Sylvain Tricot
162ffa87bd
The version is now not hardcoded anymore in the python module. We use setuptools_scm or pkg_resources instead. There was also a bug in the linkage for PED with matrix inversion using external lapack. Finally, the install script install now requirements and all requirements are stored in the requirements.txt file. setup.py looks inside to set its "install_requires" keyword. |
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| CI | ||
| doc | ||
| src | ||
| utils | ||
| .gitattributes | ||
| .gitignore | ||
| Jenkinsfile | ||
| Makefile | ||
| README.md | ||
| license.txt | ||
README.md
Introduction
This is the Python MsSpec version with support for Python 3.x and dynamic memory allocation for Phagen and Spec
To work with the git repository
It is higly recommended to work in a Python virtual environment. To create one, you can use:
virtualenv --python=python3 msspec_venv
or
virtualenv --python=python3 --system-site-packages msspec_venv
to activate the virtual environment (if you are in the folder where you created "msspec_venv"):
source ./msspec_venv/bin/activate
To get the python package dependencies, you can install the requirements with the provided requirements.txt file.
pip install --upgrade -r requirements.txt
You also need to export the path to the msspec package in the PYTHONPATH variable (replace the whereisthegitrepo part of the string with the actual absolute path of your repo.
export PYTHONPATH=/whereisthegitrepo/src:$PYTHONPATH
Finally you need to compile the fortran libs:
make pybinding
That's all. All you need to do each time you want to work with msspec is:
- To activate the virtual environment
- Export the path to msspec package in the PYTHONPATH variable
To create a self-extracible archive
If you want to create a setup program to install msspec:
At the root of the repo, type in
make selfex
This will compile the code and create the results of unit tests, then it will create a self-extractible archive in the package folder
To install the *.setup file
Just execute the file with a shell
sh ./MsSpec-###.setup
Replace ### with the version number.
To automatically accept the defaults you could type in
sh ./MsSpec-###.setup --accept -- -y
and to make the install process verbose:
sh ./MsSpec-###.setup -- -d