Merge pull request #10

Sam2 refactor. Fully refactored classes. New CLI and updated tests and runs thanks to NAIRR Startup allocation and the Jetstream 2 GPUs.

Author: preshanth

.gitattributes

@@ -1 +1 @@
-*.ipynb -linguist-detectable
+*.ipynb -linguist-detectable

.github/workflows/ci.yml

@@ -0,0 +1,81 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - sam2_refactor
+      - main
+  pull_request:
+    branches:
+      - sam2_refactor
+      - main
+
+jobs:
+  test:
+    name: Test Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["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 }}
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pandas>=2.2.0 numpy>=1.26.0 --only-binary :all:
+          pip install -e .[ci]
+
+      - name: Run unit tests
+        run: |
+          pytest tests/unit -v -m "not requires_casa"
+
+      - name: Run integration tests
+        run: |
+          pytest tests/integration -v -m "not requires_casa"
+
+  code-quality:
+    name: Code Quality
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: 'pip'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install black==24.1.1 ruff==0.1.15 isort==5.13.2
+
+      - name: Check formatting with Black
+        run: |
+          black --check --line-length=100 src/ tests/
+
+      # isort check disabled - pre-commit handles this locally
+      # - name: Check import sorting with isort
+      #   run: |
+      #     isort --check-only --profile black --line-length=100 src/ tests/
+
+      - name: Auto-fix with Ruff
+        run: |
+          ruff check --fix src/ tests/
+
+      - name: Report remaining Ruff issues (warning only)
+        continue-on-error: true
+        run: |
+          ruff check src/ tests/

.gitignore

@@ -160,3 +160,24 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# SAM-RFI specific ignores
+# Large downloaded/generated files
+models/                  # Auto-downloaded SAM2 weights from HuggingFace
+datasets/                # Generated training/validation datasets
+tmp/                     # Temporary files from training/testing
+validation_results/      # GPU validation outputs
+
+# Model files
+*.pth                    # PyTorch model checkpoints
+*.safetensors           # HuggingFace model weights
+*.pt                    # PyTorch weights
+
+# Dataset files
+*.npz                   # Numpy dataset files (can be large)
+
+# CASA logs
+casa-*.log
+
+# Archive (keep structure but ignore if regenerated)
+archive/

.pre-commit-config.yaml

@@ -0,0 +1,48 @@
+# Pre-commit hooks for SAM-RFI
+# Install: pip install pre-commit && pre-commit install
+# Run manually: pre-commit run --all-files
+
+repos:
+  # Black - Python code formatter
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+        language_version: python3.12
+        args: [--line-length=100]
+
+  # isort - Import sorting
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: [--profile=black, --line-length=100]
+
+  # Ruff - Fast Python linter
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.15
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+
+  # Basic file checks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: [--maxkb=5000]
+      - id: check-json
+      - id: check-toml
+      - id: mixed-line-ending
+
+  # MyPy - Static type checking (optional, can be slow)
+  # Uncomment if you want type checking on commit
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.8.0
+  #   hooks:
+  #     - id: mypy
+  #       additional_dependencies: [types-pyyaml, types-tqdm]
+  #       args: [--ignore-missing-imports]

.readthedocs.yaml

@@ -32,4 +32,4 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
-   - requirements: docs/requirements.txt
+   - requirements: docs/requirements.txt

LICENSE

@@ -18,4 +18,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.