Update pre-commit config and change the code accordingly

.pre-commit-config.yaml

@@ -1,20 +1,66 @@
-# # Install pre-commit hooks via
-# pre-commit install
+---
+ci:
+    autoupdat_schedule: quarterly
 
-- repo: local
-  hooks:
-  # yapf = yet another python formatter
-  - id: yapf
-    name: yapf
-    entry: yapf
-    language: system
-    types: [python]
-    args: ["-i"]
-
-  # prospector: collection of linters
-  - id: prospector
-    language: system
-    types: [file, python]
-    name: prospector
-    description: "This hook runs Prospector: https://github.com/landscapeio/prospector"
-    entry: prospector
+repos:
+    - repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+          - id: end-of-file-fixer
+          - id: trailing-whitespace
+          - id: check-yaml
+          - id: check-added-large-files
+    - repo: https://github.com/pycqa/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
+            args: [--profile, black, --filter-files]
+    - repo: https://github.com/PyCQA/autoflake
+      rev: v2.1.1
+      hooks:
+          - id: autoflake
+    - repo: https://github.com/asottile/pyupgrade
+      rev: v3.4.0
+      hooks:
+          - id: pyupgrade
+            args: [--py38-plus]
+    - repo: https://github.com/psf/black
+      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
+      hooks:
+          - id: flake8
+            args: [--count, --show-source, --statistics]
+            additional_dependencies:
+                - flake8-bugbear
+                - flake8-builtins
+                - flake8-comprehensions
+                - flake8-debugger
+                - flake8-logging-format
+                - pep8-naming
+                - pyflakes
+                - tryceratops
+    - repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v1.3.0
+      hooks:
+          - id: mypy
+            additional_dependencies:
+                - types-click-spinner
+                - types-requests
+                - types-tabulate
+                - types-toml
+    - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+      rev: 0.2.3
+      hooks:
+          - id: yamlfmt
+    - repo: https://github.com/asottile/setup-cfg-fmt
+      rev: v2.2.0
+      hooks:
+          - id: setup-cfg-fmt
+    - repo: https://github.com/kynan/nbstripout
+      rev: 0.6.1
+      hooks:
+          - id: nbstripout

LICENSE.txt

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

README.md

@@ -15,7 +15,7 @@ To get an idea of how it works, please [check out the videos](https://www.youtub
 
 ## Uploading a new structure
 File formats compatible with [ASE](https://wiki.fysik.dtu.dk/ase/) can be used.
-In the example a .mol file for a structure is generated with ChemDraw. 
+In the example a .mol file for a structure is generated with ChemDraw.
 
 The structure is uploaded, a warning message is provided if similar structures were already computed.
 

compare.ipynb

@@ -52,9 +52,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "def make_plots(pk_list):\n",

export_structure.ipynb

@@ -2,24 +2,9 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7834195bf63045f38d46585f64d12e3f",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "_ColormakerRegistry()"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "%aiida\n",
     "from aiidalab_widgets_base import viewer\n",
@@ -28,45 +13,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b13b606b7c574f279828ee27314fffdf",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "StructureDataVisualizer(children=(NGLWidget(), HBox(children=(Dropdown(description='File format:', options=('x…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "uuid = urlparse.parse_qs(urlparse.urlsplit(jupyter_notebook_url).query)['uuid'][0]\n",
     "display(viewer(load_node(uuid=uuid)))"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'676167bc-1bae-4b70-a5cc-d813731f1db2'"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "uuid"
    ]

nanoribbon/editors/__init__.py

@@ -1,8 +1,5 @@
-"""Nanoribbon AiiDA lab viewers."""
-# pylint: disable=unused-import,wrong-import-position
+"""Nanoribbon AiiDAlab viewers."""
 
-from __future__ import absolute_import
-from aiida import load_profile
-load_profile()
+from .replicate import NanoribbonReplicateEditor
 
-from .replicate import NanoribbonReplicateEditor
+__all__ = ["NanoribbonReplicateEditor"]

nanoribbon/editors/replicate.py

@@ -1,48 +1,34 @@
-import numpy as np
-from numpy.linalg import norm
-from ase import Atoms
-from ase.data import covalent_radii
-from ase.neighborlist import NeighborList
-import ase.neighborlist
-import scipy.stats
-from scipy.constants import physical_constants
-import itertools
-from IPython.display import display, clear_output, HTML
-import nglview
 import ipywidgets as ipw
-
-from traitlets import HasTraits, Instance, Dict, Unicode, dlink, link, observe
-from aiidalab_widgets_base import StructureManagerWidget
+from ase import Atoms
+from traitlets import Instance
 
 
 class NanoribbonReplicateEditor(ipw.VBox):
     structure = Instance(Atoms, allow_none=True)
-    def __init__(self, title=''):
+
+    def __init__(self, title=""):
         self.title = title
         self._molecule = None
-        self.nx_slider = ipw.IntSlider(description="nx", min=1, max=6, continuous_update=False)    
-
+        self.nx_slider = ipw.IntSlider(
+            description="nx", min=1, max=6, continuous_update=False
+        )
+
         self.create_bttn = ipw.Button(description="Replicate")
         self.create_bttn.on_click(self.replicate)
-        self.info = ipw.HTML('')
-        super().__init__(children=[
-            ipw.HBox([self.nx_slider, self.create_bttn]),
-            self.info,
-        ])
-
+        self.info = ipw.HTML("")
+        super().__init__(
+            children=[
+                ipw.HBox([self.nx_slider, self.create_bttn]),
+                self.info,
+            ]
+        )
+
     def replicate(self, _=None):
         """Create slab and remember the last molecule used."""
-        #sa = StructureAnalyzer()
-        #sa.structure = self.molecule
-        self.info.value = ''
+        # sa = StructureAnalyzer()
+        # sa.structure = self.molecule
+        self.info.value = ""
         atoms = self.structure.copy()
-        nx = self.nx_slider.value
-        
+        self.nx_slider.value
+
         self.structure = atoms.repeat((self.nx_slider.value, 1, 1))
-
-#    @observe('molecule')
-#    def on_struct_change(self, change=None):
-#        """Selected molecule from structure."""
-#
-#        if self.molecule:
-#            self.nx_slider.value = 1

nanoribbon/viewers/__init__.py

@@ -1,12 +1,13 @@
-"""Nanoribbon AiiDA lab viewers."""
-# pylint: disable=unused-import,wrong-import-position
-
-from __future__ import absolute_import
-from aiida import load_profile
-load_profile()
+"""Nanoribbon AiiDAlab viewers."""
 
+from .cdxml2gnr import CdxmlUpload2GnrWidget
+from .pdos_computed import NanoribbonPDOSWidget
 from .search import NanoribbonSearchWidget
 from .show_computed import NanoribbonShowWidget
-from .pdos_computed import NanoribbonPDOSWidget
-#from .smiles2gnr import Smiles2GnrWidget
-from .cdxml2gnr import CdxmlUpload2GnrWidget
+
+__all__ = [
+    "CdxmlUpload2GnrWidget",
+    "NanoribbonPDOSWidget",
+    "NanoribbonSearchWidget",
+    "NanoribbonShowWidget",
+]