Saravanan666/pypi-org huggingface dataset:
Package: pepsin
pepsinPython Project Initializer CLI Tool, uses pipTo install packagesDiscarded previous version for not maintaining and complexity of codeIn DevelopmentCurrently the goal is to create a simple tool to manage dependencies,
Initialize projects (django, fastapi, flask) with production ready features.
Initialize pytest, tox, github actions etc. Managing scripts to run,
(Inspired bynpm run)So primary goal is to -Create a toolchain to manage dependenciesProject initializationManaging scriptsFile generation based on templates (tox, pytest)Dockerizing and customization hookpepsin's code structure is heavily inspired bydjango.core.managementpepsin implements almost the similar strategy of code writing and work process.
pepsin cli library is written using builtin libraries likeargparseimportlibpkgutilsysosetc.
For storing libraries and managing dependencies,yamlfile has been selected
as it has a very basic and minimalistic syntax.Requirementspython 3.6+Installation$pip3installpepsinBefore usepepsin generates or usespepsin.yamlfile to store
all your metadata, project configuration, project libraries and dependenciespepsin.yamlconfig filename:GameOfChairs# Name of the projectauthor:Khan Asfi Reza# Author's nameemail:info@khanasfireza.com# Author's emailvenv:venv# Virtualenv directory namelicense:MIT# Project license typelibraries:# Installed libraries-django-psycopg2-djangorestframework-django-channelsIf any failure or error occurs afailed.pepsin.logwill be created mentioning the problemUsage1.init$pepsininitInit command generates basic python project to get start with,
It will interactively ask you to fill the required fields$pepsininit
$pepsinGenerateProject
$----------------------
$ProjectName[project]:
$Author[]:
$Email[]:
$License[]:File structureProject  Directory
|____ venv
|____ pepsin.yaml
|____ Readme.md
|____ .gitignore
|____ project
      |___ main.py
      |___ __init__.pyOptional Arguments:namethe name of the project and pepsin will create a project with the given project nameExample:$pepsininitproject_nameOptionsoptiondescriptiontyperequireddefault--venvVirtual environment directorystringfalsevenv--hHelp textbooleanfalse--no-inputIgnores input promptboolean(flag)falsevenv2.installCommand Alias:addiInstall required dependencies and libraries$pepsininstalldjangoor$pepsinidjangoor$pepsinadddjangoAlsotextfile with list of libraries can be installed with-rflag$pepsininstall-rrequirements.txtNote: install command will by default create apepsin.yamlfile and a virtualenv directory namedvenvoptiondescriptiontyperequireddefault-rInstall from the given requirements filestringfalsenull--hHelp textbooleanfalse3.uninstallUninstall a library that is installed in your envrionment$pepsinuninstall
Package: pepsyn
pepsynPeptide library designInstallationpepsynis developed for Python 3.6+ and requiresbiopython.  The CLI usesclick.pipinstallpepsynor for the latest development versiongitclonehttps://github.com/lasersonlab/pepsyn.gitcdpepsyn
pythonsetup.pyinstallTo run the testspy.testUsagepepsyncan be used as a library, but also comes with a CLI.The main CLI command ispepsynand it can read fromstdinandstdoutby
specifying-as the input or output.  Input and output files are FASTA
formatted.$pepsyn-h
Usage:pepsyn[OPTIONS]COMMAND[ARGS]...pepsyn--peptidesynthesisdesign

Options:-h,--helpShowthismessageandexit.

