Saravanan666/pypi-org huggingface dataset:
Package: pmx-biobb
Warning:this is a development version ofpmx, it is not stable or reliable yet. You are welcome to
try/test it and provide feedback, but use at your own risk. The current stable version ofpmxcan
be found in the master branch:https://github.com/deGrootLab/pmxpmxis a python library that allows users to setup and analyse molecular
dynamics simulations with theGromacspackage.
Among its main features are the setup and analysis of alchemical free energy
calculations for protein, nucleic acid, and small molecule mutations.https://degrootlab.github.io/pmx/Citationspmxis a research software. If you make use of it in scientific publications, please cite the following papers:@article{Gapsys2015pmx,
    title = {pmx: Automated protein structure and topology
    generation for alchemical perturbations},
    author = {Gapsys, Vytautas and Michielssens, Servaas
    and Seeliger, Daniel and de Groot, Bert L.},
    journal = {Journal of Computational Chemistry},
    volume = {36},
    number = {5},
    pages = {348--354},
    year = {2015},
    doi = {10.1002/jcc.23804}
}

@article{Seeliger2010pmx,
    title = {Protein Thermostability Calculations Using
    Alchemical Free Energy Simulations},
    author = {Seeliger, Daniel and de Groot, Bert L.},
    journal = {Biophysical Journal},
    volume = {98},
    number = {10},
    pages = {2309--2316},
    year = {2010},
    doi = {10.1016/j.bpj.2010.01.051}
}Licensepmxis licensed under the GNU Lesser General Public License v3.0 (LGPL v3).
Package: pmxbot-glossary
# pmxbot-glossaryGlossary extension for [pmxbot](https://bitbucket.org/yougov/pmxbot/wiki/Home).[![Build Status](https://travis-ci.org/harveyr/pmxbot-glossary.svg?branch=master)](https://travis-ci.org/harveyr/pmxbot-glossary)## CommandsGet a definition!whatis carrotAdd a definition!set carrot: An orange rodUpdate a definitionSame as adding one:!set carrot: An orange vegetable. For more, see http://en.wikipedia.org/wiki/CarrotThis creates a new definition without overwriting the old one.Get an older definition!whatis carrot: 1This returns the first definition.!whatis carrot: 2would return the second,
and so on.Get a random definition!whatisRedirect an entry to anotherredirect burger: hamburgerRemove a redirectunredirect burgerFind out who wrote something!whowrote hamburger## Why?This extension is an effort to test the following hypothesis:Maintaining definitions of domain lingo via a chat bot is the
best way to keep those definitions up to date and readily accessible
(assuming the group uses some form of internet chat).This may be the case because:It allows painless updating of the definitions (no pull requests, etc.).It allows painless retrieval of the definitions.It provides a single entry point to docs that are spread among a number
of sources (assuming you provide links).It enables somewhat automatic review of definitions as they are added
or retrieved.It creates “accidental” education: you’ll learn stuff just sitting in a
channel and seeing the definitions scroll by.It keeps the definitions in front of the eyes of the
domain experts, maximizing the chances they will spot an obsolete,
misguided, or missing entry.
Package: pmxbot.webhooks
Webhooks forpmxbot. Read the source
for details.BookmarkletThis lib provides a bookmarklet
for readily sending messages to the pmxbot HTTP interface. To install it,
just open /bookmarklet in the API service. It will present a link.
Option-click the link and add it to your bookmarks. Give it a name like
“Send to pmxbot”.To use the bookmarklet, browse to any web page, then select the bookmarklet.
You will be prompted with a dialog with a channel and message. Specify the
channel and optionally edit the message. Then hit Enter or click Submit and
that message will be broadcast on the channel indicated.
Package: pmxlock
pmxlockPython classes and CLI tools for cluster-wide Proxmox pmxcfs locks.InstallationUsepipfor install:pipinstallpmxlockCLI usageStart simple command:pmxlockmylocknameechohelloorpython3-mpmxlockmylocknameechohelloOnly one command withmylocknamelock can run in current time in cluster.
