Merge pull request #281 from SCM-NV/cp2k_job

TST: Print the CP2K .out and .err files whenever a test job crashes

Author: BvB93

src/qmflows/packages/SCM.py

@@ -105,7 +105,7 @@ def __init__(self, settings: Optional[Settings],
                  dill_path: "None | str | os.PathLike[str]" = None,
                  plams_dir: "None | str | os.PathLike[str]" = None,
                  work_dir: "None | str | os.PathLike[str]" = None,
-                 status: str = 'done',
+                 status: str = 'successful',
                  warnings: Optional[WarnMap] = None) -> None:
         # Load available property parser from yaml file.
         super().__init__(settings, molecule, job_name, dill_path,
@@ -157,7 +157,7 @@ def __init__(self, settings: Optional[Settings],
                  dill_path: "None | str | os.PathLike[str]" = None,
                  plams_dir: "None | str | os.PathLike[str]" = None,
                  work_dir: "None | str | os.PathLike[str]" = None,
-                 status: str = 'done',
+                 status: str = 'successful',
                  warnings: Optional[WarnMap] = None) -> None:
         # Read available propiety parsers from a yaml file
         super().__init__(settings, molecule, job_name, dill_path,

src/qmflows/packages/packages.py

@@ -67,7 +67,7 @@ def __init__(self, settings: Optional[Settings],
                  dill_path: "None | str | os.PathLike[str]" = None,
                  plams_dir: "None | str | os.PathLike[str]" = None,
                  work_dir: "None | str | os.PathLike[str]" = None,
-                 status: str = 'done',
+                 status: str = 'successful',
                  warnings: Optional[WarnMap] = None) -> None:
         """Initialize a :class:`Result` instance.
 

src/qmflows/test_utils.py

@@ -6,6 +6,7 @@
 .. autosummary::
     fill_cp2k_defaults
     get_mm_settings
+    validate_status
     PATH
     PATH_MOLECULES
     HAS_RDKIT
@@ -18,6 +19,7 @@
 ---
 .. autofunction:: fill_cp2k_defaults
 .. autofunction:: get_mm_settings
+.. autofunction:: validate_status
 .. autodata:: PATH
     :annotation: : pathlib.Path
 .. autodata:: PATH_MOLECULES
@@ -32,19 +34,22 @@
 """
 
 import os
+import textwrap
 from pathlib import Path
 
 import pytest
 from distutils.spawn import find_executable
 
 from .settings import Settings
 from .warnings_qmflows import Assertion_Warning
+from .packages import Result
 
 __all__ = [
     'get_mm_settings',
     'PATH',
     'PATH_MOLECULES',
     'Assertion_Warning',
+    'validate_status',
     'HAS_RDKIT',
     'requires_cp2k',
     'requires_orca'
@@ -126,6 +131,62 @@ def get_mm_settings() -> Settings:
     return s
 
 
+def _read_result_file(result: Result, extension: str, max_line: int = 100) -> "None | str":
+    """Find and read the first file in ``result`` with the provided file extension.
+
+    Returns ``None`` if no such file can be found.
+    """
+    root = result.archive["plams_dir"]
+    if root is None:
+        return None
+
+    iterator = (os.path.join(root, i) for i in os.listdir(root)
+                if os.path.splitext(i)[1] == extension)
+    for i in iterator:
+        with open(i, "r") as f:
+            ret_list = f.readlines()
+            ret = "..." if len(ret_list) > max_line else ""
+            ret += "".join(ret_list[-max_line:])
+            return textwrap.indent(ret, 4 * " ")
+    else:
+        return None
+
+
+def validate_status(result: Result, *, print_out: bool = True, print_err: bool = True) -> None:
+    """Validate the status of the ``qmflows.Result`` object is set to ``"successful"``.
+
+    Parameters
+    ----------
+    result : qmflows.Result
+        The to-be validated ``Result`` object.
+    print_out : bool
+        Whether to included the content of the ``Result`` objects' .out file in the exception.
+    print_err : bool
+        Whether to included the content of the ``Result`` objects' .err file in the exception.
+
+    Raises
+    ------
+    AssertionError
+        Raised when :code:`result.status != "successful"`.
+
+    """
+    if result.status == "successful":
+        return None
+
+    indent = 4 * " "
+    msg = f"Unexpected {result.job_name} status: {result.status!r}"
+
+    if print_out:
+        out = _read_result_file(result, ".out")
+        if out is not None:
+            msg += f"\n\nout_file:\n{out}"
+    if print_err:
+        err = _read_result_file(result, ".err")
+        if err is not None:
+            msg += f"\n\nerr_file:\n{err}"
+    raise AssertionError(msg)
+
+
 def _has_exec(executable: str) -> bool:
     """Check if the passed executable is installed."""
     path = find_executable(executable)

test/test_cp2k_mm_mock.py

@@ -2,6 +2,7 @@
 
 import os
 import shutil
+from typing import Callable
 
 import numpy as np
 from assertionlib import assertion
@@ -11,7 +12,7 @@
 from qmflows import Settings, cp2k_mm, singlepoint, geometry, freq, md, cell_opt
 from qmflows.utils import InitRestart
 from qmflows.packages.cp2k_mm import CP2KMM_Result
-from qmflows.test_utils import get_mm_settings, PATH, PATH_MOLECULES
+from qmflows.test_utils import get_mm_settings, validate_status, PATH, PATH_MOLECULES
 
