Add NEBCalculator with M3GNet and CHGNet example notebook

.github/workflows/linting.yml

@@ -11,24 +11,21 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Install dependencies
         run: |
-          pip install ruff black mypy
+          pip install ruff mypy
       - name: ruff
         run: |
           ruff --version
           ruff check matcalc
-      - name: black
-        run: |
-          black --version
-          black --check --diff --color matcalc
+          ruff format matcalc --check
       - name: mypy
         run: |
           mypy --version

.github/workflows/testing.yml

@@ -27,9 +27,9 @@ jobs:
       PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: pip
@@ -52,8 +52,8 @@ jobs:
     if: github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && inputs.task == 'release')
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: "3.11"
@@ -75,7 +75,7 @@ jobs:
       id-token: write
     steps:
       - name: Set up Python 3.11
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
       - name: Get build artifacts

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.6
+    rev: v0.1.7
     hooks:
       - id: ruff
         args: [--fix]
@@ -30,7 +30,7 @@ repos:
     hooks:
       - id: codespell
         stages: [commit, commit-msg]
-        exclude_types: [html, svg, javascript]
+        exclude_types: [html, svg, javascript, jupyter]
         exclude: ^.+\.lock$ # ignore lock files
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11