Other commands will be blocked until current command completes.You can exit with failure code instead of blocking.
Use-nflag for nonblocking mode.
Failure exit code is1by default. Use-Eflag for other failure code:pmxlock-n-E2mylocknameechohelloCommand above exits with code2ifmylocknamealready acquired.You can use timeout mode also:pmxlock-w10mylocknameechohelloCommand above waits no more than 10 seconds and exits with code1ifmylocknamecannot be acquired.If command has options use--before command in order stop options parsing bypmxlock:pmxlockmylockname--echo-nhelloFormylockname-lockpmxlockuses node-wide/run/lock/pmxlock/mylocknameflock and cluster-wide/etc/pve/priv/lock/mylocknamepmxcfs-lock. Ifpmxlockterminated abnormaly (e.g. SIGKILL)/etc/pve/priv/lock/mylocknamepmxcfs-lock
will remain locked for pmxcfs timeout period (currently 120 seconds hardcoded
in Proxmox). Other process on the same node can acquire orphaned lock
without waiting. You can usepmxlock-gccli command for clean all orphaned
locks on current node.pmxlock-gcorpython3-mpmxlock.gcClass usageCluster-wide lock implemented byClusterLockclass:frompmxlockimportClusterLocklock=ClusterLock("mylockname")Short operation in blocking mode:lock.acquire()try:# Your operation should be short or timeouted.# Hardcoded proxmox timeout == 120 seconds.# Take overheads into account and use shorter timeoutdo_work(timeout=0.8*120)finally:lock.release()ClusterLocklock implements context manager protocol for blocking mode:withClusterLock("mylockname"):do_work(timeout=0.8*120)For long operations you need to uselock.update()regularly.
You can use subprocess for it:importsubprocesswithClusterLock("mylockname")aslock:proc=subprocess.Popen(command)whileTrue:try:proc.wait(0.8*120)breakexceptsubprocess.TimeoutExpired:lock.update()You can start operation in nonblocking mode:iflock.acquire(blocking=False):try:do_work()finally:lock.release()else:cannot_acquire_lock()And timeout mode:iflock.acquire(timeout=10):try:do_work()finally:lock.release()else:cannot_acquire_lock()
Package: pmx-satumut
Warning:this is a development version ofpmx, it is not stable or reliable yet. You are welcome to
try/test it and provide feedback, but use at your own risk. The current stable version ofpmxcan
be found in the master branch:https://github.com/deGrootLab/pmxpmxis a python library that allows users to setup and analyse molecular
dynamics simulations with theGromacspackage.
Among its main features are the setup and analysis of alchemical free energy
calculations for protein, nucleic acid, and small molecule mutations.https://degrootlab.github.io/pmx/Citationspmxis a research software. If you make use of it in scientific publications, please cite the following papers:@article{Gapsys2015pmx,
    title = {pmx: Automated protein structure and topology
    generation for alchemical perturbations},
    author = {Gapsys, Vytautas and Michielssens, Servaas
    and Seeliger, Daniel and de Groot, Bert L.},
    journal = {Journal of Computational Chemistry},
    volume = {36},
    number = {5},
    pages = {348--354},
    year = {2015},
    doi = {10.1002/jcc.23804}
}

@article{Seeliger2010pmx,
    title = {Protein Thermostability Calculations Using
    Alchemical Free Energy Simulations},
    author = {Seeliger, Daniel and de Groot, Bert L.},
    journal = {Biophysical Journal},
    volume = {98},
    number = {10},
    pages = {2309--2316},
    year = {2010},
    doi = {10.1016/j.bpj.2010.01.051}
}Licensepmxis licensed under the GNU Lesser General Public License v3.0 (LGPL v3).
Package: pn4pm-nano
Welcome to Petrinets 4 Process Mininghandling Process Lists with a simple small package V0.0.6.2Content:Author InformationDescriptionClassesUsage / ExamplesOther Stuff / Last WordsLicense InformationAuthor InformationName: Daniel MullerWebsite:http://damu-analytics.deDescriptionThe purpose of this package is it to offer an easy way
to create a petrinet, you can use for process mining, without having a full PNML file.
