Merge branch 'main' into feature/aiida-control-page

.github/dependabot.yml

@@ -0,0 +1,12 @@
+---
+version: 2
+updates:
+# Maintain dependencies for GitHub Actions
+    - package-ecosystem: github-actions
+      directory: /
+      schedule:
+          interval: monthly
+      groups:
+          gha-dependencies:
+              patterns:
+                  - '*'

.github/workflows/ci.yml

@@ -13,12 +13,12 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v4
 
             - name: Setup Python
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v5
               with:
-                  python-version: 3.8
+                  python-version: 3.11
 
             - name: Install dependencies
               run: |

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
         runs-on: ubuntu-latest
 
         steps:
-            - uses: softprops/action-gh-release@v0.1.14
+            - uses: softprops/action-gh-release@v2.0.5
               name: Create release.
               with:
                   generate_release_notes: true

.pre-commit-config.yaml

@@ -5,50 +5,38 @@ ci:
 repos:
 
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
+      rev: v4.5.0
       hooks:
           - id: check-json
           - id: check-yaml
           - id: end-of-file-fixer
           - id: trailing-whitespace
             exclude: miscellaneous/structures/SiO2.xyz
 
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.3.5
+      hooks:
+          - id: ruff-format
+            exclude: ^docs/.*
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix, --show-fixes]
+
     - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
       rev: 0.2.3
       hooks:
           - id: yamlfmt
 
-    - 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
-
-    - repo: https://github.com/pycqa/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-            args: [--profile, black, --filter-files]
-
     - repo: https://github.com/asottile/setup-cfg-fmt
-      rev: v2.4.0
+      rev: v2.5.0
       hooks:
           - id: setup-cfg-fmt
 
     - repo: https://github.com/sirosen/check-jsonschema
-      rev: 0.23.2
+      rev: 0.28.1
       hooks:
           - id: check-github-workflows
 
     - repo: https://github.com/kynan/nbstripout
-      rev: 0.6.1
+      rev: 0.7.1
       hooks:
           - id: nbstripout

appstore.ipynb

@@ -19,6 +19,9 @@
     "%%javascript\n",
     "IPython.OutputArea.prototype._should_scroll = function(lines) {\n",
     "    return false;\n",
+    "}\n",
+    "if (document.getElementById('appmode-busy')) {\n",
+    "    window.onbeforeunload = function() {return}\n",
     "}"
    ]
   },

home/app_manager.py

@@ -1,5 +1,5 @@
-# -*- coding: utf-8 -*-
 """Module that contains widgets for managing AiiDAlab applications."""
+
 from subprocess import CalledProcessError
 
 import ipywidgets as ipw
@@ -69,9 +69,9 @@ def __init__(self, *args, **kwargs):
         )
 
         super().__init__(
+            *args,
             children=[self.installed_version, self.version_to_install, self.info],
             layout={"min_width": "300px"},
-            *args,
             **kwargs,
         )
 
@@ -207,7 +207,7 @@ def __init__(self, app, minimalistic=False):
         self.app.observe(
             self._refresh_prereleases, names=["has_prereleases", "installed_version"]
         )
-        self._refresh_prereleases(change=dict(owner=self.app))  # initialize
+        self._refresh_prereleases(change={"owner": self.app})  # initialize
 
         children = [
             ipw.HBox([self.header_warning]),

home/app_store.py

@@ -1,5 +1,5 @@
-# -*- coding: utf-8 -*-
 """AiiDAlab app store."""
+
 import logging
 
 import ipywidgets as ipw
@@ -21,7 +21,7 @@ def __init__(self):
             self.index = load_app_registry_index()
         except RuntimeError as error:
             logger.warning(error)
-            self.index = dict(apps=[], categories=[])
+            self.index = {"apps": [], "categories": []}
         self.output = ipw.Output()
 
         # Apps per page.
@@ -120,12 +120,8 @@ def change_vis_list(self, _=None):
 
         if self.category_filter.value:
             all_apps = self.apps_to_display
-            self.apps_to_display = (
-                []
-            )  # clear the array that contains all the apps to be displayed
-            self.app_corresponding_categories = (
-                []
-            )  # create a parallel array that contains corresponding category names
+            self.apps_to_display = []  # clear the array that contains all the apps to be displayed
+            self.app_corresponding_categories = []  # create a parallel array that contains corresponding category names
             # iterate over all categories
             for category in self.category_filter.value:
                 category_key = self.category_title_key_mapping[category]

home/start_page.py

@@ -1,4 +1,5 @@
 """Module to generate AiiDAlab home page."""
+
 import json
 from functools import wraps
 from glob import glob
@@ -60,7 +61,7 @@ class AiidaLabHome:
     def __init__(self):
         self.config_fn = ".launcher.json"
         self.output = ipw.Output()
-        self._app_widgets = dict()
+        self._app_widgets = {}
 
