Merge pull request #192 from ispg-group/reorganize-workflows

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+63d994fa6294d87eead1f8502d1476eca3a84148 # apply new pre-commit rules
+b20a1b955f654202f2014a29ab834ec1f3915e35 # reorganize workflows

.pre-commit-config.yaml

@@ -1,27 +1,17 @@
 repos:
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.3.0
     hooks:
       - id: black
         language_version: python3 # Should be a command that runs python3.6+
 
-  - repo: https://github.com/pycqa/flake8
-    rev: '6.0.0'
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.0.270
     hooks:
-    - id: flake8
-      args: [--count, --show-source, --statistics, --version]
-      additional_dependencies:
-        - flake8-bugbear
-        - flake8-builtins
-        - flake8-comprehensions
+    - id: ruff
+      args: [--show-source]
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
     hooks:
     - id: nbstripout
-
-  - repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.0
-    hooks:
-        - id: pyupgrade
-          args: [--py39-plus]

aiidalab_ispg/app/atmospec_steps.py

@@ -8,11 +8,10 @@
 import traitlets
 
 from aiida.engine import submit, ProcessState
-from aiida.orm import Bool, StructureData, TrajectoryData, WorkChainNode
+from aiida.orm import Bool
 from aiida.orm import load_code, load_node
 from aiida.plugins import WorkflowFactory
 
-from aiidalab_widgets_base import WizardAppWidgetStep
 
 from .input_widgets import (
     ExcitedStateMethod,
@@ -335,9 +334,8 @@ def submit(self, _=None):
                 nroots=bp.nstates,
             )
         else:
-            raise NotImplementedError(
-                f"Excited method {bp.excited_method} not implemented"
-            )
+            msg = f"Excited method {bp.excited_method} not implemented"
+            raise NotImplementedError(msg)
 
         builder.optimize = bp.optimize
         builder.opt.orca.parameters = gs_opt_parameters
@@ -454,7 +452,6 @@ def _observe_status(self, change):
 
 
 class ViewAtmospecAppWorkChainStatusAndResultsStep(ViewWorkChainStatusStep):
-
     workflow_status = traitlets.Instance(AtmospecWorkflowStatus, allow_none=True)
 
     def __init__(self, **kwargs):

aiidalab_ispg/app/conformers.py

@@ -69,7 +69,6 @@ class FFMethod(Enum):
 
 
 class ConformerSmilesWidget(SmilesWidget):
-
     structure = Union(
         [Instance(Atoms), Instance(StructureData), Instance(TrajectoryData)],
         allow_none=True,
@@ -232,7 +231,10 @@ def _filter_and_sort_conformers(self, conformers, energies):
                 selected_energies.append(shifted_energy)
         return selected_conformers, selected_energies
 
-    def _rdkit_opt(self, smiles, steps, algo=RDKitMethod.ETKDGV1, opt_algo=None):
+    # TODO: Refactor this to smaller functions
+    def _rdkit_opt(  # noqa: C901
+        self, smiles, steps, algo=RDKitMethod.ETKDGV1, opt_algo=None
+    ):
         """Optimize a molecule using force field and rdkit (needed for complex SMILES)."""
 
         if self.debug:
@@ -273,7 +275,8 @@ def _rdkit_opt(self, smiles, steps, algo=RDKitMethod.ETKDGV1, opt_algo=None):
                 mol, numConfs=num_confs, params=params
             )
         if len(conf_ids) == 0:
-            raise ValueError("Failed to generate conformers with RDKit")
+            msg = "Failed to generate conformers with RDKit"
+            raise ValueError(msg)
 
         ffenergies = None
         if opt_algo == FFMethod.UFF and AllChem.UFFHasAllMoleculeParams(mol):

aiidalab_ispg/app/experimental_spectra/import_experimental_spectrum.py

@@ -1,3 +1,4 @@
+# ruff: noqa: INP001
 # This script needs to be run with `verdi run`
 import argparse
 from pprint import pprint
@@ -7,6 +8,9 @@
 import numpy as np
 from rdkit import Chem
 
+from aiida.orm import QueryBuilder
+from aiida.plugins import DataFactory
+
 XyData = DataFactory("array.xy")
 
 
@@ -33,15 +37,16 @@ def parse_cmd():
 def canonicalize_smiles(smiles):
     mol = Chem.MolFromSmiles(smiles, sanitize=True)
     if mol is None:
-        raise ValueError("RDkit ERROR: Invalid SMILES string")
+        msg = "RDkit ERROR: Invalid SMILES string"
+        raise ValueError(msg)
     canonical_smiles = Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
     if not canonical_smiles:
-        raise ValueError("RDKit: Could not canonicalize SMILES")
+        msg = "RDKit: Could not canonicalize SMILES"
+        raise ValueError(msg)
     return canonical_smiles
 
 
 def main(input_file, dry_run=True):
-
     with open(opts.input_file) as f:
         data = yaml.safe_load(f)
 

