# How to install

To download the code, go to directory you want download the code to, open a terminal/command prompt there and type
```bash
git clone https://github.com/ocean-perception/oplab_pipeline.git
```

To push updates you made to the repository on github (assuming you are using the master branch, which is the default), type
```bash
git add -u
git commit -m "Some message about the change"
git push origin master
```

## Running the code ##
Requires [Python3.6.2](https://www.python.org/downloads/release/python-362/) or ([latest](https://www.python.org/downloads/release/python3)).  
You can also use [Anaconda](https://www.anaconda.com/download/), which comes with the Spyder IDE, that in turn uses the IPython shell.

### When using Python from standard terminal or the Anaconda prompt ###
The oplab_pipeline project is compiled into binaries. To do this, navigate to the oplab_pipeline folder and execute  
`pip3 install -U .` resp. if you are using Anaconda run `pip install -U .` from the Anaconda Prompt (Anaconda3). The `-U` is strictly only required in certain cases when oplab_pipeline is already installed and changes are made, but it is safer to always pip install with `-U` to avoid the latest updates being skipped when updating the binaries.

`auv_nav`, `auv_cal` and `correct_images` can now be used as a command from any folder on your computer. You can test that by trying to display the help by calling `auv_nav -h`.  
To run the unit tests, execute  
`pytest`  
from within the oplab_pipeline folder.  
To uninstall the oplab_pipeline programs run  
`pip uninstall oplab_pipeline`.

#### Building the documentation locally ####
Install the required packages and then build the documentation files by executing the following commands from the oplab_pipeline folder:
```bash
pip install -r requirements.txt
cd docs
make html
```
This generates the documentation in the subfolder \_build/html/ of the docs folder. 


### When using Spyder IDE in Anaconda ###
When installing the oplab_pipeline as described above, it is not possilbe to call `auv_nav`, `auv_cal` and `correct_images` directly from within the Spyder IDE (which uses IPython console), the reason being that IPython does not support execution of binaries.  
To get the programs to work in the the Spyder IDE, first install the required packages by navigating to the oplab_pipeline directory in an Ancaconda prompt and executing  
`pip install -r requirements.txt`  
Then open Spyder and use its shell (it is the IPython shell) to navigate to the oplab_pipeline folder and execute
```python
import auv_nav
run auv_nav/auv_nav.py -h
```
This should display the help of auv_nav. To use auv_nav, replace `-h` with the command you want to run.  
This way you can run auv_nav from within Spyder, but you always need to navigate to the oplab_pipeline directory to execute the code.  
`auv_cal` and `correct_images` can be exectuted in the same way.