add tests for inpt rewrite

.gitignore

@@ -771,3 +771,5 @@ ex0-*/
 al-eos-sparc.traj
 */ex1-sparc/
 examples/ex1-ase/
+/SPARC-master/
+/master.zip

sparc/io.py

@@ -691,7 +691,7 @@ def write_ion(filename, atoms, **kwargs):
     """
     label = Path(filename).with_suffix("").name
     parent_dir = Path(filename).parent
-    sb = SparcBundle(directory=parent_dir, label=label)
+    sb = SparcBundle(directory=parent_dir, label=label, mode="w")
     sb._write_ion_and_inpt(atoms, **kwargs)
     return atoms
 

tests/test_read_all_examples.py

@@ -6,11 +6,16 @@
 The ref
 """
 import pytest
+import numpy as np
 from pathlib import Path
 import os
 import tempfile
 import shutil
 
+skipped_names = ["Si2_domain_paral", "Si2_kpt_paral",
+                 "SiH4", "SiH4_quick",
+                 "H2O_sheet_quick", "H2O_sheet",
+                 "CdS_bandstruct"]
 
 def test_read_all_tests():
     """Search all .inpt files within the tests dir."""
@@ -24,6 +29,7 @@ def test_read_all_tests():
         pytest.skip(allow_module_level=True)
 
     tests_dir = Path(tests_dir)
+    failed_counts = 0
     for inpt_file in tests_dir.glob("**/*.inpt"):
         workdir = inpt_file.parent
         parent_name = inpt_file.parents[1].name
@@ -45,3 +51,58 @@ def test_read_all_tests():
             except Exception as e:
                 print("Failed: ", parent_name, workdir)
                 print("\t: Error is ", e)
+                failed_counts += 1
+    if failed_counts > 0:
+        raise RuntimeError("More than 1 test in output read test failed")
+
+def test_write_all_inputs():
+    """Search all .inpt files within the tests dir."""
+
+    from sparc.io import read_sparc, read_ion, write_ion
+    from sparc.sparc_parsers.inpt import _read_inpt
+
+    # Skipped tests are to avoid unwanted keywords
+    tests_dir = os.environ.get("SPARC_TESTS_DIR", "")
+    failed_counts = 0
+    print(f"Current test dir is {tests_dir}")
+    if len(tests_dir) == 0:
+        pytest.skip(allow_module_level=True)
+
+    tests_dir = Path(tests_dir)
+    for inpt_file in tests_dir.glob("**/*.inpt"):
+        workdir = inpt_file.parent
+        parent_name = inpt_file.parents[1].name
+        ion_file = inpt_file.with_suffix(".ion")
+        if parent_name in skipped_names:
+            continue
+        with tempfile.TemporaryDirectory() as tmpdir:
+            tmpdir = Path(tmpdir)
+            origin_atoms = read_ion(ion_file)
+            origin_inpt_dict = _read_inpt(inpt_file)
+            for key in ["CELL", "LATVEC_SCALE", "LATVEC", "BC"]:
+                origin_inpt_dict["inpt"]["params"].pop(key, None)
+            # Re-write the ion and inpt files
+            try:
+                write_ion(tmpdir / "test.ion", origin_atoms, **origin_inpt_dict["inpt"]["params"])
+                new_atoms = read_ion(tmpdir / "test.ion")
+                new_inpt_dict = _read_inpt(tmpdir / "test.inpt")
+                assert np.all(origin_atoms.pbc == new_atoms.pbc)
+                for key in origin_inpt_dict["inpt"]["params"].keys():
+                    origin_val = origin_inpt_dict["inpt"]["params"][key]
+                    new_val = new_inpt_dict["inpt"]["params"][key]
+                    if isinstance(origin_val, (int, bool)):
+                        assert origin_val == new_val
+                    elif isinstance(origin_val, float):
+                        assert np.isclose(origin_val, new_val, 1e-6)
+                    elif isinstance(origin_val, str):
+                        assert origin_val == new_val
+                    # Vector types can be list compared
+                    elif isinstance(origin_val, (list, np.ndarray)):
+                        assert np.all(origin_val == new_val)
+
+            except Exception as e:
+                print("Failed: ", parent_name, workdir)
+                print("\t: Error is ", e)
+                failed_counts += 1
+    if failed_counts > 0:
+        raise RuntimeError("More than 1 test in inpt write test failed")