Commands:prefixaddaprefixtoeachsequencerecodesiteremovesitefromeachsequence'sCDSby...revtransreversetranslateaminoacidsequencesinto...statscomputesomesequencestatisticssuffixaddasuffixtoeachsequencetiletileasetofsequencesFor example, to tile a set of sequences, use thepepsyn tilecommand.  Each
subcommand has its own help message with relevant options.$pepsyntile-h
Usage:pepsyntile[OPTIONS]INPUTOUTPUTtileasetofsequences

Options:-l,--lengthINTEGERLengthofoutputoligos-p,--overlapINTEGEROverlapofoligos-h,--helpShowthismessageandexit.Commands can be piped into each other.  (Note:stdinandstdoutare
signified with-.)catpepsyn/tests/proteins.fasta\|pepsyntile-l10-p3--\|pepsynrevtrans--\|pepsynprefix-pACGGG--\|pepsynsuffix-sTGCTG--\|pepsynrecodesite--siteEcoRI--clip-left5--clip-right5--
Package: pept3
PepT3Test-time training for deep MS/MS spectrum predictionGet Startedpipinstallpept3To get to knowpept3, follow the next section to run a demo data.Set up locallyclone this repo with:gitclonehttps://github.com/gusye1234/pept3.git# fetch the pre-trained model weights:gitlfsinstall
gitlfspull# install pept3 to python environmentpipinstall-e.# run pept3 like an installed commandpept3./examples/demo_data/demo_input.tab--spmodel=prosit--similarity=SA--output_tab=./examples/demo_data/demo_out.tab--need_tensor--output_tensor=./examples/demo_data/tensor.hdf5to perform a simple test-time training over Prosit(--spmodel=prosit) with Spectral Angle(--similarity=SA).
The program will take./examples/demo_data/demo_input.tabas the input file. Then the tuned features will be outputted to./examples/demo_data/demo_out.tab, which is already for the downstream task, for example, as the input of thePercolator:cdexamples
bash./percolator_demo.sh# rescoring over the tuned features set# the result will be saved in ./examples/percolator_resultAlso a python script for the above demo commands is available:cdexamples
pythonpept3_demo.pyYou should get the identical result. The scriptpept3_demo.pywill demonstrate the process of howPepT3working inside python.Input FormatPepT3 expects a tab-delimited file format as the input, just likePercolator.
Each row should contains features associated with a single PSM:SpecId <tab> Label <tab> ScanNr <tab> peak_ions <tab> peak_inten <tab> ... Charge <tab> <tab> Peptide <tab>For PepT3, the input tab file should at least include those fields:SpecId(any type):Uniqueid for each PSM.ScanNr(any type): Same meaning as thePercolator.Label({1, -1}): 1 for target PSM, -1 for decoys.peak_ions:;-delimited matched ions for PSM, only b/y types are considered currently. For exampleb10;b2;b3;peak_inten: Corresponding ions' intensities for the matched ions, also;-delimited. For example829;4154;168;Charge(int):, Percursor Chargecollision_energy_aligned_normed(float, [0,1]): Maximun-normalized NCE.Peptides(str)For the input example, have a look at./examples/demo_data/demo_input.tab.Please note that: For any feature that not on the above list, PepT3 will automaticly merge it into the output tabOutput FormatPepT3 outputs a tab-delimited file format with each row contains enlarged features associated with a single PSM. The output tab file can be directly used as the input of thePercolator. Have a look at each features meaning in./FEATURES.txt.
Also, for those who want to visit the tuned spectrum prediction, use--need_tensoroption and set--output_tensor. The prediction will be store as the format ofhfd5, with columnsSpecIdandtuned-tensor.
For the output example, please have a look at./examples/demo_data/demo_out.taband./examples/demo_data/tensor.hdf5
Package: pep-talk
Pep Talk!A little library to give your day a little pep!Install$pipinstallpep-talkRunning$pep-talkOkay,listenup:thewayyourolldeservestheNobelPrize,period.Colour OptionsThis module uses thecoloredmodule fromhttps://pypi.org/project/colored/.
