Fix release CI (#122)

* update pre-commit hooks * pre-commit run --all-files * update GHA runner to macos-14 and pypa/cibuildwheel@v2.16.5 fixes release job, see pypa/cibuildwheel#1740
CederGroupHub · Feb 8, 2024 · 38bb60b · 38bb60b
1 parent 26dda61
commit 38bb60b
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Showing 8 changed files with 91 additions and 88 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-14, windows-latest]
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -29,7 +29,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.10"
           cache: pip
           cache-dependency-path: pyproject.toml
 
@@ -81,15 +81,15 @@ jobs:
     if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-14, windows-latest]
         python-version: ["39", "310", "311"]
     runs-on: ${{ matrix.os }}
     steps:
       - name: Check out repo
         uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.2
+        uses: pypa/cibuildwheel@v2.16.5
         env:
           CIBW_BUILD: cp${{ matrix.python-version }}-*
           CIBW_ARCHS_MACOS: universal2

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.2.1
     hooks:
       - id: ruff
         args: [--fix]
@@ -30,13 +30,13 @@ repos:
         args: [--check-filenames]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.7.1
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.7
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         args: [--write] # edit files in-place
@@ -46,7 +46,7 @@ repos:
           - svelte
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v9.0.0-alpha.1
+    rev: v9.0.0-alpha.2
     hooks:
       - id: eslint
         types: [file]

diff --git a/chgnet/utils/common_utils.py b/chgnet/utils/common_utils.py
@@ -73,7 +73,7 @@ def read_json(filepath: str) -> dict:
         filepath (str): file name of json to read.
 
     Returns:
-        dictionary stored in fjson
+        dict: data stored in filepath
     """
     with open(filepath) as file:
         return json.load(file)

diff --git a/examples/basics.ipynb b/examples/basics.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "f8c75a16",
+   "id": "0",
    "metadata": {},
    "source": [
     "# This notebook shows example to load the CHGNet for prediction\n"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87432e22",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +25,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7ead933c",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16eeae1e",
+   "id": "3",
    "metadata": {},
    "source": [
     "### Read structure from a json or cif file\n"
@@ -51,7 +51,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "208fa4aa",
+   "id": "4",
    "metadata": {},
    "outputs": [
     {
@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "abcc09b4",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Define Model\n"
@@ -103,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c04a0993",
+   "id": "6",
    "metadata": {},
    "outputs": [
     {
@@ -123,7 +123,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "961d51fc",
+   "id": "7",
    "metadata": {},
    "source": [
     "# Predict energy, force, stress, magmom\n"
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2c7c1997",
+   "id": "8",
    "metadata": {
     "pycharm": {
      "name": "#%%\n"
@@ -181,7 +181,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2258f2f5",
+   "id": "9",
    "metadata": {},
    "source": [
     "# Structure Optimization\n"
@@ -190,7 +190,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27dac383",
+   "id": "10",
    "metadata": {},
    "outputs": [
     {
@@ -211,7 +211,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "04bc3159",
+   "id": "11",
    "metadata": {},
    "outputs": [
     {
@@ -270,7 +270,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "06f7e84c",
+   "id": "12",
    "metadata": {},
    "source": [
     "# Molecular Dynamics\n"
@@ -279,7 +279,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1a59a5b5",
+   "id": "13",
    "metadata": {},
    "outputs": [
     {
@@ -316,7 +316,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c6a10ec8",
+   "id": "14",
    "metadata": {},
    "source": [
     "# Magmom Visualization\n"
@@ -325,7 +325,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2d5c2f93",
+   "id": "15",
    "metadata": {},
    "outputs": [
     {
@@ -344,7 +344,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "db4c9f16",
+   "id": "16",
    "metadata": {},
    "outputs": [
     {
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a0fe8e50",
+   "id": "17",
    "metadata": {},
    "outputs": [
     {
@@ -784,7 +784,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c96fb111",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -797,7 +797,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "71ac47b1",
+   "id": "19",
    "metadata": {},
    "outputs": [
     {
@@ -1862,7 +1862,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/examples/crystaltoolkit_relax_viewer.ipynb b/examples/crystaltoolkit_relax_viewer.ipynb
@@ -3,7 +3,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "f8c75a16",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Crystaltoolkit Relaxation Viewer\n",
@@ -14,7 +14,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "a51da8f4",
+   "id": "1",
    "metadata": {},
    "source": [
     "Running the last cell in this notebook should spin up a `dash` app that looks like this:\n",
@@ -25,7 +25,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "156e8031",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7ead933c",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e6792912",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "208fa4aa",
+   "id": "5",
    "metadata": {},
    "outputs": [
     {
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5d6e9fcc",
+   "id": "6",
    "metadata": {},
    "outputs": [
     {
@@ -218,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c04ebd43",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e7a91576",
+   "id": "8",
    "metadata": {},
    "outputs": [
     {
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c9f16422",
+   "id": "9",
    "metadata": {},
    "outputs": [
     {