Saravanan666/pypi-org huggingface dataset:
Package: pyteomics
What is Pyteomics?Pyteomics is a collection of lightweight and handy tools for Python that help
to handle various sorts of proteomics data. Pyteomics provides a growing set of
modules to facilitate the most common tasks in proteomics data analysis, such as:calculation of basic physico-chemical properties of polypeptides:mass and isotopic distributioncharge and pIchromatographic retention timeaccess to common proteomics data:MS or LC-MS dataFASTA databasessearch engines outputeasy manipulation of sequences of modified peptides and proteinsThe goal of the Pyteomics project is to provide a versatile, reliable and
well-documented set of open tools for the wide proteomics community.
One of the project’s key features is Python itself, an open source language
increasingly popular in scientific programming. The main
applications of the library are reproducible statistical data analysis and rapid
software prototyping.Supported Python versionsPyteomics supports Python 2.7 and Python 3.3+.Install with pipThe main way to obtain Pyteomics is viapip Python package manager:pip install pyteomicsInstall with condaYou can also install Pyteomics fromBiocondausingconda:conda install -c bioconda pyteomicsArch-based distrosOn Arch Linux and related distros, you can install Pyteomics from AUR:python-pyteomicsProject dependenciesSome functionality in Pyteomics relies on other packages:numpy;matplotlib(used bypyteomics.pylab_aux);lxml(used by XML parsing modules andpyteomics.mass.mass.Unimod);pandas(can be used withpyteomics.pepxml,pyteomics.tandem,pyteomics.mzid,pyteomics.auxiliary);sqlalchemy(used bypyteomics.mass.unimod);pynumpress(adds support for Numpress compression in mzML);h5pyand optionallyhdf5plugin(used bypyteomics.mzmlb);psims(used pypyteomics.proforma);spectrum_utils(optionally used for spectrum annotation inpyteomics.pylab_aux).All dependencies are optional.Installing a subset of dependencies with pipYou can quickly install just the dependencies you need by specifying an“extra”. For example:pip install pyteomics[XML]This will install Pyteomics, NumPy and lxml, which are needed to read XML format. Currently provided identifiers are:XML,TDA,graphics,DF,Unimod,numpress,mzMLb,proforma.You can also use these specs as dependencies in your own packages which require specific Pyteomics functionality.
Package: pyteomics.cythonize
This package re-implements several ofPyteomicsfunctions
in C usingCythonand the Python-C API. Currently, only
commonly used functions inpyteomics.massandpyteomics.parserare implemented,
providing faster sequence manipulation and mass calculations. Every effort has been
made to make the user-facing interfaces identical to their pure Python counterparts.These functions are also exposed in the package’s C-API so that other C-Extensions can make
use of them.This package also re-implements thepyteomics.mass.Compositiontype in C using Python’sdictas a base.APIThis package provides two modules,pyteomics.cmassandpyteomics.cparser,
which mimic a subset of the APIs ofpyteomics.massandpyteomics.parserrespectively. For example:frompyteomicsimportcmass,massassertcmass.fast_mass("PEPTIDE")==mass.fast_mass("PEPTIDE")
Package: pyteomics.pepxmltk
pyteomics.pepxmltk - a pepXML writer and Tandem2XML converterpyteomics.pepxmltkis a module based on the
[pyteomics](https://pyteomics.readthedocs.io/) package that
allows creation of
[pepXML](http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML)
files from Python objects of a certain structure. The structure corresponds to
tokens generated by the pyteomics TandemXML parser.This package provides a module that can be used for writing pepXML files
from your Python code, as well as a command-line script for conversion, merging
or filtering of X!Tandem files to pepXML. Unlike its analog from Trans-Proteomic
Pipeline (TPP), the script is capable of handling non-standard enzymes.The package contains two scripts:pepxmltk.pyandruntandem.pepxmltk.pydoes conversion from X!Tandem XML to pepXML, or from pepXML to pepXML, while optionally
combining multiple files and performing FDR filtering.runtandemis a CLI wrapper that simplifies the repetitive actions of creatingtaxonomy.xml,
running X!Tandem, and converting the result to pepXML.Dependenciespyteomicsnumpylxmljinja2LinksPyPI:https://pypi.org/project/pyteomics.pepxmltk/BitBucket repo & issue tracker:https://bitbucket.org/markmipt/pyteomics.pepxmltkMailing list:pyteomics@googlegroups.com
Package: pyteomics-utils
# pyteomics-utils
Simple but handy CLI tools for everyday data analysis tasks.The commands operate on stdin and write to stdout whenever possible.## Supported commands (run each command with-hfor help)pyteomics fasta decoy– generate a decoy database for one or more files.pyteomics fasta describe– check contents of a FASTA file.pyteomics fasta combine– combine multiple FASTA files, optionally adding decoys in the process.pyteomics pepxml info– list number of PSMs (with and without FDR filtering) in pepXML files.