Check the link to see the colour options.To enable the colour features, use the following:--fgForegroundcolour
--bgBackgroundcolour
--attrTextattributes,boldetc.$pep-talk--bgblack--fggreen--attrbold
Package: peptide
Bravo!  You have received a Medical Diploma in "peptide" fromthe Orbital Convergence University International Air and Water Embassy of the Tangerine Planet.You are now officially certified to include "peptide" in your practice.🌑 🌘 🌗 🌖 🌕 🌔 🌓 🌒 🌑🌑 🌒 🌓 🌔 🌕 🌖 🌗 🌘 🌑🌑 🌘 🌗 🌖 🌕 🌔 🌓 🌒 🌑peptide🌊 descriptionThis is a module that can ascertain
the health status of software with
a python3 testing interface.(It's like a testing framework)⛵ install[ZSH] pip install peptide🪸 documentation (this opens a server process that sends HTML)[ZSH] peptide shares🛟 internal status tests of the module[ZSH] peptide internal-statusThese checks are run with pypi "body_scan""peptide" is built from a fork of "body_scan"("body_scan" checks are written with "unittest")🧭 TutorialChecks are started simultaneously, unless "--simultaneous no"Create a status file (glob pattern "**/status_*.py").(The glob pattern can be modified with the progammatic python3 interface)# status_1.py

def check_1 ():
	print ("check 1")
	
def check_2 ():
	print ("check 2")
	
def check_3 ():
	raise Exception ("not 110%")

checks = {
	"check 1": check_1,
	"check 2": check_2,
	"check 3": check_3
}from a directory deeper than the status file "status_1.py"[ZSH] peptide statusThis is the equivalent of:[ZSH] peptide status --glob-string "**/status_*.py"The report then should appear like thispaths: [
	{
		"path": "../status_1.py",
		"empty": false,
		"parsed": true,
		"stats": {
			"passes": 2,
			"alarms": 1
		},
		"checks": [
			{
				"check": "check 1",
				"passed": true,
				"elapsed": [
					4.054199962411076e-05,
					"seconds"
				]
			},
			{
				"check": "check 2",
				"passed": true,
				"elapsed": [
					1.72930003827787e-05,
					"seconds"
				]
			},
			{
				"check": "check 3",
				"passed": false,
				"exception": "Exception('not 110%')",
				"exception trace": [
					"Traceback (most recent call last):",
					"  File \"/home/veganecology/.local/lib/python3.11/site-packages/peptide/processes/scan/process/keg/check.py\", line 68, in start",
					"    checks [ check ] ()",
					"  File \"<string>\", line 13, in check_3",
					"Exception: not 110%"
				]
			}
		]
	}
]
alarms: [
	{
		"path": "../status_1.py",
		"checks": [
			{
				"check": "check 3",
				"passed": false,
				"exception": "Exception('not 110%')",
				"exception trace": [
					"Traceback (most recent call last):",
					"  File \"/home/veganecology/.local/lib/python3.11/site-packages/peptide/processes/scan/process/keg/check.py\", line 68, in start",
					"    checks [ check ] ()",
					"  File \"<string>\", line 13, in check_3",
					"Exception: not 110%"
				]
			}
		]
	}
]
stats: {
	"alarms": 0,
	"empty": 0,
	"checks": {
		"passes": 2,
		"alarms": 1
	}
}🤿 Advanced TutorialIt's recommended to run peptide programmatilly.An example of this can be found in the "_book/advanced tutorial"section of the documentation.🏖️ Contactsbgrace2468@pm.me
Package: pepubot
PePuBot is a Slack bot that can arrange Friday bottle lotteries on a
Slack channel with a specific set of rules.The NamePePu comes from Finnish words “Perjantai Pullo”, which means “Friday
Bottle”.  Bot is shortened from Robot, as you may know. ;-)The RulesPePu is arranged in rounds, usually a round is arranged on every
Friday, but it’s also possible to arrange a round on any other day
or to skip rounds.When a PePu round is running in a channel anyone in the channel can
attend and get a new ticket to the lottery box by posting a funny
picture or video to the channel.Each attendee may get at most one new ticket to the lottery box per a
PePu round.  If the same person posts several pictures or videos to
the PePu channel, only the first one is awarded with a ticket.When the round is ended, the winner will be selected by randomly
picking one of the tickets from the lottery box.  Then all tickets of
the winner will be removed from the lottery box and the rest of the
tickets will be stored for the next PePu round.  I.e. your chances to
win increase on every round until you win.Anyone can arrange a PePu round, but the person who starts the round
should also arrange the prize bottle.The person who starts the round also decides when the round ends and
is responsible to do so before the day ends.RequirementsTo run PePuBot you need Python 3.7 and a Slack account.InstallingAdd a new app to Slack inhttps://api.slack.com/appsand add a bot
