Migrate GitHub Actions from cellify

.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug Report
+description: Report a reproducible bug in VisualizePhonon
+labels: [bug]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for reporting a bug. Please provide enough detail to reproduce the issue with a minimal OUTCAR when possible.
+  - type: input
+    id: title
+    attributes:
+      label: Bug Summary
+      placeholder: Short and descriptive summary of the bug
+    validations:
+      required: true
+  - type: textarea
+    id: steps
+    attributes:
+      label: Steps to Reproduce
+      placeholder: |
+        1. Run `vaspvis generate -i OUTCAR -f xsf -m 0 -s 1.0`
+        2. Observe the error
+      description: Please provide a minimal, reproducible example.
+    validations:
+      required: true
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected Behavior
+      description: What did you expect to happen instead?
+    validations:
+      required: false
+  - type: textarea
+    id: logs
+    attributes:
+      label: Error Traceback or Logs
+      description: Include the traceback, command output, or relevant OUTCAR parser message.
+      render: shell
+    validations:
+      required: false
+  - type: input
+    id: environment
+    attributes:
+      label: Environment
+      placeholder: "e.g., macOS, Python 3.11, VisualizePhonon 0.0.2"
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/feature_request.yml

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+name: Feature Request
+description: Suggest a new feature or improvement
+labels: [enhancement]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thank you for your suggestion. Please describe the workflow or visualization need you want VisualizePhonon to support.
+  - type: input
+    id: summary
+    attributes:
+      label: Summary
+      placeholder: e.g., Add support for exporting selected modes to another visualization format
+    validations:
+      required: true
+  - type: textarea
+    id: motivation
+    attributes:
+      label: Motivation
+      description: Why is this feature important? What problem does it solve?
+    validations:
+      required: false
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed Solution
+      description: Describe how you would like the feature to work.
+    validations:
+      required: false
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives
+      description: Any alternative solutions or tools you have considered?
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/question.yml

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+name: Question
+description: Ask a question related to usage or development
+labels: [question]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        If you have a question, please provide enough context about your VASP output, command, or development task.
+  - type: input
+    id: summary
+    attributes:
+      label: Question Summary
+      placeholder: e.g., How should I visualize one imaginary phonon mode from OUTCAR?
+    validations:
+      required: true
+  - type: textarea
+    id: context
+    attributes:
+      label: Context or Background
+      description: What are you trying to do? Include relevant commands, files, modes, formats, or errors.
+    validations:
+      required: false

.github/labeler.yml

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+Python:
+  - changed-files:
+      - any-glob-to-any-file:
+          - src/VisualizePhonon/**/*
+          - pyproject.toml
+          - setup.py
+Docs:
+  - changed-files:
+      - any-glob-to-any-file:
+          - "*.md"
+          - docs/**/*
+Examples:
+  - changed-files:
+      - any-glob-to-any-file: examples/**/*
+Test:
+  - changed-files:
+      - any-glob-to-any-file: test/**/*
+CICD:
+  - changed-files:
+      - any-glob-to-any-file: .github/**/*

.github/workflows/autorelease.yml

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+name: Auto Release on Version Bump
+
+on:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: write
+  id-token: write
+
+jobs:
+  autorelease:
+    name: Check version and create release
+    runs-on: ubuntu-latest
+    outputs:
+      tag_exists: ${{ steps.check_tag.outputs.exists }}
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Get current version
+        id: get_version
+        run: |
+          VERSION=$(python - <<'PY'
+          import tomllib
+
+          with open("pyproject.toml", "rb") as f:
+              print(tomllib.load(f)["project"]["version"])
+          PY
+          )
+          echo "VERSION=$VERSION" >> "$GITHUB_ENV"
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      - name: Check if tag exists
+        id: check_tag
+        run: |
+          TAG_NAME="v${{ env.VERSION }}"
+          if git rev-parse "$TAG_NAME" >/dev/null 2>&1; then
+            echo "Tag $TAG_NAME already exists. Skipping release."
+            echo "exists=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "Tag $TAG_NAME does not exist. A new release will be created."
+            echo "exists=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Create GitHub Release
+        if: steps.check_tag.outputs.exists == 'false'
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          TAG_NAME="v${{ env.VERSION }}"
+          echo "Creating release for $TAG_NAME..."
+          gh release create "$TAG_NAME" \
+            --title "$TAG_NAME" \
+            --generate-notes
+
+  publish:
+    name: Build & Publish to PyPI
+    needs: autorelease
+    if: needs.autorelease.outputs.tag_exists == 'false'
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/VisualizePhonon
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build dependencies
+        run: pip install build
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/check_cmdline.yml

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+name: Test if cmdlines work
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  check-cmdline:
+    name: Check CLI
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .
+
+      - name: Check vaspvis commands
+        run: |
+          vaspvis --help
+          vaspvis generate --help
+          tmpdir="$(mktemp -d)"
+          cp test/OUTCAR "$tmpdir/OUTCAR"
+          cd "$tmpdir"
+          vaspvis generate -i OUTCAR -f xsf -m 0 -s 1.0
+          test -f mode_0.xsf

.github/workflows/labeler.yml

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+name: Pull Request Labeler
+
+on:
+  - pull_request_target
+
+jobs:
+  labeler:
+    permissions:
+      contents: read
+      pull-requests: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/labeler@v5
+        with:
+          configuration-path: .github/labeler.yml

.github/workflows/pre-commit.yml

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+name: pre-commit
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install pre-commit
+        run: |
+          python -m pip install --upgrade pip
+          pip install pre-commit
+
+      - name: Run pre-commit
+        run: pre-commit run --all-files --show-diff-on-failure

.github/workflows/tests.yml

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+name: Test Suite
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    env:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run tests with coverage
+        run: pytest --cov=src/ --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        if: ${{ matrix.python-version == '3.12' && env.CODECOV_TOKEN != '' }}
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          token: ${{ env.CODECOV_TOKEN }}
+
+      - name: Build package verification
+        if: ${{ matrix.python-version == '3.12' }}
+        run: |
+          pip install build
+          python -m build

.pre-commit-config.yaml

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+exclude: ^(examples/(OUTCAR|POSCAR|\.latexmkrc|test\.py)|test/(OUTCAR|test_vibrationalanalysis\.py))$
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+        args: ["--maxkb=2048"]