Merge remote-tracking branch 'origin/main' into 127-implement-mims

Author: frey-perez

.dockerignore

@@ -0,0 +1,7 @@
+docs/
+tests/sample_data
+*.png
+*.csv
+*.xlsx
+*.md
+!README.md

.github/workflows/release.yaml

@@ -0,0 +1,52 @@
+name: Publish Docker image
+
+on:
+  push:
+    branches:
+    - main
+    tags:
+    - v*
+
+
+permissions:
+  contents: read
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out the repo
+      uses: actions/checkout@v4
+      with:
+        lfs: true
+
+    - name: Set up QEMU
+      uses: docker/setup-qemu-action@29109295f81e9208d7d86ff1c6c12d2833863392
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2
+
+    - name: Log in to Docker Hub
+      uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+
+    - name: Extract metadata (tags, labels) for Docker
+      id: meta
+      uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804
+      with:
+        images: cmidair/wristpy
+
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@1dc73863535b631f98b2378be8619f83b136f4a0
+      with:
+        platforms: linux/amd64,linux/arm64
+        context: .
+        file: ./Dockerfile
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}

README.md

@@ -50,6 +50,8 @@ pip install wristpy
 
 ## Quick start
 
+`wristpy` provides three flexible interfaces: a command-line tool for direct execution, an importable Python library, and a Docker image for containerized deployment.
+
 ### Using Wristpy through the command-line:
 #### Run single files:
 ```sh
@@ -117,6 +119,49 @@ nonwear_array = subject1.nonwear_epoch
 sleep_windows = subject1.sleep_windows_epoch
 ```
 
+### Using Wristpy Through Docker
+
+
+1. **Install Docker**: Ensure you have Docker installed on your system. [Get Docker](https://docs.docker.com/get-docker/)
+
+2. **Pull the Docker image**:
+   ```bash
+   docker pull cmidair/wristpy:main
+   ```
+
+3. **Run the Docker image** with your data:
+   ```bash
+   docker run -it --rm \
+     -v "/local/path/to/data:/data" \
+     -v "/local/path/to/output:/output" \
+     cmidair/wristpy
+   ```
+   Replace `/local/path/to/data` with the path to your input data directory and `/local/path/to/output` with where you want results saved.
+
+   To run a single file, we simply need to modify the mounting structure for the docker call slightly:
+    ```bash
+    docker run -it --rm \
+     -v "/local/path/to/data/file.bin:/data/file.bin" \
+     -v "/local/path/to/output:/output" \
+     cmidair/wristpy
+   ```
+
+### Customizing the Pipeline:
+
+The Docker image supports multiple input variables to customize processing. You can set these by simply chaining these inputs as you would for the CLI input:
+
+```bash
+docker run -it --rm \
+  -v "/local/path/to/data/file.bin:/data/file.bin" \
+  -v "/local/path/to/output:/output" \
+  cmidair/wristpy /data --output /output --epoch-length 5 --nonwear-algorithm ggir --nonwear-algorithm detach --thresholds 0.1 0.2 0.4
+```
+
+
+
+For more details on available options, see the [orchestrator documentation](https://childmindresearch.github.io/wristpy/wristpy/core/orchestrator.html#run).
+
+
 ## References
 1. van Hees, V.T., Sabia, S., Jones, S.E. et al. Estimating sleep parameters
               using an accelerometer without sleep diary. Sci Rep 8, 12975 (2018).

dockerfile

@@ -0,0 +1,20 @@
+FROM python:3.11-buster
+
+WORKDIR /app
+COPY . /app/
+
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    gfortran \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip install poetry && \
+    poetry config virtualenvs.create false && \
+    poetry install --only main
+
+RUN mkdir -p /data /output
+
+ENTRYPOINT ["poetry", "run", "wristpy"]
+
+CMD ["/data", "--output", "/output", "--output-filetype", ".csv", "--calibrator", "none", \
+     "--activity-metric", "enmo", "--epoch-length", "5", "--nonwear-algorithm", "ggir"]