for that app.Enable the following permissions for the app:botTo act as a bot user in Slackchat:write:botFor writing to the channelreactions:writeFor marking ticket additions with reactions to the picture or
video message.users:readFor filling user names to the ticketsInstall PePuBot and its dependencies to a Python virtual environment
or to a Docker container or using whatever isolation you prefer.  You
may do this with a command like:pip install .Copy the “Bot User OAuth Access Token” value to environment variable
namedSLACK_API_TOKENor to a line in a configuration file namedpepubot.conf.  There is apepubot.conf.templatewhich you can
use as a base.Note: Each configuration option can be set in the configuration
file or with an environment variable with the same name.  If a
variable is defined in both places, the value will be read from the
environment.Start the PePuBot with the script installed by Pip:pepubotBy default the configuration file will be read from the current
working directory by namepepubot.conf, but alternative location
can be given via command line argument:pepubot --config-file /path/to/pepubot.conf
Package: pepver
pepverPEP-440 version parsing, interpretation and manipulation.>>>frompepverimportVersion>>>version=Version.parse("0!1.2.3.4a5.post6.dev7+8.9")>>>version.epoch0>>>version.release(1,2,3,4)>>>version.major1>>>version.minor2>>>version.micro3>>>version.pre('a',5)>>>version.post6>>>version.dev7>>>version.local'8.9'UsageThe main star of the library is theVersionclass, which encompasses the semantics of a version string.
It can be instantiated directly or be parsed from a string:>>>frompepverimportVersion>>>Version(1,2,3,4)Value(release=(1,),pre=2,post=3,dev=4)>>>Version((0,1,2,3),post=11,epoch=1)Value(epoch=1,release=(0,1,2,3),post=11)>>>Version.parse("11.2")Value(release=(11,2))Versions can be updated to suit one's needs:>>>frompepverimportVersion>>>version=Version.parse("0!1.2.3.4a5.post6.dev7+8.9")>>>version.update("minor")Value(epoch=0,release=(1,3))>>>version.update("post",-2)Value(epoch=0,release=(1,2,3,4),pre=('a',5),post=4)>>>version.update("release")Value(epoch=0,release=(1,2,3,5))>>>version.update("release").is_final()TrueVersions correctly convert into strings. Note that the conversion is "normalized" ie
standard representation that is the same for the same version:>>>frompepverimportVersion>>>str(Version.parse("010.12-11"))'10.12.post11'>>>str(Version.parse("1.2.3preview11dev"))'1.2.3rc11.dev0'
Package: pequenawebview
https://pywebview.flowrl.compywebviewis a lightweight cross-platform wrapper around a webview component that allows to display HTML content in its own native GUI window. It gives you power of web technologies in your desktop application, hiding the fact that GUI is browser based. You can use pywebview either with a lightweight web framework likeFlaskorBottleor on its own with a two way bridge between Python and DOM.pywebviewuses native GUI for creating a web component window: WinForms on Windows, Cocoa on macOS and QT or GTK on Linux. If you choose to freeze your application, pywebview does not bundle a heavy GUI toolkit or web renderer with it keeping the executable size small.pywebviewis compatible with Python 3.pywebviewis created byRoman Sirokov.Getting startedInstallpipinstallpywebviewCurrently only python version 3.8 or older supported on Windows.On Linux you need additional libraries. Refer to theinstallationpage for details.Hello worldimportwebviewwebview.create_window('Hello world','https://pywebview.flowrl.com/hello')webview.start()Explorepywebviewfurther by readingdocumentation,examplesorcontributing. If React is your thing, get started right away withReact boilerplate.ContributorsCode ContributorsThis project exists thanks to all the people who contribute. [Contribute].Financial ContributorsBecome a financial contributor and help us sustain our community. More donation options are outlined on theDonatingpage.IndividualsOrganizationsSupport this project with your organization. Your logo will show up here with a link to your website. [Contribute]
Package: pera-transcript