     def _create_app_widget(self, name):
         """Create the widget representing the app on the home screen."""
@@ -92,7 +93,7 @@ def write_config(self, config):
 
     def read_config(self):
         if path.exists(self.config_fn):
-            return json.load(open(self.config_fn, "r"))
+            return json.load(open(self.config_fn))
         return {"order": [], "hidden": []}  # default config
 
     def render(self):
@@ -124,7 +125,7 @@ def load_apps(self):
         apps.sort(key=lambda x: order.index(x) if x in order else -1)
         config["order"] = apps
         self.write_config(config)
-        return ["home"] + apps
+        return ["home", *apps]
 
     def move_updown(self, name, delta):
         """Move the app up/down on the start page."""

home/utils.py

@@ -33,15 +33,15 @@ def load_start_py(name):
         except TypeError:
             return mod.get_start_widget(appbase=appbase, jupbase=jupbase)
     except Exception:  # pylint: disable=broad-except
-        return ipw.HTML("<pre>{}</pre>".format(sys.exc_info()))
+        return ipw.HTML(f"<pre>{sys.exc_info()}</pre>")
 
 
 def load_start_md(name):
     """Load app appearance from a Markdown file."""
     fname = path.join(AIIDALAB_APPS, name, "start.md")
     try:
         md_src = open(fname).read()
-        md_src = md_src.replace("](./", "](../{}/".format(name))
+        md_src = md_src.replace("](./", f"](../{name}/")
         html = markdown(md_src)
 
         # open links in new window/tab
@@ -52,7 +52,7 @@ def load_start_md(name):
         return ipw.HTML(html)
 
     except Exception as exc:  # pylint: disable=broad-except
-        return ipw.HTML("Could not load start.md: {}".format(str(exc)))
+        return ipw.HTML(f"Could not load start.md: {exc!s}")
 
 
 def load_logo(app):

home/widgets.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """AiiDAlab basic widgets."""
 
 from threading import Timer
@@ -104,7 +103,7 @@ class AppStatusInfoWidget(ipw.HTML):
         "and avoid compatibility isssues."
     )
 
-    MESSAGES_UPDATES = {
+    MESSAGES_UPDATES = {  # noqa: RUF012
         AppStatus.CANNOT_REACH_REGISTRY: f'<div title="Unable to reach the registry server ({AIIDALAB_REGISTRY}).">'
         f'<font color="{Theme.COLORS.GRAY}">{Theme.ICONS.APP_UPDATE_AVAILABLE_UNKNOWN} '
         "Cannot reach server.</font></div>",

open_app.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1e6a8c8c",
+   "id": "0",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -14,7 +14,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7e7e205e",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b3e749de",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -55,7 +55,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c25a71a5",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [

pyproject.toml

@@ -0,0 +1,31 @@
+[build-system]
+# this version is required to support reading of version in setup.cfg
+requires = ["setuptools>=46.4.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.ruff]
+line-length = 88
+show-fixes = true
+target-version = "py38"
+
+[tool.ruff.lint]
+ignore = ["E501", "E402", "B904", "TRY003"]
+select = [
+  "A",    # flake8-builtins
+  "ARG",  # flake8-unused-arguments
+  "B",    # flake8-bugbear
+  "C4",   # flake8-comprehensions
+  "E",    # pycodestyle
+  "F",    # pyflakes
+  "I",    # isort
+  "N",    # pep8-naming
+  "PLE",  # pylint error rules
+  "PLW",  # pylint warning rules
+  "PLC",  # pylint convention rules
+  "RUF",  # ruff-specific rules
+  "TRY",  # Tryceratops
+  "UP"    # pyupgrade
+]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["ARG001"]

setup.cfg

@@ -28,12 +28,12 @@ install_requires =
     ipywidgets~=7.6
     traitlets~=5.0
     widgetsnbextension<3.6.3  # Hotfix. Remove when #149 is fixed
-python_requires = >=3.8
+python_requires = >=3.9
 
 [options.extras_require]
 dev =
     bumpver==2022.1118
-    pre-commit==2.15.0
+    pre-commit==3.6.0
 
 [flake8]
 ignore =

setup.py

@@ -1,5 +1,5 @@
-# -*- coding: utf8 -*-
 """This file is required for editable installs of the package."""
+
 from setuptools import setup
 
 setup()

single_app.ipynb

@@ -9,6 +9,9 @@
     "%%javascript\n",
     "IPython.OutputArea.prototype._should_scroll = function(lines) {\n",
     "    return false;\n",
+    "}\n",
+    "if (document.getElementById('appmode-busy')) {\n",
+    "    window.onbeforeunload = function() {return}\n",
     "}"
    ]
   },