fix: ci slurm check (#388)

This is a fix for breaking 3rd party workflows: Bioconda was unable to
build (i.e.
https://github.com/bioconda/bioconda-recipes/actions/runs/20041946577/job/57478140127?pr=61020)
because an import of this plugin immediately threw an error due to the
missing SLURM setup. This had repercussions in other repos, too.

Some bits of the test suite have been refactored.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Bug Fixes**
* Detects absence of SLURM tools and disables the default status command
to avoid misconfiguration when SLURM is not available.
* Provides a clear user-facing message when SLURM is not detected and no
status command can be used.

* **Tests**
* Added focused parsing and time-conversion tests that run without SLURM
present.
* Removed older redundant tests and reorganized the test suite for
clarity.

<sub>✏️ Tip: You can customize this high-level summary in your review
settings.</sub>
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

Author: cmeesters

snakemake_executor_plugin_slurm/__init__.py

@@ -10,6 +10,7 @@
 from pathlib import Path
 import re
 import shlex
+import shutil
 import subprocess
 import time
 from dataclasses import dataclass, field
@@ -59,6 +60,10 @@ def _get_status_command_default():
     squeue_available = is_query_tool_available("squeue")
     # squeue is assumed to always be available on SLURM clusters
 
+    is_slurm_available = shutil.which("sinfo") is not None
+    if not is_slurm_available:
+        return None
+
     if not squeue_available and not sacct_available:
         raise WorkflowError(
             "Neither 'sacct' nor 'squeue' commands are available on this "
@@ -74,6 +79,15 @@ def _get_status_command_default():
 def _get_status_command_help():
     """Get help text with computed default."""
     default_cmd = _get_status_command_default()
+
+    # if SLURM is not available (should not occur, only
+    # in 3rd party CI tests)
+    if default_cmd is None:
+        return (
+            "Command to query job status. Options: 'sacct', 'squeue'. "
+            "SLURM not detected on this system, so no status command can be used."
+        )
+
     sacct_available = is_query_tool_available("sacct")
     squeue_recommended = should_recommend_squeue_status_command()
 

