+"""Main entry point for ecpac."""
+
 import dataclasses
 import itertools
 import math
@@ -7,7 +9,6 @@
 import stat
 import subprocess
 from datetime import datetime, timedelta
-from typing import List, Optional
 
 import click
 
@@ -16,18 +17,19 @@
 
 @dataclasses.dataclass
 class FsPlan:
-    """Planned file system change"""
+    """Planned file system change."""
 
     path: pl.Path
     is_file: bool = False
-    contents_text: Optional[str] = None
+    contents_text: str | None = None
     make_executable: bool = False
 
     def apply(self) -> None:
+        """Apply the file system change."""
         if self.is_file:
             self.path.parent.mkdir(parents=True, exist_ok=True)
             txt = "" if self.contents_text is None else self.contents_text
-            with open(self.path, "w", encoding="utf-8") as handle:
+            with self.path.open("w", encoding="utf-8") as handle:
                 handle.write(txt)
 
             if self.make_executable:
@@ -66,7 +68,7 @@ def apply(self) -> None:
     "--analysis_level",
     "arg_analysis_level",
     type=str,
-    help='Analysis level ("participant", "group", ' '"test_config").',
+    help='Analysis level ("participant", "group", "test_config").',
 )
 @click.option("-c", "--cpac", "arg_cpac", type=str, help="C-PAC folder for patching image.")
 @click.option("-m", "--memory_gb", "arg_memory_gb", type=str, help="Memory (GB) for each job.")
@@ -98,21 +100,22 @@ def apply(self) -> None:
     type=str,
     help="Additional arguments that will be passed to C-PAC.",
 )
-def main(
-    arg_input: Optional[str] = None,
-    arg_output: Optional[str] = None,
-    arg_run: Optional[str] = None,
-    arg_image: Optional[str] = None,
-    arg_subject: Optional[str] = None,
-    arg_pipeline: Optional[str] = None,
-    arg_analysis_level: Optional[str] = None,
-    arg_cpac: Optional[str] = None,
-    arg_memory_gb: Optional[str] = None,
-    arg_threads: Optional[str] = None,
-    arg_duration_h: Optional[str] = None,
-    arg_save_working_dir: Optional[str] = None,
-    arg_extra_cpac_args: Optional[str] = None,
+def main(  # noqa: C901, PLR0912, PLR0913, PLR0915
+    arg_input: str | None = None,
+    arg_output: str | None = None,
+    arg_run: str | None = None,
+    arg_image: str | None = None,
+    arg_subject: str | None = None,
+    arg_pipeline: str | None = None,
+    arg_analysis_level: str | None = None,
+    arg_cpac: str | None = None,
+    arg_memory_gb: str | None = None,
+    arg_threads: str | None = None,
+    arg_duration_h: str | None = None,
+    arg_save_working_dir: str | None = None,
+    arg_extra_cpac_args: str | None = None,
 ) -> None:
+    """CLI entry point."""
     if not consts.PSC_PROJECT_USER.exists():
         click.secho(
             f'Error: User directory does not exist! "{consts.PSC_PROJECT_USER}" '
@@ -127,7 +130,7 @@ def main(
     run_id = cli.option_or_prompt(
         opt=arg_run,
         prompt=icons.ICON_JOB + click.style("Run name", fg="blue"),
-        default=datetime.now().strftime("run_%y-%m-%d_%H-%M-%S"),
+        default=datetime.now().strftime("run_%y-%m-%d_%H-%M-%S"),  # noqa: DTZ005
     )
 
     # Resources
@@ -138,15 +141,15 @@ def main(
             prompt=icons.ICON_THREADS
             + click.style(" Number of threads/cores (int) (C-PAC will get 1 less)", fg="blue"),
             default=str(8),
-        )
+        ),
     )
 
     res_memory_gb = float(
         cli.option_or_prompt(
             opt=arg_memory_gb,
             prompt=icons.ICON_MEMORY + click.style(" Memory (GB, float) (C-PAC will get 1GB less)", fg="blue"),
             default=f"{2 * res_threads:.1f}",
-        )
+        ),
     )
 
     res_duration = timedelta(
@@ -155,8 +158,8 @@ def main(
                 opt=arg_duration_h,
                 prompt=icons.ICON_DURATION + click.style(" Duration (hours, float)", fg="blue"),
                 default=f"{48.0:.1f}",
-            )
-        )
+            ),
+        ),
     )
 
     # Image
@@ -167,7 +170,7 @@ def main(
                 opt=arg_image,
                 prompt=icons.ICON_SINGULARITY + click.style(" Image file", fg="blue"),
                 default=str(consts.PSC_IMAGE_DEFAULT),
-            )
+            ),
         )
 
         if cli.check_exist_file(path_image, label="Singularity image"):
@@ -195,8 +198,7 @@ def main(
 
         if not patch_cpac or utils.cpac_dir_valid(path_cpac):
             break
-        else:
-            click.secho(f'Error: Not a valid cpac dir! "{path_cpac}"', fg="red")
+        click.secho(f'Error: Not a valid cpac dir! "{path_cpac}"', fg="red")
 
     # Input directory
 
@@ -205,7 +207,7 @@ def main(
             cli.option_or_prompt(
                 opt=arg_input,
                 prompt=icons.ICON_FOLDER + click.style(" Input directory", fg="blue"),
-            )
+            ),
         )
 
         if cli.check_exist_dir(path_input, label="Input"):
@@ -251,7 +253,7 @@ def main(
             opt=arg_output,
             prompt=icons.ICON_FOLDER + click.style(" Output directory", fg="blue"),
             default=str(consts.PSC_OUTPUT_DEFAULT),
-        )
+        ),
     )
 
