Add tests for CLI yaml summary

tests/test_geomopt_cli.py

@@ -5,6 +5,7 @@
 from ase.io import read
 import pytest
 from typer.testing import CliRunner
+import yaml
 
 from janus_core.cli import app
 from tests.utils import read_atoms
@@ -14,17 +15,19 @@
 runner = CliRunner()
 
 
-def test_geomopt_help():
+def test_help():
     """Test calling `janus geomopt --help`."""
     result = runner.invoke(app, ["geomopt", "--help"])
     assert result.exit_code == 0
     # Command is returned as "root"
     assert "Usage: root geomopt [OPTIONS]" in result.stdout
 
 
-def test_geomopt():
+def test_geomopt(tmp_path):
     """Test geomopt calculation."""
     results_path = Path("./NaCl-opt.xyz").absolute()
+    summary_path = tmp_path / "summary.yml"
+
     assert not results_path.exists()
 
     result = runner.invoke(
@@ -35,16 +38,20 @@ def test_geomopt():
             DATA_PATH / "NaCl.cif",
             "--max-force",
             "0.2",
+            "--summary",
+            summary_path,
         ],
     )
 
     read_atoms(results_path)
     assert result.exit_code == 0
 
 
-def test_geomopt_log(tmp_path, caplog):
+def test_log(tmp_path, caplog):
     """Test log correctly written for geomopt."""
     results_path = tmp_path / "NaCl-opt.xyz"
+    log_path = tmp_path / "test.log"
+    summary_path = tmp_path / "summary.yml"
 
     with caplog.at_level("INFO", logger="janus_core.geom_opt"):
         result = runner.invoke(
@@ -56,18 +63,21 @@ def test_geomopt_log(tmp_path, caplog):
                 "--out",
                 results_path,
                 "--log",
-                f"{tmp_path}/test.log",
+                log_path,
+                "--summary",
+                summary_path,
             ],
         )
         assert result.exit_code == 0
         assert "Starting geometry optimization" in caplog.text
         assert "Using filter" not in caplog.text
 
 
-def test_geomopt_traj(tmp_path):
+def test_traj(tmp_path):
     """Test trajectory correctly written for geomopt."""
     results_path = tmp_path / "NaCl-opt.xyz"
     traj_path = f"{tmp_path}/test.xyz"
+    summary_path = tmp_path / "summary.yml"
 
     result = runner.invoke(
         app,
@@ -79,6 +89,8 @@ def test_geomopt_traj(tmp_path):
             results_path,
             "--traj",
             traj_path,
+            "--summary",
+            summary_path,
         ],
     )
     assert result.exit_code == 0
@@ -89,6 +101,7 @@ def test_geomopt_traj(tmp_path):
 def test_fully_opt(tmp_path, caplog):
     """Test passing --fully-opt without --vectors-only"""
     results_path = tmp_path / "NaCl-opt.xyz"
+    summary_path = tmp_path / "summary.yml"
 
     with caplog.at_level("INFO", logger="janus_core.geom_opt"):
         result = runner.invoke(
@@ -100,6 +113,8 @@ def test_fully_opt(tmp_path, caplog):
                 "--out",
                 results_path,
                 "--fully-opt",
+                "--summary",
+                summary_path,
             ],
         )
         assert result.exit_code == 0
@@ -114,6 +129,9 @@ def test_fully_opt(tmp_path, caplog):
 def test_fully_opt_and_vectors(tmp_path, caplog):
     """Test passing --fully-opt with --vectors-only."""
     results_path = tmp_path / "NaCl-opt.xyz"
+    log_path = tmp_path / "test.log"
+    summary_path = tmp_path / "summary.yml"
+
     with caplog.at_level("INFO", logger="janus_core.geom_opt"):
         result = runner.invoke(
             app,
@@ -126,7 +144,9 @@ def test_fully_opt_and_vectors(tmp_path, caplog):
                 "--out",
                 results_path,
                 "--log",
-                f"{tmp_path}/test.log",
+                log_path,
+                "--summary",
+                summary_path,
             ],
         )
         assert result.exit_code == 0
@@ -141,6 +161,8 @@ def test_fully_opt_and_vectors(tmp_path, caplog):
 def test_vectors_not_fully_opt(tmp_path, caplog):
     """Test passing --vectors-only without --fully-opt."""
     results_path = tmp_path / "NaCl-opt.xyz"
+    summary_path = tmp_path / "summary.yml"
+
     with caplog.at_level("INFO", logger="janus_core.geom_opt"):
         result = runner.invoke(
             app,
@@ -151,15 +173,19 @@ def test_vectors_not_fully_opt(tmp_path, caplog):
                 "--out",
                 results_path,
                 "--vectors-only",
+                "--summary",
+                summary_path,
             ],
         )
         assert result.exit_code == 0
         assert "hydrostatic_strain: True" in caplog.text
 
