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# Installation and configuration

## Installation on Windows/Linux with pip/conda
## Installing SANDY on Windows/Linux with pip/conda
The recommended way to install SANDY both on Windows and Linux is on an Anaconda virtual environment that already includes several python packages. Click [here](#anaconda) for more details on Anaconda.

We advise to install the SANDY dependences in a python environment that was not previously altered. You can do so from a terminal/Anaconda Prompt using the package/environment management system `conda` included in Anaconda, as
Expand All @@ -27,11 +27,9 @@ To manage your python environments read the [conda cheatsheet](https://docs.cond
Once the virtual environment is set up and active, you can install SANDY with `pip`.

```sh
pip install -i https://test.pypi.org/simple/ sandy
pip install sandy
```

> This distribution is only temporarily available on a separate instance of the [Python Package index](https://test.pypi.org/project/sandy/).
## Running SANDY in a python shell
1. Open a terminal/Anaconda Prompt.
2. Switch to the correct python environment (if any).
Expand All @@ -41,21 +39,10 @@ pip install -i https://test.pypi.org/simple/ sandy
import sandy
```

Now, if `sandy` is available you are ready to roll!

Still, many of the features of SANDY require running NJOY.
Here we assume that

Now, if `sandy` is available and if you have a running version of NJOY2016 you are ready to roll!

## Installation using Anaconda

### Downloading Anaconda
The recommended way to install the SANDY requirements (especially on Windows) is with the Anaconda distribution, which already includes several python packages and few other cool tools. The installer for the most recent Anaconda distributions can be found [here](https://www.anaconda.com/products/individual). For the Anaconda installation documentation, click [here](https://docs.anaconda.com/anaconda/install/).

### Getting started with Anaconda
The user guide to get yourself acquainted with Anaconda is available [here](https://docs.anaconda.com/anaconda/user-guide/). On a Windows machine we recommend that you use the Anaconda Prompt terminal.

# Installation from source
## Installing SANDY from source
The source code of SANDY is available as a git repository. The recommended way to get SANDY is by cloning the source package using your local git distribution (*click [here](https://git-scm.com/downloads) to download it!*).

```sh
Expand All @@ -69,69 +56,15 @@ If a `SSL Certificate problem` appears when pushing or pulling with git, one can
git config --global http.sslVerify false
```

Move to the folder `sandy` that you cloned with git and install the requirements

**with conda**
```sh
conda install --force-reinstall -y -c conda-forge --file requirements_conda.txt
```

**with pip**
```sh
pip install -r requirements.txt
```

> The difference between files `'requirements.txt'` and `'requirements_conda.txt'` is all in how they call the python package `pytables`. For more info have a look at the pytables [installation website](https://www.pytables.org/usersguide/installation.html). If you are aware of a better way of doing it, please get in touch with us!
Now you can simply add the `sandy` folder to your `PYTHONPATH` and you are ready to go.

**in Linux**
```sh
export PYTHONPATH="/path/to/sandy:${PYTHONPATH}"
```
> Add the previous command to your `${HOME}/.bashrc` or `${HOME}/.bash_profile` file to make your changes permanent.
**in Windows**
```dos
set PYTHONPATH=%PYTHONPATH%;C:\path\to\sandy
```
> Alternatively, use the environment variable editor in **Control panel** → **View advanced system settings**.
Alternatively, you can add sandy to the python packages of your environent (although not necessary). Then, once you are in the folder `sandy`, run the installation command,
Move to the folder `sandy` that you cloned with git and run the installation command,
```sh
cd sandy
python setup.py install --user
```
> Don't forget to activate the virtual environment if you are using one.
SANDY is installed! Now go back to run it in a python shell.

## Testing SANDY
If you installed SANDY from source you can test if it works correctly by runnning a number (far away from being extensive enough) of unit tests. First, make sure you istalled the following packages

```sh
conda install -y --name sandy-devel -c conda-forge numpydoc nbval
```

Then, you can run the tests from a terminal/Anaconda Prompt from the `sandy` folder with
```sh
conda activate sandy-devel
mkdir tests
cd tests
pytest ../sandy
```

Hopefully they are all green!


## Running SANDY in a Jupyter notebook

For combatibility issues we recommend installing a python kernel specific for the `sandy-devel` environment.
For that, you can run the following after making sure that `ipykernel` is installed in the virtual environment.

```sh
conda activate sandy-devel
python -m ipykernel install --user --name sandy-devel --display-name "Python3 (sandy-devel)"
```

## Running SANDY with NJOY
SANDY also works as a wrapper to the NJOY code to process nuclear data files into PENDF and ACE formats.
Expand All @@ -142,11 +75,25 @@ You can find the source on its [github repository](https://github.com/njoy/NJOY2

To install NJOY you can do the following

**in Linux**
### NJOY on Linux

Clone NJOY2016 with `git` and follow the installation instructions provided on the [NJOY website](https://docs.njoy21.io/install.html).

**in Windows**
Then, add the NJOY executable to the environment variables, as
```sh
export NJOY=/path/to/njoy
```

or make this permanent by adding it to your `.bashrc`.

You can see that `sandy` recongnizes the NJOY executable if you open a python terminal and type
```sh
import sandy
sandy.get_njoy()
```


### NJOY on Windows

1. Download [Cygwin64](https://cygwin.com/install.html).
2. Follow the instructions of the installation wizard.
Expand Down Expand Up @@ -218,4 +165,34 @@ To check if NJOY works you can:
* make sure `C:\path\to\cygwin64\bin` is in your list of environemnt variables (juste type `set` and look at `Path`);
* run `C:\path\to\cygwin64\home\your_username\NJOY2016\bin\njoy.exe`.

NJOY should now be running in your terminal!
NJOY should now be running in your terminal!


## Testing SANDY
If you installed SANDY from source you can test if it works correctly by runnning a number of unit tests.
First, make sure you istalled the following packages

```sh
conda install -y --name sandy-devel -c conda-forge pytest numpydoc nbval
```

Then, you can run the tests from a terminal/Anaconda Prompt from the `sandy` folder with
```sh
conda activate sandy-devel
mkdir tests
cd tests
pytest ../sandy
```

Hopefully they are all green!


## Running SANDY in a Jupyter notebook

For combatibility issues we recommend installing a python kernel specific for the `sandy-devel` environment.
For that, you can run the following after making sure that `ipykernel` is installed in the virtual environment.

```sh
conda activate sandy-devel
python -m ipykernel install --user --name sandy-devel --display-name "Python3 (sandy-devel)"
```

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