Merge branch 'jupyter-book' into 'main'

doc: update gh-action; update toc

See merge request cheng-group/ai2-kit!41

.github/workflows/doc.yml

@@ -11,21 +11,20 @@ jobs:
   deploy-book:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     # Install dependencies
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.8
+        python-version: 3.9
 
     - name: Run image
       uses: abatilo/actions-poetry@v2
-      with:
-        poetry-version: 1.4.2
 
     - name: Install dependencies
       run: |
+        rm -f poetry.lock
         poetry install
     
     - name: Sphinx APIDoc
@@ -39,7 +38,7 @@ jobs:
 
     # Push the book's HTML to github-pages
     - name: GitHub Pages action
-      uses: peaceiris/actions-gh-pages@v3.6.1
+      uses: peaceiris/actions-gh-pages@v3
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: jupyter-book/_build/html

jupyter-book/_toc.yml

@@ -7,18 +7,24 @@ parts:
   - caption: Featuring Tools
     chapters:
       - file: doc/manual/ai2cat.md
-  - caption: Domain Specific Tools
+  - caption: Workflows
     chapters:
-      - file: doc/manual/proton-transfer
       - file: doc/manual/cll-workflow
       - file: doc/manual/fep-workflow
+  - caption: Domain Specific Tools
+    chapters:
+      - file: doc/manual/proton-transfer
+      - file: doc/manual/aos-analysis
   - caption: Build-in Functionalities
     chapters:
       - file: doc/manual/checkpoint
       - file: doc/manual/hpc-executor
       - file: doc/manual/ase
       - file: doc/manual/dpdata
       - file: doc/manual/tips
+  - caption: Notebooks
+    chapters:
+      - file: notebook/ai2cat.ipynb
   - caption: 中文文档
     chapters:
       - file: doc/manual/cll-workflow.zh

jupyter-book/intro.md

@@ -1,8 +1,10 @@
 # ai<sup>2</sup>-kit
 
 [![PyPI version](https://badge.fury.io/py/ai2-kit.svg)](https://badge.fury.io/py/ai2-kit)
+[![PyPI - Downloads](https://img.shields.io/pypi/dm/ai2-kit)](https://pypi.org/project/ai2-kit/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ai2-kit)](https://pypi.org/project/ai2-kit/)
 
+
 A toolkit featured _**a**rtificial **i**ntelligence × **a**b **i**nitio_ for computational chemistry research.
 
 *Please be advised that `ai2-kit` is still under heavy development and you should expect things to change often. We encourage people to play and explore with `ai2-kit`, and stay tuned with us for more features to come.*

jupyter-book/notebook

@@ -0,0 +1 @@
+../notebook