# pysciencedock

**Repository Path**: mirrors_Kitware/pysciencedock

## Basic Information

- **Project Name**: pysciencedock
- **Description**: Scientific and statistical methods from Python exposed through Docker.
- **Primary Language**: Unknown
- **License**: Apache-2.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-08-09
- **Last Updated**: 2026-03-14

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# pysciencedock

Scientific and statistical methods from Python exposed through Docker.

## Local usage

List methods available with JSON descriptions of inputs and outputs:
```
python -m pysciencedock
```

Print help information for a method:
```
python -m pysciencedock <method> --help
```

Run one of the methods:
```
python -m pysciencedock <method> <arg1> ...
```

## Usage through Docker

List the methods available through Docker:
```
docker run kitware/pysciencedock
```

Run a method through Docker:
```
docker run <docker_options> kitware/pysciencedock <method> <arg1> ...
```

In order to send data files to Docker, mount a volume and use the mounted
volume prefix for the input and output paths. For example, if `myinput.csv`
is in your current directory, the following will produce `myoutput.csv` in
the current directory:
```
docker run -v $PWD:/data kitware/pysciencedock normalize --data=/data/myinput.csv --output=/data/myoutput.csv
```

Build the Docker image:
```
git clone https://github.com/Kitware/pysciencedock.git
cd pysciencedock
docker build -t pysciencedock .
```

Now use `pysciencedock` instead of `kitware/pysciencedock` in the commands
above to use your local version.

## Usage through Girder

* Install Girder.
* Enable the "Item tasks" plugin.
* Start a `girder_worker` Celery worker and point it and the Worker plugin settings to use the same task queue.
* From any folder you have write access to (you must be admin), select
  "Add tasks" from the actions menu.
* Enter "kitware/pysciencedock" as the image name and click Run.
* When that task completes, navigate to a created task item and select
  "Run task" from the actions menu.
* Fill in the task parameters and click Run.

## Testing

To run the unit tests:

```
python -m unittest tests
```