 MOL = Molecule(PATH_MOLECULES / 'Cd68Cl26Se55__26_acetate.xyz')
 WORKDIR = PATH / 'output_cp2k_mm'
@@ -46,7 +47,7 @@ def overlap_coords(xyz1: np.ndarray, xyz2: np.ndarray) -> np.ndarray:
 
 def mock_runner(mocker_instance: MockFixture,
                 settings: Settings = SETTINGS,
-                jobname: str = 'job') -> CP2KMM_Result:
+                jobname: str = 'job') -> Callable[..., CP2KMM_Result]:
     """Create a Result instance using a mocked runner."""
     run_mocked = mocker_instance.patch("qmflows.run")
 
@@ -72,7 +73,7 @@ def test_cp2k_singlepoint_mock(mocker: MockFixture) -> None:
     run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_sp")
 
     result = run_mocked(job)
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     # Compare energies
     ref = -15.4431781758
@@ -88,7 +89,7 @@ def test_c2pk_opt_mock(mocker: MockFixture) -> None:
     run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_opt")
 
     result = run_mocked(job)
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     # Compare energies
     ref = -16.865587192150834
@@ -114,7 +115,7 @@ def test_c2pk_freq_mock(mocker: MockFixture) -> None:
     run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_freq")
 
     result = run_mocked(job)
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     freqs = result.frequencies
     freqs_ref = np.load(PATH / 'Cd68Cl26Se55__26_acetate.freq.npy')
@@ -136,7 +137,7 @@ def test_c2pk_md_mock(mocker: MockFixture) -> None:
     run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_md")
 
     result = run_mocked(job)
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     assertion.isfile(result.results['cp2k-1_1000.restart'])
 
@@ -172,7 +173,7 @@ def test_c2pk_cell_opt_mock(mocker: MockFixture) -> None:
     job = cp2k_mm(s, mol)
     run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_cell_opt")
     result = run_mocked(job)
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     ref_volume = np.load(PATH / 'volume.npy')
     ref_coordinates = np.load(PATH / 'coordinates.npy')
@@ -191,6 +192,7 @@ def test_c2pk_npt_mock(mocker: MockFixture) -> None:
     job = cp2k_mm(s, None)
     run_mocked = mock_runner(mocker, settings=s, jobname="cp2k_mm_npt")
     result = run_mocked(job)
+    validate_status(result)
 
     ref_pressure = np.load(PATH / 'pressure.npy')
     np.testing.assert_allclose(result.pressure, ref_pressure)

test/test_cp2k_mock.py

@@ -1,5 +1,6 @@
 """Mock CP2K funcionality."""
 import copy
+from typing import Callable
 
 import pytest
 import numpy as np
@@ -9,25 +10,34 @@
 
 from qmflows import cp2k, templates
 from qmflows.packages.cp2k_package import CP2K_Result
-from qmflows.test_utils import PATH, PATH_MOLECULES, fill_cp2k_defaults, requires_cp2k
 from qmflows.utils import init_restart
 from qmflows.common import CP2KVersion
 from qmflows.parsers.cp2KParser import get_cp2k_version_run
+from qmflows.test_utils import (
+    PATH,
+    PATH_MOLECULES,
+    fill_cp2k_defaults,
+    requires_cp2k,
+    validate_status,
+)
 
 try:
     CP2K_VERSION = get_cp2k_version_run("cp2k.popt")
 except Exception:
     CP2K_VERSION = CP2KVersion(0, 0)
 
 
-def mock_runner(mocker_instance, jobname: str) -> CP2K_Result:
+def mock_runner(mocker_instance, jobname: str) -> Callable[..., CP2K_Result]:
     """Create a Result instance using a mocked runner."""
     run_mocked = mocker_instance.patch("qmflows.run")
-    dill_path = WORKDIR / jobname / f"{jobname}.dill"
-    plams_dir = WORKDIR / jobname
-    run_mocked.return_value = CP2K_Result(templates.geometry, ETHYLENE, jobname,
-                                          dill_path=dill_path, plams_dir=plams_dir)
-
+    run_mocked.return_value = CP2K_Result(
+        templates.geometry,
+        ETHYLENE,
+        jobname,
+        status="successful",
+        dill_path=WORKDIR / jobname / f"{jobname}.dill",
+        plams_dir=WORKDIR / jobname,
+    )
     return run_mocked
 
 # module constants
@@ -71,6 +81,7 @@ def test_cp2k_singlepoint_mock(mocker: MockFixture):
     jobname = "cp2k_job"
     run_mocked = mock_runner(mocker, jobname)
     rs = run_mocked(job)
+    validate_status(rs)
 
