TST: Redirect test stdout to the qmflows logger and re-enable sphinx tests

conftest.py

@@ -1,12 +1,19 @@
 """A pytest ``conftest.py`` file."""
 
+import os
 import sys
 import types
+import tempfile
 import importlib
+import contextlib
 from typing import Generator
 from pathlib import Path
 
 import pytest
+from scm.plams import config
+
+from qmflows import InitRestart, logger
+from qmflows._logger import stdout_handler
 
 _ROOT = Path("src") / "qmflows"
 _collect_ignore = [
@@ -54,3 +61,29 @@ def reload_qmflows() -> Generator[None, None, None]:
         _del_all_attr(module)
 
     importlib.import_module("qmflows")
+
+
+@pytest.fixture(autouse=True, scope="session")
+def configure_plams_logger() -> "Generator[None, None, None]":
+    """Remove the date/time prefix from the PLAMS logging output."""
+    # Ensure the plams.config dict is populated by firing up plams.init once
+    with open(os.devnull, "w") as f1, tempfile.TemporaryDirectory() as f2:
+        with contextlib.redirect_stdout(f1), InitRestart(f2):
+            pass
+
+    assert "log" in config
+    log_backup = config.log.copy()
+    config.log.time = False
+    config.log.date = False
+
+    yield None
+    config.log = log_backup
+
+
+@pytest.fixture(autouse=True, scope="session")
+def prepare_logger() -> "Generator[None, None, None]":
+    """Remove logging output to the stdout stream while running tests."""
+    assert stdout_handler in logger.handlers
+    logger.removeHandler(stdout_handler)
+    yield None
+    logger.addHandler(stdout_handler)

docs/_packages.rst

@@ -117,8 +117,8 @@ API
 
 |
 
-.. autofunction:: qmflows.packages.adf
-.. autofunction:: qmflows.packages.dftb
-.. autofunction:: qmflows.packages.cp2k
-.. autofunction:: qmflows.packages.cp2k_mm
-.. autofunction:: qmflows.packages.orca
+.. autofunction:: qmflows.adf
+.. autofunction:: qmflows.dftb
+.. autofunction:: qmflows.cp2k
+.. autofunction:: qmflows.cp2k_mm
+.. autofunction:: qmflows.orca

docs/conf.py

@@ -21,6 +21,7 @@
 # import sys
 # sys.path.insert(0, os.path.abspath('.'))
 
+import qmflows
 
 # -- General configuration ------------------------------------------------
 
@@ -68,16 +69,16 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.12'
+version = qmflows.__version__
 # The full version, including alpha/beta/rc tags.
-release = '0.12.0'
+release = qmflows.__version__
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -204,16 +205,3 @@
 #     'none' – Do not show typehints
 # New in version 2.1.
 autodoc_typehints = 'none'
-
-# This value contains a list of modules to be mocked up.
-# This is useful when some external dependencies are not met at build time and break the building process.
-# You may only specify the root package of the dependencies themselves and omit the sub-modules:
-autodoc_mock_imports = [
-    'rdkit',
-    'h5py',
-]
-
-rst_epilog = """
-.. |Package| replace:: :class:`~qmflows.packages.Package`
-.. |Settings| replace:: :class:`~qmflows.Settings`
-"""

docs/settings.rst

@@ -1,7 +1,7 @@
 Settings
 --------
 
-|Settings| is a :class:`dict` subclass implemented in PLAMS_ and modified in *Qmflows*.
+:class:`~qmflows.Settings` is a :class:`dict` subclass implemented in PLAMS_ and modified in *Qmflows*.
 This class represents the data in a hierarchical tree-like structure. for example:
 
 .. code:: python
@@ -19,7 +19,7 @@ This class represents the data in a hierarchical tree-like structure. for exampl
     >>> input_settings = templates.singlepoint.overlay(s)  # (4)
 
 
-The above code snippet shows how to create a |Settings| instance object in **(1)**,
+The above code snippet shows how to create a :class:`~qmflows.Settings` instance object in **(1)**,
 then in **(2)** the generic keyword *basis*  declares that the "DZP" should be used together with the *large* keyword
 of *ADF* as shown at **(3)**.
 Finally in line **(4)** the user's keywords are merged with the defaults resultin in a input like:

src/qmflows/__init__.py

@@ -6,7 +6,7 @@
 from ._version import __version__ as __version__
 from ._version_info import version_info as version_info
 