aiidalab_ispg/app/input_widgets.py

@@ -42,7 +42,6 @@ class ExcitedStateMethod(Enum):
 
 
 class MolecularGeometrySettings(ipw.VBox):
-
     title = ipw.HTML(
         """<div style="padding-top: 0px; padding-bottom: 0px">
         <h4>Molecular geometry</h4></div>"""
@@ -234,14 +233,13 @@ def _observe_excited_method(self, change):
             self.tddft_functional.disabled = False
 
     def reset(self):
-        self.excited_method.value = _DEFAULT_EXCITED_METHOD
+        self.excited_method.value = self._DEFAULT_EXCITED_METHOD
         self.method.value = self._DEFAULT_FUNCTIONAL
         self.basis.value = self._DEFAULT_BASIS
         self.nstate.value = self._DEFAULT_NSTATES
 
 
 class WignerSamplingSettings(ipw.VBox):
-
     disabled = traitlets.Bool(default=False)
 
     title = ipw.HTML(
@@ -296,7 +294,6 @@ def reset(self):
 
 
 class CodeSettings(ipw.VBox):
-
     codes_title = ipw.HTML(
         """<div style="padding-top: 10px; padding-bottom: 0px">
         <h4>Codes</h4></div>"""
@@ -311,7 +308,6 @@ class CodeSettings(ipw.VBox):
     _DEFAULT_ORCA_CODES = ("orca@slurm", "orca@localhost")
 
     def __init__(self, **kwargs):
-
         self.orca = ComputationalResourcesWidget(
             default_calc_job_plugin="orca.orca",
             description="ORCA program",

aiidalab_ispg/app/optimization_steps.py

@@ -8,16 +8,10 @@
 import traitlets
 
 from aiida.engine import submit, ProcessState
-from aiida.orm import Bool, StructureData, TrajectoryData, WorkChainNode
+from aiida.orm import Bool
 from aiida.orm import load_code, load_node
 from aiida.plugins import WorkflowFactory
 
-from aiidalab_widgets_base import (
-    WizardAppWidgetStep,
-    AiidaNodeViewWidget,
-    ProcessMonitor,
-    ProcessNodesTreeWidget,
-)
 
 from .input_widgets import (
     ResourceSelectionWidget,
@@ -27,7 +21,6 @@
 )
 from .widgets import TrajectoryDataViewer, spinner
 from .steps import SubmitWorkChainStepBase, ViewWorkChainStatusStep
-from .utils import MEMORY_PER_CPU
 
 ConformerOptimizationWorkChain = WorkflowFactory("ispg.conformer_opt")
 

aiidalab_ispg/app/qeapp/process.py

@@ -3,7 +3,6 @@
 
 import ipywidgets as ipw
 import traitlets as tl
-from aiida import orm
 from aiida.tools.query.calculation import CalculationQueryBuilder
 
 

aiidalab_ispg/app/qeapp/widgets.py

@@ -24,7 +24,6 @@
 
 
 class RollingOutput(ipw.VBox):
-
     style = (
         "background-color: #253239; color: #cdd3df; line-height: normal; custom=test"
     )
@@ -107,7 +106,8 @@ def _default_tooltip(self):
         return "Download"
 
     def __on_click(self, _):
-        digest = hashlib.md5(self.payload).hexdigest()  # bypass browser cache
+        # bypass browser cache
+        digest = hashlib.md5(self.payload).hexdigest()  # noqa: S324
         payload = base64.b64encode(self.payload).decode()
 
         link_id = f"dl_{digest}"
@@ -134,7 +134,6 @@ def __on_click(self, _):
 
 
 class FilenameDisplayWidget(ipw.Box):
-
     value = traitlets.Unicode()
 
     def __init__(self, max_width=None, **kwargs):
@@ -158,7 +157,6 @@ def _observe_filename(self, change):
 
 
 class LogOutputWidget(ipw.VBox):
-
     filename = traitlets.Unicode()
     value = traitlets.Unicode()
 
@@ -236,7 +234,6 @@ def _observe_value(self, change):
 
 
 class CalcJobOutputFollower(traitlets.HasTraits):
-
     calcjob_uuid = traitlets.Unicode(allow_none=True)
     filename = traitlets.Unicode(allow_none=True)
     output = traitlets.List(trait=traitlets.Unicode)

aiidalab_ispg/app/spectrum.py

@@ -147,7 +147,8 @@ def get_spectrum(
         elif kernel is BroadeningKernel.LORENTZ:
             self._calc_lorentzian_spectrum(x, y, width)
         else:
-            raise ValueError(f"Invalid broadening kernel {kernel}")
+            msg = f"Invalid broadening kernel {kernel}"
+            raise ValueError(msg)
 