tests/test_parsing.py

@@ -0,0 +1,146 @@
+"""Tests for parsing functions that don't require SLURM to be installed."""
+from io import StringIO
+import pandas as pd
+from snakemake_executor_plugin_slurm.efficiency_report import (
+    parse_sacct_data,
+    time_to_seconds,
+)
+
+
+def test_parse_sacct_data():
+    test_data = [
+        "10294159|b10191d0-6985-4c3a-8ccb-"
+        "aa7d23ebffc7|rule_bam_bwa_mem_mosdepth_"
+        "simulate_reads|00:01:31|00:24.041|1|1||32000M",
+        "10294159.batch|batch||00:01:31|00:03.292|1|1|71180K|",
+        "10294159.0|python3.12||00:01:10|00:20.749|1|1|183612K|",
+        "10294160|b10191d0-6985-4c3a-8ccb-"
+        "aa7d23ebffc7|rule_bam_bwa_mem_mosdepth_"
+        "simulate_reads|00:01:30|00:24.055|1|1||32000M",
+        "10294160.batch|batch||00:01:30|00:03.186|1|1|71192K|",
+        "10294160.0|python3.12||00:01:10|00:20.868|1|1|184352K|",
+    ]
+    df = parse_sacct_data(
+        lines=test_data, e_threshold=0.0, run_uuid="test", logger=None
+    )
+    output = StringIO()
+    df.to_csv(output, index=False)
+    print(output.getvalue())
+    # this should only be two rows once collapsed
+    assert len(df) == 2
+    # check that RuleName is properly inherited from main jobs
+    assert all(df["RuleName"] == "rule_bam_bwa_mem_mosdepth_simulate_reads")
+    # check that RequestedMem_MB is properly inherited
+    assert all(df["RequestedMem_MB"] == 32000.0)
+    # check that MaxRSS_MB is properly calculated from job steps
+    assert df.iloc[0]["MaxRSS_MB"] > 0  # Should have actual memory usage from job step
+
+
+class TestTimeToSeconds:
+    """Test the time_to_seconds function with SLURM sacct time formats."""
+
+    def test_elapsed_format_with_days(self):
+        """
+        Test Elapsed format: [D-]HH:MM:SS or
+        [DD-]HH:MM:SS (no fractional seconds).
+        """
+        # Single digit days
+        assert time_to_seconds("1-00:00:00") == 86400  # 1 day
+        assert (
+            time_to_seconds("1-12:30:45") == 86400 + 12 * 3600 + 30 * 60 + 45
+        )  # 131445
+        assert time_to_seconds("9-23:59:59") == 9 * 86400 + 23 * 3600 + 59 * 60 + 59
+
+        # Double digit days
+        assert (
+            time_to_seconds("10-01:02:03") == 10 * 86400 + 1 * 3600 + 2 * 60 + 3
+        )  # 867723
+
+    def test_elapsed_format_hours_minutes_seconds(self):
+        """Test Elapsed format: HH:MM:SS (no fractional seconds)."""
+        assert time_to_seconds("00:00:00") == 0
+        assert time_to_seconds("01:00:00") == 3600  # 1 hour
+        assert time_to_seconds("23:59:59") == 23 * 3600 + 59 * 60 + 59  # 86399
+        assert time_to_seconds("12:30:45") == 12 * 3600 + 30 * 60 + 45  # 45045
+
+    def test_totalcpu_format_with_days(self):
+        """
+        Test TotalCPU format: [D-][HH:]MM:SS or [DD-][HH:]MM:SS
+        (with fractional seconds).
+        """
+        # With days and hours
+        assert time_to_seconds("1-12:30:45.5") == 86400 + 12 * 3600 + 30 * 60 + 45.5
+        assert (
+            time_to_seconds("10-01:02:03.123")
+            == 10 * 86400 + 1 * 3600 + 2 * 60 + 3.123
+        )
+
+        # With days, no hours (MM:SS format)
+        assert time_to_seconds("1-30:45") == 86400 + 30 * 60 + 45
+        assert time_to_seconds("1-30:45.5") == 86400 + 30 * 60 + 45.5
+
+    def test_totalcpu_format_minutes_seconds(self):
+        """Test TotalCPU format: MM:SS with fractional seconds."""
+        assert time_to_seconds("00:00") == 0
+        assert time_to_seconds("01:00") == 60  # 1 minute
+        assert time_to_seconds("59:59") == 59 * 60 + 59  # 3599
+        assert time_to_seconds("30:45") == 30 * 60 + 45  # 1845
+        assert time_to_seconds("30:45.5") == 30 * 60 + 45.5  # 1845.5
+
+    def test_totalcpu_format_seconds_only(self):
+        """Test TotalCPU format: SS or SS.sss (seconds only with fractional)."""
+        assert time_to_seconds("0") == 0
+        assert time_to_seconds("1") == 1
+        assert time_to_seconds("30") == 30
+        assert time_to_seconds("59") == 59
+
+        # Fractional seconds
+        assert time_to_seconds("30.5") == 30.5
+        assert time_to_seconds("0.5") == 0.5
+
+    def test_real_world_sacct_examples(self):
+        """Test with realistic sacct time values from actual output."""
+        # From your test data
+        assert time_to_seconds("00:01:31") == 91  # 1 minute 31 seconds
+        assert time_to_seconds("00:24.041") == 24.041  # 24.041 seconds
+        assert time_to_seconds("00:03.292") == 3.292  # 3.292 seconds
+        assert time_to_seconds("00:20.749") == 20.749  # 20.749 seconds
+
+        # Longer running jobs
+        assert time_to_seconds("02:15:30") == 2 * 3600 + 15 * 60 + 30  # 2h 15m 30s
+        assert time_to_seconds("1-12:00:00") == 86400 + 12 * 3600  # 1 day 12 hours
+        assert time_to_seconds("7-00:00:00") == 7 * 86400  # 1 week
+
+    def test_empty_and_invalid_inputs(self):
+        """Test empty, None, and invalid inputs."""
+        assert time_to_seconds("") == 0
+        assert time_to_seconds("   ") == 0
+        assert time_to_seconds(None) == 0
+        assert time_to_seconds(pd.NA) == 0
+        assert time_to_seconds("invalid") == 0
+        assert time_to_seconds("1:2:3:4") == 0  # Too many colons
+        assert time_to_seconds("abc:def") == 0
+        assert time_to_seconds("-1:00:00") == 0  # Negative values
+
+    def test_whitespace_handling(self):
+        """Test that whitespace is properly handled."""
+        assert time_to_seconds(" 30 ") == 30
+        assert time_to_seconds("  1-02:30:45  ") == 86400 + 2 * 3600 + 30 * 60 + 45
+        assert time_to_seconds("\t12:30:45\n") == 12 * 3600 + 30 * 60 + 45
+
+    def test_pandas_na_values(self):
+        """Test pandas NA and NaN values."""
+        assert time_to_seconds(pd.NA) == 0
+        assert (
+            time_to_seconds(pd.NaType()) == 0 if hasattr(pd, "NaType") else True
+        )  # Skip if not available
+
+    def test_edge_case_values(self):
+        """Test edge case values that might appear in SLURM output."""
+        # Zero padding variations (should work with datetime parsing)
+        assert time_to_seconds("01:02:03") == 1 * 3600 + 2 * 60 + 3
+        assert time_to_seconds("1:2:3") == 1 * 3600 + 2 * 60 + 3
+
+        # Single digit values
+        assert time_to_seconds("5") == 5
+        assert time_to_seconds("1:5") == 1 * 60 + 5

