Merge pull request #290 from SCM-NV/cp2k_version

MAINT: Do not extract the CP2K version via `cp2k.popt --version`

src/qmflows/parsers/cp2KParser.py

@@ -32,7 +32,7 @@
 
 __all__ = ['readCp2KBasis', 'read_cp2k_coefficients', 'get_cp2k_freq',
            'read_cp2k_number_of_orbitals', 'read_cp2k_xyz', 'read_cp2k_table',
-           'read_cp2k_table_slc', 'get_cp2k_version', 'get_cp2k_version_run']
+           'read_cp2k_table_slc', 'get_cp2k_version']
 
 
 # Starting logger
@@ -97,11 +97,10 @@ def read_cp2k_coefficients(
 
     file_in = fnmatch.filter(os.listdir(plams_dir), '*in')[0]
     file_out = fnmatch.filter(os.listdir(plams_dir), '*out')[0]
-    file_run = fnmatch.filter(os.listdir(plams_dir), '*run')[0]
 
     path_in = plams_dir / file_in
     path_out = plams_dir / file_out
-    cp2k_version = get_cp2k_version_run(plams_dir / file_run)
+    cp2k_version = get_cp2k_version(plams_dir / file_out)
 
     orbitals_info = read_cp2k_number_of_orbitals(path_out)
     _, range_mos = read_mos_data_input(path_in)
@@ -677,50 +676,25 @@ def read_cp2k_pressure(
         return np.fromiter(islice(iterator, start, stop, step), dtype=dtype)
 
 
+PATTERN = re.compile(r"CP2K version ([0-9]+)\.([0-9]+)")
+
+
 def get_cp2k_version(out_file: PathLike) -> CP2KVersion:
     """Read the CP2K major and minor version from the passed .out file.
 
     Returns :code:`(0, 0)` if the versions cannot be identified.
     """
     with open(out_file, 'r') as f:
         for i in f:
-            if i.startswith(" CP2K| version string:"):
-                version_str = i.split()[-1]
-
-                # if an error is encoutered here then we must be dealing with
-                # a very old CP2K version; fall back to `major = 0` in such case
-                try:
-                    return CP2KVersion._make(int(i) for i in version_str.split("."))
-                except ValueError:
-                    pass
-    warnings.warn("Failed to identify the CP2K version", QMFlows_Warning, stacklevel=2)
+            i = i.strip()
+            if i.startswith("CP2K| version string:"):
+                match = PATTERN.search(i)
+                if match is None:
+                    continue
+                return CP2KVersion(int(match[1]), int(match[2]))
+
+    warnings.warn(
+        f"Failed extract the CP2K version from {os.fsdecode(out_file)!r}",
+        QMFlows_Warning, stacklevel=2,
+    )
     return CP2KVersion(0, 0)
-
-
-EXECUTABLE_PATTERN = re.compile(r"""(".+"|'.+'|\S+)\s+-i""")
-VERSION_PATTERN = re.compile(r"CP2K version (\d+).(\d+)")
-
-
-def get_cp2k_version_run(run_file: PathLike) -> CP2KVersion:
-    """Get the CP2K version using the PLAMS .run."""
-    # Extract the executable
-    with open(run_file, 'r') as f:
-        match = EXECUTABLE_PATTERN.search(f.read())
-    if match is None:
-        raise ValueError(f"Failed to extract the CP2K executable from {f.name!r}")
-    executable = match.groups()[0]
-
-    # Get the `--version` of the executable
-    try:
-        out = subprocess.run(
-            f"{executable} --version",
-            check=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding="utf8", shell=True
-        )
-    except subprocess.CalledProcessError as ex:
-        raise ValueError(f"Failed to execute `{executable} --version`:\n\n{ex.stderr}") from ex
-
-    # Parse the `--version` output
-    match = VERSION_PATTERN.search(out.stdout)
-    if match is None:
-        raise ValueError(f"Failed to parse the `{executable} --version` output:\n\n{out.stdout}")
-    return CP2KVersion._make(int(i) for i in match.groups())

test/test_cp2k_mock.py

@@ -12,7 +12,6 @@
 from qmflows.packages.cp2k_package import CP2K_Result
 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,
@@ -21,11 +20,6 @@
     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) -> Callable[..., CP2K_Result]:
     """Create a Result instance using a mocked runner."""
@@ -63,7 +57,6 @@ def test_deepcopy():
 
