stepup-queue 1.1.0__tar.gz → 1.1.1__tar.gz

{stepup_queue-1.1.0/stepup_queue.egg-info → stepup_queue-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stepup-queue
-Version: 1.1.0
+Version: 1.1.1
 Summary: StepUp Queue integrates queued jobs into a StepUp workflow.
 Author-email: Toon Verstraelen <toon.verstraelen@ugent.be>
 License-Expression: GPL-3.0-or-later
@@ -25,6 +25,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: path>=16.14.0
+Requires-Dist: rich>=13.0.0
 Requires-Dist: stepup<4.0.0,>=3.2.0
 Provides-Extra: dev
 Requires-Dist: psutil; extra == "dev"

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/pyproject.toml

@@ -29,6 +29,7 @@ classifiers = [
 dependencies = [
     # Ensure changes to these dependencies are reflected in .github/requirements-old.txt
     "path>=16.14.0",
+    "rich>=13.0.0",
     "stepup>=3.2.0,<4.0.0",
 ]
 dynamic = ["version"]

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/__init__.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/actions.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/api.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/canceljobs.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #
@@ -24,6 +24,7 @@ import subprocess
 import sys
 
 from path import Path
+from rich.console import Console
 
 from .sbatch import DONE_STATES, parse_sbatch, read_log, read_status
 from .utils import search_jobs
@@ -31,12 +32,17 @@ from .utils import search_jobs
 
 def canceljobs_tool(args: argparse.Namespace):
     """Iterate over all slurmjob.log files, read the SLURM job IDs, and cancel them."""
+    console = Console(highlight=False)
+    if not args.commit:
+        console.print("[yellow]# Note: No jobs are actually cancelled.[/]")
+        console.print("[yellow]# Use the --commit option to execute the cancellations.[/]")
+
     jobs = {}
-    for path_log in search_jobs(args.paths, verbose=True):
+    for path_log in search_jobs(args.paths, console):
         try:
             job_id, cluster, status = read_jobid_cluster_status(path_log)
         except ValueError as e:
-            print(f"# WARNING: Could not read job ID from {path_log}: {e}")
+            console.print(f"[red]# WARNING: Could not read job ID from {path_log}: {e}[/]")
             continue
         if args.all or status not in DONE_STATES:
             jobs.setdefault(cluster, []).append((job_id, path_log, status))
@@ -56,24 +62,22 @@ def canceljobs_tool(args: argparse.Namespace):
                 command_args.extend(str(job_id) for job_id, _, _ in cancel_jobs)
 
                 # Using subprocess.run for better control and error handling
-                print(" ".join(command_args))
+                print_cancel_command(
+                    console, [job_id for job_id, _, _ in cancel_jobs], cluster, None
+                )
                 result = subprocess.run(command_args, check=False)
                 all_good &= result.returncode == 0
         else:
             for job_id, path_log, status in cluster_jobs:
-                command = "scancel"
-                if cluster is not None:
-                    command += f" -M {cluster}"
-                command += f" {job_id}  # {path_log} {status}"
-                print(command)
+                print_cancel_command(console, [job_id], cluster, f"{path_log} {status}")
     if not all_good:
-        print("Some jobs could not be cancelled. See messages above.")
+        console.print("[red]Some jobs could not be cancelled. See messages above.[/]")
         sys.exit(1)
 
 
 def read_jobid_cluster_status(path_log: str) -> tuple[int, str | None, str | None]:
     """Read the job ID, cluster, and job status from the job log file."""
-    lines = read_log(path_log, False)
+    lines = read_log(path_log, None)
     if len(lines) < 1:
         raise ValueError(f"Incomplete file: {path_log}.")
     words = lines[0].split()
@@ -115,3 +119,16 @@ def canceljobs_subcommand(subparser: argparse.ArgumentParser) -> callable:
         help="Select all jobs, including the ones that seem to be done already.",
     )
     return canceljobs_tool
+
+
+def print_cancel_command(
+    console: Console, job_ids: list[int], cluster: str | None, comment: str | None
+) -> str:
+    """Print the job cancellation command."""
+    parts = ["[green]scancel[/]"]
+    if cluster is not None:
+        parts.append(f"[cyan]-M {cluster}[/]")
+    parts.extend(str(job_id) for job_id in job_ids)
+    if comment is not None:
+        parts.append(f" [bright_black]# {comment}[/]")
+    console.print(" ".join(parts))

