Merge pull request #287 from SCM-NV/linting

TST: Move linting checks to their own dedicated workflow

.github/workflows/pythonapp.yml

@@ -7,7 +7,7 @@ on:
   pull_request:
 
 jobs:
-  build:
+  Test:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -126,3 +126,34 @@ jobs:
       with:
         file: ./coverage.xml
         name: codecov-umbrella
+
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python 3.10 on ubuntu-latest
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install linters
+        run: pip install pydocstyle pycodestyle mypy "numpy>=1.21" pytest more_itertools types-PyYAML types-setuptools
+
+      - name: Python info
+        run: |
+          which python
+          python --version
+
+      - name: Installed packages
+        run: pip list
+
+      - name: Run pycodestyle
+        run: pycodestyle src test
+
+      - name: Run pydocstyle
+        run: pydocstyle src
+
+      - name: Run mypy
+        run: mypy src
+        continue-on-error: true

pyproject.toml

@@ -0,0 +1,27 @@
+[tool.mypy]
+plugins = "numpy.typing.mypy_plugin"
+show_error_codes = true
+
+[[tool.mypy.overrides]]
+module = "scm.plams.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "scm.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "noodles.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "rdkit.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "pandas.*"
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "pyparsing.*"
+ignore_missing_imports = true

setup.cfg

@@ -17,7 +17,7 @@ max-line-length = 100
 
 [tool:pytest]
 testpaths = src test
-addopts = --pycodestyle --pydocstyle --tb=short --cov --doctest-modules --cov-report xml --cov-report term --cov-report html
+addopts = --tb=short --cov --doctest-modules --cov-report xml --cov-report term --cov-report html
 markers = slow: A marker for slow tests requiring external quantum-chemical packages.
 
 # Define `python setup.py build_sphinx`
@@ -29,5 +29,5 @@ builder = html
 
 [pydocstyle]
 convention = numpy
-add-ignore = D401  # First line should be in imperative mood
+add-ignore = D401,D105  # First line should be in imperative mood
 ignore-decorators = overload

setup.py

@@ -27,17 +27,10 @@ def readme():
     'pytest>=5.4',
     'pytest-cov',
     'pytest-mock',
-    'pytest-pycodestyle',
-    'pytest-pydocstyle>=2.1',
     'typing_extensions'
 ]
 
-tests_require =  [
-    'mypy',
-    'types-PyYAML',
-    'types-setuptools',
-]
-tests_require += tests_no_optional_require
+tests_require = tests_no_optional_require.copy()
 tests_require += docs_require
 
 setup(

src/qmflows/packages/SCM.py

@@ -99,6 +99,19 @@ class ADF_Result(Result):
 
     prop_mapping: ClassVar[_Settings] = load_properties('ADF', prefix='properties')
 
+    # Attributes accessed via `__getattr__`
+    charges: "None | Any"
+    dipole: "None | Any"
+    energy: "None | Any"
+    enthalpy: "None | Any"
+    free_energy: "None | Any"
+    frequencies: "None | Any"
+    hessian: "None | Any"
+    homo: "None | Any"
+    lumo: "None | Any"
+    optcycles: "None | Any"
+    runtime: "None | Any"
+
     def __init__(self, settings: Optional[Settings],
                  molecule: Optional[plams.Molecule],
                  job_name: str,
@@ -151,6 +164,15 @@ class DFTB_Result(Result):
 
     prop_mapping: ClassVar[_Settings] = load_properties('DFTB', prefix='properties')
 
