refactor sander_mdru

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

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

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

@@ -7,9 +7,7 @@ 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/amber/sander-mdrun-tool/tests/test_sander_mdrun.py

@@ -0,0 +1,39 @@
+"""Tests for sander_mdrun."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_sander_mdrun() -> None:
+    """Test sander_mdrun CWL."""
+    cwl_file_str = "sander_mdrun.cwl"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    input_top_path = Path(__file__).resolve().parent / Path("cln025.prmtop")
+    input_crd_path = Path(__file__).resolve().parent / Path("cln025.inpcrd")
+    input_mdin_path = Path(__file__).resolve().parent / Path("npt.mdin")
+
+    sander_mdrun = Step(clt_path=cwl_file)
+    sander_mdrun.input_top_path = input_top_path
+    sander_mdrun.input_crd_path = input_crd_path
+    sander_mdrun.input_mdin_path = input_mdin_path
+    sander_mdrun.output_log_path = "system.log"
+    sander_mdrun.output_traj_path = "system.trj"
+    sander_mdrun.output_rst_path = "system.rst"
+    sander_mdrun.output_cpout_path = "system.cpout"
+    sander_mdrun.output_cprst_path = "system.cprst"
+    sander_mdrun.output_mdinfo_path = "system.mdinfo"
+
+    steps = [sander_mdrun]
+    filename = "sander_mdrun"
+    viz = Workflow(steps, filename)
+
+    viz.run()
+
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.rst"))
+
+    assert (
+        files
+    ), f"The file 'system.rst' does not exist in any subdirectory of '{outdir}'."