from fluiddoc import mock_modules

mock_modules(('nbstripout', 'scipy', 'scipy.fftpack', 'scipy.interpolate',
              'skimage', ''))

Main features of the fluiddyn package

We here give an overview of the main features of the package. Fluiddyn contains pure python code useful when developing and using fluiddyn packages. It is like the Ali Baba’s cave of the fluiddyn project. Here, we just show typical import commands and point towards pages in the documentation.

Just importing the main package can be useful:

import fluiddyn as fld
<function fluiddyn.util.util.ipydebug()>

Subpackage fluiddyn.output

from fluiddyn.output import show, set_rcparams, gradient_colors


from import (
    binary, txt, mycsv, hdf5, digiflow, dantec, davis, multitiff, in_py, image)
from import query_yes_no, query, query_number
from import MultiFile

There is also a function to disable the standard output which we use a lot in unittests.

from import stdout_redirected


This package also contains the code of a very simple utility to dump hdf5 and netcdf files (without dependency in the netcdf library and in the program h5dump)

from import dump_h5_file, dump_nc_file
! fluiddump -h
usage: fluiddump [-h] [-pv] file

Utility to print the hierarchy of hdf5 and netcdf files.

positional arguments:
  file                  str indicating which file has to be dump.

  -h, --help            show this help message and exit
  -pv, --print-variables
                        also print the content of the variables

Subpackage fluiddyn.util

from fluiddyn.util import (
    time_as_str, get_memory_usage, print_memory_usage,
    import_class, is_run_from_ipython)

# very simple use of mpi (no dependency on mpi4py if the process is run without mpi)
from fluiddyn.util import mpi

# storing parameters
from fluiddyn.util.paramcontainer import ParamContainer
from fluiddyn.util.paramcontainer_gui import QtParamContainer

# handling series of arrays in files
from fluiddyn.util.serieofarrays import SerieOfArraysFromFiles, SeriesOfArrays

# "tickers"
from fluiddyn.util.timer import Timer, TimerIrregular

# daemon
from fluiddyn.util.daemons import DaemonThread, DaemonProcess

# emails
from fluiddyn.util import mail

# matlab to py (command line utility fluidmat2py)
from fluiddyn.util.matlab2py import cleanmat, mat2wrongpy


from fluiddyn.util.logger import Logger
from fluiddyn.util import terminal_colors
from fluiddyn.util import config_logging

from fluiddyn.util.terminal_colors import cprint
cprint("RED", color="RED")
cprint.light_blue("bold light blue", bold=True)
bold light blue

fluidinfo: gather information on your Python environment

from fluiddyn.util import info
!fluidinfo -h
usage: fluidinfo [-h] [-s] [-o OUTPUT_DIR] [-v] [-W]

Displays all important information related to software and hardware. It also
includes detailed information such as currently installed FluidDyn packages,
other third-party packages, C compiler, MPI and NumPy configuration.

>>> fluidinfo  # print package, Python, software and hardware info
>>> fluidinfo -v  # also print Numpy info
>>> fluidinfo -s  # save all information into sys_info.xml
>>> fluidinfo -o /tmp  # save all information into /tmp/sys_info.xml

.. todo::
    Use a YAML package to print.

  -h, --help            show this help message and exit
  -s, --save            saves system information to an xml file (sys_info.xml)
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR
                        save to directory
  -v, --verbosity       increase output verbosity (max: -vvv)
  -W, --warnings        show warnings

Subpackage fluiddyn.calcul

from fluiddyn.calcul import easypyfft
from fluiddyn.calcul import sphericalharmo
from fluiddyn.calcul import signal
from fluiddyn.calcul.setofvariables import SetOfVariables

Subpackage fluiddyn.clusters

from fluiddyn.clusters.legi import Calcul8 as Cluster
Useful commands
oarsub -S
oarstat -u
oardel $JOB_ID
oarsub -C $JOB_ID
from fluiddyn.clusters.cines import Occigen as Cluster
Useful commands

squeue -u $USER
squeue --format="%.12i %.9P %.25j %.8u %.8T %.10M %.6D %R" -u $USER
scontrol hold
scontrol release
scontrol show <jobid>
scontrol update jobid=<jobid> TimeLimit=1-00:00:00

Package fluiddoc: helping to build nice web documentations

import fluiddoc
<function fluiddoc.mock_modules(modules)>
from fluiddoc.ipynb_maker import ipynb_to_rst