All you need is a simple list of your process steps, the number of your step and the number
of all Previous Steps.This is just the first Version of the Package. I will try to develop more possible outputs when i got time.ClassesThe package offers the following classes:Petrinet(labels,[places, transitions, edges, inc_gateways, exc_gateways, parall_gateways])output([tablename])cel_out([tablename])Usage / ExamplesIt's very easy to use the package. Just import the packagecreate your activity list with an activity, position of the activity, all direct previous activity rangescall the Petrinet function with your list and create your outputsfrom pn4pm_nano import petrinets as pnlist = [['Activity1',0,[-1]],['Activity2',1,[0]],['A....']]petriobject = pn.Petrinet(list)
print(petriobject.out())
print(petriobject.cel_out())
print(petrionject.cel_out("YourActivityTable"))For silencing the activities just give an empty string as name['',0,[-1]]
In this case a transition is created but not returned in the frontendOther Stuff / Last WordsIf you have some issues with the package or ideas what functionalities could be added,
feel free to contact me.Changes to Last Versioninternal fixes and optimization for gateway calculations [0.0.5.3] -> [0.0.6]multiple changes on the calculations - enabled the handling of loops [0.0.5 - 0.0.5.3]Added the handling of duplicated activities in the petrinet Input [0.0.4 - 0.0.5]Added Handling of 'Silent' Activitys and Bug Fix in the cel_out() function [0.0.3.2 -> 0.0.4]Bug Fix in function cel_out() [0.0.3.1 -> 0.0.3.2]Bug Fix after calling the class Petrinet the second time [0.0.1 -> 0.0.3]License InformationThis Project is using the MIT License
Package: pn532pi
NFC library for Raspberry PiThis is a port ofSeeed Studios's PN532 Arduino Libraryfor using the PN532 chip with Raspberry Pi.FeaturesSupport all interfaces of PN532 (I2C, SPI, HSU)Read/write Mifare Classic CardCommunicate with android 4.0+(Lists of devices supported)Card emulation (NFC Type 4 tag)To DoWorks withDon's NDEF LibraryTo support more than one INFO PDU of P2P communicationTo read/write NFC Type 4 tagGetting StartedPyPIInstall with pippip install pn532piFollow examplesDirect DownloadDownloadzip fileand extract the 4 folders(pn532pi, quick2wire, examples and test)Follow the examples of the two libraries.Clone Git RepositoryGet pn532 librarygit clone --recursive https://github.com/gassajor000/pn532pi.gitFollow the examples of the two librariesPowerThe Raspberry Pi 3.3v regulator does not provide enough current to drive the PN532 chip.
If you try to run the PN532 off your Raspberry Pi it will reset randomly and may not respond to commands.
Instead you will need another power source (3.3v) to power the PN532. Some people have been able to run
the PN532 off of the 5V rail of the raspberry pi but this is not the recommended way of powering it.I2C InterfaceI2C is short for Inter-integrated Circuit. I2C interface needs only 4 wires to connect PN532 with Raspbeery Pi.To use the I2C bus 1 to control PN532, refer to the code below.frompn532piimportPn532I2c,Pn532i2c=Pn532I2c(1)nfc=Pn532(i2c)defsetup():nfc.begin()# ...ExamplesTo run an example you will need to change the interface flags to the interface you are using.
For SPI you may also have to change the slave select pin to the pin you have connected.# Set the desired interface to TrueSPI=TrueI2C=FalseHSU=False...ifSPI:PN532_SPI=Pn532Spi(Pn532Spi.SS0_GPIO8)nfc=Pn532(PN532_SPI)Then you can just callpython <example file>.pyfrom a terminal.Help debuggingWe are willing to provide debug help for this library however there is currently only one maintainer doing this in his free time.
