semvec/pypi-packages huggingface dataset:
clusterpolate 0.2.0
Clusterpolate: Inter- and extrapolation for clustered data.
License: MIT
Keywords: interpolation,extrapolation,data,cluster,scattered,heatmap,scatterplot

Traditional approaches for inter- and extrapolation of scattered data
work on a filled rectangular area surrounding the data points or in
their filled convex hull. However, scattered data often consists of
different clusters of irregular shapes and usually contains areas where
there simply is no data. Forcing such data into a traditional inter-
or extrapolation scheme often does not lead to the desired results.

Heatmaps, on the other hand, deal well with scattered data but often do
not provide real interpolation: Instead they usually use raw sums of
kernel functions which overestimate the target value in densely
populated areas.

Clusterpolation is a hybrid inter- and extrapolation scheme to fix this.
It uses kernel functions for a weighted inter- and extrapolation of
local values, as well as for a density estimation of the data. The
latter is used to assign a membership degree to clusterpolated points:
Points with a low membership degree lie in an area where there's just
not enough data.
goodreads_quotes 0.1.0
Fetches popular quotes and quote of the day from goodreads.com website
License: MIT
Keywords: goodreads,quotes,motivation,daily-quotes,popular-quotes

goodreads-quotes
================

A Python module to fetch popular quotes and quote of the day from `Goodreads <https://goodreads.com/quotes>`_ page.

Dependencies
------------

This package depends on the following packages:

- requests
- lxml
- u

They can be installed using ``pip``.

::

    sudo pip install -r requirements.txt


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

- You will need [Python 3](https://www.python.org/download/).
- [pip](http://pip.readthedocs.org/en/latest/installing.html) is recommended for installing dependencies.

::

    sudo pip install goodreads_quotes

Getting Started
---------------

.. code:: python

    from goodreads_quotes import Goodreads

    print(Goodreads.get_popular_quotes())
    print(Goodreads.get_popular_quotes_as_json())
    print(Goodreads.get_daily_quote())
    print(Goodreads.get_daily_quote_json())

Features
--------

- Popular quotes
- Daily quote

Contribution
------------

Feel free to create a Github issue. Also, you are more than welcome to submit
a pull request for a bug fix or additional feature.

License
-------

`MIT License <http://opensource.org/licenses/mit-license.php>`_
calltree 0.26
Show Callgraph from cscope database
License: MIT


.. sectnum::
.. contents:: Table Of Contents

********
calltree
********

Show Callgraph of a given function

=======
Purpose
=======
The understanding of the codeflow in a larger source of codebase, requires to list the caller and callee relationships for a given function. For linux and unix developers, cscope has been the primary utitlity to search and browse through the code.

This utility uses the generated cscope database to list and display the
callgraph, which is stored in a image format. 

=====
Usage
=====

    Command Line
    ------------

Usage: python -m calltree [options] functionname

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  --everything          Recursively show all callers and callees
  -a, --showall         Show all callers and callees
  -c, --callers         Recursively show all callers
  -e, --callees         Recursively show all callees
  -l LEVEL, --level=LEVEL
                        Show Level of callers/callees
  -f OUTPUTFORMAT, --format=OUTPUTFORMAT
                        output format jpg/png
  -o OUTPUTDIR, --outputdir=OUTPUTDIR
                        Storage directory for output files
  -d SOURCEDB, --db=SOURCEDB
                        cscope database (cscope.out)

.. code-block::        
    import calltree
    f = calltree.calltree.calltree()
    f.showtree()
    f.showgraph()
pelican_vimeo 0.1.1
Easily embed Vimeo videos in your posts
License: MIT

=============
Pelican Vimeo
=============

Pelican Vimeo is a plugin to enabled you to embed Vimeo videos in your pages
and articles.

Installation
============

To install pelican-vimeo, simply install it from PyPI:

.. code-block:: bash

    $ pip install pelican-vimeo

Then enabled it in your pelicanconf.py

.. code-block:: python

    PLUGINS = [
        # ...
        'pelican_vimeo',
        # ...
    ]

Usage
=====

In your article or page, you simply need to add a line to embed you video.

.. code-block:: rst

    .. vimeo:: VIDEO_ID

Which will result in:

.. code-block:: html

    <div class="vimeo" align="left">
    <iframe width="420" height="315" src="https://player.vimeo.com/video/VIDEO_ID" frameborder="0"></iframe>
    </div>

Additional arguments
--------------------

You can also specify a `width`, `height` and `alignment`

.. code-block:: rst

	.. vimeo:: 37818131
        :width: 800
        :height: 500
        :align: center

Which will result in:

.. code-block:: html

    <div class="vimeo" align="center">
    <iframe width="800" height="500" src="https://player.vimeo.com/video/37818131" frameborder="0"></iframe>
    </div>

License
=======

`MIT`_ license.