 
-def duplicate_traj(tmp_path):
+def test_duplicate_traj(tmp_path):
     """Test trajectory file cannot be not passed via traj_kwargs."""
     traj_path = tmp_path / "NaCl-traj.xyz"
+    summary_path = tmp_path / "summary.yml"
+
     result = runner.invoke(
         app,
         [
@@ -168,6 +194,8 @@ def duplicate_traj(tmp_path):
             DATA_PATH / "NaCl.cif",
             "--opt-kwargs",
             f"{{'trajectory': '{str(traj_path)}'}}",
+            "--summary",
+            summary_path,
         ],
     )
     assert result.exit_code == 1
@@ -179,6 +207,7 @@ def test_restart(tmp_path):
     data_path = DATA_PATH / "NaCl-deformed.cif"
     restart_path = tmp_path / "NaCl-res.pkl"
     results_path = tmp_path / "NaCl-opt.xyz"
+    summary_path = tmp_path / "summary.yml"
 
     result = runner.invoke(
         app,
@@ -192,6 +221,8 @@ def test_restart(tmp_path):
             f"{{'restart': '{str(restart_path)}'}}",
             "--steps",
             2,
+            "--summary",
+            summary_path,
         ],
     )
     assert result.exit_code == 0
@@ -210,9 +241,46 @@ def test_restart(tmp_path):
             f"{{'restart': '{str(restart_path)}'}}",
             "--steps",
             2,
+            "--summary",
+            summary_path,
         ],
     )
     assert result.exit_code == 0
     atoms = read(results_path)
     final_energy = atoms.get_potential_energy()
     assert final_energy < intermediate_energy
+
+
+def test_summary(tmp_path):
+    """Test summary file can be read correctly."""
+    results_path = tmp_path / "NaCl-results.xyz"
+    summary_path = tmp_path / "summary.yml"
+
+    result = runner.invoke(
+        app,
+        [
+            "geomopt",
+            "--struct",
+            DATA_PATH / "NaCl.cif",
+            "--out",
+            results_path,
+            "--summary",
+            summary_path,
+        ],
+    )
+
+    assert result.exit_code == 0
+
+    # Read geomopt summary file
+    with open(summary_path, encoding="utf8") as file:
+        md_summary = yaml.safe_load(file)
+
+    assert "command" in md_summary[0]
+    assert "janus geomopt" in md_summary[0]["command"]
+    assert "start_time" in md_summary[1]
+    assert "end_time" in md_summary[3]
+
+    assert "inputs" in md_summary[2]
+    assert "opt_kwargs" in md_summary[2]["inputs"]
+    assert "struct" in md_summary[2]["inputs"]
+    assert "n_atoms" in md_summary[2]["inputs"]["struct"]

tests/test_md_cli.py

@@ -67,7 +67,7 @@ def test_md(ensemble, tmp_path):
     assert isinstance(atoms, Atoms)
 
 
-def test_md_log(tmp_path, caplog):
+def test_log(tmp_path, caplog):
     """Test log correctly written for MD."""
     file_prefix = tmp_path / "nvt-T300"
     stats_path = tmp_path / "nvt-T300-stats.dat"
@@ -225,6 +225,7 @@ def test_summary(tmp_path):
         summary = yaml.safe_load(file)
 
     assert "command" in summary[0]
+    assert "janus md" in summary[0]["command"]
     assert "start_time" in summary[1]
     assert "inputs" in summary[2]
     assert "end_time" in summary[3]