Don't be surprised if responses take a couple days. Also, as hardware issues can be quite difficult to debug remotely,
if your issue cannot be replicated using the test setup (pi 3B+) then there may not be much we can do.ForRemote IO Errors(I2C communciation errors) we also require that you take a logic capture
of the i2c failure. This is needed to determine whether the pi or the nfc chip is the cause of the communication failure. Below is a
recommendation for an affordable logic analyzer that can be run with the opensourcePulse Viewapplication or with the Selaea app.HiLetgo USB Logic AnalyzerContributionIt's based onAdafruit_NFCShield_I2C.Seeed Studiorewrite the library to make it easy to support different interfaces and platforms.
@Don writes theNDEF libraryto make it more easy to use.
@JiapengLi adds HSU interface.
@awieser adds card emulation function.
@gassajor000 ported to python/Raspberry Pi[Mega]:http://arduino.cc/en/Main/arduinoBoardMega
[DUE]:http://arduino.cc/en/Main/arduinoBoardDue[Leonardo]:http://arduino.cc/en/Main/arduinoBoardLeonardo[SoftwareSerial]:https://www.arduino.cc/en/Reference/softwareSerialImages courtesy ofpinout.xyz,components101.com,sparkfun.com
Package: pnadc
This is an unofficial and simple python package to deal with IBGE-PNADc microdata. Aims to help you with quick functions to work with thePesquisa Nacional por Amostra de Domicílios ContínuaThis package will provide you with tools to download, save, build and analyze all the survey data in the most effective way possible.Free software: GNU Lesser General Public License v3 or later (LGPLv3+)Installationpip install pnadcYou can also install the in-development version with:pip install https://github.com/ppnasser/pnadc/archive/master.zipDocumentationhttps://pnadc.readthedocs.io/DevelopmentTo run all the tests run:toxNote, to combine the coverage data from all the tox environments run:Windowsset PYTEST_ADDOPTS=--cov-append
toxOtherPYTEST_ADDOPTS=--cov-append toxChangelog0.0.0 (2020-07-26)First release on PyPI.
Package: pname
PyPI Package NameCheck whether a package name is available on PyPIScreenshotInstall$ pip install pnameUsageimportpnamepname.check('standard')#=> ✔ standard is availablepname.check('standardbucks')#=> ✘ standardbucks is unavailableGet HelpThere are few ways to get help:Pleasepost questions on Stack Overflow. You can open issues with questions, as long you add a link to your Stack Overflow question.For bug reports and feature requests, open issues.For direct and quick help, you canemail me.How to contributeHave an idea? Found a bug? Seehow to contribute.Thanks!LicenseMIT
Package: pnap-audit-api
The Audit Logs API lets you read audit log entries and track API calls or activities in the Bare Metal Cloud Portal.<br> <br> <span class='pnap-api-knowledge-base-link'> Knowledge base articles to help you can be found <a href='https://phoenixnap.com/kb/bmc-server-management-via-api#audit-log-api&#39; target='_blank'>here</a> </span><br> <br> <b>All URLs are relative to (https://api.phoenixnap.com/audit/v1/)&lt;/b>
Package: pnap-bmc-api
Create, power off, power on, reset, reboot, or shut down your server with the Bare Metal Cloud API.  Deprovision servers, get or edit SSH key details, assign public IPs, assign servers to networks and a lot more.  Manage your infrastructure more efficiently using just a few simple API calls.<br> <br> <span class='pnap-api-knowledge-base-link'> Knowledge base articles to help you can be found <a href='https://phoenixnap.com/kb/how-to-deploy-bare-metal-cloud-server&#39; target='_blank'>here</a> </span><br> <br> <b>All URLs are relative to (https://api.phoenixnap.com/bmc/v1/)&lt;/b>
Package: pnap-ip-api
Public IP blocks are a set of contiguous IPs that allow you to access your servers or networks from the internet. Use the IP Addresses API to request and delete IP blocks.<br> <br> <span class='pnap-api-knowledge-base-link'> Knowledge base articles to help you can be found <a href='https://phoenixnap.com/kb/public-ip-management#bmc-public-ip-allocations-api&#39; target='_blank'>here</a> </span><br> <br> <b>All URLs are relative to (https://api.phoenixnap.com/ips/v1/)&lt;/b>
Package: pnap-network-api
