Fix entrypoint

Move to cmidair dockerhub

Author: Asanto32

.github/workflows/release.yaml

@@ -3,7 +3,7 @@ name: Publish Docker image
 on:
   push:
     branches:
-    - main
+    - feature/issue-178/build-docker-image
     tags:
     - v*
 
@@ -35,7 +35,7 @@ jobs:
       id: meta
       uses: docker/metadata-action@v5.5.1
       with:
-        images: adamsanto/wristpy
+        images: cmidair/wristpy
 
 
     - name: Build and push Docker image

README.md

@@ -126,15 +126,15 @@ sleep_windows = subject1.sleep_windows_epoch
 
 2. **Pull the Docker image**:
    ```bash
-   docker pull adamsanto/wristpy:latest
+   docker pull cmidair/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
+     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.
 
@@ -143,38 +143,20 @@ sleep_windows = subject1.sleep_windows_epoch
     docker run -it --rm \
      -v "/local/path/to/data/file.bin:/data/file.bin" \
      -v "/local/path/to/output:/output" \
-     adamsanto/wristpy
+     cmidair/wristpy
    ```
 
 ### Customizing the Pipeline:
 
-The Docker image supports multiple environment variables to customize processing. You can set these using the `-e` flag:
+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 "$(pwd)/my_data:/data" \
-  -v "$(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 \
-  adamsanto/wristpy
+  -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
 ```
 
-### 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).

dockerfile

@@ -3,17 +3,6 @@ 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 \
@@ -23,9 +12,9 @@ RUN pip install poetry && \
     poetry config virtualenvs.create false && \
     poetry install --only main
 
-RUN mkdir -p $INPUT_DIR $OUTPUT_DIR
+RUN mkdir -p /data /output
 
-COPY entrypoint.sh /entrypoint.sh
-RUN chmod +x /entrypoint.sh
+ENTRYPOINT ["poetry", "run", "wristpy"]
 
-ENTRYPOINT ["/entrypoint.sh"]
+CMD ["/data", "--output", "/output", "--output-filetype", ".csv", "--calibrator", "none", \
+     "--activity-metric", "enmo", "--epoch-length", "5", "--nonwear-algorithm", "ggir"]