     # Pipeline configs
@@ -265,8 +267,8 @@ def main(
         ),
     )
 
-    preconfig_ids: List[str] = []
-    pipeline_config_files: List[str] = []
+    preconfig_ids: list[str] = []
+    pipeline_config_files: list[str] = []
     for pipe in pipeline_ids:
         if pipe in consts.CPAC_PRECONFIGS:
             preconfig_ids.append(pipe)
@@ -329,8 +331,6 @@ def main(
     # Reconstruct ecpac cli call
 
     reargs: list[str] = ["ecpac"]
-    # Don't add run_id, if the user runs ecpac again, they should always change it
-    # reargs.extend(["--run", run_id])
     reargs.extend(["--input", str(path_input)])
     reargs.extend(["--output", str(path_output)])
     reargs.extend(["--image", str(path_image)])
@@ -349,7 +349,7 @@ def main(
 
     # Plan out dirs and job files
 
-    fs_plans: List[FsPlan] = []
+    fs_plans: list[FsPlan] = []
     job_paths = []
     example_job = None
     example_path_stdout_log = None
@@ -362,7 +362,7 @@ def main(
         path_job = path_out / "run_job.sh"
         path_stdout_log = path_out / "out.log"
 
-        extra_args: List[str] = [extra_cpac_args]
+        extra_args: list[str] = [extra_cpac_args]
         if save_working_dir:
             extra_args.append(f"--save_working_dir {path_out_wd.absolute()}")
 
@@ -380,7 +380,7 @@ def main(
                     f"- Image: `{path_image.absolute()}`\n"
                     f"- Threads: {res_threads}\n"
                     f"- Memory: {res_memory_gb} GB\n"
-                    f"- Analysis level: `{analysis_level}`"
+                    f"- Analysis level: `{analysis_level}`",
                 )
                 + "\n\n"
             )
@@ -390,7 +390,7 @@ def main(
                 f"- Pipeline: `{pipe_id}`\n"
                 f"- Subject: `{sub}`\n"
                 f"- Analysis level: `{analysis_level}`\n"
-                f"- Output: `{path_out.absolute()}`\n"
+                f"- Output: `{path_out.absolute()}`\n",
             )
 
         # Adjust ressources for ACCESS limits
@@ -464,7 +464,7 @@ def main(
             is_file=True,
             contents_text=executor,
             make_executable=True,
-        )
+        ),
     )
 
     # Add reproducible ecpac call
@@ -474,7 +474,7 @@ def main(
             is_file=True,
             contents_text=shlex.join(reargs),
             make_executable=True,
-        )
+        ),
     )
 
     # User sanity check
@@ -499,7 +499,7 @@ def main(
         plan.apply()
 
     if click.confirm(icons.ICON_LAUNCH + click.style(" Launch now?", bg="blue"), default=None):
-        subprocess.run([path_executor], shell=True)
+        subprocess.run([path_executor], shell=True, check=False)  # noqa: S602
 
         click.secho("Jobs were executed!", bg="blue")
         click.secho("Some commands you might find helpful:", fg="blue")

src/ecpac/slack.py

@@ -1,3 +1,5 @@
+"""Slack-related functions."""
+
 import json
 import os
 import shlex
@@ -15,7 +17,7 @@ def slack_message_bash(data: dict) -> str:
     if not slack_webhook_available():
         return ""
     return shlex.join(
-        ["curl", "-X", "POST", "-H", "Content-type: application/json", "--data", json.dumps(data), SLACK_WEBHOOK_URL]
+        ["curl", "-X", "POST", "-H", "Content-type: application/json", "--data", json.dumps(data), SLACK_WEBHOOK_URL],
     )
 
 

src/ecpac/utils.py

@@ -1,26 +1,27 @@
+"""Utility functions."""
+
 import datetime
 import os
 import pathlib as pl
 import re
-from typing import Optional, Union
 
 
 def filesafe(f: str) -> str:
     """Convert a string to a file-safe string."""
     return re.sub(r"[^a-zA-Z0-9_\-]", "_", f)
 
 
-def option_truthy(opt: Optional[str]) -> Optional[bool]:
-    """
-    Convert a string option to a boolean option.
+def option_truthy(opt: str | None) -> bool | None:
+    """Convert a string option to a boolean option.
+
     Common truthy values like "true", "y", "yes", and "1" are converted to True.
     None is converted to None.
     All other values are converted to False.
     """
     if opt is None:
         return None
     opt_lower = opt.lower()
-    return opt_lower == "true" or opt_lower == "y" or opt_lower == "yes" or opt_lower == "1"
+    return opt_lower in ("true", "y", "yes", "1")
 
 
 def timedelta_to_hms(t: datetime.timedelta) -> str:
@@ -34,7 +35,7 @@ def bullet_str_list(list_: list) -> str:
     return "\n".join([f" - {i}" for i in list_])
 
 
-def cpac_dir_valid(path: Union[str, os.PathLike]) -> bool:
+def cpac_dir_valid(path: str | os.PathLike) -> bool:
     """Check if a directory is a valid C-PAC source code directory."""
     p = pl.Path(path)
     return (
@@ -44,6 +45,6 @@ def cpac_dir_valid(path: Union[str, os.PathLike]) -> bool:
     )
 
 
-def bridges_gb_to_mb(gb: float | int) -> float | int:
+def bridges_gb_to_mb(gb: float) -> float:
     """ACCESS/Bridges uses 1000 MB per GB instead of 1024 MB per GB."""
     return gb * 1000

tests/__init__.py

@@ -0,0 +1 @@
+"""Tests."""

tests/dummy_test.py

@@ -1,2 +1,6 @@
+"""Dummy test."""
+
+
 def test_dummy() -> None:
-    assert 1 == 1
+    """Dummy test."""
+    assert 1 == 1  # noqa: PLR0133, S101