bugfix replace-output-directory

a3fe/_version.py

@@ -1 +1 @@
-__version__ = "0.3.1"
+__version__ = "0.3.2"

a3fe/run/leg.py

@@ -259,11 +259,12 @@ def setup(
                     relative_simulation_cost=self.relative_simulation_cost,
                     ensemble_size=self.ensemble_size,
                     lambda_values=cfg.lambda_values[self.leg_type][stage_type],
-                    base_dir=self.stage_input_dirs[stage_type].replace("/input", ""),
+                    base_dir=self.stage_input_dirs[stage_type].rsplit("/input", 1)[0],
                     input_dir=self.stage_input_dirs[stage_type],
-                    output_dir=self.stage_input_dirs[stage_type].replace(
-                        "input", "output"
-                    ),
+                    output_dir="/".join(
+                        self.stage_input_dirs[stage_type].split("/")[:-1]
+                    )
+                    + "/output",
                     stream_log_level=self.stream_log_level,
                 )
             )

a3fe/tests/test_run.py

@@ -12,6 +12,7 @@
 import BioSimSpace.Sandpit.Exscientia as BSS
 import numpy as np
 import pytest
+import shutil
 
 import a3fe as a3
 from a3fe.analyse.detect_equil import dummy_check_equil_multiwindow
@@ -348,6 +349,38 @@ def setup_calc(mock_run_process):
             setup_calc.setup(bound_leg_sysprep_config=cfg, free_leg_sysprep_config=cfg)
             yield setup_calc
 
+    @pytest.fixture
+    def setup_calc_with_input_path(self, setup_calc):
+        """Based on the setup_calc fixture,
+        create a new calculation with a temporary directory containing "input"."""
+        temp_parent_dir = "input_temp_a3fe"
+        os.makedirs(temp_parent_dir, exist_ok=True)
+
+        with TemporaryDirectory(prefix="temp_input_", dir=temp_parent_dir) as dirname:
+            # Copy the example input directory to the temporary directory
+            subprocess.run(
+                [
+                    "cp",
+                    "-r",
+                    "a3fe/data/example_run_dir/input",
+                    f"{dirname}/input",
+                ]
+            )
+
+            calc = a3.Calculation(
+                base_dir=dirname,
+                input_dir=f"{dirname}/input",
+                ensemble_size=1,
+                stream_log_level=logging.CRITICAL,
+            )
+            cfg = SystemPreparationConfig()
+            cfg.slurm = False
+            calc.setup(bound_leg_sysprep_config=cfg, free_leg_sysprep_config=cfg)
+            yield calc
+
+        if os.path.exists(temp_parent_dir):
+            shutil.rmtree(temp_parent_dir, ignore_errors=True)
+
     def test_setup_calc_overall(self, setup_calc, mock_run_process):
         """Test that setting up the calculation was successful at a high level."""
         assert setup_calc.setup_complete
@@ -463,6 +496,17 @@ def test_setup_calc_sims(self, setup_calc):
                         base_dir_files = set(os.listdir(sim.base_dir))
                         assert base_dir_files == expected_base_files
 
+    def test_stage_output_path_replacement(self, setup_calc_with_input_path):
+        """Test that stage output paths are correctly derived from input paths by only
+        replacing the last 'input' with 'output'."""
+        for leg in setup_calc_with_input_path.legs:
+            for stage in leg.stages:
+                if leg.leg_type == a3.LegType.BOUND:
+                    expected_output_dir = "output".join(
+                        stage.input_dir.rsplit("input", 1)
+                    )
+                    assert stage.output_dir == expected_output_dir
+
 
 ######################## Tests Requiring SLURM ########################
 

docs/CHANGELOG.rst

@@ -5,6 +5,7 @@ Change Log
 0.3.2
 ====================
 - Fix bug which caused somd.rst7 files in the ensemble equilibration directories to be incorrectly numbered in some cases.
+- Fix bug which caused the output directory to be incorrectly replaced with "output" in some cases.
 
 0.3.1
 ====================