         # Conversion factor from eV to given energy unit
         if x_unit == EnergyUnit.NM:
@@ -170,7 +171,6 @@ def _convert_to_nanometers(self, x, y):
 
 
 class SpectrumWidget(ipw.VBox):
-
     disabled = traitlets.Bool(default=True)
     conformer_transitions = traitlets.List(
         trait=traitlets.Dict, allow_none=True, default=None
@@ -645,7 +645,8 @@ def _validate_conformers(self, change):
         if not all(
             self._validate_transitions(c["transitions"]) for c in conformer_transitions
         ):
-            raise ValueError("Invalid conformer transitions")
+            msg = "Invalid conformer transitions"
+            raise ValueError(msg)
         return conformer_transitions
 
     @traitlets.validate("conformer_structures")
@@ -659,7 +660,8 @@ def _validate_conformer_structures(self, change):
         elif isinstance(structures, StructureData):
             return TrajectoryData(structurelist=(structures,))
         else:
-            raise ValueError(f"Unsupported type {type(structures)}")
+            msg = f"Unsupported type {type(structures)}"
+            raise ValueError(msg)
 
     @traitlets.observe("selected_conformer_id")
     def _observe_selected_conformer(self, change):
@@ -704,7 +706,7 @@ def find_experimental_spectrum_by_smiles(self, smiles: str):
         and plot it if it is available in our DB"""
 
         self.set_trait("experimental_spectrum_uuid", None)
-        if smiles is None or smiles == "":
+        if not smiles:
             return
 
         qb = QueryBuilder()

aiidalab_ispg/app/spectrum_analysis.py

@@ -5,16 +5,13 @@
 """
 
 from dataclasses import dataclass
-from enum import Enum, unique
 
 import bokeh.plotting as plt
 import bokeh.palettes
-from bokeh.models import ColumnDataSource, Scatter
 
 import ipywidgets as ipw
 import traitlets
 import scipy
-from scipy import constants
 import numpy as np
 
 from .utils import BokehFigureContext
@@ -105,8 +102,8 @@ def _init_figure(self, *args, **kwargs) -> BokehFigureContext:
         """Initialize Bokeh figure. Arguments are passed to bokeh.plt.figure()"""
         figure = BokehFigureContext(plt.figure(*args, **kwargs))
         f = figure.get_figure()
-        f.xaxis.axis_label = f"Excitation Energy (eV)"
-        f.yaxis.axis_label = f"Oscillator strength (-)"
+        f.xaxis.axis_label = "Excitation Energy (eV)"
+        f.yaxis.axis_label = "Oscillator strength (-)"
         return figure
 
     @traitlets.observe("conformer_transitions")
@@ -130,7 +127,8 @@ def _update_density_plot(self, plot_type: str):
         elif plot_type == "DENSITY":
             self.plot_density(energies, osc_strengths)
         else:
-            raise ValueError(f"Unexpected value for toggle: {plot_type}")
+            msg = f"Unexpected value for toggle: {plot_type}"
+            raise ValueError(msg)
 
     def _flatten_transitions(self):
         # Flatten transitions for all conformers.

aiidalab_ispg/app/steps.py

@@ -5,15 +5,12 @@
     * Daniel Hollas <daniel.hollas@durham.ac.uk>
 """
 import ipywidgets as ipw
-import numpy as np
 import re
 import traitlets
 
-from aiida.common import MissingEntryPointError, LinkType
-from aiida.engine import ProcessState, submit
+from aiida.engine import ProcessState
 from aiida.orm import load_node
 from aiida.orm import WorkChainNode, StructureData, TrajectoryData
-from aiida.plugins import WorkflowFactory
 
 from aiidalab_widgets_base import (
     AiidaNodeViewWidget,
@@ -87,7 +84,8 @@ def _on_submit_button_clicked(self, _):
 
     def submit(self):
         """Submit workflow, implementation must be provided by the the child class"""
-        raise NotImplementedError("FATAL: submit method not implemented")
+        msg = "FATAL: submit method not implemented"
+        raise NotImplementedError(msg)
 
     def _get_state(self):
         # Process is already running.
@@ -212,11 +210,9 @@ def _update_workflow_state(self, _=None):
         """To be implemented by child workflows
         to power the workflow-specific progress bar
         """
-        pass
 
     def _display_results(self, _=None):
         """Optional function to be called when the process is finished"""
-        pass
 
     @traitlets.observe("process_uuid")
     def _observe_process(self, change):

aiidalab_ispg/app/utils.py

@@ -26,6 +26,7 @@
 # https://github.com/pzarabadip/aiida-orca/issues/45
 MEMORY_PER_CPU = 3000  # Mb
 
+
 # TODO: Use numpy here? Measure the speed...
 # Energies expected in kJ / mole, Absolute temperature in Kelvins
 def calc_boltzmann_weights(energies, T):
@@ -48,7 +49,8 @@ def get_formula(data_node):
     elif isinstance(data_node, CifData):
         return data_node.get_ase().get_chemical_formula()
     else:
-        raise ValueError(f"Cannot get formula from node {type(data_node)}")
+        msg = f"Cannot get formula from node {type(data_node)}"
+        raise ValueError(msg)
 
 
 # https://stackoverflow.com/a/3382369