cgat_rebuild_extensions.py - rebuild all cython extensions

Tags

Python

Purpose

This script rebuilds all cython extensions in the source directory.

Some scripts in the repository make use of pyximport to compile associated cython scripts with embedded C code. Theses scripts are automatically re-compiled if the script has changed, but this process can fail if:

• the script is executed on a machine without a C-compiler

• some underlying libraries have changed.

Thus, it is safer to rebuild all scripts on a machine with a C compiler before running a script in production on a cluster, where not all nodes might be fully configured for compilation.

Usage

Example:

python cgat_rebuild_extensions.py

Type:

python cgat_rebuild_extensions.py --help

for command line help.

Command line options

usage: cgat-rebuild-extensions [-h] [-i TEST_OPTION] [--timeit TIMEIT_FILE]
                               [--timeit-name TIMEIT_NAME] [--timeit-header]
                               [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                               [--log-config-filename LOG_CONFIG_FILENAME]
                               [--tracing {function}] [-? ?] [-I STDIN]
                               [-L STDLOG] [-E STDERR] [-S STDOUT]
cgat-rebuild-extensions: error: argument -?: expected one argument