Create, list, edit and delete public/private networks with the Network API. Use public networks to place multiple  servers on the same network or VLAN. Assign new servers with IP addresses from the same CIDR range. Use private  networks to avoid unnecessary egress data charges. Model your networks according to your business needs.<br> <br> <span class='pnap-api-knowledge-base-link'> Helpful knowledge base articles are available for  <a href='https://phoenixnap.com/kb/bmc-server-management-via-api#multi-private-backend-network-api&#39; target='_blank'>multi-private backend networks</a> and <a href='https://phoenixnap.com/kb/bmc-server-management-via-api#ftoc-heading-15&#39; target='_blank'>public networks</a>. </span><br> <br> <b>All URLs are relative to (https://api.phoenixnap.com/networks/v1/)&lt;/b>
Package: pnap-network-storage-api
Create, list, edit, and delete storage networks with the Network Storage API. Use storage networks to expand storage capacity on a private network. <br> <span class='pnap-api-knowledge-base-link'> Knowledge base articles to help you can be found <a href='https://phoenixnap.com/kb/bare-metal-cloud-storage&#39; target='_blank'>here</a> </span> <br> <b>All URLs are relative to (https://api.phoenixnap.com/network-storage/v1/)&lt;/b>
Package: pnap-rancher-solution-api
Simplify enterprise-grade Kubernetes cluster operations and management with Rancher on Bare Metal Cloud. Deploy Kubernetes clusters using a few API calls.<br> <br> <span class='pnap-api-knowledge-base-link'> Knowledge base articles to help you can be found <a href='https://phoenixnap.com/kb/rancher-bmc-integration-kubernetes&#39; target='_blank'>here</a> </span><br> <br> <b>All URLs are relative to (https://api.phoenixnap.com/solutions/rancher/v1beta)&lt;/b>
Package: pnap-tag-api
Tags are case-sensitive key-value pairs that simplify resource management. The Tag Manager API allows you to create and manage such tags to later assign them to related resources in your Bare Metal Cloud (through the respective resource apis) in order to group and categorize them.<br> <br> <span class='pnap-api-knowledge-base-link'> Knowledge base articles to help you can be found <a href='https://phoenixnap.com/kb/bmc-server-management-via-api#server-tag-manager-api&#39; target='_blank'>here</a> </span><br> <br> <b>All URLs are relative to (https://api.phoenixnap.com/tag-manager/v1/)&lt;/b>
Package: pnb
More screenshotsIntroductionPnb is an interactive environment for python programming which
follows the notebook concept of mathematica and jupyter. Notebooks are
a pleasant way to develop and document python code and to store ideas.Unlike other python notebook applications such as jupyter or spyder,
pnb is very lightweight and easy to install. It has only two
dependencies: wxpython and pynotebook.FeaturesMost notable features are:syntax highlightingcommand completion (tab-key)introspection (F1-key)built-in vector graphicsplotting via matplotlibBSD-licenseLinkspynotebook moduleR-Notebookgithub page
Package: pnc-cli
#pnc-cli
A python CLI around the PNC REST APIInstallation:python setup.py install –userUsage:Configure the REST endpoint for PNC in USER_HOME/.config/pnc-cli/pnc-cli.confpnc -h for a list of valid operations.Currently outputs the raw JSON. More refined output is definitely in the works :)#TestsRequirements:py.test (pip install pytest)mock (pip install mock)GitPython (pip install GitPython)Run any of the testing scripts to see results. The tested instance is configured by the local file ~/.config/pnc-cli/pnc-cli.conf
Package: pncl
Welcome to PencilPencil is a small Python library to create plots in the browser usingCharts.js.Pencil makes it easy to draw your charts in a dynamic and responsive grid, and lets you update your plots live as the data is created.With Pencil, you can draw seven different types of charts:LineBarRadarPieDoughnutPolar areaScatterRead the documentationhere.InstallationPencil is available on the Python Package Index and can be installed withpip:$pipinstallpnclIf you want, you can also install the package from source with:$gitclonehttps://github.com/danielegrattarola/pncl.git
$cdpncl
$pipinstall.Pencil requires Python 3.6.5+, and works on Linux and MacOS.ContributingFeel free to open an issue or a pull request if you find any problems with the package or if you want to add a new functionality to Pencil.
