167 lines
4.8 KiB
Markdown
167 lines
4.8 KiB
Markdown
Introduction
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============
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This is the Python MsSpec version with support for Python 3.x and dynamic memory allocation for Phagen and Spec
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Installation
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============
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Requirements
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------------
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To compile MsSpec shared libraries, you need:
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- Python >= 3.6
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- gfortran compiler
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- cairo library (runtime files and header files)
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Depending on your OS and Python version, you may need all the requirements (runtime libraries
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and header files) to build wxPython (please consult your distribution's package list for the
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appropriate package names) and their dependencies:
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- python-dev (for your version of python)
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- gtk (preferably version 3, but depends on your needs)
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- gstreamer
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- gstreamer-plugins-base
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- glut
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- libwebkitgtk (matching your gtk version)
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- libjpeg
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- libpng
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- libtiff
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- libsdl
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- libnotify
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- libsm
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You also need a tool to create and manage Python virtual environments. For now only
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*virtualenv* is supported. So if you plan to install msspec with the one-step command,
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you need to install it.
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Fetching the code
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-----------------
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You first need to clone the repository with the command below:
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```Bash
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git clone https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git
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```
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If you want to pull the devel branch (unstable):
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```Bash
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git clone --branch devel https://git.ipr.univ-rennes1.fr/epsi/msspec_python3.git
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```
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This will create a msspec\_python3 folder with a local copy of the repository.
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One step install
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----------------
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The command below will do all the stuff to install msspec in its dedicated Python
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virtual environment provided all the above requirements are fullfilled:
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```Bash
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cd msspec_python3
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make install
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```
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This will:
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- Create a Python virtual environment in your '~/.local/src' folder
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- Install all the required Python packages in this virtual environment.
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- Install (or even maybe build) wxPython for your OS and Python version in this virtual environment.
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- Build the msspec shared librarires.
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- Install the Python msspec package in this virtual environment.
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- Install a frontend script called 'msspec' in the '~/.local/bin' folder.
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You can tweak the process by specifying space separated key=value pairs on the command line.
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Allowed keys are:
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- PYTHON, to give the executable name of the python interpreter to use rather than the default (python)
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- VERBOSE, set to 1 if you want the install process to be more verbose
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- NO\_VENV, set to 1 to not create a virtual environment
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- VENV\_PATH, specify the path to a virtual environment root folder
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- DEBUG, set to 1 to add debugging symbols
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- BUILDDIR, to set a different name than the default to store building artifacts (./build)
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- FC, the Fortran compiler to use (gfortran)
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- F2PY
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To install msspec in developpment mode, use:
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```Bash
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cd msspec_python3
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make devel
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```
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This will do the same steps as above except that the virtual environment will be located in
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the "\_venv" folder inside the "msspec\_python3" folder and the frontend script will not be
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installed.
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Working with msspec
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-------------------
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Use the frontend command to process a Python script with msspec.
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```Bash
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msspec -p myscript.py
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```
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This will execute the myscript.py inside the msspec virtual environment.
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You can also load a hdf5 file with the '-l' option:
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```Bash
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msspec -l results.hdf5
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```
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You can load an iPython console with "msspec -i". It is a good way to modify the virtual environment
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of MsSpec since you can add or remove packages withe the "%pip" command.
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If you want to activate the MsSpec virtual environment in your current shell session:
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```Bash
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eval $(msspec -e)
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```
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You can then run scripts using the 'python' command directly.
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Type in 'deactivate' to go back to your standard shell.
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See the online [tutorials](https://msspec.cnrs.fr/tutorials/index.html) for more information on how to use msspec.
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Uninstall MsSpec
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----------------
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To remove MsSpec, use the command:
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```Bash
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msspec -u
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```
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This will simply remove the virtual environment folder in '~/.local/src' and the frontend script in '~/.local/bin'.
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When Installed in "devel mode", nothing is created outside the msspec\_python3 folder, so you just have to remove
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that folder to get rid of msspec on your computer
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Manual control over the install
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-------------------------------
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If for any reason you want to control each step of the building process (for example you do not have *virtualenv* but you
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are using *conda*), here is how:
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- Create a virtual environment or use an existing one and activate it
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- Install the list of requirements that are listed in the src/pip.freeze file
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- Install wxPython
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- Build the msspec shared librarires with the command "make pybinding"
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- Install the msspec Python package with "pip install -e src/"
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The last step can be replaced by adding the src/ path to your PYTHONPATH, but bear in mind that the package will then
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be also visible to other virtual environments no matter they fit the msspec requirements.
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