.. _MIT: http://opensource.org/licenses/MIT
storjcore 0.0.6
Client for storing and auditing data. http://storj.io
License: MIT

=========
storjcore
=========

|BuildLink|_ |CoverageLink|_ |LicenseLink|_ |IssuesLink|_


.. |BuildLink| image:: https://travis-ci.org/Storj/storjcore.svg?branch=master
.. _BuildLink: https://travis-ci.org/Storj/storjcore

.. |CoverageLink| image:: https://coveralls.io/repos/Storj/storjcore/badge.svg
.. _CoverageLink: https://coveralls.io/r/Storj/storjcore

.. |LicenseLink| image:: https://img.shields.io/badge/license-MIT-blue.svg
.. _LicenseLink: https://raw.githubusercontent.com/Storj/storjcore

.. |IssuesLink| image:: https://img.shields.io/github/issues/Storj/storjcore.svg
.. _IssuesLink: https://github.com/Storj/storjcore/issues

Storj core library.
rvenv 0.2
Install and manage R packages in a python virtualenv
License: MIT

=======
 rvenv
=======

Install and manage R packages in a python virtualenv.

Why?
====

I need someplace to put project-specific R packages. The python
virtualenv I inevitably have installed in any given
project/analysis/pipeline seems as good a place as any.

Installation
============

Install to an active virtualenv using pip (or simply copy ``rvenv`` to
``$VIRTUAL_ENV/bin``)::

  % virtualenv r-env
  % source r-env/bin/activate
  % pip install rvenv

Or to install from the GitHub repository::

  % pip install git+https://github.com/nhoffman/rvenv.git

You can use the ``rvenv`` script from the command line to install
packages to ``$VIRTUAL_ENV/lib/R.%v-library``::

  % rvenv dplyr

Including the following lines in an R script will set the library path
to use locally-installed packages::

  #!/usr/bin/env Rscript
  if(Sys.getenv("VIRTUAL_ENV") == ""){ stop("An active virtualenv is required") }
  source(file.path(Sys.getenv('VIRTUAL_ENV'), 'bin', 'rvenv'))

Loading ``rvenv`` as above prepends ``$VIRTUAL_ENV/lib/R.%v-library``
to the library search path. See example script ``script.R``

To start an interactive R session with the library path defined::

  % eval $(rvenv -e)
  % R

And to define the library path within an already running R session::

  > Sys.setenv(VIRTUAL_ENV='some/path/to/virtualenv')
  > source(file.path(Sys.getenv("VIRTUAL_ENV"), "bin", "rvenv"))


usage
=====

::

  usage: ./rvenv [-h] [-r REQUIREMENTS] [--rm] [-U] [-l] [-e] [-R REPOS] [-v]
		 [packages [packages ...]]

  Install R packages to a python virtualenv

  Include the following in an R script to add "$VIRTUAL_ENV/lib/R.%v-library"
  to the library search path:

    #!/usr/bin/env Rscript
    if(Sys.getenv("VIRTUAL_ENV") == ""){ stop("An active virtualenv is required") }
    source(file.path(Sys.getenv("VIRTUAL_ENV"), "bin", "rvenv"))

  Also see https://github.com/nhoffman/rvenv

  positional arguments:
    packages              one or more package names

  optional arguments:
    -h, --help            show this help message and exit
    -r REQUIREMENTS, --requirements REQUIREMENTS
			  a file listing packages
    --rm                  remove listed packages
    -U, --update          update existing packages
    -l, --list            list packages installed locally
    -e, --environ         print shell command to set R_LIBS
    -R REPOS, --repos REPOS
			  value for "install.packages(repos)" [http://cran.fhcrc.org/]
    -v, --verbose         be verbose when installing packages
pg_jts 0.0.1
Create JSON-table-schema from a live PostgreSQL database
License: MIT
Keywords: PostgreSQL Postgres extract schema JTS JSON table schema

pg_jts
======

Create JSON-table-schemas from a live PostgreSQL database

Python3 alpha code

(JSON table schema is an extensible standard for describing tabular data:
http://dataprotocols.org/json-table-schema
)

Documentation: https://pg_jts.readthedocs.org/

If you provide patches, please also consider patching https://github.com/iburadempa/jts_erd/ accordingly.
SQLAlchemyViz 0.4
Package to create ER diagrams from SQLAlchemy schemas using Graphviz.
License: MIT

=============
SQLAlchemyViz
=============

SQLAlchemyViz is a command line utility to create entity-relations diagrams
from database schemas modeled with `SQLAlchemy <http://www.sqlalchemy.org/>`_
using `Graphviz <http://www.graphviz.org/>`_.