Package: pndatapush
# pndatapush
Python module to push data to the Pervasive Nation IoT network. It saves data locally until there is internet access.#To install`python pip install--upgradepndatapush `#To run an example`python python examples/gatherdata.py `# Easiest way to add to your project
Create an instance of the Offline class.`python from pndatapush.offline import Offline from pndatapush.pushdata import PNPushData #Set the PervasiveNation Auth token pnpushdata =PNPushData(pervasivenation_authtoken="MYREALLYLONGTOKENIGOTSECRET")offline =Offline(payload_consumers=[pnpushdata])`## OR if you want to use environment variables:` #set your PervasiveNation Auth token by using an environment variable before starting your applicaiton exportPERVASIVENATION_AUTHTOKEN="MYREALLYLONGTOKENIGOTSECRET"``python from pndatapush.offline import Offline from pndatapush.pushdata import PNPushData offline =Offline(payload_consumers=[PNPushData])#PNPushData is a data consumer class. see pnpushdata.pushdata.PNPushData `## AND if you want the local database in your current directory:`python import os from pndatapush.offline import Offline from pndatapush.pushdata import PNPushData #Set the PervasiveNation Auth token pnpushdata =PNPushData(pervasivenation_authtoken="MYREALLYLONGTOKENIGOTSECRET")#Set the local SQLite DB path offline =Offline(payload_consumers=[pnpushdata],dbpath='sqlite:///%s/sensordata.db'%os.path.dirname(os.path.realpath(__file__)))`Then when sensor data is received save the data`python device_identifier = '12456' offline.save(device_identifier, 30.00) #save(self, deviceid, payload): `Changelog0.0.1 (2016-04-13)First release on PyPI.
Package: pndex
A Python package to manage all python files in a folder at once in console and do operation on itto download pndexpip install pndexusage :import pndex---------------pndex.running()screenshot of the toolcustom function you can usecolorchanger() - to change console color
  	enter_file_to_open() - to open py file
  	readit() - to read content of py file in console
  	open_in_notepad() - open file in notepad
  	open_in_vscode() - open file in vs code
  	reading_read_me() - read readme of python file if function is defined
  	install_py__module() - download python module directly
  	check_quality() - check quality of python file
  	file_info() - get information about file
  	clearscreen() - clear terminal
  	quitscreen() - quit programopen this in folder where all .py file existsview in githubhttps://github.com/adityadand/pndexthanks for reading readme
Package: pnet
A fast and simple packet creation and parsing lib for Python, currently nothing
more then a proof of concept. Inspired by both the pythonpypackerlibrary and Rust’spnet,DesignBuilt around trying to minimize copying data by taking advantage ofmemoryviewsfor fast slicing and zero copy memory operations.This library takes either abytesorbytearrayobject and parses out
various protocols in a similar fashion to the Rust library. The resulting
packet objects can be inspected, or, in the case its backed by abytearray,
also written to. In this case, the backing memory is immediately updated.Instead of mapping packet fields to attributes, I expose them instead with a
collection-like API. This is my personal taste, as I don’t like how
autogenerated attributes end up with akward names that can overlap with Python
keywords.PerformanceInitial testing on my machine has shown that this library is abouttwiceas
fast at parsing packets, but I haven’t determined yet if this can be attributed
to design differences, or if I’m just simply doing less.TODOThis is one part of a slew of network inspecting code I’m releasing.rich BPF support and mini-languageasyncio support for raw sockets and packet capturingasyncio based dhcp server and client library