Package: pyteos_air
This package is still in beta testing phase and some of its functions are
likely to evolve over time.Includes:Sea-Ice-Water (SIA) Library 3.0 + simple code fixes (for easy compilation)An extra module layerLiq_Ice_Air_5a.F90,Liq_Ice_Air_5b.F90,Liq_Ice_Air_5c.F90andLiq_Ice_Air_5d.F90with the temperature, the entropy, the potential temperature,
the equivalent potential temperature and the pseudo equivalent potential temperature
valid over the whole region of validity of TEOS-10.Two other extra modulesLiq_Air_4d.F90andIce_Air_4d.F90that are very similar
toLiq_Air_4b.F90andIce_Air_4b.F90but where one can specify a maximum
saturation mass fraction in the definition of the Gibbs function. This allows
to compute the equivalent potential temperature in a clean manner.A framework to add python bindings to the Fortran version of TEOS-10 with basic examples.This package provides a simple way to import the TEOS-10 SIA Library into python.
The current beta version offers a very basic interface to the library. Future versions
will include a better interface and a more extensive physical description of the different
routines available.NOTE:This package requires a Fortran 90 compiler. Sometimes numpy.disutils will not find
the installed Fortran compiler and will return an error. It this happens, download the
source code and run:$ f2py -c --help-fcompilerTo find the list of available compilers and then compile:$ python setup.py build --fcompiler=gnu95if ‘gnu95’ was in the list.VERSION HISTORY1.0.4 : New equivalent potential temperature and its approximate version.1.0.3 : Must compute f2py insetup.pybut now using a more portable method.1.0.1 : Package comes with pre-computed f2py files for easier portability.1.0 : Important bug fix on PYPI0.9.5 : Some minimal testing and code publication improvements0.9.2 : Finished moving netCDF interface to packagepyteos_nc0.9.1 : Moved netCDF interface to packagepyteos_nc0.9 : Improve netCDF interface0.8 : Fixed a warning signal with missing values0.7 : The interpolation is now much faster0.6 : Faster netcdf interface for computing interpolated thermodynamic quantities.Frederic Laliberte, February 17 2015
Package: pyteos_nc
Command-line tool to compute thermodynamic quantities from netCDF4 files.It requires a thermodynamic data file (table of values) produced by a
data file generator that relies on thepyteos_airpackage:VERSION HISTORY0.4.2: Potential temperatures generators cover more of thermal space andthe exact potential temperature can now be used.0.4.1: Bug fix.0.4 : Clean-up PYPI repository.0.3 : Added some pre-cooked recipes0.2 : Finished disentangling frompyteos_airFrederic Laliberte, March 2017
Package: pyter
pyterpyter is a simple Translation Error Rate evaluation command.Currentry under development state.Installationpip install pyteror checkout the repository:git clone git://github.com/aflc/pyter.git
cd pyter
pip install -e .UsageIn Python code(Python2.x case)import>>> import pyterTo get a TER score, both hypothesis sentence and reference sentence have to a list of word.>>> ref = u'SAUDI ARABIA denied THIS WEEK information published in the AMERICAN new york times'.split()
>>> hyp = u'THIS WEEK THE SAUDIS denied information published in the new york times'.split()
>>> '%.3f' % pyter.ter(hyp, ref)
'0.308'If you want to use a charactor based matching, write a code like that.>>> ref = list(u"Pythonは、より素早く、効果的にシステムとの統合が可能なプログラミング言語です。")
>>> hyp = list(u"Pythonは、より迅速に動作するとより効果的にシステムを統合できるプログラミング言語です。")
>>> '%.3f' % pyter.ter(hyp, ref)
'0.357'Command line interfacePlease type:pyter --helpReleaseNotev0.2.2.1bugfix releasev0.2.2fixed #1, invalid scoreing.v0.2.1New CLI interfaceRefactoring the whole codeThis version is incompatible with the previous version.v0.2Replace normal DP based edit distance with cached version. A little performance improvement.v0.1.1Minor fix, and register to PyPiv0.1Initial releaseLicenseIt is released under the MIT license.Copyright (c) 2011 Hiroyuki TanakaPermission 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.
