Fix bug in get_slurm_file_base so = is correctly handled

This partially addresses #6.
Now both = and spaces are correctly handled when reading the slurm
script to extract the output file name.

a3fe/_version.py

@@ -1 +1 @@
-__version__ = "0.1.1"
+__version__ = "0.1.2"

a3fe/data/alternative_input/alternative_run_somd.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+#SBATCH --account=qt
+#SBATCH --nodes=1
+#SBATCH --time=24:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --ntasks-per-node=1
+#SBATCH --cpus-per-task=2
+#SBATCH --exclude=node018
+#SBATCH --mem=50G
+#SBATCH --output=somd-array-gpu-%A.%a.out
+
+lam=$1
+echo "lambda is: " $lam
+
+srun somd-freenrg -C somd.cfg -l $lam -p CUDA

a3fe/read/_process_slurm_files.py

@@ -1,6 +1,7 @@
 """Functionality for processing slurm files."""
 
 import os as _os
+import re as _re
 
 
 def get_slurm_file_base(slurm_file: str) -> str:
@@ -22,7 +23,7 @@ def get_slurm_file_base(slurm_file: str) -> str:
     # Find the slurm output file
     with open(slurm_file, "r") as f:
         for line in f:
-            split_line = line.split()
+            split_line = _re.split(" |=", line)
             if len(split_line) > 0 and split_line[0] == "#SBATCH":
                 if split_line[1] == "--output" or split_line[1] == "-o":
                     slurm_pattern = split_line[2]

a3fe/tests/test_read.py

@@ -15,6 +15,8 @@
     write_truncated_sim_datafile,
 )
 
+from ..read._process_slurm_files import get_slurm_file_base
+
 
 def test_read_mbar_result():
     """Test that the read_mbar_result function works correctly"""
@@ -112,3 +114,14 @@ def test_write_truncated_sim_datafile_end_and_start():
             lines = f.readlines()
         assert lines[13].split()[0] == "5000"
         assert lines[-2].split()[0] == "9000"
+
+def test_process_slurm_file_base():
+    """
+    Test that the SLURM file base name is correctly extracted from a SLURM file.
+    """
+    slurm_file_base = get_slurm_file_base("a3fe/data/example_run_dir/input/run_somd.sh")
+    assert slurm_file_base == "a3fe/data/example_run_dir/input/somd-array-gpu-"
+
+    # Test alternative formatting
+    slurm_file_base = get_slurm_file_base("a3fe/data/alternative_input/alternative_run_somd.sh")
+    assert slurm_file_base == "a3fe/data/alternative_input/somd-array-gpu-"

docs/CHANGELOG.rst

@@ -2,7 +2,13 @@
 Change Log
 ===============
 
+0.1.2
+====================
+
+- Fixed bug in ``get_slurm_file_base`` which caused the function to fail to read the output name if an "=" instead of a space was used to separate the argument and value.
+
 v0.1.1
+====================
 
 - Ensured that ``simulation_runner`` objects only get pickled once they've been fully initialised. This avoids issues where an error occurs during initialisation and the object is pickled in an incomplete state. Addresses https://github.com/michellab/a3fe/issues/1.
 

pyproject.toml

@@ -40,7 +40,7 @@ dependencies = [
 "Documentation" = "https://a3fe.readthedocs.io/"
 
 [metadata]
-version = "0.1.1"
+version = "0.1.2"
 
 [project.optional-dependencies]
 test = [
@@ -97,7 +97,7 @@ distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 method = "git"  # <- The method name
 # Parameters to pass to the method:
 match = ["*"]
-default-tag = "0.1.1"
+default-tag = "0.1.2"
 
 [tool.versioningit.write]
 file = "a3fe/_version.py"