tests/tests.py

@@ -7,16 +7,11 @@
 from unittest.mock import MagicMock, patch
 import pytest
 from snakemake_executor_plugin_slurm import ExecutorSettings
-from snakemake_executor_plugin_slurm.efficiency_report import (
-    parse_sacct_data,
-    time_to_seconds,
-)
 from snakemake_executor_plugin_slurm.utils import set_gres_string
 from snakemake_executor_plugin_slurm.submit_string import get_submit_command
 
 from snakemake_executor_plugin_slurm.validation import validate_slurm_extra
 from snakemake_interface_common.exceptions import WorkflowError
-import pandas as pd
 
 
 class TestWorkflows(snakemake.common.tests.TestWorkflowsLocalStorageBase):
@@ -32,147 +27,6 @@ def get_executor_settings(self) -> Optional[ExecutorSettingsBase]:
         )
 
 
-def test_parse_sacct_data():
-    from io import StringIO
-
-    test_data = [
-        "10294159|b10191d0-6985-4c3a-8ccb-"
-        "aa7d23ebffc7|rule_bam_bwa_mem_mosdepth_"
-        "simulate_reads|00:01:31|00:24.041|1|1||32000M",
-        "10294159.batch|batch||00:01:31|00:03.292|1|1|71180K|",
-        "10294159.0|python3.12||00:01:10|00:20.749|1|1|183612K|",
-        "10294160|b10191d0-6985-4c3a-8ccb-"
-        "aa7d23ebffc7|rule_bam_bwa_mem_mosdepth_"
-        "simulate_reads|00:01:30|00:24.055|1|1||32000M",
-        "10294160.batch|batch||00:01:30|00:03.186|1|1|71192K|",
-        "10294160.0|python3.12||00:01:10|00:20.868|1|1|184352K|",
-    ]
-    df = parse_sacct_data(
-        lines=test_data, e_threshold=0.0, run_uuid="test", logger=None
-    )
-    output = StringIO()
-    df.to_csv(output, index=False)
-    print(output.getvalue())
-    # this should only be two rows once collapsed
-    assert len(df) == 2
-    # check that RuleName is properly inherited from main jobs
-    assert all(df["RuleName"] == "rule_bam_bwa_mem_mosdepth_simulate_reads")
-    # check that RequestedMem_MB is properly inherited
-    assert all(df["RequestedMem_MB"] == 32000.0)
-    # check that MaxRSS_MB is properly calculated from job steps
-    assert df.iloc[0]["MaxRSS_MB"] > 0  # Should have actual memory usage from job step
-
-
-class TestTimeToSeconds:
-    """Test the time_to_seconds function with SLURM sacct time formats."""
-
-    def test_elapsed_format_with_days(self):
-        """
-        Test Elapsed format: [D-]HH:MM:SS or
-        [DD-]HH:MM:SS (no fractional seconds).
-        """
-        # Single digit days
-        assert time_to_seconds("1-00:00:00") == 86400  # 1 day
-        assert (
-            time_to_seconds("1-12:30:45") == 86400 + 12 * 3600 + 30 * 60 + 45
-        )  # 131445
-        assert time_to_seconds("9-23:59:59") == 9 * 86400 + 23 * 3600 + 59 * 60 + 59
-
-        # Double digit days
-        assert (
-            time_to_seconds("10-01:02:03") == 10 * 86400 + 1 * 3600 + 2 * 60 + 3
-        )  # 867723
-
-    def test_elapsed_format_hours_minutes_seconds(self):
-        """Test Elapsed format: HH:MM:SS (no fractional seconds)."""
-        assert time_to_seconds("00:00:00") == 0
-        assert time_to_seconds("01:00:00") == 3600  # 1 hour
-        assert time_to_seconds("23:59:59") == 23 * 3600 + 59 * 60 + 59  # 86399
-        assert time_to_seconds("12:30:45") == 12 * 3600 + 30 * 60 + 45  # 45045
-
-    def test_totalcpu_format_with_days(self):
-        """
-        Test TotalCPU format: [D-][HH:]MM:SS or [DD-][HH:]MM:SS
-        (with fractional seconds).
-        """
-        # With days and hours
-        assert time_to_seconds("1-12:30:45.5") == 86400 + 12 * 3600 + 30 * 60 + 45.5
