151 lines
5.2 KiB
ReStructuredText
151 lines
5.2 KiB
ReStructuredText
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.. |LINUXSCRIPT| replace:: https://git.ipr.univ-rennes1.fr/epsi/msspec_python3/raw/branch/devel/utils/dockerized/linux/msspec
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##########################
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Download and install notes
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##########################
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************
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Installation
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************
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There are 2 ways to install MsSpec. You can either:
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- Use a Docker image. This is, by far, the most straightforward and easy way to work with MsSpec.
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- Compile your own version for your system.
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1. Using a Docker image
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-----------------------
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You first need `Docker <https://www.docker.com>`_ to be installed on your system.
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This is really straightforward. Please see the `Docker documentation
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<https://docs.docker.com/engine/install/>`_ for more information depending on
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your OS.
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* **For Linux**,
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* Download :download:`this script <../../utils/dockerized/linux/msspec>` and
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make it executable (with the *chmod u+x msspec* command)
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* Place it in a location known to your $PATH (or add this location to your $PATH if needed).
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The *~/.local/bin* folder is a good choice.
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* **For Windows**
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* You need a running X server. Download and install `VcXsrv <https://sourceforge.net/projects/vcxsrv/>`_
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* Install the small :download:`MsSpec frontend <../../utils/dockerized/windows/msspec_setup.exe>`
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* While not necessary, it is also a good idea to use a better terminal application than the default one.
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`Windows Terminal <https://www.microsoft.com/fr-fr/p/windows-terminal/9n0dx20hk701#activetab=pivot:overviewtab>`_
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may be a good choice.
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* **For Mac**
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* *To be documented*
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Open a terminal in Linux, or a powershell in Windows and type in::
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msspec
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The first time you run the command, it will download the msspec image (it may takes several minutes or half an hour
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depending on your internet connexion).
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The command will automatically create a new container and start it.
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As the command was entered without any argument on the command-line, the help message should be printed on the screen
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.. code-block:: text
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Usage: 1) msspec -p [PYTHON OPTIONS] SCRIPT [ARGUMENTS...]
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2) msspec [-l FILE | -i | -h]
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3) msspec [bash | reset]
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Form (1) is used to launch a script
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Form (2) is used to load a hdf5 data file
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Form (3) is used to control the Docker container/image.
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List of possible options:
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-p Pass every arguments after this option to the msspec
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virtual environment Python interpreter.
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-i Run the interactive Python interpreter within msspec
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virtual environment.
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-l Load and display a *.hdf5 data file in a graphical
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window.
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-v Print the version.
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-h Show this help message.
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bash This command starts an interactive bash shell in the
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MsSpec container.
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reset This command removes the MsSpec container (but not the
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image). Changes made in the container will be lost and
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any new call to msspec will recreate a new fresh container.
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2. Compile your own version
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---------------------------
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To install MsSpec this way, follow the instructions `here <https://git.ipr.univ-rennes1.fr/epsi/msspec_python3/src/branch/devel>`_
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***************************
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Running your Python scripts
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***************************
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You can run your MsSpec Python scripts (e.g. *my_script.py*) by typing in::
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msspec -p my_script.py
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This command is equivalent to activating the Python virtual environment MsSpec is intsalled in
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and to run the Python interpreter of that environment (everything that follows the -p option is
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passed to the python command).
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You can also launch the Interactive Python (iPython) of MsSpec::
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msspec -i
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Inside this interactive session, you can run a script with the command::
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%run my_script.py
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You can interact with your filesystem with the classical *cd*, *ls*, *cp*, *rm*... commands.
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and you can edit your script with::
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%ed my_script.py
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.. warning::
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**If using the Docker image of MsSpec in Linux**, your home folder on the host machine is bind mounted
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in the same location in the container and your UID and GID are also set so that creating files within
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your home file hierarchy is totally transparent.
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**If using the Docker image of MsSpec in Windows**, the drive containing your "My Documents" folder on the
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host machine is bind mounted on the container at the root of the filesystem. For example, if your
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"My documents" folder on Windows are in 'D:\\Home\\Bob\\MyDocuments', it will be available in the container as
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'/D/Home/Bob/MyDocuments'. It has two consequences:
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#. The msspec command will fail if running on another drive than the one where is located "My Documents"
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#. You have to specify filenames with the Unix slashes. For example if you want to run the script located
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in *.\\results\\my_script.py*, you will have to enter *msspec -p ./results/my_script.py*
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**************
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Uninstallation
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**************
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* **Under Linux**, type in::
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msspec -u
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* **Under Windows**, simply `uninstall the application from the Settings page
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<https://support.microsoft.com/en-us/windows/uninstall-or-remove-apps-and-programs-in-windows-10-4b55f974-2cc6-2d2b-d092-5905080eaf98>`_.
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A command window will pop-up and you will have to answer 'y' to remove MsSpec.
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* **Under Mac OS**, *to be documented.*
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