Utility functions for python
The python functions are organized in packages and modules in the subdirectory
utils. Unittests reside in subdirectories tests in the respective packages.
The top-level folder tests provides shell scripts to run all unittests and
determine the test coverage. Finally, the top-level folder scripts contains
python code that can be executed as a command directly from the shell.
The following external packages are required for many of the functions
| Package | Usage |
|---|---|
| numpy | Array library used for manipulating data |
| scipy | Miscellaneous scientific functions |
| six | Compatibility layer between python 2 and 3 |
The following packages are only necessary for some packages and need thus not
all be installed. These packages can be installed through pip, macports,
or similar repositories:
| Package | Usage |
|---|---|
| cython | Compiling code to accelerate some calculations |
| h5py | Handling hdf5 files |
| pandas | Managing data |
| ply | Parsing text |
| portalocker | Locking files on different platforms |
| matplotlib | Plotting graphs |
| networkx | Handling graph theory |
| numba | Just-in time compiling of python code |
| tqdm | Displaying progress bars |
| yaml | Reading and writing structured data (package name: pyyaml) |