Update package for Python 3.10+ with Cython 3.x support

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,34 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: '[BUG] '
+labels: bug
+assignees: ''
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Import module '...'
+2. Call function '...' with parameters '...'
+3. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Error output**
+If applicable, paste the full error traceback:
+```
+Paste error here
+```
+
+**Environment:**
+ - OS: [e.g., Ubuntu 22.04, macOS 13.0]
+ - Python version: [e.g., 3.11]
+ - pyfk version: [e.g., 0.4.0]
+ - MPI enabled: [yes/no]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: '[FEATURE] '
+labels: enhancement
+assignees: ''
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,31 @@
+## Description
+
+Please include a summary of the changes and the related issue. 
+
+Fixes # (issue)
+
+## Type of change
+
+Please delete options that are not relevant.
+
+- [ ] Bug fix (non-breaking change which fixes an issue)
+- [ ] New feature (non-breaking change which adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] Documentation update
+
+## How Has This Been Tested?
+
+Please describe the tests that you ran to verify your changes.
+
+- [ ] Test A
+- [ ] Test B
+
+## Checklist:
+
+- [ ] My code follows the style guidelines of this project
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have made corresponding changes to the documentation
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes

.github/dependabot.yml

@@ -0,0 +1,22 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+    commit-message:
+      prefix: "deps"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+      - "github-actions"
+    commit-message:
+      prefix: "ci"

.github/workflows/codeql.yml

@@ -0,0 +1,36 @@
+name: "CodeQL"
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+  schedule:
+    - cron: '0 0 * * 0'  # Weekly on Sunday
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v3
+        with:
+          languages: ${{ matrix.language }}
+
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v3
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v3
+        with:
+          category: "/language:${{matrix.language}}"

.github/workflows/lint.yml

@@ -0,0 +1,30 @@
+name: lint
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install linting tools
+        run: |
+          pip install ruff
+
+      - name: Run Ruff linter
+        run: |
+          ruff check pyfk --ignore E501,F401,E402,F841,E711,E712,F541
+
+      - name: Run Ruff formatter check
+        run: |
+          ruff format --check pyfk || echo "Formatting issues found (non-blocking)"

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

@@ -3,25 +3,58 @@ on:
   release:
     types: [published]
 jobs:
+  # Run all tests including MPI tests before publishing
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install OpenMPI
+        run: |
+          sudo apt update
+          sudo apt install openmpi-bin libopenmpi-dev -y
+
+      - name: Set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Run standard tests
+        run: |
+          pip install .
+          pip install pytest pytest-mpi
+          pytest --pyargs pyfk
+
+      - name: Run MPI tests
+        run: |
+          pip uninstall pyfk -y
+          pip install mpi4py
+          PYFK_USE_MPI=1 pip install ".[mpi]"
+          export OMPI_ALLOW_RUN_AS_ROOT=1
+          export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+          mpirun --oversubscribe -np 1 pytest --with-mpi --pyargs pyfk
+          mpirun --oversubscribe -np 3 pytest --with-mpi --pyargs pyfk
+
   pypi:
+    needs: test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.2.0b1
+          version: "1.8.5"
           virtualenvs-create: true
           virtualenvs-in-project: true
           installer-parallel: true
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}

.github/workflows/publish-to-test-pypi.yml

@@ -4,25 +4,58 @@ on:
     branches:    
       - 'test/**'
 jobs:
+  # Run all tests including MPI tests before publishing
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install OpenMPI
+        run: |
+          sudo apt update
+          sudo apt install openmpi-bin libopenmpi-dev -y
+
+      - name: Set up python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Run standard tests
+        run: |
+          pip install .
+          pip install pytest pytest-mpi
+          pytest --pyargs pyfk
+
+      - name: Run MPI tests
+        run: |
+          pip uninstall pyfk -y
+          pip install mpi4py
+          PYFK_USE_MPI=1 pip install ".[mpi]"
+          export OMPI_ALLOW_RUN_AS_ROOT=1
+          export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+          mpirun --oversubscribe -np 1 pytest --with-mpi --pyargs pyfk
+          mpirun --oversubscribe -np 3 pytest --with-mpi --pyargs pyfk
+
   testpypi:
+    needs: test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up python
         id: setup-python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
-          version: 1.2.0b1
+          version: "1.8.5"
           virtualenvs-create: true
           virtualenvs-in-project: true
           installer-parallel: true
       - name: Load cached venv
         id: cached-poetry-dependencies
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: .venv
           key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
@@ -33,4 +66,5 @@ jobs:
         run: |
           poetry build -f sdist
           poetry config repositories.testpypi https://test.pypi.org/legacy/
-          poetry publish --repository testpypi --username xiziyi --password ${{ secrets.TestPypiPassWord }}
+          poetry config pypi-token.testpypi ${{ secrets.TEST_PYPI_TOKEN }}
+          poetry publish --repository testpypi

.github/workflows/sphinx.yml

@@ -7,24 +7,24 @@ jobs:
   sphinx:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
       - name: run doc
         run: |
-          pip install poetry-core@https://github.com/python-poetry/poetry-core/archive/refs/tags/1.1.0a7.zip
+          pip install poetry-core
           pip install numpy obspy cython scipy cysignals
           pip install . --no-build-isolation
-          pip install sphinx==4.5 pydata-sphinx-theme sphinx-autoapi jupyter-sphinx sphinx-copybutton pytest
+          pip install sphinx pydata-sphinx-theme sphinx-autoapi jupyter-sphinx sphinx-copybutton pytest
           cd docs
           make html
           echo "pyfk.ziyixi.science" > _build/html/CNAME
           cd ..
       - name: push to github page
         if: ${{ !env.ACT }}
-        uses: peaceiris/actions-gh-pages@v3
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./docs/_build/html