Merge pull request #280 from nlesc-nano/qmflows

DEP: Bump qmflows and deal with deprecations

FOX/armc/package_manager.py

@@ -35,7 +35,7 @@
 from scm.plams import config, Molecule, JobManager  # type: ignore
 from qmflows import Settings as QmSettings
 from qmflows.cp2k_utils import prm_to_df
-from qmflows.packages.cp2k_package import CP2K, CP2K_Result
+from qmflows.packages import CP2K, CP2K_Result
 from noodles import gather, schedule, has_scheduled_methods, run_parallel
 from nanoutils import set_docstring, TypedDict
 
@@ -93,7 +93,7 @@ def __init__(self, data: Union[DataMap, DataIter],
         data : :class:`~collections.abc.Mapping` [:class:`str`, :class:`~collections.abc.Iterable` [:class:`~scm.plams.core.basejob.SingleJob`]]
             A mapping with user-defined job descriptor as keys and an iterable of Job
             instances as values.
-        hook : :class:`~collections.abc.Iterator` [:class:`~collections.abc.Iterable` [:class:`~qmflows.packages.packages.Result`]], optional
+        hook : :class:`~collections.abc.Iterator` [:class:`~collections.abc.Iterable` [:class:`~qmflows.packages.Result`]], optional
             An iterator yielding multiple qmflows Result objects.
             Can be used as a hook for the purpose of unit-testing.
         **kwargs : :data:`~typing.Any`

FOX/armc/sanitization.py

@@ -359,7 +359,7 @@ def get_param(dct: ParamMapping_) -> Tuple[ParamMapping, dict, dict, ValidationD
             data2[['min', 'max']] = min_max2
             data2['unit'] = units2
             data2['frozen'] = True
-            data = data.append(data2)
+            data = pd.concat([data, data2])
     data.sort_index(inplace=True)
 
     param_type = prm_dict.pop('type')  # type: ignore

FOX/properties/bulk_modulus.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 from scm.plams import Units
-from qmflows.packages.cp2k_package import CP2K_Result
+from qmflows.packages import CP2K_Result
 from qmflows.warnings_qmflows import QMFlows_Warning
 from nanoutils import warning_filter
 
@@ -85,7 +85,7 @@ def _(
 
     Parameters
     ----------
-    result : :class:`qmflows.CP2K_Result <qmflows.packages.cp2k_package.CP2K_Result>`
+    result : :class:`qmflows.CP2K_Result <qmflows.packages.CP2K_Result>`
         The Result instance that **self** should operator on.
     reduce : :class:`str` or :class:`Callable[[Any], Any] <collections.abc.Callable>`, optional
         A callback for reducing the output of **self**.

FOX/properties/pressure.py

@@ -7,7 +7,7 @@
 import numpy as np
 from scipy import constants
 from scm.plams import Units
-from qmflows.packages.cp2k_package import CP2K_Result
+from qmflows.packages import CP2K_Result
 from qmflows.warnings_qmflows import QMFlows_Warning
 from nanoutils import warning_filter
 
@@ -104,7 +104,7 @@ def _(
 
     Parameters
     ----------
-    result : :class:`qmflows.CP2K_Result <qmflows.packages.cp2k_package.CP2K_Result>`
+    result : :class:`qmflows.CP2K_Result <qmflows.packages.CP2K_Result>`
         The Result instance that **self** should operator on.
     reduce : :class:`str` or :class:`Callable[[Any], Any] <collections.abc.Callable>`, optional
         A callback for reducing the output of **self**.

FOX/testing_utils.py

@@ -34,7 +34,7 @@
 from assertionlib import assertion
 from scm.plams import Molecule
 from qmflows import Settings as QmSettings
-from qmflows.packages.cp2k_mm import CP2KMM_Result
+from qmflows.packages import CP2KMM_Result
 from nanoutils import Literal, PathType, recursive_keys
 
 from .functions.cp2k_utils import get_xyz_path

FOX/type_alias.py

@@ -44,8 +44,8 @@
 
     'NDFrame': 'pandas.core.generic.NDFrame',
 
-    'Result': 'qmflows.packages.packages.Result',
-    'Package': 'qmflows.packages.packages.Package',
+    'Result': 'qmflows.packages.Result',
+    'Package': 'qmflows.packages.Package',
 
     'Registry': 'noodles.serial.registry.Registry',
     'PromisedObject': 'noodles.interface.decorator.PromisedObject'

setup.cfg

@@ -25,13 +25,15 @@ max-line-length = 100
 
 [tool:pytest]
 testpaths = FOX tests
-addopts = --tb=short --cov=FOX --cov-report xml --cov-report term --cov-report html
+addopts = --tb=short --cov=FOX --cov-report xml --cov-report term --cov-report html --pdbcls=IPython.terminal.debugger:TerminalPdb
 markers = slow: A marker for slow tests requiring external quantum-chemical packages.
 filterwarnings =
     ignore::pandas.errors.PerformanceWarning
     ignore:numpy\.ufunc size changed, may indicate binary incompatibility\. Expected [0-9]+ from C header, got [0-9]+ from PyObject:RuntimeWarning
     ignore::DeprecationWarning:numpy.distutils.*
     ignore:elementwise comparison failed:FutureWarning:pandas
+    error::qmflows.warnings_qmflows.QMFlows_Warning
+    ignore:Generic keyword '_pytestfixturefunction' not implemented for package \w:qmflows.warnings_qmflows.Key_Warning
 
 # Define `python setup.py build_sphinx`
 [build_sphinx]

setup.py

@@ -27,6 +27,7 @@
 tests_require = [
     'ase>=3.21.1',
     'nlesc-CAT>=0.10.0',
+    'ipython>=5.0.0',
 ]
 tests_require += tests_require_no_optional
 tests_require += docs_require
@@ -110,7 +111,7 @@
         'AssertionLib>=2.3',
         'noodles>=0.3.3',
         'h5py>=2.10',
-        'qmflows>=0.11.0',
+        'qmflows>=0.12.0',
         'plams>=1.5.1',
     ],
     tests_require=tests_require,

tests/test_properties.py

@@ -12,7 +12,7 @@
 import pytest
 import numpy as np
 from assertionlib import assertion
-from qmflows.packages.cp2k_mm import CP2KMM_Result
+from qmflows.packages import CP2KMM_Result
 
 from FOX.properties import FromResult, get_pressure, get_bulk_modulus, get_attr