Package: pyter3
=====
pyterpyter is a simple Translation Error Rate evaluation package.============
InstallationCheckout the repository.. code-block:: bashgit clone https://github.com/BramVanroy/pyter.git
cd pyter
pip install -e .=====
Usage.. code-block:: pythonimport pyter

# To get a TER score, both hypothesis sentence and reference sentence have to be tokenised (a list of words).

ref = 'SAUDI ARABIA denied THIS WEEK information published in the AMERICAN new york times'.split()
hyp = 'THIS WEEK THE SAUDIS denied information published in the new york times'.split()
print(pyter.ter(hyp, ref))
# 0.308===========
ReleaseNotev0.3only kept essentials for use as module (removed CLI)turned it into Python 3 scriptsv0.2.2.1bugfix releasev0.2.2fixed #1, invalid scoreing.v0.2.1New CLI interfaceRefactoring the whole codeThis version is incompatible with the previous version.v0.2Replace normal DP based edit distance with cached version. A little performance improvement.
v0.1.1Minor fix, and register to PyPi
v0.1Initial release===============
AcknowledgmentsBased on the original version by user afcl at afcl/pyter_... _pyter:https://github.com/aflc/pyter=======
LicenseIt is released under the MIT license.Copyright (c) 2011 Hiroyuki Tanaka

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.
Package: pytere
pyterePython Template repositoryDescription•Install•Usage•Use this template•FAQ•ContributeDocumentationDescriptionpyterestands forPythontemplaterepository.It's just a template repository for python, with the following features :📚 Beautiful documentation withMaterial for Mkdocs, published as a Github page withmikeautomatically✨ Modern code style checks withblackandruff🅿️ Easy development withpre-commit hooks✅ Tests withpytestand coverage without external tools:octocat: CI withGithub actions📝 Issues & PR templates🤖 Stale bot & Dependabot🚀 Releases automatically published to PyPiInstallInstallpytereby running :pip install pytereFor development, you can install it locally by first cloning the repository :git clone https://github.com/astariul/pytere.git
cd pytere
pip install -e .Usagepyteredoes not contain any useful code because it's a template repository.But you can check if the package is correctly installed with :frompytereimportis_oddprint(is_odd(2))# FalseUse this templateTo use this template, click the button "Use this template" :It will prompt you to create a new Github repository.Then replace the content  in your freshly created repository, with your own package name, own code, and update the links to point to your own repository.More details in thedocumentation.FAQ❓Why creating yet another template, there is already plenty on the internet ?True, but I couldn't find one that entirely satisfies my needs and uses
the tools I want.For example, a lot of templates useSphinxfor the documentation, but I'm much more comfortable withMkDocs. Or the test coverage was provided by an external tool, but I wanted everything in Github. Etc...Hence the creation of this repository.❓Can I use this template for a private repository ?Absolutely !But some things might not work (for example the release badge), and you might want to remove some features (like automatically pushing to PyPi, or publishing the documentation to Github page)ContributeTo contribute, install the package locally, create your own branch, add your code (and tests, and documentation), and open a PR !Pre-commit hooksPre-commit hooks are set to check the code added whenever you commit something.If you never ran the hooks before, install it with :pre-commitinstallThen you can just try to commit your code. If your code does not meet the quality required by linters, it will not be committed. You can just fix your code and try