-from .logger import logger
+from ._logger import logger
 
 from .utils import InitRestart
 

src/qmflows/_logger.py

@@ -0,0 +1,18 @@
+"""A module containing the :class:`~logging.Logger` of QMFlows."""
+
+import sys
+import logging
+
+__all__ = ['logger', 'stdout_handlet']
+
+#: The QMFlows :class:`~logging.Logger`.
+logger = logging.getLogger(__package__)
+logger.setLevel(logging.DEBUG)
+
+stdout_handler = logging.StreamHandler(stream=sys.stdout)
+stdout_handler.setLevel(logging.DEBUG)
+stdout_handler.setFormatter(logging.Formatter(
+    fmt='[%(asctime)s] %(levelname)s: %(message)s',
+    datefmt='%H:%M:%S',
+))
+logger.addHandler(stdout_handler)

src/qmflows/_settings.py

@@ -60,7 +60,7 @@ def __deepcopy__(self: _Self, _: object) -> _Self:
         return self.copy()
 
     def overlay(self: _Self, other: Mapping[str, Any]) -> _Self:
-        """Return new instance of |Settings| that is a copy of this instance updated with *other*."""  # noqa: E501
+        """Return new instance of :class:`~qmflows.Settings` that is a copy of this instance updated with *other*."""  # noqa: E501
         ret = self.copy()
         ret.update(other)
         return ret

src/qmflows/packages/__init__.py

@@ -1,5 +1,7 @@
 """A set of modules for managing various quantum-chemical packages."""
 
+from typing import TYPE_CHECKING
+
 from ._packages import (
     Package, Result, run,
     _load_properties as load_properties,
@@ -24,3 +26,8 @@
     'ORCA_Result', 'ORCA', 'orca',
     'PackageWrapper', 'ResultWrapper', 'JOB_MAP',
 ]
+
+if not TYPE_CHECKING:
+    #: Placeholder docstring for sphinx.
+    JOB_MAP: "dict[type[plams.Job], Package]"
+del TYPE_CHECKING

src/qmflows/packages/_cp2k_mm.py

@@ -30,7 +30,7 @@ class CP2KMM(CP2K):
     It uses plams together with the templates to generate the stucture input
     and also uses Plams to invoke the binary CP2K code.
     This class is not intended to be called directly by the user, instead the
-    :func:`~qmflows.packages.cp2k_mm` function should be called.
+    :class:`~qmflows.cp2k_mm` function should be called.
 
     """  # noqa: E501
 

src/qmflows/packages/_package_wrapper.py

@@ -7,9 +7,9 @@
 appropiate instance of Package subclas instance is called.
 
 For example, passing :class:`plams.ADFJob<scm.plams.interfaces.adfsuite.adf.ADFJob>` will
-automatically call :data:`~qmflows.packages.adf`,
+automatically call :data:`~qmflows.adf`,
 :class:`plams.Cp2kJob<scm.plams.interfaces.thirdparty.cp2k.Cp2kJob>` will
-call :data:`~qmflows.packages.cp2k`, *etc*.
+call :data:`~qmflows.cp2k`, *etc*.
 
 When no appropiate Package is found, let's say after passing the :class:`MyFancyJob` type,
 the PackageWrapper class will still run the job as usual and return the matching
@@ -77,7 +77,7 @@
     :annotation: : dict[type[plams.Job], Package]
 
     A dictionary mapping PLAMS :class:`Job<scm.plams.core.basejob.Job>` types
-    to appropiate QMFlows :class:`~qmflows.packages.Package` instance
+    to appropiate QMFlows :class:`~qmflows.packages.Package` instance.
 
     .. code:: python
 
@@ -119,7 +119,7 @@
 plams.Job = plams.core.basejob.Job
 plams.ORCAJob = plams.interfaces.thirdparty.orca.ORCAJob
 
-__all__ = ['PackageWrapper', 'ResultWrapper']
+__all__ = ['PackageWrapper', 'ResultWrapper', 'JOB_MAP']
 
 JT = TypeVar("JT", bound=plams.core.basejob.Job)
 
@@ -177,7 +177,7 @@ class PackageWrapper(Package, Generic[JT]):
 
     See Also
     --------
-    :data:`~qmflows.packages.package_wrapper.JOB_MAP` : :class:`dict[type[plams.Job], Package] <dict>`
+    :data:`~qmflows.packages.JOB_MAP`
         A dictionary mapping PLAMS Job types to appropiate QMFlows Package instances.
 
     """  # noqa

src/qmflows/packages/_scm.py

@@ -236,7 +236,7 @@ def run_job(cls, settings: Settings, mol: plams.Molecule,
         """Execute ADF job.
 
         :param settings: user input settings.
-        :type settings: |Settings|
+        :type settings: :class:`~qmflows.Settings`
         :param mol: Molecule to run the simulation
         :type mol: Plams Molecule
         :parameter input_file_name: The user can provide a name for the

src/qmflows/test_utils.py

@@ -32,17 +32,20 @@
 .. autodata:: requires_ams
 .. autodata:: requires_adf
 .. autofunction:: find_executable
+.. autodata:: stdout_to_logger
 
 """
 
 import os
 import sys
 import textwrap
+import logging
+import contextlib
 from pathlib import Path
 
 import pytest
 
-from ._settings import Settings
+from . import logger, Settings
 from .warnings_qmflows import Assertion_Warning
 from .packages import Result
 