+    # Attributes accessed via `__getattr__`
+    charges: "None | Any"
+    dipole: "None | Any"
+    energy: "None | Any"
+    enthalpy: "None | Any"
+    free_energy: "None | Any"
+    frequencies: "None | Any"
+    hessian: "None | Any"
+
     def __init__(self, settings: Optional[Settings],
                  molecule: Optional[plams.Molecule],
                  job_name: str,

src/qmflows/packages/cp2k_package.py

@@ -3,7 +3,7 @@
 
 import os
 from os.path import join
-from typing import Any, Dict, Iterable, ClassVar, Type
+from typing import Any, Dict, Iterable, ClassVar, Type, TYPE_CHECKING
 from warnings import warn
 
 import numpy as np
@@ -14,6 +14,11 @@
 from ..settings import Settings
 from ..warnings_qmflows import cp2k_warnings, Key_Warning
 from ..type_hints import Final, _Settings, Generic2Special
+from ..common import InfoMO
+
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+    from numpy import float64 as f8
 
 __all__ = ['cp2k']
 
@@ -131,6 +136,20 @@ class CP2K_Result(Result):
 
     prop_mapping: ClassVar[_Settings] = load_properties('CP2K', prefix='properties')
 
+    # Attributes accessed via `__getattr__`
+    energy: "None | float"
+    frequencies: "None | NDArray[f8]"
+    geometry: "None | plams.Molecule"
+    enthalpy: "None | float"
+    free_energy: "None | float"
+    orbitals: "None | InfoMO | tuple[InfoMO, InfoMO]"
+    forces: "None | NDArray[f8]"
+    coordinates: "None | NDArray[f8]"
+    temperature: "None | NDArray[f8]"
+    volume: "None | NDArray[f8]"
+    lattice: "None | NDArray[f8]"
+    pressure: "None | NDArray[f8]"
+
     @property
     def molecule(self) -> "None | plams.Molecule":
         """Return the current geometry.

src/qmflows/packages/orca.py

@@ -4,7 +4,7 @@
 import os
 from os.path import join
 from warnings import warn
-from typing import Any, Union, Optional, ClassVar, List, Type
+from typing import Any, Union, Optional, ClassVar, List, Type, TYPE_CHECKING
 
 import numpy as np
 from scm import plams
@@ -15,6 +15,11 @@
 from ..type_hints import Final, _Settings
 from ..utils import get_tmpfile_name
 from ..warnings_qmflows import Key_Warning
+from ..common import InfoMO
+
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+    from numpy import float64 as f8
 
 # ============================= Orca ==========================================
 
@@ -24,6 +29,19 @@ class ORCA_Result(Result):
 
     prop_mapping: ClassVar[_Settings] = load_properties('ORCA', prefix='properties')
 
+    # Attributes accessed via `__getattr__`
+    charges: "None | list[float]"
+    dipole: "None | list[float]"
+    energy: "None | float"
+    enthalpy: "None | float"
+    free_energy: "None | float"
+    frequencies: "None | NDArray[f8]"
+    hessian: "None | NDArray[f8]"
+    normal_modes: "None | NDArray[f8]"
+    optcycles: "None | int"
+    orbitals: "None | InfoMO"
+    runtime: "None | float"
+
     @property
     def molecule(self) -> Optional[plams.Molecule]:
         """Retrieve the molecule from the output file."""

src/qmflows/packages/package_wrapper.py

@@ -99,7 +99,9 @@
 
 import os
 from os.path import join
-from typing import Type, TypeVar, Union, ClassVar, Any, Dict, Optional, TypeVar, Generic, Tuple
+from typing import (
+    Type, TypeVar, Union, ClassVar, Any, Dict, Optional, TypeVar, Generic, Tuple, TYPE_CHECKING
+)
 from warnings import warn
 
 from scm import plams
@@ -187,6 +189,9 @@ class PackageWrapper(Package, Generic[JT]):
     result_type: ClassVar[Type[ResultWrapper]] = ResultWrapper
     job_type: Type[JT]
 
+    if TYPE_CHECKING:
+        def __getattr__(self, name: str) -> Any: ...
+
     def __init__(self, job_type: Type[JT], name: Optional[str] = None) -> None:
         """Initialize this instance.
 