============
Requirements
============

Requires `Graphviz <http://www.graphviz.org/>`_ installed on your machine and the
`SQLAlchemy <http://www.sqlalchemy.org/>`_ and `pydot <https://pypi.python.org/pypi/pydot>`_ packages.

=======
License
=======

SQLAlchemyViz is distributed under the `MIT License <http://www.opensource.org/licenses/mit-license.php>`_.

==========
Quickstart
==========
Create an ER diagram from a sqlalchemy schema object.

positional arguments:
  pkg.module:metadata   Import path for the metadata identifier.

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  Write diagram to specified file {default:
                        diagram.pdf}.
  -p PROG, --prog PROG  Name of the graphviz layout program to use {default:
                        "dot"}. Other choices are: "dot", "twopi", "circo" or
                        "fdp".
  -o OPTION, --opt OPTION
                        Where OPTION is e.g. "graph_bgcolor=red". May be
                        supplied multiple times.
  -g GRAPHVIZ_PATH, --graphviz GRAPHVIZ_PATH
                        Path to folder containing the graphviz executables.
  -i INCLUDE_TABLES, --include INCLUDE_TABLES
                        Include the given comma separated list of tables or
                        classes. If omitted, create diagram for all.
  -x EXCLUDE_TABLES, --exclude EXCLUDE_TABLES
                        Exclude the given comma separated list of tables or
                        classes.
  --sort-columns        Sort columns by whether they are primary or foreign
                        keys and (case-insensitive) alphabetically.
  --unique-relations    Draw relations between tables only once (if multiple
                        foreign keys reference the same table).
  --show-constraints    Show table constraints.
  --max-cols MAX_COLS   Limit amount of columns shown per table.
beout 0.1.0
beout  is a library for easily generating beautiful output for long-running processes
License: MIT
Keywords: terminal

beout
=====

``beout`` is a library for easily generating beautiful output for
long-running processes. It was originally conceived as part of
improving the usability of internal tools at Prezi.

Example
-------

[`example/example.py`](example/example.py) provides a full-fledged
example of all the features. The output looks like this:

|Example screencast|

.. |Example screencast| image:: https://raw.githubusercontent.com/abesto/beout/master/example/example.gif
urlreplacer 0.1.1
Find and replace URLs in plain text messages
License: MIT
Keywords: url,email,replace

Library for replacing emails and urls in plain text messages
============================================================

To parse your text use :code:`urlreplacer.urls` or/and :code:`urlreplacer.emails`. They will only find urls and emails which has a known TLD; meaning example.com will match but example.ujh will not.

Installation:
-------------

.. code::

    $ pip install urlreplacer


Usage
=====

.. code:: python

    from urlreplacer import urls, emails

    message = """Hi!
    Please try example.com/one.html, test.com or test.com/a/?b=1.
    Or email me john@example.com! Bye.
    """

    # This will only parse for urls, emails will be left alone.
    parsed_message = urls(message)

    print(parsed_message)
    >>> Hi!
    >>> Please try <example.com/one.html>, <test.com> or <test.com/a/?b=1>.
    >>> Or email me john@example.com! Bye.

    # Now parse for emails, urls will be left alone.
    parsed_message = emails(parsed_message)

    print(parsed_message)
    >>> Hi!
    >>> Please try <example.com/one.html>, <test.com> or <test.com/a/?b=1>.
    >>> Or email me <john@example.com>! Bye.

Custom marker function
----------------------

By default it will surround all urls and emails with :code:`<>`. But you can also supply your own marker function to both :code:`urls()` and :code:`emails()`.

Example:

.. code:: python

    def marker(a, b):
        return u'<a href="{}">{}</a>'.format(a, b)

    parsed_message = urls('Is this the website: example.com?', marker)
    print(parsed_message)
    >>> Is this the website: <a href="http://example.com">example.com</a>?

Contributing
============

There is a makefile setup:

- :code:`$ make install` - installs all requirements.
- :code:`$ make test` - runs all tests under coverage
- :code:`$ make clean` - cleans caches/.pyc etc.

There is also a script for updating the list with known TLDs.

