Merge v2.0 branch into master

- Resolved merge conflicts by keeping v2.0 changes
- Removed deprecated files that were deleted in v2.0
- Updated visualizer.py to use v2.0 version
- Major refactoring: moved from engine/ to lightning/, model/ to models/
- Added new features: auto-config, hydra integration, monai transforms
- Updated documentation and added new tutorials
- Removed legacy projects and configs

Author: Donglai Wei

.github/two_stream_overview.png

@@ -0,0 +1,85 @@
+name: Build Wheels
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, macos-11, windows-2019]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build wheel setuptools
+
+      - name: Build wheel
+        run: python -m build --wheel
+
+      - name: Upload wheels
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build sdist
+        run: python -m build --sdist
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v3
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    name: Upload to PyPI
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+      - uses: actions/download-artifact@v3
+        with:
+          name: sdist
+          path: dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/build-wheels.yml

@@ -0,0 +1,35 @@
+name: Documentation
+
+on:
+  push:
+    branches: [ main, master, v2.0 ]
+  pull_request:
+    branches: [ main, master, v2.0 ]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[docs]
+
+    - name: Build documentation
+      run: |
+        cd docs
+        make html
+
+    - name: Deploy to GitHub Pages
+      if: github.event_name == 'push' && github.ref == 'refs/heads/master'
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./docs/build/html

.github/workflows/docs.yml

@@ -0,0 +1,67 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main, master, v2.0 ]
+  pull_request:
+    branches: [ main, master, v2.0 ]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pytest-cov
+        pip install -e .
+
+    - name: Run tests
+      run: |
+        pytest tests/ -v --cov=connectomics --cov-report=xml
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
+
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install linters
+      run: |
+        python -m pip install --upgrade pip
+        pip install black flake8 isort mypy
+
+    - name: Run black
+      run: black --check connectomics/
+
+    - name: Run flake8
+      run: flake8 connectomics/ --max-line-length=100
+
+    - name: Run isort
+      run: isort --check connectomics/
+
+    - name: Run mypy
+      run: mypy connectomics/ --ignore-missing-imports

.github/workflows/tests.yml

@@ -126,11 +126,28 @@ dmypy.json
 .vscode/
 *~
 
-datasets/
+datasets/*
 others/
 locals/
 outputs/
 tmpwdir/
 *.iml
 .idea/
 docs/pytorch_sphinx_theme
+lightning_logs/
+slurm_outputs/
+
+# Build artifacts
+build/
+*.egg-info/
+
+# Editor configs
+.vscode/
+.idea/
+
+# OS files
+.DS_Store
+Thumbs.db
+
+# Development logs and documentation
+.claude/

.gitignore

@@ -108,7 +108,7 @@ For example:
 
 * [connectomics](connectomics) - The actual Pytorch Connectomics library.
     * [data](connectomics/data) - Dataset and dataloader for large-scale volumetric data
-    * [model](connectomics/model) - Model zoo for 3D segmentation
+    * [models](connectomics/models) - Model zoo for 3D segmentation
     * [engine](connectomics/engine) - Training and inference routines
     * [config](connectomics/config) - Configuration files for training and inference