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/removejobs.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #
@@ -23,6 +23,7 @@ import argparse
 import shutil
 
 from path import Path
+from rich.console import Console
 
 from .sbatch import read_log, read_status
 from .utils import search_jobs
@@ -45,26 +46,31 @@ FAILED_STATES = {
 
 def removejobs_tool(args: argparse.Namespace):
     """Iterate over all slurmjob.log files and remove their parent job directories."""
+    console = Console(highlight=False)
+    if not args.commit:
+        console.print("[yellow]# Note: No job directories are actually removed.[/]")
+        console.print("[yellow]# Use the --commit option to execute the removals.[/]")
+
     jobs = []
-    for path_log in search_jobs(args.paths, verbose=True):
+    for path_log in search_jobs(args.paths, console):
         try:
             status = read_last_status(path_log)
         except ValueError as e:
-            print(f"Warning: Could not read job status from {path_log}: {e}")
+            console.print(f"[red]# WARNING: Could not read job status from {path_log}: {e}[/]")
             status = None
         if args.all or status in FAILED_STATES:
             jobs.append((path_log, status))
 
     for path_log, status in jobs:
-        command = f"rm -rf {path_log.parent}  # state={status}"
-        print(command)
+        command = f"[cyan]rm -rf[/] {path_log.parent}  [bright_black]# state={status}[/]"
+        console.print(command)
         if args.commit:
             shutil.rmtree(path_log.parent)
 
 
 def read_last_status(path_log: str) -> str | None:
     """Read the last job status from the job log file."""
-    lines = read_log(path_log, False)
+    lines = read_log(path_log, None)
     return read_status(lines[-1:])[1]
 
 

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/sbatch.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #
@@ -68,9 +68,17 @@ def submit_once_and_wait(
         The return code of the job.
         0 if successful, 1 if the job failed.
     """
+    inp_digest = os.getenv("STEPUP_STEP_INP_DIGEST")
+    if inp_digest is None:
+        raise ValueError("The environment variable STEPUP_STEP_INP_DIGEST is not set.")
+
     # Read previously logged job states
     path_log = Path("slurmjob.log")
-    previous_lines = read_log(path_log, validate_inp_digest) if path_log.is_file() else []
+    previous_lines = (
+        read_log(path_log, inp_digest if validate_inp_digest else None)
+        if path_log.is_file()
+        else []
+    )
 
     # Go through or skip states.
     submit_time, status = read_status(previous_lines)
@@ -79,7 +87,7 @@ def submit_once_and_wait(
         submit_time = time.time()
         sbatch_stdout = submit_job(work_thread, job_ext, sbatch_rc)
         # Create a new log file after submitting the job.
-        _init_log(path_log)
+        _init_log(path_log, inp_digest)
         log_status(path_log, f"Submitted {sbatch_stdout}")
         rndsleep()
     else:
@@ -117,7 +125,7 @@ def submit_once_and_wait(
     raise RuntimeError(f"Job ended with status '{status}'.")
 
 
-def read_log(path_log: str, do_inp_digest: bool = True) -> list[str]:
+def read_log(path_log: str, expected_inp_digest: str | None = None) -> list[str]:
     """Read lines from a previously created log file."""
     lines = []
     with open(path_log) as f:
@@ -126,11 +134,11 @@ def read_log(path_log: str, do_inp_digest: bool = True) -> list[str]:
         except StopIteration as exc:
             raise ValueError("Existing log file is empty.") from exc
         try:
-            inp_digest = next(f).strip()
+            actual_inp_digest = next(f).strip()
         except StopIteration as exc:
             raise ValueError("Existing log file has no input digest.") from exc
-        if do_inp_digest:
-            check_log_inp_digest(inp_digest)
+        if expected_inp_digest is not None:
+            check_log_inp_digest(actual_inp_digest, expected_inp_digest)
         for line in f:
             line = line.strip()
             lines.append(line)
@@ -145,11 +153,8 @@ def check_log_version(line: str):
         )
 