to commit again !You can manually run the pre-commit hooks with :pre-commitrun--all-filesTestsWhen you contribute, you need to make sure all the unit-tests pass. You should also add tests if necessary !You can run the tests with :pytestTests are not included in the pre-commit hooks, because running the tests might be slow, and for the sake of developpers we want the pre-commit hooks to be fast !Pre-commit hooks will not run the tests, but it will automatically update the coverage badge !DocumentationThe documentation should be kept up-to-date. You can visualize the documentation locally by running :mkdocsserve
Package: pytermcanvas
pytermcanvasRequirementsterminal emulator (withtrue color support)python3pipPILcursorInstallpipinstallpytermcanvasUsageclassTerminalCanvas(x_size, y_size, auto_render, empty_char)Parameters:x_size(Int) - number of columns to use, stored inself.colsy_size(Int) - number of rows to use, stored inself.rowsauto_render(Bool) [default:True]True- enable automatic canvas renderingFalse- disable automatic canvas renderingempty_char(Char) [default:SPACE] - character used to fill the canvas on creationMethods:render()Renders canvasclear()Clears canvasresize(x_size, y_size)x_size(Int) - number of columns to use, stored inself.colsy_size(Int) - number of rows to use, stored inself.rowsdrawImage(*path, ***kwargs)Draws image on canvaspath(Str) - path to imagemode(Str) [default:bg] - mode to use for renderingbg- change color behind characterfg- change color of specified charactersize(List or Tuple) [default: canvas size] - desired size of imagesize[0] (Int) - number of columns to usesize[1] (Int) - number of rows to usechar(Char) [defualt:SPACE] - character to print, mainly used forfgrenderingdrawRect(*col, row, width, height, ***kwargs)Draws rectangle on canvascol(Int) - position of top left corner in columnrow(Int) - position of top left corner in rowwidth(Int) - width of rectangleheight(Int) - height of rectanglemode(Str) [default:bg] - mode to use for renderingbg- change color behind characterfg- change color of specified charactercolor(List or Tuple) [default:(255, 255, 255)] - RGB color of rectanglecolor[0] (Int) - Red,0 - 255color[1] (Int) - Green,0 - 255color[2] (Int) - Blue,0 - 255char(Char) [defualt:SPACE] - character to print, mainly used forfgrenderinginsertRow(row, data, offset)Inserts set of characters to specified rowrow(Int) - row to insert data todata(Str, List or Tuple) - data inserted into desired row(Str) - standard string(List or Tuple) - sequence of charactersoffset(Int) [default:0] - defines the starting columninsertCol(col, data, offset)Inserts set of characters to specified columncol(Int) - column to insert data todata(Str, List or Tuple) - data inserted into desired column(Str) - standard string(List or Tuple) - sequence of charactersoffset(Int) [default:0] - defines the starting rowgetRow(row)Returns list of characters from specified rowrow(Int) - row to fetch data fromgetCol(col)Returns list of characters from specified columncol(Int) - column to fetch data fromsetChar(col, row, char)Changes character on specified locationcol(Int) - column of characterrow(Int) - row of characterchar(Char) - replacement charactergetChar(col, row)Returns character from specified locationcol(Int) - column of characterrow(Int) - row of character
Package: pytermcolor
Tool for coloring print output in terminalFork ofhttps://pypi.org/project/termcolor/Exampleimport sys
from pytermcolor import colored, cprint

text = colored('Hello, World!', 'red', attrs=['reverse', 'blink'])
print(text)
cprint('Hello, World!', 'green', 'red')

print_red_on_cyan = lambda x: cprint(x, 'red', 'cyan')
print_red_on_cyan('Hello, World!')
print_red_on_cyan('Hello, Universe!')