- :code:`$ make update_tlds`

This will update the :code:`urlreplacer/tlds.py` file with the latest list.

LICENSE
=======

The MIT License (MIT)

Copyright (c) [2015] [Tictail]

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
controlspeed 2.3
Control function call speed ,support network mode by redis
License: MIT
Keywords: controlspeed,fengyun

# ControlSpeed  
这项目是用来控制函数调用的频率, 不仅支持本地的同步线程模式, 而且支持分布式模式.   
[更多开发描述,请点击链接](http://xiaorui.cc)

ControlSpeed(本地版)还不兼容多进程多线程的场景, 当然你可以用ControlSpeedNetwork分布式版解决. 缺点是每次访问都会有一次网络io消耗.
#Usage:

装饰器使用方法
```
from controlspeed import ControlSpeed
@ControlSpeed(max_calls=10, period=1.0)
def do_something():
    pass
```

with关键词控制上下文
```
from controlspeed import ControlSpeed
rate = ControlSpeed(max_calls=10, period=1.0)
for i in range(100):
    with rate:
        do_something()
```

支持回调函数的控速
```
from controlspeed import ControlSpeed
import time
def limited(until):
    duration = int(round(until - time.time()))
    print 'Speed limited, sleeping for %d seconds' % duration

rate = ControlSpeed(max_calls=2, period=3, callback=limited)
for i in range(3):
    with rate:
        print i
```

在2.1加入了分布式限频, 借助于redis实现.
```
import redis
redis_conn = redis.StrictRedis()
key = 'xiaorui.cc'

@ControlSpeedNetwork(redis_conn, key, max_calls=10, period=3.0)
def do_something(args):
    print args
    time.sleep(0.1)

for i in xrange(20):
    do_something(i)
```
PPeg 0.9.4
A Python port of Lua's LPeg pattern matching library
License: MIT
Keywords: parsing peg grammar regex

====
PPeg
====

*PPeg* is a pattern matching library for Python, based on
`Parsing Expression Grammars`_ (PEGs).
It's a port of the `LPeg`_ library from Lua.

.. warning::
    PPeg is still experimental. The API and semantics are not stable.

.. _Parsing Expression Grammars: https://en.wikipedia.org/wiki/Parsing_expression_grammar
.. _LPeg: http://www.inf.puc-rio.br/~roberto/lpeg/

Usage
=====

Unlike the ``re`` module [#]_, PPeg patterns can handle balanced sequences

.. code:: python

    >>> from _ppeg import Pattern as P
    >>> pattern = P.Grammar('(' + ( (P(1)-P.Set('()')) | P.Var(0) )**0 + ')')
    >>> pattern('(foo(bar()baz))').pos
    15
    >>> pattern('(foo(bar(baz)').pos
    -1
    >>> capture = P.Cap(pattern)
    >>> capture('(foo(bar()baz))').captures
    ['(foo(bar()baz))']

This example corresponds roughly to the following LPeg example

.. code:: lua

    > lpeg = require "lpeg"
    > pattern = lpeg.P{ "(" * ((1 - lpeg.S"()") + lpeg.V(1))^0 * ")" }
    > pattern:match("(foo(bar()baz))") -- Lua indexes begin at 1
    16
    > pattern:match("(foo(bar(baz)")
    nil
    > capture = lpeg.C(pattern)
    > capture:match("(foo(bar()baz))")
    "(foo(bar()baz))"

.. [#] Some regular expression implementations (e.g. PCRE_, regex_)
   support `recursive patterns`_, which can match balanced sequences.

.. _pcre: http://www.pcre.org/
.. _regex: https://pypi.python.org/pypi/regex
.. _recursive patterns: http://www.regular-expressions.info/recurse.html

Modules
=======
- _cpeg.c
- _ppeg.c
    - includes lpeg.c
metaseq 0.5.6
Integrative analysis of high-thoughput sequencing data
License: MIT

Metaseq
=======
.. image:: https://travis-ci.org/daler/metaseq.png?branch=master
    :target: https://travis-ci.org/daler/metaseq

.. image:: https://badge.fury.io/py/metaseq.svg
    :target: http://badge.fury.io/py/metaseq

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
    :target: http://bioconda.github.io

Briefly, the goal of `metaseq` is to tie together lots of existing software into
a framework for exploring genomic data.  It focuses on flexibility and
interactive exploration and plotting of disparate genomic data sets.

The main documentation for `metaseq` can be found at https://daler.github.io/metaseq.