Auto-Generate Tool for eng.pdn.ac.lk Interim Transcript Template (Unofficial)Installationpip install pera-transcriptUsing the toolGenerate the latex file:The tool provides three ways of specifying metadata in order to generate the latex file. Choose any of the following methods that you find convenient.Specify metadata as a set of command-line arguments:autogen_transcript--user"E/XX/YYY"--passwd"password"--DOB"DD Month YYYY"--dept_head"Prof. John A. Doe"Using a "metadata.yml" file: Create a "metadata.yml" file with your registeration number, course registeration portal password, your date of birth, and the name of your head of department as following:user:E/XX/YYY# Your registeration numberpasswd:xxxxxx# Your password for the course registeration / degree claim accountDOB:DD Month YYYY# Your date of birthdept_head:Prof. John A. Doe# The name of your head of departmentThen, run the tool as follows:autogen_transcript--meta_path="/path/to/metadata.yml"Specify the metadata as a JSON formatted string in the command-line argument:If using Windows,autogen_transcript--meta_cfg"{\"user\": \"E/XX/YYY\", \"passwd\": \"password\", \"DOB\": \"DD Month YYYY\", \"dept_head\": \"Prof. John A. Doe\"}"If using Linux,autogen_transcript--meta_cfg'{"user": "E/XX/YYY", "passwd": "password", "DOB": "DD Month YYYY", "dept_head": "Prof. John A. Doe"}'Generate both latex and pdf files:autogen_transcript--compile(--meta_pathMETA_PATH|--meta_cfgMETA_CFG|--userUSER--passwdPASSWD--DOBDOB--dept_headDEPT_HEAD)Thelatex templateused in this tool was originally created for the convinience of obtaining interim transcripts by@samurdhilbk.Youmustget the interim transcript approved with the signature and seal of the head of the department.Frequently Asked QuestionsCan I add or drop technical electvies when I am filling this?Should I round off/up/down my GPA? --- the python script rounds up to the nearest 0.05How can I mention me completing the internship even when TR400 results are not officially released?The previous semester results are not added to the degree claim page. Can I add them to this transcript?Answer to all FAQs:Ask the head of your department.Disclaimer:The creator(s) do not take any responsibility for how you ue this template or what you run into in the process, including but not limited to:Head of department declining to approve this template.Any institution declining to accept this unofficial transcript.Mistakes you make while filling your information.You intentionally filling fake information.Someone using the logo or any other information in this document for any malicious purpose.
Package: percato
reverse video searchPerCato (Short for Persian Character OCR) is a python library for detecting Persian/Farsi letters in an image or pdf file.
PerCato is both a image-from-text generation program for other OCR projects and also a deep learning model made using Detectron2.RequirementsPython 3 or greaterDetectron2CUDAInstallation:pip install percatoUsage:You can work directly with PerCato's command line interface:percato image.pngInput:Output:Advance Usage:LicenseCopyright (c) 2021 bysadiqush. All rights reserved.PerCatois licensed under the GLPv3 License as stated in theLICENSEfile.
Package: percentage
open source and free to use!!<br>
if you have question,feel free to emailseojin04230423@gmail.com!<br>
Changelogs:<br>
0.0.0b1 first release(changed from percstat)<br>
0.0.0b3 debug and added AmB function<br>
0.0.0b4 import error fixed<br>
how to use:<br>
1.Class etc:<br>
coin=[0,1]<br>
dice=[1,2,3,4,5,6]<br>
2.Class percentage:<br>
2-1.functions that returns integer:<br>
Factorial(n)=n*(n-1)*…*2*1<br>
nPr(n,r)=n!/(n-r)!(! is factorial)<br>
nPIr(n,r)=n**r((ex)nPIr(3,2)=3**2= 3*3,nPIr(4,4)=4**4=4*4*4*4<br>
nHr(n,r)=n+r-1Cr(=nCr(n+r-1,r))<br>
nCr(n,r)=nPr(=nPr(n,r))/n!<br>
P(A,S)=len(A)/len(S)(if A is in S,if not, returns 0)(A and S are NON-TUPLE list)<br>
P_BlA(A,B,S)=returns P(AnB(A,B)/P(A))<br>
2-2.functions that returns NON-TUPLE list:<br>
Ac(A,S)=returns all of S’s elements except A’s elements.<br>
AnB(A,B)=returns (A and B)’s elements.<br>
AUB(A,B)=returns (A or B’)s elements.<br>
AmB(A,B,S)=returns AnB(A,Ac(B,S))’s elements.<br>
2-3.Functions that returns boolean(True/False)<br>
AcB(A,B)=returns true if list A is in B<br>
AEB(A,B)=returns true if element A(only one elements!) is in B<br>
Package: percentcoding
An example of percent encoding is the one defined for URIs in RFC 3986. Percent encoding can also be used for general purpose text escaping. Unlike C backslash escaping, which requires that every reserved character be explicitly named (eg. 0x0a corresponds to n), percent encoding can easily accommodate an arbitrary set of reserved characters. For the specific case of URI escaping, the percentcoding library provides 10x faster drop-in replacement for the urllib.quote, urllib.unquote, urllib.quote_plus, and urllib.unquote_plus.