@@ -58,6 +61,7 @@
     'requires_ams',
     'requires_adf',
     'find_executable',
+    'stdout_to_logger',
 ]
 
 try:
@@ -261,3 +265,37 @@ def _has_env_vars(*env_vars: str) -> bool:
     not _has_env_vars("ADFBIN", "ADFHOME", "ADFRESOURCES"),
     reason="Requires ADF <=2019",
 )
+
+
+class _StdOutToLogger(contextlib.redirect_stdout, contextlib.ContextDecorator):
+    """A context decorator and file-like object for redirecting the stdout stream to a logger.
+
+    Attributes
+    ----------
+    logger : logging.Logger
+        The wrapped logger.
+    level : int
+        The logging level.
+
+    """
+
+    __slots__ = ("logger", "level")
+
+    def __init__(self, logger: logging.Logger, level: int = logging.INFO) -> None:
+        super().__init__(self)
+        self.logger = logger
+        self.level = level
+
+    def write(self, msg: str) -> None:
+        """Log '`msg'` with the integer severity :attr:`level`."""
+        self.logger.log(self.level, msg)
+
+    def flush(self) -> None:
+        """Ensure aqll logging output has been flushed."""
+        for handler in self.logger.handlers:
+            handler.flush()
+
+
+#: A context decorator and file-like object for redirecting the stdout
+#: stream to the qmflows logger.
+stdout_to_logger = _StdOutToLogger(logger)

test/test_adf_mock.py

@@ -10,7 +10,7 @@
 
 from qmflows import adf, templates
 from qmflows.packages import ADF_Result
-from qmflows.test_utils import PATH, PATH_MOLECULES
+from qmflows.test_utils import PATH, PATH_MOLECULES, stdout_to_logger
 from qmflows.warnings_qmflows import QMFlows_Warning
 from qmflows.utils import InitRestart
 
@@ -51,6 +51,7 @@ def test_adf_mock(mocker: MockFixture):
     ("bob", "Generic property 'bob' not defined", None),
     ("energy", "It is not possible to retrieve property: 'energy'", "crashed"),
 ], ids=["undefined_property", "job_crashed"])
+@stdout_to_logger
 def test_getattr_warning(tmp_path: Path, name: str, match: str, status: Optional[str]) -> None:
     mol = Molecule(PATH_MOLECULES / "acetonitrile.xyz")
     jobname = "ADFjob"

test/test_cp2k_mm_mock.py

@@ -1,7 +1,5 @@
 """Mock CP2K funcionality."""
 
-import os
-import shutil
 from typing import Callable
 
 import numpy as np
@@ -10,7 +8,6 @@
 from scm.plams import Molecule
 
 from qmflows import Settings, cp2k_mm, singlepoint, geometry, freq, md, cell_opt
-from qmflows.utils import InitRestart
 from qmflows.packages import CP2KMM_Result
 from qmflows.test_utils import get_mm_settings, validate_status, PATH, PATH_MOLECULES
 
@@ -20,12 +17,6 @@
 #: Example input Settings for CP2K mm calculations.
 SETTINGS: Settings = get_mm_settings()
 
-# Ensure that plams.config is populated with a JobManager
-with InitRestart(PATH, 'tmp'):
-    pass
-if os.path.isdir(PATH / 'tmp'):
-    shutil.rmtree(PATH / 'tmp')
-
 
 def overlap_coords(xyz1: np.ndarray, xyz2: np.ndarray) -> np.ndarray:
     """Rotate *xyz1* such that it overlaps with *xyz2* using the Kabsch algorithm."""

test/test_sphinx.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 
 import pytest
+from qmflows.test_utils import stdout_to_logger
 
 try:
     from sphinx.application import Sphinx
@@ -17,7 +18,6 @@
 
 
 @pytest.mark.skipif(not HAS_SPHINX, reason='Requires Sphinx')
-@pytest.mark.xfail
 def test_sphinx_build(tmp_path: Path) -> None:
     """Test :meth:`sphinx.application.Sphinx.build`."""
     try:
@@ -28,6 +28,7 @@ def test_sphinx_build(tmp_path: Path) -> None:
             tmp_path / "build" / "doctrees",
             buildername='html',
             warningiserror=True,
+            status=stdout_to_logger,
         )
         app.build(force_all=True)
     except SphinxWarning as ex:
@@ -38,3 +39,4 @@ def test_sphinx_build(tmp_path: Path) -> None:
             warning = RuntimeWarning(str(ex))
             warning.__cause__ = ex
             warnings.warn(warning)
+            pytest.xfail(str(ex))

test/test_utils.py

@@ -12,7 +12,7 @@
 from qmflows import Settings
 from qmflows.packages import CP2K_Result
 from qmflows.utils import to_runtime_error, file_to_context, init_restart, InitRestart
-from qmflows.test_utils import PATH_MOLECULES, PATH, validate_status
+from qmflows.test_utils import PATH_MOLECULES, PATH, validate_status, stdout_to_logger
 
 PSF_STR: str = """
 PSF EXT
@@ -63,6 +63,7 @@ def test_file_to_context() -> None:
     assertion.assert_(file_to_context, 5.0, exception=TypeError)
 
 
+@stdout_to_logger
 def test_restart_init(tmp_path: Path) -> None:
     """Tests for :func:`restart_init` and :class:`RestartInit`."""
     workdir = tmp_path / 'test_restart_init'