 
-def _init_log(path_log: str):
+def _init_log(path_log: str, inp_digest: str):
     """Initialize a new log file."""
-    inp_digest = os.getenv("STEPUP_STEP_INP_DIGEST")
-    if inp_digest is None:
-        raise ValueError("The environment variable STEPUP_STEP_INP_DIGEST is not set.")
     with open(path_log, "w") as fh:
         print(FIRST_LINE, file=fh)
         print(inp_digest, file=fh)
@@ -279,15 +284,12 @@ class InpDigestError(ValueError):
     """The input digest in the log file does not match the one in the environment."""
 
 
-def check_log_inp_digest(line: str):
+def check_log_inp_digest(actual: str, expected: str):
     """Validate the log input digest, abort if there is a mismatch."""
-    inp_digest = os.getenv("STEPUP_STEP_INP_DIGEST")
-    if inp_digest is None:
-        raise ValueError("The environment variable STEPUP_STEP_INP_DIGEST is not set.")
-    if line != inp_digest:
+    if actual != expected:
         raise InpDigestError(
             "The second line of the log contains the wrong input digest.\n"
-            f"Expected: {inp_digest}\nFound:    {line}"
+            f"Actual:   {actual}\nExpected: {expected}\n"
         )
 
 

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup/queue/utils.py

@@ -1,5 +1,5 @@
 # StepUp Queue integrates queued jobs into a StepUp workflow.
-# © 2025 Toon Verstraelen
+# Copyright 2025-2026 Toon Verstraelen
 #
 # This file is part of StepUp Queue.
 #
@@ -22,19 +22,20 @@
 from itertools import chain
 
 from path import Path
+from rich.console import Console
 
 __all__ = ("search_jobs",)
 
 
-def search_jobs(paths: list[Path], verbose: bool = False) -> list[Path]:
+def search_jobs(paths: list[Path], console: Console | None = None) -> list[Path]:
     """Recursively search for slurmjob.log files in the specified directories.
 
     Parameters
     ----------
     paths
         List of directories to search in.
-    verbose
-        Whether to print warnings when paths do not exist or are not directories.
+    console
+        Rich console for printing warnings. If None, no warnings are printed.
 
     Returns
     -------
@@ -44,12 +45,12 @@ def search_jobs(paths: list[Path], verbose: bool = False) -> list[Path]:
     paths_log = set()
     for path in paths:
         if not path.exists():
-            if verbose:
-                print(f"# WARNING: Path {path} does not exist.")
+            if console is not None:
+                console.print(f"[red]# WARNING: Path {path} does not exist.[/]")
             continue
         if not path.is_dir():
-            if verbose:
-                print(f"# WARNING: Path {path} is not a directory.")
+            if console is not None:
+                console.print(f"[red]# WARNING: Path {path} is not a directory.[/]")
             continue
         for path_sub in chain([path], path.walkdirs()):
             path_log = path_sub / "slurmjob.log"

{stepup_queue-1.1.0 → stepup_queue-1.1.1/stepup_queue.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: stepup-queue
-Version: 1.1.0
+Version: 1.1.1
 Summary: StepUp Queue integrates queued jobs into a StepUp workflow.
 Author-email: Toon Verstraelen <toon.verstraelen@ugent.be>
 License-Expression: GPL-3.0-or-later
@@ -25,6 +25,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: path>=16.14.0
+Requires-Dist: rich>=13.0.0
 Requires-Dist: stepup<4.0.0,>=3.2.0
 Provides-Extra: dev
 Requires-Dist: psutil; extra == "dev"

{stepup_queue-1.1.0 → stepup_queue-1.1.1}/stepup_queue.egg-info/requires.txt

@@ -1,4 +1,5 @@
 path>=16.14.0
+rich>=13.0.0
 stepup<4.0.0,>=3.2.0
 
 [dev]