Saravanan666/pypi-org huggingface dataset:
Package: pyicare
Py-iCAREPy-iCAREis a Python distribution of iCARE, a tool forindividualizedCoherentAbsoluteRiskEstimation. iCARE allows users to build, validate, and apply absolute risk models.Absolute riskquantifies the chance of an event occurring. For example, the likelihood that a healthy individual, of a given age and a risk factor profile, will develop the disease of interest over a specified time interval.The original iCARE was written in R and its archived version (1.26.0) is available via Bioconductor at:https://www.bioconductor.org/packages/release/bioc/html/iCARE.html.MotivationThe main motivation of porting iCARE from R to Python was to enable its use as aWebAssemblymodule (viaPyodide) for the proliferation of portable and privacy-preserving web applications that can build, validate, and apply absolute risk models. Python also enables researchers to leverage its rapidly evolving data science ecosystem— includingTensorFlow,PyTorch,statsmodels, andscikit-learn— to explore novel absolute risk models that can incorporate evidence from wider sources of data.InstallationThis repository contains a Python package. It can be installed via PyPI as shown below. It is also compiled into WebAssembly via Pyodide. The wrapper JavaScript library, as ES6 modules, is also distributed in this repository at GitHub Pages. It can be accessed by any JavaScript runtime environment, including Node.js, web browsers, and Quarto notebooks in RStudio (to interface with R, Julia, and/or Python). Specifically, the steps to access it via JavaScript and R are also shown below.PythonIf you want to access iCARE from a purely Python runtime environment, you can install it via PyPI:pipinstallpyicareiCARE is supported on Python 3.7 and above.JavaScriptES6 import JS SDK via GitHub Pages.RES6 import JS SDK via Quarto.UsageOnce installed, Py-iCARE can be imported into your Python scripts as follows:importicarePy-iCARE is a library with three main functions: 1)compute_absolute_risk(), a method to build and apply absolute risk models; 2)compute_absolute_risk_split_interval(), a method to build and apply absolute risk models that relaxes the proportional hazard assumption to some extent by allowing you to specify different model parameters before and after a cut-point in time; and 3)validate_absolute_risk_model(), a method to validate absolute risk models on an independent cohort study data or a case-control study nested within a cohort.Example usages of these functions are shown in Jupyter notebooks at theexamples/Pythondirectory.RQuartoJavaScriptES6 import into scriptLicensePy-iCARE is open-source licensed under the MIT License.ReferencesPal Choudhury, Parichoy, Paige Maas, Amber Wilcox, William Wheeler, Mark Brook, David Check, Montserrat Garcia-Closas, and Nilanjan Chatterjee. "iCARE: an R package to build, validate and apply absolute risk models." PloS one 15, no. 2 (2020): e0228198.
Package: pyIcarus
To automatically install SRE related dependencies run:pip install pyicarusThe actual code in pyicarus is just some commonly used functionsInteresting repos:https://github.com/Nalen98/GhidraEmu.githttps://github.com/justfoxing/ghidra_bridge.githttps://github.com/justfoxing/jfx_bridge_ida.githttps://github.com/wtsxDev/reverse-engineering.githttps://github.com/OWASP/owasp-mstg.githttps://github.com/geohot/qira.githttps://github.com/pwndbg/pwndbg.git
Package: pyicat-plus
PyIcat-PlusA python client for ICAT+.Getting startedRegister raw datasets with ICATicat-store-raw--beamlineid00\--proposalid002207\--path/data/visitor/path/to/dataset1\--datasettest1\--samplemysample

