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Installation

There are 2 ways to install MsSpec. You can either:

Use a Docker image. This is, by far, the most straightforward and easy way to work with MsSpec.
Compile your own version for your system.

1. Using a Docker image

You first need Docker to be installed on your system. This is really straightforward. Please see the Docker documentation for more information depending on your OS.

For Linux,
- Download :download:`this script <../../utils/dockerized/linux/msspec>` and make it executable (with the chmod u+x msspec command)
  
  System Message: ERROR/3 (<stdin>, line 32); backlink
  
  Unknown interpreted text role "download".
- Place it in a location known to your $PATH (or add this location to your $PATH if needed). The ~/.local/bin folder is a good choice.
For Windows
- You need a running X server. Download and install VcXsrv
- Install the small :download:`MsSpec frontend <../../utils/dockerized/windows/msspec_setup.exe>`
  
  System Message: ERROR/3 (<stdin>, line 42); backlink
  
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- While not necessary, it is also a good idea to use a better terminal application than the default one. Windows Terminal may be a good choice.
For Mac
- To be documented

Open a terminal in Linux, or a powershell in Windows and type in:

msspec

The first time you run the command, it will download the msspec image (it may takes several minutes or half an hour depending on your internet connexion). The command will automatically create a new container and start it. As the command was entered without any argument on the command-line, the help message should be printed on the screen

Usage: 1) msspec -p [PYTHON OPTIONS] SCRIPT [ARGUMENTS...]
       2) msspec [-l FILE | -i | -h]
       3) msspec [bash | reset]

Form (1) is used to launch a script
Form (2) is used to load a hdf5 data file
Form (3) is used to control the Docker container/image.

List of possible options:
    -p   Pass every arguments after this option to the msspec
         virtual environment Python interpreter.
    -i   Run the interactive Python interpreter within msspec
         virtual environment.
    -l   Load and display a *.hdf5 data file in a graphical
         window.
    -v   Print the version.
    -h   Show this help message.

    bash        This command starts an interactive bash shell in the
                MsSpec container.
    reset       This command removes the MsSpec container (but not the
                image). Changes made in the container will be lost and
                any new call to msspec will recreate a new fresh container.

2. Compile your own version

To install MsSpec this way, follow the instructions here

Running your Python scripts

You can run your MsSpec Python scripts (e.g. my_script.py) by typing in:

msspec -p my_script.py

This command is equivalent to activating the Python virtual environment MsSpec is intsalled in and to run the Python interpreter of that environment (everything that follows the -p option is passed to the python command).

You can also launch the Interactive Python (iPython) of MsSpec:

msspec -i

Inside this interactive session, you can run a script with the command:

%run my_script.py

You can interact with your filesystem with the classical cd, ls, cp, rm... commands. and you can edit your script with:

%ed my_script.py

Warning

If using the Docker image of MsSpec in Linux, your home folder on the host machine is bind mounted in the same location in the container and your UID and GID are also set so that creating files within your home file hierarchy is totally transparent.

If using the Docker image of MsSpec in Windows, the drive containing your "My Documents" folder on the host machine is bind mounted on the container at the root of the filesystem. For example, if your "My documents" folder on Windows are in 'D:\Home\Bob\MyDocuments', it will be available in the container as '/D/Home/Bob/MyDocuments'. It has two consequences:

The msspec command will fail if running on another drive than the one where is located "My Documents"
You have to specify filenames with the Unix slashes. For example if you want to run the script located in .\results\my_script.py, you will have to enter msspec -p ./results/my_script.py

Uninstallation

Under Linux, type in:
```
msspec -u
```
Under Windows, simply uninstall the application from the Settings page. A command window will pop-up and you will have to answer 'y' to remove MsSpec.
Under Mac OS, to be documented.

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