 # See https://github.com/SCM-NV/qmflows/issues/225
 @pytest.mark.xfail(raises=AssertionError)
-@pytest.mark.skipif(CP2K_VERSION >= (8, 2), reason="Requires CP2K < 8.2")
 @requires_cp2k
 def test_cp2k_singlepoint_mock(mocker: MockFixture):
     """Mock a call to CP2K."""

test/test_cp2k_parser.py

@@ -9,7 +9,7 @@
 import pytest
 from assertionlib import assertion
 
-from qmflows.parsers.cp2KParser import parse_cp2k_warnings, readCp2KBasis, get_cp2k_version_run
+from qmflows.parsers.cp2KParser import parse_cp2k_warnings, readCp2KBasis
 from qmflows.test_utils import PATH, requires_cp2k
 from qmflows.warnings_qmflows import QMFlows_Warning, cp2k_warnings
 from qmflows.common import AtomBasisKey
@@ -57,49 +57,3 @@ def test_raise(self, filename: str, lineno: int) -> None:
         pattern = r"Failed to parse the '.+' basis set on line {}".format(lineno)
         with pytest.raises(ValueError, match=pattern):
             readCp2KBasis(PATH / filename)
-
-
-@requires_cp2k
-class TestGetCP2KVersion:
-    @classmethod
-    def setup_class(cls) -> None:
-        """Add ``cp2k.popt`` to a space-containing directory and add it to ``$PATH``."""
-        cp2k_popt = shutil.which("cp2k.popt")
-        assert cp2k_popt is not None
-
-        os.mkdir(PATH / "test dir")
-        shutil.copy2(cp2k_popt, PATH / "test dir" / "cp2k.popt")
-
-    @classmethod
-    def teardown_class(cls) -> None:
-        """Restore the old ``$PATH`` environment variable."""
-        shutil.rmtree(PATH / "test dir")
-
-    PASS_DICT = {
-        "mpirun": "bin/mpirun cp2k.popt -i file.in -o file.out",
-        "srun": "srun cp2k.popt -i file.in -o file.out",
-        "none": "cp2k.popt -i file.in -o file.out",
-        "space": " cp2k.popt -i file.in -o file.out",
-        "single_quote": f"'{PATH}/test dir/cp2k.popt' -i file.in -o file.out",
-        "double_quote": f'"{PATH}/test dir/cp2k.popt" -i file.in -o file.out',
-    }
-
-    @pytest.mark.parametrize("name,txt", PASS_DICT.items(), ids=PASS_DICT)
-    def test_pass(self, name: str, txt: str, tmp_path: Path) -> None:
-        with open(tmp_path / f"{name}.run", "w") as f:
-            f.write(txt)
-        out = get_cp2k_version_run(tmp_path / f"{name}.run")
-        assertion.truth(out)
-
-    RAISE_DICT = {
-        "invalid_run": "cp2k.popt -j file.in -o file.out",
-        "invalid_exec": "cp2k.bob -i file.in -o file.out",
-        "invalid_exec_version": "python -i file.in -o file.out",
-    }
-
-    @pytest.mark.parametrize("name,txt", RAISE_DICT.items(), ids=RAISE_DICT)
-    def test_raise(self, name: str, txt: str, tmp_path: Path) -> None:
-        with open(tmp_path / f"{name}.run", "w") as f:
-            f.write(txt)
-        with pytest.raises(ValueError):
-            get_cp2k_version_run(tmp_path / f"{name}.run")