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drop jupyter-dash (now included in regular dash) and update CTK relax…
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… viewer (#37)
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@janosh
janosh authored Jun 23, 2023
1 parent df4b1e6 commit 959ffcb
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Expand Up @@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg]

repos:
- repo: https://github.com/charliermarsh/ruff-pre-commit
rev: v0.0.274
rev: v0.0.275
hooks:
- id: ruff
args: [--fix]
Expand All @@ -27,7 +27,7 @@ repos:
- id: trailing-whitespace

- repo: https://github.com/codespell-project/codespell
rev: v2.2.4
rev: v2.2.5
hooks:
- id: codespell
stages: [commit, commit-msg]
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170 changes: 72 additions & 98 deletions examples/crystaltoolkit_relax_viewer.ipynb
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Expand Up @@ -93,18 +93,9 @@
"name": "stdout",
"output_type": "stream",
"text": [
"('Pmmn', 59)\n"
"original: ('Pmmn', 59)\n",
"perturbed: ('P1', 1)\n"
]
},
{
"data": {
"text/plain": [
"('P1', 1)"
]
},
"execution_count": null,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
Expand Down Expand Up @@ -134,89 +125,73 @@
"CHGNet will run on cpu\n",
" Step Time Energy fmax\n",
"*Force-consistent energies used in optimization.\n",
"FIRE: 0 16:14:42 -50.368877* 32.5095\n",
"FIRE: 1 16:14:42 -54.143169* 5.8680\n",
"FIRE: 2 16:14:42 -54.461754* 5.6230\n",
"FIRE: 3 16:14:42 -54.960907* 5.8534\n",
"FIRE: 4 16:14:42 -55.480988* 5.6906\n",
"FIRE: 5 16:14:42 -55.956520* 5.1693\n",
"FIRE: 6 16:14:42 -56.459927* 4.8143\n",
"FIRE: 7 16:14:42 -56.851875* 3.3015\n",
"FIRE: 8 16:14:42 -57.091263* 4.1499\n",
"FIRE: 9 16:14:42 -57.331764* 3.1478\n",
"FIRE: 10 16:14:42 -57.515900* 4.0483\n",
"FIRE: 11 16:14:42 -57.575695* 3.7472\n",
"FIRE: 12 16:14:42 -57.666180* 3.2176\n",
"FIRE: 13 16:14:42 -57.757183* 2.6150\n",
"FIRE: 14 16:14:42 -57.842495* 2.6404\n",
"FIRE: 15 16:14:42 -57.929653* 2.8689\n",
"FIRE: 16 16:14:42 -58.019592* 2.3735\n",
"FIRE: 17 16:14:42 -58.102535* 1.5942\n",
"FIRE: 18 16:14:42 -58.176746* 1.5989\n",
"FIRE: 19 16:14:42 -58.243935* 2.1723\n",
"FIRE: 20 16:14:42 -58.310703* 1.9688\n",
"FIRE: 21 16:14:43 -58.363392* 1.4786\n",
"FIRE: 22 16:14:43 -58.389481* 1.7102\n",
"FIRE: 23 16:14:43 -58.418602* 1.8503\n",
"FIRE: 24 16:14:43 -58.471935* 1.1974\n",
"FIRE: 25 16:14:43 -58.517002* 1.7578\n",
"FIRE: 26 16:14:43 -58.553810* 1.8129\n",
"FIRE: 27 16:14:43 -58.613503* 1.6485\n",
"FIRE: 28 16:14:43 -58.704597* 1.0232\n",
"FIRE: 29 16:14:43 -58.729168* 2.2496\n",
"FIRE: 30 16:14:43 -58.753529* 1.2002\n",
"FIRE: 31 16:14:43 -58.771957* 0.7578\n",
"FIRE: 32 16:14:43 -58.777966* 1.5446\n",
"FIRE: 33 16:14:43 -58.780994* 1.3726\n",
"FIRE: 34 16:14:43 -58.786022* 1.0541\n",
"FIRE: 35 16:14:43 -58.791451* 0.6607\n",
"FIRE: 36 16:14:43 -58.795883* 0.6259\n",
"FIRE: 37 16:14:43 -58.798832* 0.5877\n",
"FIRE: 38 16:14:43 -58.801147* 0.6803\n",
"FIRE: 39 16:14:43 -58.804146* 0.8653\n",
"FIRE: 40 16:14:44 -58.809155* 0.8536\n",