src/qmflows/packages/packages.py

@@ -13,7 +13,8 @@
 from os.path import join
 from warnings import warn
 from typing import (
-    Any, Callable, Optional, Union, ClassVar, Mapping, Iterator, Type, Dict, TypeVar, Tuple, List
+    Any, Callable, Optional, Union, ClassVar, Mapping, Iterator,
+    Type, Dict, TypeVar, Tuple, List, TYPE_CHECKING,
 )
 
 import numpy as np
@@ -109,48 +110,50 @@ def __deepcopy__(self, memo: Optional[Dict[int, Any]] = None) -> 'Result':
         copy_instance.__dict__ = self.__dict__.copy()
         return copy_instance
 
-    def __getattr__(self, prop: str) -> Any:
-        """Return a section of the results.
+    # Hide `__getattr__` from the type checker and use explicit attribute annotations
+    if not TYPE_CHECKING:
+        def __getattr__(self, prop: str) -> Any:
+            """Return a section of the results.
 
-        For example:
+            For example:
 
-        ..code:: python
+            ..code:: python
 
-            >>> from qmflows.packages.packages import Result
+                >>> from qmflows.packages.packages import Result
 
-            >>> result = Result(...)  # doctest: +SKIP
-            >>> dipole = result.dipole  # doctest: +SKIP
+                >>> result = Result(...)  # doctest: +SKIP
+                >>> dipole = result.dipole  # doctest: +SKIP
 
-        """
-        is_private = prop.startswith('__') and prop.endswith('__')
-        has_crashed = self.status in {'failed', 'crashed'}
-
-        if not has_crashed and prop in self.prop_mapping:
-            return self.get_property(prop)
-
-        elif not (has_crashed or is_private or prop in self.prop_mapping):
-            if self._results_open:
-                warn(f"Generic property {prop!r} not defined",
-                     category=QMFlows_Warning, stacklevel=2)
-
-            # Do not issue this warning if the Results object is still pickled
-            else:  # Unpickle the Results instance and try again
-                self._unpack_results()
-                try:
-                    return vars(self)[prop]  # Avoid recursive `getattr` calls
-                except KeyError:
-                    warn(f"Generic property {prop!r} not defined",
-                         category=QMFlows_Warning, stacklevel=2)
+            """
+            is_private = prop.startswith('__') and prop.endswith('__')
+            has_crashed = self.status in {'failed', 'crashed'}
 
-        elif has_crashed and not is_private:
-            warn(f"""
-            It is not possible to retrieve property: {prop!r}
-            Because Job: {self.job_name!r} has {self.status}. Check the output.\n
-            Are you sure that you have the package installed or
-             you have loaded the package in the cluster. For example:
-            `module load AwesomeQuantumPackage/3.141592`
-            """, category=QMFlows_Warning, stacklevel=2)
-        return None
+            if not has_crashed and prop in self.prop_mapping:
+                return self.get_property(prop)
+
+            elif not (has_crashed or is_private or prop in self.prop_mapping):
+                if self._results_open:
+                    warn(f"Generic property {prop!r} not defined",
+                        category=QMFlows_Warning, stacklevel=2)
+
+                # Do not issue this warning if the Results object is still pickled
+                else:  # Unpickle the Results instance and try again
+                    self._unpack_results()
+                    try:
+                        return vars(self)[prop]  # Avoid recursive `getattr` calls
+                    except KeyError:
+                        warn(f"Generic property {prop!r} not defined",
+                            category=QMFlows_Warning, stacklevel=2)
+
+            elif has_crashed and not is_private:
+                warn(f"""
+                It is not possible to retrieve property: {prop!r}
+                Because Job: {self.job_name!r} has {self.status}. Check the output.\n
+                Are you sure that you have the package installed or
+                you have loaded the package in the cluster. For example:
+                `module load AwesomeQuantumPackage/3.141592`
+                """, category=QMFlows_Warning, stacklevel=2)
+            return None
 
     def __dir__(self) -> List[str]:
         """Implement ``dir(self)``."""