refactor mdrun (#158)

Co-authored-by: Brandon Duane Walker <[email protected]>

utils/mdrun-plugin/ict.yml → utils/molecular-dynamics/gromacs/mdrun-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: mdrun
 version: 0.1.0
-container: mdrun-plugin
+container: mdrun-tool
 entrypoint:
 title: mdrun
 description: Wrapper of the GROMACS mdrun module.
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/mdrun-plugin/pyproject.toml → utils/molecular-dynamics/gromacs/mdrun-tool/pyproject.toml

@@ -8,8 +8,7 @@ readme = "README.md"
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 typer = "^0.7.0"
-cwl-utils = "0.33"
-cwltool = "3.1.20240404144621"
+sophios = "0.1.1"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

utils/molecular-dynamics/gromacs/mdrun-tool/tests/test_mdrun.py

@@ -0,0 +1,39 @@
+"""Tests for mdrun."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_mdrun() -> None:
+    """Test mdrun."""
+    # Define paths and setup input properties
+    cwl_file_str = "mdrun_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+    file_path_str = "mdrun.tpr"
+    file_path = Path(__file__).resolve().parent / Path(file_path_str)
+
+    # Create the CWL step
+    mdrun_step = Step(clt_path=cwl_file)
+    mdrun_step.input_tpr_path = file_path
+    mdrun_step.output_crd_path = "system.gro"
+    mdrun_step.output_edr_path = "system.edr"
+    mdrun_step.output_log_path = "system.log"
+    mdrun_step.output_trr_path = "system.trr"
+    mdrun_step.output_xtc_path = "system.xtc"
+    mdrun_step.output_cpt_path = "system.cpt"
+    mdrun_step.output_dhdl_path = "system.xvg"
+
+    # Create the workflow and run it
+    steps = [mdrun_step]
+    filename = "mdrun_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # Define output directory and check for expected output
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.trr"))
+
+    assert (
+        files
+    ), f"The file 'system.trr' does not exist in any subdirectory of '{outdir}'."