Fix colab button links in website attempt 2 (#105)

* Replace symbolic link to docs/notebooks by files copy in website.yaml

* Update pytest configuration

* Use MacOS instead of Windows OS becauase PySCF does not support windows

* Update the website building workflow

- Build the website for multiple-cases
- Only push to the gh-pages when in master branch

* Use the latest version of actions-gh-pages

* Add the information of `PySCF` in the installation guide

---------

Co-authored-by: Gabriela Sanchez-Diaz <[email protected]>, Fanwang Meng <[email protected]>

.github/workflows/pytest.yaml

@@ -15,14 +15,16 @@ jobs:
 
     strategy:
       matrix:
-        os: ["ubuntu-latest", "windows-latest"]
-        py: ["3.9", "3.10", "3.11"]
+        # windows-latest is not supported because pyscf is not supported on windows
+        # https://pyscf.org/user/install.html
+        os: ["ubuntu-latest", "macos-latest"]
+        py: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: "actions/checkout@v3"
+      - uses: "actions/checkout@v4"
 
       - name: Setup python for test ${{ matrix.py }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.py }}
 
@@ -56,4 +58,4 @@ jobs:
           job-summary: true
           click-to-expand: true
           report-title: 'Dev Test Report'
-          pytest-args: '-m dev'
+          pytest-args: '-m dev'

.github/workflows/website.yaml

@@ -3,30 +3,32 @@ name: build_website
 on:
 
   push:
+    branches:
+      - master
+      - main
 
+  # this ensures that the website is built when a PR is opened, synchronized, reopened, or closed
+  # and the PR is not breaking the website building process
+  pull_request:
+    types: [opened, synchronize, reopened, closed]
     branches:
+      - main
       - master
 
 permissions:
-
   contents: write
   deployments: write
   pages: write
 
 jobs:
-
   build:
-
     runs-on: ubuntu-latest
-
     permissions:
-
       contents: write
       deployments: write
       pages: write
 
     steps:
-
     - name: Checkout repository
       uses: actions/checkout@v4
 
@@ -48,8 +50,7 @@ jobs:
     - name: Create soft links
       run: |
         cd website
-        ln -s ../docs/notebooks ./examples
-        ln -s ../docs/notebooks/images ./examples/images
+        cp -lR ../docs/notebooks ./examples
         ln -s ../docs/source ./api
         cd ../
 
@@ -65,10 +66,10 @@ jobs:
       # inspired by https://github.com/orgs/community/discussions/26724
       # only push to gh-pages if the master branch has been updated
     - name: GitHub Pages Action
-      # if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
-      uses: peaceiris/actions-gh-pages@v3
+      if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/master' }}
+      uses: peaceiris/actions-gh-pages@v4.0.0
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: ./website/_build/html
         publish_branch: gh-pages
-        cname: atomdb.qcdevs.org
+        cname: atomdb.qcdevs.org

website/installation.rst

@@ -3,6 +3,11 @@
 Installation
 ############
 
+.. note::
+   Because the dependency `PySCF <https://pyscf.org/user/install.html>`
+   does not support Windows, `AtomDB` is not supported on Windows. But we can use
+   `AtomDB` with `Windows Subsystem for Linux (WSL) <https://learn.microsoft.com/en-us/windows/wsl/>`_.
+
 Downloading Code
 ================
 
@@ -136,4 +141,4 @@ formats, run,
 
 .. code-block:: bash
 
-    make
+    make