Package: percentiles
Find x-th percentile of a sequence without numpyBecause sometimes you need one function only.Installpip install percentilesUse>>>importpercentiles>>>percentiles.percentile([100,120,130,1000],75)347.5>>>fromnumpyimportpercentile>>>percentile([100,120,130,1000],75)347.5CreditsOriginal code was posted onhttp://code.activestate.com/recipes/511478-finding-the-percentile-of-the-values/
Package: percent-max-diff
READMETutorialsBlahhWhat is this repository for?PMDHow do I get set up?PyMINEr is now pip installable:python3 -m pip pmdNote that there was another package called pyminer for mining bit-coin - this is definitely not that, so be sure to install bio-pyminer instead!You can also install using the setup.py script in the distribution like so:python3 setup.py installHow do I run PyMINEr?Video TutorialsBlahhhimport numpy as np
from percent_max_diff.percent_max_diff import pmd
pmd_res = pmd(np.array([[100,0,0],[0,100,0],[0,0,100]]))
print(pmd_res.pmd)LicenseFor non-commercial use, PyMINEr is available via the AGPLv3 license. Commercial entities should inquire withscottyler89@gmail.comWho do I talk to?Repo owner/admin:scottyler89+bitbucket@gmail.com
Package: percentum
Percentumpercentumis a Python command-line interface (CLI) package designed to provide a clear perception of time in terms of hours, minutes, and working hours as a percentage of total time.The primary intention behind creating and publishing this package is to assist individuals who tend to be workaholics and often lose track of time. They may find themselves immersed in work, losing sight of the passage of time. This phenomenon is well-explained inPsychology Stack Exchange.The secondary purpose is that we often say, "What's the big deal? It's only 15 minutes." Essentially, we don't value time, as 14.4 minutes represent 1% of your day, and we all know that 1% is a significant portion.UsageTo usepercentum, follow these simple steps:Install the package:$pipinstallpercentumUsage$sand
TimeUsed:|████████████████████████--------------------------|48.91%Licensepercentum is released under the MIT License. See theLICENSEfile for more details.
Package: percepthor
PyPercepthorLocalexport PYTHONPATH=/path/to/pypercepthor:$PYTHONPATHDockerBuid localdevelopmentdocker imagebash development.shRundevelopmentimage with local sourcesudo docker run \
  -it \
  --name pypercepthor --rm \
  -v /home/ermiry/Documents/Work/pypercepthor:/home/pypercepthor \
  itpercepthor/pypercepthor:development /bin/bashHandlepypercepthormoduleexport PYTHONPATH=$pwd:$PYTHONPATH
Package: perceptible
Observable versions of python data structuresThis library is meant to be API compatible with standard Python objects, but with the addition of observability.  Currently supports Lists and Dictionaries.A simple use looks like this:>>>fromperceptibleimportObservableDictionary>>>defobserver(o):...print('observer was called with',o)...>>>o_dict=ObservableDictionary()>>>o_dict.add_observer(observer)>>>o_dict['key']='value'observerwascalledwith{'key':'value'}Installation is as simple as installing via pip.pipinstallperceptible