refactor process-mdout

utils/molecular-dynamics/amber/process-mdout-tool/.gitattributes

@@ -0,0 +1 @@
+*.log filter=lfs diff=lfs merge=lfs -text

utils/process-mdout-plugin/ict.yml → utils/molecular-dynamics/amber/process-mdout-tool/ict.yml

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

utils/process-mdout-plugin/pyproject.toml → utils/molecular-dynamics/amber/process-mdout-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/amber/process-mdout-tool/tests/test_process_mdout.py

@@ -0,0 +1,30 @@
+"""Tests for process_mdout."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_process_mdout() -> None:
+    """Test process_mdout CWL."""
+    cwl_file_str = "process_mdout_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    input_log_path = Path(__file__).resolve().parent / Path("sander.heat.log")
+
+    process_mdout = Step(clt_path=cwl_file)
+    process_mdout.input_log_path = input_log_path
+    process_mdout.output_dat_path = "system.dat"
+
+    steps = [process_mdout]
+    filename = "process_mdout"
+    viz = Workflow(steps, filename)
+
+    viz.run()
+
+    outdir = Path("outdir")
+    output_files = list(outdir.rglob("system.dat"))
+
+    assert (
+        output_files
+    ), f"The file 'system.dat' does not exist in any subdirectory of '{outdir}'."