Feature/issue 178/build docker image

.github/workflows/release.yaml

@@ -0,0 +1,49 @@
+name: Publish Docker image
+
+on:
+  push:
+    branches:
+    - main
+    tags:
+    - v*
+
+
+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@v3
+
+    - 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: Extract metadata (tags, labels) for Docker
+      id: meta
+      uses: docker/metadata-action@v5.5.1
+      with:
+        images: adamsanto/wristpy
+
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5.1.0
+      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 +119,60 @@ 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 adamsanto/wristpy:latest
+   ```
+
+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" \
+     adamsanto/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.
+
+### Customizing the Pipeline:
+
+The Docker image supports multiple environment variables to customize processing. You can set these using the `-e` flag:
+
+```bash
+docker run -it --rm \
+  -v "$(pwd)/my_data:/data" \
+  -v "$(pwd)/results:/output" \
+  -e CALIBRATOR=ggir \
+  -e ACTIVITY_METRIC=mad \
+  -e NONWEAR=ggir,cta \
+  -e THRESHOLDS=0.1,1.0,1.5 \
+  -e EPOCH_LENGTH=10 \
+  -e VERBOSITY=1 \
+  adamsanto/wristpy
+```
+
+### Available Environment Variables:
+
+| Variable | Description | Default | Options |
+|----------|-------------|---------|---------|
+| `INPUT_DIR` | Path for input data inside container | `/data` | Any valid path |
+| `OUTPUT_DIR` | Path for output data inside container | `/output` | Any valid path |
+| `OUTPUT_TYPE` | Format for output files | `csv` | `csv`, `parquet` |
+| `CALIBRATOR` | Calibration method | `none` | `none`, `ggir`, `gradient` |
+| `ACTIVITY_METRIC` | Activity metric for analysis | `enmo` | `enmo`, `mad`, `ag_count` |
+| `EPOCH_LENGTH` | Sampling rate in seconds | `5` | Any integer ≥ 1 |
+| `NONWEAR` | Non-wear detection algorithm(s) | `ggir` | `ggir`, `cta`, `detach` or comma-separated list. |
+| `THRESHOLDS` | Activity level thresholds | `""` | Specify three threshold values as comma-separated numbers. |
+
+
+
+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 +1,31 @@
+FROM python:3.11-buster
+
+WORKDIR /app
+COPY . /app/
+
+
+ENV INPUT_DIR=/data
+ENV OUTPUT_DIR=/output
+ENV OUTPUT_TYPE=.csv
+ENV CALIBRATOR=none
+ENV ACTIVITY_METRIC=enmo
+ENV EPOCH_LENGTH=5
+ENV NONWEAR=ggir
+ENV THRESHOLDS=""
+
+
+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 $INPUT_DIR $OUTPUT_DIR
+
+COPY entrypoint.sh /entrypoint.sh
+RUN chmod +x /entrypoint.sh
+
+ENTRYPOINT ["/entrypoint.sh"]

entrypoint.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+# Wristpy Docker Entrypoint Script
+
+CMD="poetry run wristpy $INPUT_DIR --output $OUTPUT_DIR"
+
+
+if [ -n "$OUTPUT_TYPE" ]; then
+  CMD="$CMD --output-filetype $OUTPUT_TYPE"
+fi
+
+CMD="$CMD --calibrator $CALIBRATOR"
+CMD="$CMD --activity-metric $ACTIVITY_METRIC"
+CMD="$CMD --epoch-length $EPOCH_LENGTH"
+
+
+if [ -n "$NONWEAR" ]; then
+  IFS="," read -ra ALGOS <<< "$NONWEAR"
+  for algo in "${ALGOS[@]}"; do
+    CMD="$CMD --nonwear-algorithm $algo"
+  done
+fi
+
+if [ -n "$THRESHOLDS" ]; then
+  THRESHOLD_VALUES=$(echo $THRESHOLDS | tr "," " ")
+  if [ -n "$THRESHOLD_VALUES" ]; then
+    CMD="$CMD --thresholds $THRESHOLD_VALUES"
+  fi
+fi
+
+echo "Running: $CMD"
+exec $CMD