semvec/pypi-packages huggingface dataset:
groio 1.0
A simple library for gro files
License: MIT

groIO
=======================

.. image:: https://travis-ci.org/HubLot/groio.svg?branch=master
   :target: https://travis-ci.org/HubLot/groio
.. image:: https://coveralls.io/repos/HubLot/groio/badge.svg?branch=master&service=github
  :target: https://coveralls.io/github/HubLot/groio?branch=master


A library to handle the reading and writing of a gro file.


Installation
------------

    pip install groio

Usage
-----

.. code:: python

    import groio

    #Read a gro file
    title, atoms, box = groio.parse_file("filin.gro")

    #Write a gro file
    with open("filout.gro", "w") as f:
        for line in groio.write_gro(title, output_atoms, box):
            print(line, end='', file=f)

    #Renumber the atoms to avoid number above 100 000
    atoms = groio.renumber(atoms)


The function ``parse_file`` returns :

- ``title``: the title of the system as written on line 1 of the file  as a string
- ``atoms``: a list of atom, each atom is stored as a dictionary
- ``box``: the box description as written on the last line as a string


Run tests
---------

Unit tests are available through `nosetests python module <https://nose.readthedocs.org>`_.
    nosetests tests/test_groio.py
Flask-Beanstalk 0.0.3
Utilities for using Beanstalk with Flask
License: MIT

===============
Flask-Beanstalk
===============

.. image:: http://img.shields.io/pypi/v/Flask-Beanstalk.png

Utilities for using Beanstalk with Flask

------
Client
------

``flask_beanstalk.Beanstalk`` is a simple wrapper for ``beanstalkc.Connection``
that allows reading configuration from ``app.config``.

::

  from flask import Flask
  from flask_beanstalk import Beanstalk

  app = Flask(__name__)
  beanstalk = Beanstalk(app)  # or beanstalk.init_app(app)

Configuration
=============

::

  app.config['BEANSTALK_HOST']
  app.config['BEANSTALK_PORT']
  app.config['BEANSTALK_PARSE_YAML']
  app.config['BEANSTALK_CONN_TIMEOUT']

------
Worker
------

Define and spawn workers by subclassing from ``flask_beanstalk.Worker``.
``flask_beanstalk.Worker`` inherits from ``gevent.Greenlet`` but ``gevent``
is an optional dependency in case you just want to use the client.

::

  import gevent
  from flask_beanstalk import Worker as _Worker

  class Worker(_Worker):
    def run(self, job):
      self._logger.info('Received: %r' % job.body)
      job.delete()

  workers = Worker.spawn_workers(10)
  try:
    while True:
      gevent.sleep(10000)
  except KeyboardInterrupt:
    Worker.stop_workers(workers)

----------
Try it out
----------

Install and run ``beanstalkd`` if you haven't done so yet.

::

  git clone https://github.com/marksteve/flask-beanstalk.git
  cd flask-beanstalk
  mkvirtualenv flask-beanstalk
  workon flask-beanstalk
  python setup.py develop
  python example_worker.py

On another terminal::

  workon flask-beanstalk
  python example.py

Go to localhost:5000 in your browser to send a job.
The worker should be able to accept and process it.
Try to send multiple jobs before sending a SIGINT
to the worker. Jobs being worked on should be
processed first before the worker shuts down.
clean-directories 1.1.0
A script to clean your directories
License: MIT
Keywords: script clean directories

clean
=====

## Objective

The python script "clean" allow the user to clean directory off temporary files with its default behavior.
With anoter configuration, it can allow you to clean a working directory before committing.

The final goal is to provide multiple configurations to clean a directory the exact way you want it.

## Suggestion

The best way to use this script at its fullest is to place clean.py in a personnal bin directory.
For example, you can create a directory "bin" in your home and add it to the variable $PATH.
Then, place the binaries and script you want to execute them wherever you are.
You can of course rename clean.py to clean or another name you prefer.

## Important options

### Help

./clean.py -h or ./clean.py --help

Print basical informations to the user, with a summary of the available commands.

### Pattern

./clean.py -p PATTERN or ./clean.py --pattern PATTERN

Allow the user to search for one or more pattern, overridding the default patterns.
You can use this option multiple times. For example, this command imitate the normal behavior : "./clean.py -p '#*#' -p '*~'"

### Force

./clean.py -f or ./clean.py --force

Skip the prompt for all the files targeted.
Use this command with prudence, and verify that the command will not remove a file you want to keep.

### Recursive

./clean.py -r or ./clean.py --recursive

Make a recursion to clean every subdirectory found.
Usefull if your working directory is subdivised into multiple directories.

### Configuration

./clean.py -c CONFIGURATION or ./clean.py --configuration CONFIGURATION

Override the default behavior with the given configuration.
The argument for this option must be the name of the configuration placed in $HOME/.config/clean.