refactor grompp (#157)

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

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

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

utils/grompp-plugin/pyproject.toml → utils/molecular-dynamics/gromacs/grompp-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/grompp-tool/tests/test_grompp.py

@@ -0,0 +1,35 @@
+"""Tests for the GROMACS grompp tool."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_grompp_cwl() -> None:
+    """Tests grompp.cwl."""
+    # Define paths and setup input properties
+    cwl_file_str = "grompp_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    input_crd_path = Path(__file__).resolve().parent / Path("grompp.gro")
+    input_top_zip_path = Path(__file__).resolve().parent / Path("grompp.zip")
+
+    # Create the CWL step
+    grompp_step = Step(clt_path=cwl_file)
+    grompp_step.input_crd_path = input_crd_path
+    grompp_step.input_top_zip_path = input_top_zip_path
+    grompp_step.output_tpr_path = "system.tpr"
+
+    # Create the workflow and run it
+    steps = [grompp_step]
+    filename = "grompp_workflow"
+    workflow = Workflow(steps, filename)
+    workflow.run()
+
+    # Define output directory and check for expected output
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.tpr"))
+
+    assert (
+        files
+    ), f"The file 'system.tpr' does not exist in any subdirectory of '{outdir}'."