If you use `metaseq` in your work, please cite the following publication:

    Dale, R. K., Matzat, L. H. & Lei, E. P. metaseq: a Python package for
    integrative genome-wide analysis reveals relationships between chromatin
    insulators and associated nuclear mRNA. Nucleic Acids Res. 42, 9158–9170
    (2014). http://www.ncbi.nlm.nih.gov/pubmed/25063299


Example 1: Average ChIP-seq signal over promoters
-------------------------------------------------

`Example 1 <https://daler.github.io/metaseq/example_session.html>`_ walks you
through the creation of the following heatmap and line-plot figure:

.. figure:: demo.png

    Top: Heatmap of ATF3 ChIP-seq signal over transcription start sites (TSS) on
    chr17 in human K562 cells.  Middle: average ChIP enrichment over all TSSs
    +/- 1kb, with 95% CI band.  Bottom: Integration with ATF3 knockdown RNA-seq
    results, showing differential enrichment over transcripts that went up,
    down, or were unchanged upon ATF3 knockdown.

Example 2: Differential expression scatterplots
-----------------------------------------------

`Example 2 <https://daler.github.io/metaseq/example_session_2.html>`_ walks
you through the creation of the following scatterplot and marginal histogram
figure:


.. figure:: expression-demo.png

    Control vs knockdown expression (log2(FPKM + 1)) for an ATF3 knockdown
    experiment.  Each point represents one transcript on chromosome 17.
    Marginal distributions are shown on top and side.  1:1 line shown as
    a dotted line.  Up- and downregulated genes determined by a simple 2-fold
    cutoff.

Other features
--------------
In addition, `metaseq` offers:

* A format-agnostic API for accessing "genomic signal" that allows you to work
  with BAM, BED, VCF, GTF, GFF, bigBed, and bigWig using the same API.

* Parallel data access from the file formats mentioned above

* "Mini-browsers", zoomable and pannable Python-only  figures that show genomic
  signal and gene models and are spawned by clicking on features of interest

* A wrapper around pandas.DataFrames to simplify the manipulation and plotting
  of tabular results data that contain gene information (like DESeq results
  tables)

* Integrates data keyed by genomic interval (think BAM or BED files) with data
  keyed by gene ID (e.g., Cufflinks or DESeq results tables)

Check out the `full documentation <https://daler.github.io/metaseq/>`_ for
more.
songvid 1.0.1
A tool to create a video with a still image and a given audio track
License: MIT

songvid
=======

A tool to create a video with a still image and a given audio track

Needs ffmpeg compiled with ``--enable-libfdk-aac`` and
``--enable-nonfree``

Usage
-----

::

    usage: songvid [-h] image audio

    positional arguments:
      image       Image filename
      audio       Audio filename

    optional arguments:
      -h, --help  show this help message and exit

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

Via ``pip``:

::

    pip3 install songvid

Alternatively:

-  Clone the repository, ``cd songvid``
-  Run ``python3 setup.py install`` or ``pip3 install -e``
prompter 0.3.10
Simple CUI input prompt
License: MIT

prompter
========

.. image:: https://travis-ci.org/tylerdave/prompter.svg?branch=master
  :target: https://travis-ci.org/tylerdave/prompter

.. image:: http://badge.fury.io/py/prompter.png
  :target: http://badge.fury.io/py/prompter

.. image:: https://coveralls.io/repos/tylerdave/prompter/badge.svg?branch=master
  :target: https://coveralls.io/r/tylerdave/prompter?branch=master 

Simple CUI prompt input for Python

Installing
----------

Install the latest stable from PyPi::

 pip install prompter

Install the latest development version from master::

  pip install git+git://github.com/tylerdave/prompter

Using
-----

.. code-block:: python

  >>> from prompter import prompt, yesno

  >>> prompt('What is your name?')
  What is your name? Dave
  'Dave'

  >>> prompt('What is your name?', default='Jenn')
  What is your name? [Jenn]
  'Jenn'

  >>> prompt('What is your name?', default='Jenn', suffix='\n > ')
  What is your name? [Jenn]
  >
  'Jenn'

  >>> prompt('Enter text surrounded by spaces.', strip=False)
  Enter text surrounded by spaces.    text
  '   text   '

  >>> yesno('Really?')
  Really? [Y/n]
  True

  >>> yesno('Really?')
  Really? [Y/n] no
  False

  >>> yesno('Really?', default='no')
  Really? [y/N]
  True

  >>> yesno('')
  [Y/n] n
  False

Note
----

Please open an issue on Github if you notice problems or have
suggestions!