update gh actions and docs

Author: taoliu

.github/workflows/build-and-test-MACS3-macos.yml

@@ -23,22 +23,22 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [macos-13]
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        os: [macos-latest]
+        python-version: ["3.12", "3.13", "3.14"]
     runs-on: ${{ matrix.os }}
     name: Build on ${{ matrix.os }} with Python ${{ matrix.python-version }}
 
     steps:
       - name: Checkout MACS
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: 'true'
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache pip
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           # This path is specific to Ubuntu
           path: ~/.cache/pip
@@ -76,7 +76,7 @@ jobs:
           source macs3venv/bin/activate
           python3 setup.py sdist
       - name: Archive sdist
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: sdist-${{ matrix.os }}-${{ matrix.python-version }}
           path: |

.github/workflows/build-and-test-MACS3-non-x64-others.yml

@@ -8,8 +8,8 @@ on:
 
 jobs:
   build_job:
-    runs-on: ubuntu-22.04
-    name: Build on ${{ matrix.arch }} with Python 3.10
+    runs-on: ubuntu-24.04
+    name: Build on ${{ matrix.arch }} with Python 3.12
     strategy:
       matrix:
         include:
@@ -19,16 +19,16 @@ jobs:
 
     steps:
       - name: Checkout MACS
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: 'true'
 
       - name: Set up arch and run
-        uses: uraimo/run-on-arch-action@v2
+        uses: uraimo/run-on-arch-action@v3
         id: build
         with:
           arch: ${{ matrix.arch }}
-          distro: ubuntu22.04
+          distro: ubuntu24.04
 
           githubToken: ${{ github.token }}
 
@@ -89,7 +89,7 @@ jobs:
 
       - name: Archive cmdlinetest results
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: cmdlinetest-hmmratac-results-${{ matrix.arch }}
           path: temp/macs3_run_hmmratac/

.github/workflows/build-and-test-MACS3-non-x64.yml

@@ -21,25 +21,25 @@ on:
 
 jobs:
   build_job:
-    runs-on: ubuntu-22.04
-    name: Build on ${{ matrix.arch }} with Python 3.10
+    runs-on: ubuntu-24.04
+    name: Build on ${{ matrix.arch }} with Python 3.12
     strategy:
       matrix:
         include:
           - arch: aarch64
 
     steps:
       - name: Checkout MACS
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: 'true'
 
       - name: Set up arch and run
-        uses: uraimo/run-on-arch-action@v2
+        uses: uraimo/run-on-arch-action@v3
         id: build
         with:
           arch: ${{ matrix.arch }}
-          distro: ubuntu22.04
+          distro: ubuntu-24.04
 
           githubToken: ${{ github.token }}
 
@@ -100,7 +100,7 @@ jobs:
 
       - name: Archive cmdlinetest results
         if: always()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: cmdlinetest-hmmratac-results-${{ matrix.arch }}
           path: temp/macs3_run_hmmratac/

.github/workflows/build-and-test-MACS3-website.yml

@@ -1,5 +1,7 @@
 name: Build and Test MACS3 website using Sphinx
 
+# This action is to test document building
+
 on: 
   push: 
     paths: 
@@ -13,18 +15,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v4
+      uses: actions/checkout@v6
+      with:
+        submodules: 'true'
 
-    - name: Set up Python 3.11
-      uses: actions/setup-python@v5
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v6
       with:
-        python-version: "3.11"
+        python-version: "3.12"
 
     - name: Install dependencies
       run: |
         python3 -m pip install --upgrade pip
         python3 -m pip install sphinx myst-parser sphinx-rtd-theme sphinx-autodoc-typehints
         python3 -m pip install -r requirements.txt
+        python3 -m pip install -e .
 
     - name: Build Sphinx Documentation
       run: |
@@ -33,7 +38,7 @@ jobs:
         cd ..
 
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v3
+      uses: actions/upload-pages-artifact@v4
       with:
         # Archive and upload entire website
         path: './docs/build/html'

.github/workflows/build-and-test-MACS3-x64.yml

@@ -21,24 +21,24 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
         arch: ['x64']
     name: Build on x64 with Python ${{ matrix.python-version }}
     steps:
       - name: Checkout MACS
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: 'true'
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           architecture: ${{ matrix.arch }}
       - name: Cache pip
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           # This path is specific to Ubuntu
           path: ~/.cache/pip
@@ -70,7 +70,7 @@ jobs:
         run: |
           python3 setup.py sdist
       - name: Archive sdist
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v6
         with:
           name: sdist-${{ matrix.arch }}-${{ matrix.python-version }}
           path: |

.github/workflows/publish-to-anaconda.yml

@@ -22,12 +22,13 @@ jobs:
   build-and-publish:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4  # Checks-out your repository under $GITHUB_WORKSPACE
+    - name: Checkout
+      uses: actions/checkout@v6  # Checks-out your repository under $GITHUB_WORKSPACE
       with:
         submodules: 'true'
 
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.12'  # Set up the Python version you need
         architecture: 'x64'
@@ -43,15 +44,15 @@ jobs:
 
     - name: Build Sphinx Documentation
       run: |
-        cd docs  # Change to your documentation directory if needed
+        cd docs
         make html
         cd ..
 
     - name: Setup Pages
-      uses: actions/configure-pages@v4
+      uses: actions/configure-pages@v5
 
     - name: Upload artifact
-      uses: actions/upload-pages-artifact@v3
+      uses: actions/upload-pages-artifact@v4
       with:
         # Upload entire repository
         path: './docs/build/html'

.github/workflows/publish-to-gh-with-sphinx.yml

@@ -20,12 +20,12 @@ jobs:
     steps:
     # retrieve your distributions here
       - name: Check out MACS3 with submodules 
-        uses: actions/checkout@v4 
+        uses: actions/checkout@v6
         with: 
           submodules: 'true'
 
       - name: Set up Python 
-        uses: actions/setup-python@v5 
+        uses: actions/setup-python@v6
         with: 
           python-version: '3.12'