Obia release prep

.dockerignore

@@ -0,0 +1,15 @@
+.git
+.github
+.cache
+.pytest_cache
+*.egg-info
+__pycache__/
+*.py[cod]
+site/
+build/
+dist/
+docs/
+tests/
+notebooks/
+archive/
+data/

.github/workflows/docs.yml

@@ -0,0 +1,44 @@
+name: Build and Deploy Docs
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "obia/**"
+      - "docs/**"
+      - "mkdocs.yml"
+      - "pyproject.toml"
+      - ".github/workflows/docs.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install package and docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[docs,detection]"
+
+      - name: Build MkDocs site
+        run: mkdocs build --strict
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./site
+          cname: obia.sefa.ai

.github/workflows/publish-docker.yml

@@ -0,0 +1,43 @@
+name: Publish Docker Image
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+env:
+  IMAGE_NAME: iosefa/obia
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Generate Docker metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE_NAME }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=raw,value=latest
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/publish-pypi.yml

@@ -0,0 +1,52 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - "v*.*.*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install build tool
+        run: python -m pip install --upgrade build
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/obia
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/tests.yml

@@ -0,0 +1,46 @@
+name: Tests
+
+on:
+  pull_request:
+    paths:
+      - "obia/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - "environment.yml"
+      - ".github/workflows/tests.yml"
+  push:
+    branches:
+      - main
+    paths:
+      - "obia/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - "environment.yml"
+      - ".github/workflows/tests.yml"
+  workflow_dispatch:
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install package and test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[test]"
+
+      - name: Run tests
+        run: pytest -q

.gitignore

@@ -159,21 +159,19 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
 
-notebooks/data
-
-*.png
-*.gpkg
+# Local geospatial data and generated outputs
+notebooks/
 *.gpkg-shm
 *.gpkg-wal
-*.yaml
-*.tif
 *.laz
 *.las
-*.json
-*.jpeg
-*.jpg
-*.xml
 *.npy
+*.pth
+*.pt
+*.ckpt
+*.parquet
+*.pkl
+
 scripts/SAM copy
 archive/
 
@@ -182,8 +180,8 @@ archive/
 
 # Data directories and outputs
 data/
-notebooks/lightning_logs/
-notebooks/tiles/
+output_tiles*/
+lightning_logs/
 scripts/lightning_logs/
 scripts/SAM/backup/
 scripts/SAM/crowns/
@@ -201,11 +199,6 @@ scripts/SegmentationSAM/data/
 scripts/SegmentationSAM/training_crowns/
 scripts/SegmentationSAM/training_crowns_raw/
 
-# Model files and serialized artifacts
-*.pth
-*.pt
-*.ckpt
-*.parquet
-*.pkl
+# Serialized graph artifacts
 scripts/segments_graph.pkl*
 scripts/segments_labeled.parquet*

Dockerfile

@@ -0,0 +1,40 @@
+FROM condaforge/miniforge3:latest
+
+LABEL org.opencontainers.image.title="OBIA"
+LABEL org.opencontainers.image.description="Object-based image analysis tools for geospatial rasters"
+LABEL org.opencontainers.image.source="https://github.com/iosefa/obia"
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
+
+WORKDIR /opt/obia
+
+COPY pyproject.toml README.md LICENSE MANIFEST.in ./
+COPY obia ./obia
+
+RUN conda install -y -c conda-forge \
+        "python=3.11" \
+        pip \
+        "setuptools>=68" \
+        wheel \
+        "numpy>=2.1.1" \
+        "rasterio>=1.3.11" \
+        "shapely>=2.0.3" \
+        "pillow>=10.3.0" \
+        "pandas>=2.2.2" \
+        "geopandas>=1.0.1" \
+        "scipy>=1.14.1" \
+        "scikit-image>=0.23.2" \
+        "tqdm>=4.66.2" \
+        "scikit-learn>=1.4.2" \
+        "affine>=2.4.0" \
+        "pyproj>=3.6.1" \
+        "matplotlib>=3.8" \
+        requests \
+        opencv \
+        gdal \
+        pdal \
+        python-pdal \
+    && pip install --no-cache-dir --no-deps pyforestscan . \
+    && conda clean -afy
+
+CMD ["python"]