for i in range(10):
    cprint(i, 'magenta', end=' ')

cprint("Attention!", 'red', attrs=['bold'], file=sys.stderr)Text PropertiesText colors:greyredgreenyellowbluemagentacyanwhiteText background:on_greyon_redon_greenon_yellowon_blueon_magentaon_cyanon_whiteAttributes:bolddarkunderlineblinkreverseconcealedTerminal propertiesTerminalbolddarkunderlineblinkreverseconcealedxtermyesnoyesboldyesyeslinuxyesyesboldyesyesnorxvtyesnoyesbold/blackyesnodttermyesyesyesreverseyesyesteratermreversenoyesrev/redyesnoaixtermnormalnoyesnoyesyesPuTTYcolornoyesnoyesnoWindowsnonononononoCygwin SSHyesnocolorcolorcoloryesMac Terminalyesnoyesyesyesyes
Package: pytermcontrol
PyTermControlPython only version ofhttps://github.com/axiros/termcontrolStarts a command within a pty from a controlling process, which reads "keystrokes" from a fifo and forwards into the child.
User input may be forwarded to another fifo, instead of sending it into the child process' pty.This way any terminal process waiting for user input can be controlled from outside.USAGE: with_termcontrol [Params] COMMANDThe fifo filename (fn_fifo) is available as$STDIN_FIFOwithin the child. All data on this fifo will be sent into the pty.If fn_fifo is set to 'auto' then we'll create a tempfile fifoIf you configure a forward fifo (fn_user), then alluserinput will be forwarded to it,
instead of sending into the ptyThe program will block(!) until a reader is attached to that user fifofn_usersimply set to true will result in its filename set to$STDIN_FIFO+ '.user' (and exported as$USER_INPUT_FIFO)Fifos will be created only if they don't exist at process startFifos will be unlinked at exit only if they where created by usParams:
--fn_user[=False]
--fn_fifo[=auto]
Package: pytermgame
pytermgameYou've seen frameworks for making terminal apps (textual,pytermgraphics,asciimaticsetc.), but how about a framework for games ... likepygame?Installationpip install pytermgameFeaturespygame-inspired structurecustomizable terminal behaviour (alternate screen, cursor visibility)optimized rendering: game figures out which sprites requires erase and re-render(it takes care of overlapping sprites too!)provides both tick-based and thread-based event systemscross-platform support for reading and identifying keysExamplesExamples are included in the repo root (there's 2 currently)Instructions are in the file of the example (docstrings)Future planscross-platform support for more keyssimulated scrolling (extended axis)a "Scene" or "Screen" systemuse integer IDs to reference sprites (for performance?)support color using ANSI (Char class?)option to remain black and white (less memory)cross-platform mouse supportmore examples
Package: py-term-helpers
py-term-helpersPublished package on pypihttps://pypi.org/project/py-term-helpers/OverviewThepy-term-helpersis a lightweight Python terminal debug helper tool designed to streamline the debugging process for developers. Creates a more dynamic output for the terminal with star lines and any console testing visuals. It provides essential functions and utilities to assist in identifying and resolving issues in Python applications directly from the terminal.Features.term_size:Returns current size of terminal in characters.star_line(char="*"):Prints terminal widechar.center_string_stars(string,char="*"):Prints thestringin the center of terminal widechar.term_wrap(string,char="*"):Prints thestringin the center of terminal widecharwith 2.star_lineabove and belowEssentially:.star_line() => .center_string_stars() => .star_line().top_wrap(string, char="*"*):Clears console and runs.term_wrap().kv_print(arg):Prints any given arg as '{arg_variable_name} => {arg_value}'Similar to JavaScript'sconsole.log({ arg }) => "{arg_name: arg_value}"Getting StartedInstallation:pipinstallpy-term-helpersUsage:frompy_term_helpersimportterm_wrap,star_line,kv_printterm_wrap("TerminalWrap")# Output:#****************************TerminalWrap***********************************star_line()# Output:#***************************************************************************my_dict=dict({'key':'value'})kv_print(my_dict)# Output:# key => 'value'
Package: pytermichat
PyTermiChatchat without GUIDisclaimer:This is notyetencrypted.Not To Be Confused withTermChatinstalling:pipinstallpytermichatrunning:python-mpychat[-h][-s][-u]note:this will only to connect to instances hosted on127.0.0.1Running as a serverpython-mpychat-sthis will run the server on0.0.0.0:80current port is notyetchangeableCustom Serverspython-mpychat-u"url to the server"Credits:Pythonwebsocketsmodule