From 2c4d288bc020c1eac8ad1deba7d94321876084b9 Mon Sep 17 00:00:00 2001
From: Zhen-Qi Liu <liuzhenqi77@gmail.com>
Date: Mon, 18 Nov 2024 16:51:34 -0500
Subject: [PATCH] [ENH] update GitHub Actions workflows (#143)

---
 .github/workflows/docker-release.yml |  8 ++++----
 .github/workflows/docs.yml           | 10 +++++-----
 .github/workflows/tests.yml          | 22 +++++++++-------------
 3 files changed, 18 insertions(+), 22 deletions(-)

diff --git a/.github/workflows/docker-release.yml b/.github/workflows/docker-release.yml
index 8d70732..67c575b 100644
--- a/.github/workflows/docker-release.yml
+++ b/.github/workflows/docker-release.yml
@@ -18,13 +18,13 @@ jobs:
         uses: actions/checkout@v4
       
       - name: Log in to Docker Hub
-        uses: docker/login-action@v1.14.1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_HUB_USERNAME }}
           password: ${{ secrets.DOCKER_HUB_PASSWORD }}
       
       - name: Log in to the Container registry
-        uses: docker/login-action@v1.14.1
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
@@ -32,14 +32,14 @@ jobs:
       
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@v3.8.0
+        uses: docker/metadata-action@v5
         with:
           images: |
             ${{ secrets.DOCKER_HUB_USERNAME }}/netneurotools
             ghcr.io/netneurolab/netneurotools
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v2.10.0
+        uses: docker/build-push-action@v6
         with:
           context: .
           push: true
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 5ffcd7b..c700a36 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -18,10 +18,10 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.12
       - name: Install dependencies
         run: |
           pip install -r docs/requirements.txt
@@ -32,8 +32,8 @@ jobs:
         run: |
           cd docs && make clean html
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
             path: 'docs/_build/html'
       - name: Deploy to GitHub Pages
-        uses: actions/deploy-pages@v2
\ No newline at end of file
+        uses: actions/deploy-pages@v4
\ No newline at end of file
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 11c62ff..ca61230 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -4,7 +4,7 @@ on:
   workflow_dispatch:
   push:
     branches:
-      - master
+      - main
   pull_request:
 
 jobs:
@@ -15,10 +15,10 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v4
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: '3.12'
       - name: Install dependencies
         run: |
             python -m pip install --upgrade pip
@@ -32,14 +32,14 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Display Python version
@@ -53,18 +53,14 @@ jobs:
         run: python -m pip install .
       - name: Print netneurotools version
         run: python -c "import netneurotools; print(netneurotools.__version__)" 
-      - name: Test submodule import
-        run: |
-          cd ..
-          python -c "from netneurotools import metrics; from netneurotools.datasets import fetch_cammoun2012"
       - name: Run tests
         run: pytest --doctest-modules --cov=netneurotools --cov-report=xml --junitxml=junit/test-results.xml --verbose --pyargs netneurotools
       - name: Upload coverage
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v5
         with:
-          file: coverage.xml
+          files: coverage.xml
       - name: Upload pytest test results
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
           path: junit/test-results.xml