     # electronic energy
     assertion.isfinite(rs.energy)
@@ -91,6 +102,8 @@ def test_c2pk_opt_mock(mocker: MockFixture):
 
     job = cp2k(s, ETHYLENE, job_name=jobname)
     rs = run_mocked(job)
+    validate_status(rs)
+
     # check the optimized geometry
     mol = rs.geometry
     assertion.len_eq(mol, 6)
@@ -110,6 +123,7 @@ def test_c2pk_freq_mock(mocker: MockFixture):
     run_mocked = mock_runner(mocker, jobname)
     job = cp2k(s, ETHYLENE, job_name=jobname)
     rs = run_mocked(job)
+    validate_status(rs)
 
     # check properties
     assertion.isfinite(rs.enthalpy)
@@ -123,5 +137,6 @@ def test_dir(mocker: MockFixture) -> None:
 
     job = cp2k(s, ETHYLENE, job_name=jobname)
     r = run_mocked(job)
+    validate_status(r)
 
     assertion.issubset(CP2K_Result.prop_mapping.keys(), dir(r))

test/test_using_plams/test_cp2k.py

@@ -9,7 +9,13 @@
 from scm.plams import Molecule
 
 from qmflows import Settings, cp2k, run, templates
-from qmflows.test_utils import PATH, PATH_MOLECULES, fill_cp2k_defaults, requires_cp2k
+from qmflows.test_utils import (
+    PATH,
+    PATH_MOLECULES,
+    fill_cp2k_defaults,
+    requires_cp2k,
+    validate_status,
+)
 
 
 @requires_cp2k
@@ -28,7 +34,7 @@ def test_cp2k_opt(tmp_path: Path) -> None:
     job = cp2k(s, water)
     result = run(job, path=tmp_path, folder="test_cp2k_opt")
 
-    assertion.eq(result.status, "successful")
+    validate_status(result)
     assertion.isinstance(result.molecule, Molecule)
 
 
@@ -57,7 +63,7 @@ def test_cp2k_singlepoint(tmp_path: Path, mo_index_range: str) -> None:
         key = f"test_using_plams/test_cp2k/test_cp2k_singlepoint/{mo_index_range}"
         ref = f[key][...].view(np.recarray)
 
-    assertion.eq(result.status, "successful")
+    validate_status(result)
     orbitals = result.orbitals
     assertion.is_not(orbitals, None)
     np.testing.assert_allclose(orbitals.eigenvalues, ref.eigenvalues)
@@ -74,7 +80,7 @@ def test_cp2k_freq(tmp_path: Path) -> None:
     job = cp2k(s, mol)
     result = run(job, path=tmp_path, folder="test_cp2k_freq")
 
-    assertion.eq(result.status, "successful")
+    validate_status(result)
     assertion.isclose(result.free_energy, -10801.971213467135)
     assertion.isclose(result.enthalpy, -10790.423489727531)
     np.testing.assert_allclose(result.frequencies, [1622.952012, 3366.668885, 3513.89377])

test/test_using_plams/test_cp2k_mm.py

@@ -6,7 +6,7 @@
 from scm.plams import Molecule
 
 from qmflows import Settings, run, cp2k_mm, singlepoint, geometry, freq, md, cell_opt
-from qmflows.test_utils import get_mm_settings, PATH, PATH_MOLECULES, requires_cp2k
+from qmflows.test_utils import get_mm_settings, validate_status, PATH, PATH_MOLECULES, requires_cp2k
 
 MOL = Molecule(PATH_MOLECULES / 'Cd68Cl26Se55__26_acetate.xyz')
 
@@ -41,7 +41,7 @@ def test_singlepoint(tmp_path: Path) -> None:
 
     job = cp2k_mm(settings=s, mol=MOL, job_name='cp2k_mm_sp')
     result = run(job, path=tmp_path, folder="test_singlepoint")
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     # Compare energies
     ref = -15.4431781758
@@ -57,7 +57,7 @@ def test_geometry(tmp_path: Path) -> None:
 
     job = cp2k_mm(settings=s, mol=MOL, job_name='cp2k_mm_opt')
     result = run(job, path=tmp_path, folder="test_geometry")
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     # Compare energies
     ref = -16.865587192150834
@@ -84,7 +84,7 @@ def test_freq(tmp_path: Path) -> None:
 
     job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_freq')
     result = run(job, path=tmp_path, folder="test_freq")
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     freqs = result.frequencies
     freqs_ref = np.load(PATH / 'Cd68Cl26Se55__26_acetate.freq.npy')
@@ -109,7 +109,7 @@ def test_md(tmp_path: Path) -> None:
 
     job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_md')
     result = run(job, path=tmp_path, folder="test_md")
-    assertion.eq(result.status, 'successful')
+    validate_status(result)
 
     plams_results = result.results
     assertion.isfile(plams_results['cp2k-1_1000.restart'])
@@ -147,4 +147,4 @@ def test_c2pk_cell_opt(tmp_path: Path) -> None:
 
     job = cp2k_mm(settings=s, mol=mol, job_name='cp2k_mm_cell_opt')
     result = run(job, path=tmp_path, folder="test_c2pk_cell_opt")
-    assertion.eq(result.status, 'successful')
+    validate_status(result)