-        assert (
-            time_to_seconds("10-01:02:03.123")
-            == 10 * 86400 + 1 * 3600 + 2 * 60 + 3.123
-        )
-
-        # With days, no hours (MM:SS format)
-        assert time_to_seconds("1-30:45") == 86400 + 30 * 60 + 45
-        assert time_to_seconds("1-30:45.5") == 86400 + 30 * 60 + 45.5
-
-    def test_totalcpu_format_minutes_seconds(self):
-        """Test TotalCPU format: MM:SS with fractional seconds."""
-        assert time_to_seconds("00:00") == 0
-        assert time_to_seconds("01:00") == 60  # 1 minute
-        assert time_to_seconds("59:59") == 59 * 60 + 59  # 3599
-        assert time_to_seconds("30:45") == 30 * 60 + 45  # 1845
-        assert time_to_seconds("30:45.5") == 30 * 60 + 45.5  # 1845.5
-
-    def test_totalcpu_format_seconds_only(self):
-        """Test TotalCPU format: SS or SS.sss (seconds only with fractional)."""
-        assert time_to_seconds("0") == 0
-        assert time_to_seconds("1") == 1
-        assert time_to_seconds("30") == 30
-        assert time_to_seconds("59") == 59
-
-        # Fractional seconds
-        assert time_to_seconds("30.5") == 30.5
-        assert time_to_seconds("0.5") == 0.5
-
-    def test_real_world_sacct_examples(self):
-        """Test with realistic sacct time values from actual output."""
-        # From your test data
-        assert time_to_seconds("00:01:31") == 91  # 1 minute 31 seconds
-        assert time_to_seconds("00:24.041") == 24.041  # 24.041 seconds
-        assert time_to_seconds("00:03.292") == 3.292  # 3.292 seconds
-        assert time_to_seconds("00:20.749") == 20.749  # 20.749 seconds
-
-        # Longer running jobs
-        assert time_to_seconds("02:15:30") == 2 * 3600 + 15 * 60 + 30  # 2h 15m 30s
-        assert time_to_seconds("1-12:00:00") == 86400 + 12 * 3600  # 1 day 12 hours
-        assert time_to_seconds("7-00:00:00") == 7 * 86400  # 1 week
-
-    def test_empty_and_invalid_inputs(self):
-        """Test empty, None, and invalid inputs."""
-        assert time_to_seconds("") == 0
-        assert time_to_seconds("   ") == 0
-        assert time_to_seconds(None) == 0
-        assert time_to_seconds(pd.NA) == 0
-        assert time_to_seconds("invalid") == 0
-        assert time_to_seconds("1:2:3:4") == 0  # Too many colons
-        assert time_to_seconds("abc:def") == 0
-        assert time_to_seconds("-1:00:00") == 0  # Negative values
-
-    def test_whitespace_handling(self):
-        """Test that whitespace is properly handled."""
-        assert time_to_seconds(" 30 ") == 30
-        assert time_to_seconds("  1-02:30:45  ") == 86400 + 2 * 3600 + 30 * 60 + 45
-        assert time_to_seconds("\t12:30:45\n") == 12 * 3600 + 30 * 60 + 45
-
-    def test_pandas_na_values(self):
-        """Test pandas NA and NaN values."""
-        assert time_to_seconds(pd.NA) == 0
-        assert (
-            time_to_seconds(pd.NaType()) == 0 if hasattr(pd, "NaType") else True
-        )  # Skip if not available
-
-    def test_edge_case_values(self):
-        """Test edge case values that might appear in SLURM output."""
-        # Zero padding variations (should work with datetime parsing)
-        assert time_to_seconds("01:02:03") == 1 * 3600 + 2 * 60 + 3
-        assert time_to_seconds("1:2:3") == 1 * 3600 + 2 * 60 + 3
-
-        # Single digit values
-        assert time_to_seconds("5") == 5
-        assert time_to_seconds("1:5") == 1 * 60 + 5
-
-
 class TestEfficiencyReport(snakemake.common.tests.TestWorkflowsLocalStorageBase):
     __test__ = True