"FIRE: 41 16:14:44 -58.816200* 0.6149\n",
"FIRE: 42 16:14:44 -58.823708* 0.4149\n",
"FIRE: 43 16:14:44 -58.829689* 0.3795\n",
"FIRE: 44 16:14:44 -58.835079* 0.6436\n",
"FIRE: 45 16:14:44 -58.842659* 0.5568\n",
"FIRE: 46 16:14:44 -58.851486* 0.3081\n",
"FIRE: 47 16:14:44 -58.857994* 0.5840\n",
"FIRE: 48 16:14:44 -58.865871* 0.6220\n",
"FIRE: 49 16:14:44 -58.875755* 0.2659\n",
"FIRE: 50 16:14:44 -58.883583* 0.5791\n",
"FIRE: 51 16:14:44 -58.895329* 0.2525\n",
"FIRE: 52 16:14:44 -58.904892* 0.6525\n",
"FIRE: 53 16:14:44 -58.918137* 0.2268\n",
"FIRE: 54 16:14:44 -58.928265* 0.4081\n",
"FIRE: 55 16:14:44 -58.935215* 0.8279\n",
"FIRE: 56 16:14:44 -58.938522* 0.2784\n",
"FIRE: 57 16:14:44 -58.939091* 0.4389\n",
"FIRE: 58 16:14:44 -58.939426* 0.3746\n",
"FIRE: 59 16:14:45 -58.939934* 0.2563\n",
"FIRE: 60 16:14:45 -58.940437* 0.1812\n",
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"FIRE: 62 16:14:45 -58.941128* 0.1983\n",
"FIRE: 63 16:14:45 -58.941517* 0.2484\n",
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"FIRE: 65 16:14:45 -58.942848* 0.1787\n",
"FIRE: 66 16:14:45 -58.943714* 0.1757\n",
"FIRE: 67 16:14:45 -58.944485* 0.1723\n",
"FIRE: 68 16:14:45 -58.945293* 0.2152\n",
"FIRE: 69 16:14:45 -58.946426* 0.1687\n",
"FIRE: 70 16:14:45 -58.947723* 0.1692\n",
"FIRE: 71 16:14:45 -58.948978* 0.1853\n",
"FIRE: 72 16:14:45 -58.950665* 0.1663\n",
"FIRE: 73 16:14:45 -58.952576* 0.1604\n",
"FIRE: 74 16:14:46 -58.954712* 0.1559\n",
"FIRE: 75 16:14:46 -58.957211* 0.1533\n",
"FIRE: 76 16:14:46 -58.959904* 0.1449\n",
"FIRE: 77 16:14:46 -58.962624* 0.2165\n",
"FIRE: 78 16:14:46 -58.965687* 0.1903\n",
"FIRE: 79 16:14:46 -58.968777* 0.1781\n",
"FIRE: 80 16:14:46 -58.971272* 0.3301\n",
"FIRE: 81 16:14:46 -58.970631* 0.8330\n",
"FIRE: 82 16:14:46 -58.973919* 0.0508\n"
"FIRE: 0 14:01:10 -51.912251* 27.2278\n",
"FIRE: 1 14:01:10 -54.259518* 12.3964\n",
"FIRE: 2 14:01:10 -54.778671* 8.5672\n",
"FIRE: 3 14:01:11 -55.339821* 5.5388\n",
"FIRE: 4 14:01:11 -55.653206* 7.1592\n",
"FIRE: 5 14:01:11 -56.225849* 6.6752\n",
"FIRE: 6 14:01:11 -56.975388* 4.2375\n",
"FIRE: 7 14:01:11 -57.431259* 4.4837\n",
"FIRE: 8 14:01:11 -57.696171* 5.3055\n",
"FIRE: 9 14:01:11 -57.933193* 3.3038\n",
"FIRE: 10 14:01:11 -57.887894* 6.1535\n",
"FIRE: 11 14:01:11 -57.981998* 4.7339\n",
"FIRE: 12 14:01:12 -58.107471* 3.2390\n",
"FIRE: 13 14:01:12 -58.196518* 2.3609\n",
"FIRE: 14 14:01:12 -58.237015* 2.6211\n",
"FIRE: 15 14:01:12 -58.271477* 3.3198\n",
"FIRE: 16 14:01:12 -58.323418* 3.1086\n",
"FIRE: 17 14:01:12 -58.385509* 2.3118\n",
"FIRE: 18 14:01:12 -58.443253* 1.6311\n",
"FIRE: 19 14:01:12 -58.478363* 2.3351\n",
"FIRE: 20 14:01:12 -58.506485* 2.9915\n",
"FIRE: 21 14:01:13 -58.553890* 2.3584\n",
"FIRE: 22 14:01:13 -58.591610* 1.3229\n",
"FIRE: 23 14:01:13 -58.600597* 2.5641\n",
"FIRE: 24 14:01:13 -58.612297* 2.2842\n",
"FIRE: 25 14:01:13 -58.631424* 1.7666\n",
"FIRE: 26 14:01:13 -58.651585* 1.1141\n",
"FIRE: 27 14:01:14 -58.667530* 1.0229\n",
"FIRE: 28 14:01:14 -58.678112* 1.0305\n",
"FIRE: 29 14:01:14 -58.686382* 1.3254\n",
"FIRE: 30 14:01:14 -58.695862* 1.3551\n",
