Fix new ruff lints

Author: danielhollas

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.15.4
     hooks:
-    - id: ruff
+    - id: ruff-check
       args: [--output-format=full, --fix]
     - id: ruff-format
 

aiidalab_ispg/app/spectrum.py

@@ -4,7 +4,10 @@
     * Daniel Hollas <daniel.hollas@bristol.ac.uk>
 """
 
+import base64
+import csv
 from enum import Enum, unique
+from tempfile import SpooledTemporaryFile
 
 import bokeh.plotting as plt
 import ipywidgets as ipw
@@ -332,7 +335,7 @@ def __init__(self, **kwargs):
 
     def _download_spectrum(self, btn):
         """Download spectrum lines as CSV file"""
-        from IPython.display import Javascript, display
+        from IPython.display import Javascript, display  # noqa: PLC0415
 
         filename = "spectrum.tsv"
         if self.smiles:
@@ -354,10 +357,6 @@ def _download_spectrum(self, btn):
         display(js)
 
     def _prepare_tsv(self):
-        import base64
-        import csv
-        from tempfile import SpooledTemporaryFile
-
         column_names = [
             f"Energy / ({self.energy_unit_selector.value.value})",
             f"Cross section / {self.intensity_unit}, "

aiidalab_ispg/app/spectrum_analysis.py

@@ -22,6 +22,13 @@
 from .utils import BokehFigureContext
 from .widgets import HeaderWarning
 
+try:
+    # For numpy 1.x
+    from numpy import trapz as trapezoid
+except ImportError:
+    # for numpy >=2.4
+    from numpy import trapezoid
+
 
 @unique
 class ActinicFlux(Enum):
@@ -310,7 +317,7 @@ def _update_j_plot(self, flux_type: ActinicFlux, quantumY: float):
         )
         # Integrate the differential j plot to get the total rate.
         # Use trapezoid rule.
-        j_total = np.trapz(j_diff, x=wavelengths)
+        j_total = trapezoid(j_diff, x=wavelengths)
         self.total_rate.value = f"<b>{np.format_float_scientific(j_total, 3)}</b>"
 
         # Plot slightly smoothed j_diff to make it less rugged.

aiidalab_ispg/app/steps.py

@@ -11,6 +11,7 @@
 import traitlets
 
 from aiida.engine import ProcessState
+from aiida.engine.processes.control import kill_processes
 from aiida.orm import StructureData, TrajectoryData, WorkChainNode, load_node
 from aiidalab_widgets_base import (
     AiidaNodeViewWidget,
@@ -273,8 +274,6 @@ def _on_click_kill_button(self, _=None):
 
         First kill the process, then update the kill button layout.
         """
-        from aiida.engine.processes.control import kill_processes
-
         self.kill_button.disabled = True
 
         workchain = [load_node(self.process_uuid)]

aiidalab_ispg/app/widgets.py

@@ -9,6 +9,7 @@
 import io
 import re
 from pathlib import Path
+from tempfile import NamedTemporaryFile
 from typing import Optional
 
 import ase
@@ -302,8 +303,6 @@ def _update_structure_viewer(self, change):
     # TODO: Maybe we want to have a separate button for this?
     def _prepare_payload(self, file_format=None):
         """Prepare binary information."""
-        from tempfile import NamedTemporaryFile
-
         file_format = file_format if file_format else self.file_format.value
         tmp = NamedTemporaryFile()
 

aiidalab_ispg/wigner/wigner.py

@@ -9,6 +9,8 @@
 import copy
 import math
 import random
+import sys
+from pathlib import Path
 
 # some constants
 CM_TO_HARTREE = (
@@ -124,9 +126,8 @@ def _convert_orca_normal_modes(self, modes, masses):
                     norm += modes[imode]["move"][j][xyz] ** 2 * mass / U_TO_AMU
             norm = math.sqrt(norm)
             if norm == 0.0 and freq >= self.low_freq_thr:
-                raise ValueError(
-                    "Displacement vector of mode %i is null vector!" % (imode + 1)
-                )
+                msg = f"Displacement vector of mode {imode + 1} is null vector!"
+                raise ValueError(msg)
 
             converted_mode = copy.deepcopy(modes[imode])
             for j, mass in enumerate(masses):
@@ -150,7 +151,7 @@ def wigner(Q, P):
 
 # Below are functions for CLI standalone use
 def parse_cmd():
-    import argparse
+    import argparse  # noqa: PLC0415
 
     desc = "Program for harmonic Wigner sampling"
     prog = "harmonwig"
@@ -199,16 +200,12 @@ def parse_cmd():
 
 
 def error(msg: str):
-    import sys
-
     print(f"ERROR: {msg}")
     sys.exit(1)
 
 
 def read_qm_output(fname: str, fmt: str = "auto") -> dict:
-    from pathlib import Path
-
-    from cclib.io import ccread
+    from cclib.io import ccread  # noqa: PLC0415
 
     path = Path(fname)
     try:

notebooks/workflow_workspace.ipynb

@@ -161,7 +161,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# from aiida.plugins import load_code\n",
+    "from aiida.plugins import load_code\n",
+    "\n",
     "Dict = DataFactory(\"core.dict\")\n",
     "old_workchain = load_node(pk=223)\n",
     "builder.structure = old_workchain.inputs.structure.get_structure(index=0)\n",

pyproject.toml

@@ -12,6 +12,7 @@ line-length = 88
 # TODO: Enable ruff for notebooks
 src = ["aiidalab_ispg", "tests"]
 target-version = "py39"
+extend-exclude = ["notebooks/workflow_workspace.ipynb"]
 
 [tool.ruff.lint]
 # Enable pyflakes and pyf-builtins, pyflakes, f=bugbear

tests/app/conftest.py

@@ -6,8 +6,8 @@
 
 import pytest
 import requests
+import requests.exceptions
 import selenium.webdriver.support.expected_conditions as EC
-from requests.exceptions import ConnectionError
 from selenium.webdriver.common.by import By
 from selenium.webdriver.support.wait import WebDriverWait
 
@@ -17,7 +17,7 @@ def is_responsive(url):
         response = requests.get(url, timeout=200)
         if response.status_code == 200:
             return True
-    except ConnectionError:
+    except requests.exceptions.ConnectionError:
         return False