refactor zip_top

utils/pre-process/structure-change/.gitattributes

@@ -0,0 +1,2 @@
+*.top filter=lfs diff=lfs merge=lfs -text
+*.itp filter=lfs diff=lfs merge=lfs -text

utils/zip-top-plugin/ict.yml → utils/pre-process/structure-change/zip-top-tool/ict.yml

@@ -1,12 +1,12 @@
 specVersion: "0.1.0"
 name: zip_top
 version: 0.1.0
-container: zip-top-plugin
+container: zip-top-tool
 entrypoint:
 title: zip_top
 description: zips a gromacs topology TOP file (and/or itp include file).
-author: Data Scientist
-contact: [email protected]
+author: Brandon Walker, Nazanin Donyapour
+contact: [email protected], [email protected]
 repository:
 documentation:
 citation:

utils/zip-top-plugin/pyproject.toml → utils/pre-process/structure-change/zip-top-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/pre-process/structure-change/zip-top-tool/tests/test_zip_top.py

@@ -0,0 +1,35 @@
+"""Tests for zip_top."""
+from pathlib import Path
+
+from sophios.api.pythonapi import Step
+from sophios.api.pythonapi import Workflow
+
+
+def test_zip_top() -> None:
+    """Test zip topology CWL."""
+    input_top_path = Path(__file__).resolve().parent / Path(
+        "ALL.Ala115Pro_step8_gio_gio.top",
+    )
+    input_itp_path = Path(__file__).resolve().parent / Path(
+        "ALL.Ala115Pro_step4_p2g_p2g_Protein_chain_A.itp",
+    )
+    cwl_file_str = "zip_top_0@[email protected]"
+    cwl_file = Path(__file__).resolve().parent.parent / Path(cwl_file_str)
+
+    zip_top = Step(clt_path=cwl_file)
+    zip_top.input_top_path = input_top_path
+    zip_top.input_itp_path = input_itp_path
+    zip_top.output_top_zip_path = "system.zip"
+
+    steps = [zip_top]
+    filename = "zip_top"
+    viz = Workflow(steps, filename)
+
+    viz.run()
+
+    outdir = Path("outdir")
+    files = list(outdir.rglob("system.zip"))
+
+    assert (
+        files
+    ), f"The file 'system.zip' does not exist in any subdirectory of '{outdir}'."