"FIRE: 31 14:01:14 -58.708542* 1.1167\n",
"FIRE: 32 14:01:14 -58.721897* 0.8152\n",
"FIRE: 33 14:01:14 -58.732655* 0.9976\n",
"FIRE: 34 14:01:14 -58.743347* 1.2707\n",
"FIRE: 35 14:01:14 -58.759544* 1.0066\n",
"FIRE: 36 14:01:15 -58.777481* 0.5213\n",
"FIRE: 37 14:01:15 -58.788338* 1.0805\n",
"FIRE: 38 14:01:15 -58.805302* 1.2441\n",
"FIRE: 39 14:01:15 -58.834023* 0.4629\n",
"FIRE: 40 14:01:15 -58.856319* 1.0140\n",
"FIRE: 41 14:01:15 -58.881325* 0.5240\n",
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"FIRE: 49 14:01:16 -58.949738* 0.3384\n",
"FIRE: 50 14:01:16 -58.950603* 0.2155\n",
"FIRE: 51 14:01:16 -58.951290* 0.2596\n",
"FIRE: 52 14:01:16 -58.951885* 0.2818\n",
"FIRE: 53 14:01:16 -58.952572* 0.2948\n",
"FIRE: 54 14:01:17 -58.953487* 0.2832\n",
"FIRE: 55 14:01:17 -58.954651* 0.1820\n",
"FIRE: 56 14:01:17 -58.955776* 0.1377\n",
"FIRE: 57 14:01:17 -58.956646* 0.1858\n",
"FIRE: 58 14:01:17 -58.957542* 0.2483\n",
"FIRE: 59 14:01:17 -58.958771* 0.1507\n",
"FIRE: 60 14:01:17 -58.959930* 0.1098\n",
"FIRE: 61 14:01:17 -58.960972* 0.2491\n",
"FIRE: 62 14:01:17 -58.962578* 0.1265\n",
"FIRE: 63 14:01:17 -58.964127* 0.1622\n",
"FIRE: 64 14:01:18 -58.965885* 0.1447\n",
"FIRE: 65 14:01:18 -58.967422* 0.2064\n",
"FIRE: 66 14:01:18 -58.968880* 0.0730\n"
]
}
],
Expand Down Expand Up @@ -315,12 +290,11 @@
"import crystal_toolkit.components as ctc\n",
"import plotly.graph_objects as go\n",
"from crystal_toolkit.settings import SETTINGS\n",
"from dash import dcc, html\n",
"from dash import Dash, dcc, html\n",
"from dash.dependencies import Input, Output\n",
"from jupyter_dash import JupyterDash\n",
"from pymatgen.core import Structure\n",
"\n",
"app = JupyterDash(prevent_initial_callbacks=True, assets_folder=SETTINGS.ASSETS_PATH)\n",
"app = Dash(prevent_initial_callbacks=True, assets_folder=SETTINGS.ASSETS_PATH)\n",
"\n",
"step_size = max(1, len(trajectory) // 20) # ensure slider has max 20 steps\n",
"slider = dcc.Slider(\n",
Expand Down Expand Up @@ -437,7 +411,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.0"
"version": "3.11.4"
}
},
"nbformat": 4,
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -32,7 +32,7 @@ classifiers = [
[project.optional-dependencies]
test = ["pytest", "pytest-cov"]
# needed to run interactive example notebooks
crystal-toolkit = ["crystal-toolkit", "jupyter-dash"]
crystal-toolkit = ["crystal-toolkit"]

[project.urls]
Source = "https://github.com/CederGroupHub/chgnet"
Expand All @@ -55,6 +55,7 @@ select = [
"E", # pycodestyle error
"EXE", # flake8-executable
"F", # pyflakes
"FA", # flake8-future-annotations
"FLY", # flynt
"I", # isort
"ICN", # flake8-import-conventions
Expand Down Expand Up @@ -84,7 +85,6 @@ ignore = [
"D100", # Missing docstring in public module
"D104", # Missing docstring in public package
"D205", # 1 blank line required between summary line and description
"PLC1901", # compare-to-empty-string
"PLR", # pylint refactor
"PLW2901", # Outer for loop variable overwritten by inner assignment target
"PT006", # pytest-parametrize-names-wrong-type
Expand Down

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