icat-store-raw--beamlineid00\--proposalid002207\--path/data/visitor/path/to/dataset2\--datasettest2\--samplemysampleRegister processed data with ICATicat-store-processed--beamlineid00\--proposalid002207\--path/data/visitor/path/to/processed\--datasettestproc\--samplemysample\--raw/data/visitor/path/to/dataset1\--raw/data/visitor/path/to/dataset2TestWith threadspython-mpipinstall-e.[test]pytestWith geventpython-mpipinstall-e.[test]python-mpipinstallgevent
python-mgevent.monkey--modulepytestDocumentationhttps://pyicat-plus.readthedocs.io/
Package: pyiced
PyIcedPython bindings forIced.Iced is a cross-platform GUI library focused on simplicity and type-safety. Inspired by Elm.InstallationPrecompiled wheel:$pipinstallpyicedFrom source:$pipinstall.To install from source you need to have a recent version ofRustinstalled in your $PATH.Rustupis probably the most easy to use option to install and updateRuston your system.Quick Examplefrompyicedimport(Align,button,ButtonState,column,container,IcedApp,Length,text,)classExampleApp(IcedApp):def__init__(self):self.__incr_button_state=ButtonState()self.__decr_button_state=ButtonState()self.__value=0deftitle(self):return'Counter'defview(self):increment_button=button(self.__incr_button_state,# To track the state across redraws.text('Increment'),# This is content on the button.on_press='incr',# This value is received in update().)value_label=text(f'{self.__value}',size=50)decrement_button=button(self.__decr_button_state,text('Decrement'),on_press='decr',)returncontainer(column([increment_button,value_label,decrement_button],align_items=Align.CENTER,),padding=20,align_x=Align.CENTER,align_y=Align.CENTER,width=Length.FILL,height=Length.FILL,)defupdate(self,msg,clipboard):# When an event occurs, this method is called.# It can optionally return a list of async functions,# to handle the event.matchmsg:case'incr':self.__value+=1case'decr':self.__value-=1if__name__=='__main__':# This function only returns if there is an error on start-up.# Otherwise the program gets terminated when the window is closed.ExampleApp().run()Bigger ExamplePlease find the source code inexamples/chess.py.
Package: pyicmd
# Python port of the iRODS icommands.---## Install```bashpip3 install --user pyicmd```## Usage```bashusage: pyicmd [--host HOST] [--port PORT] [--user USER] [--passwd PASSWD][--zone ZONE] [--version][cmd]Python port of the iRODS icommands.Supports irods_environment.json file created by iinit. File can be at itsdefault location ('~/.irods/irods_environment.json') or set via theIRODS_ENVIRONMENT_FILE variable.If user is set via the command line irods_environment.json is ignoredand given (or default) command line arguments are used to open the session.positional arguments:cmd               The icommand to run:rm [file(s)]          Remove the files listed from the iRODS serverls [path]             List the files and folders at the given pathput [loc] [file(s)]   Copy file(s) and folder(s) from the local computer to [loc] on the serverget [files(s)] [loc]  Copy file(s) and folder(s) from the server to [loc] on the local computertest                  Test the connection to the iRODS server.To learn more about a function, type pyicmd [cmd] -hoptional arguments:--host HOST      Address of iRODS server--port PORT      iRODS server port--user USER      iRODS username--passwd PASSWD  iRODS user password--zone ZONE      iRODS zone--version        show programs version number and exit```## Speed TestBy default, icommands uses multi-threading for uploads greater than ~35MB. pyicmd does not currently support multiple threaded uploads, causing it to be slower for large files.![Speed Test](assets/UploadTimes.png)# Contributing----## TestingTests for the functional.py API are written in pytest format and can be runwith```bashmake test```Tests require a valid iRODS server and configured irods_environment.json file created by iinit. [This iRODS docker container](https://github.com/mjstealey/irods-provider-postgres) was used to run the tests.## Code StandardCode should follow [Python's PEP8 style guide](https://www.python.org/dev/peps/pep-0008/). All contributions should pass standard pylint tests. These can be run using:```bashmake lint```
Package: pyicoshift
pyicoshiftThis is a rewrite in python of theicoshiftfor MATLAB by F. Savorani, G. Tomasi, S.B. Engelsen.
This implementation provides all the core features as icoshift for matlab version XXX.Snapshot of the originalicoshift webpageNew, additional features:New target mode: select the signal with the highest correlation with all input signals
as target.Auto interval picking: detected peaks get clustered based on distance and intervaled accordinglySome utility functions for more convinient import of Bruker NMR dataAutophasing based on the "automics" algorithmExperimental multi-threading support for the optimal shift finding phaseExperimental syntethic target generation from HMDB spectraInstallpip install pyicoshiftUsageInstance a new object of the class Icoshift, asign signals, choose intervals and target mode, call run()
; see scripts in test folder for some examples
Package: pyICSParser
pyICSParser - ICALENDAR ParserpyICSParser is an icalendar parser (parser for .ics or ical parser files) as defined by RFC5545 (previously RFC2445) into typed structure and returns json structure with explicit dates [[dates, description, uid]] for each instanceTypical installationpip install pyICSParserTypical usage for explicit date calculation:#!/usr/bin/env python

import pyiCalendar

mycal = pyiCalendar.iCalendar()

#ics_fp being a string for the local full path to the icalendar file
mycal.local_load(ics_fp)
#dtstart and dtend are string objects of yyyymmdd formatting (%Y%M%d)
#dates will contain the json with all explicit dates of the events spec'ed by the icalendar file
dates = mycal.get_event_instances(dtstart,dtend)VersionsPre-alphav0.0.1: first pre-alphav0.0.27: fixed the dtstart to dtend problem for holidayalpha0.4.x: first fully tested handling days - remains to be done is handling of time of events (test vectors are actual icalendar files)0.5.x: added support for EXDATE0.6.x: added support for DURATION and when DTEND no present0.7.x: added support for python 3; 9/10 cottage cheese with pyroma0.7.3: fixing issue #12Release Flowrun unit testcd pyICSParser\test
python test.pyrun pyromacd pyICSParser
pyroma .build and uploadpy -m build
py -m twine upload --repository pypi dist/*Future developmentshandle of datetime (currently only handles date)handle of multiple EXRULE,  RRULE as per icalendar specCreditshttp://www.tele3.cz/jbar/rest/rest.html: reST to HTML & reST validatorhttp://guide.python-distribute.org/contributing.html: registering a package on pypi and password informationhttp://guide.python-distribute.org/creation.html: uploading a package to pypihttp://blog.msbbc.co.uk/2007/06/using-googles-free-svn-repository-with.html: how to use google codes, subclipse and eclipse
Package: pyid
PyIDTurn any python object into an exactly equivalent object with anidattribute.Exampleimportrandomimportpyidmylist=[random.sample(range(10),k=3)foriinrange(20)]# Uses python uuid module to assign ID by defaultmylist=[pyid.idfy(item)foriteminmylist]foriteminmylist:print(item,item.id)# Assign a custom IDmylist=[pyid.idfy(item,'myid')foriteminmylist]foriteminmylist:print(item,item.id)InstallationpipinstallpyidMotivationWhen referencing related objects, we use unique IDs. In python, we might handle this pattern with a dictionary mapping IDs to objects, or use an item's position in a list as its ID. Either case requires we create variables separate from the object to represent those IDs, and that each time we iterate we explicitly include the ID by iterating with the ID dict or the enumerate function for lists. I built this to test the idea that having an ID attribute is easier and cleaner.How it worksIt takes thetypeof the passed object, creates a subclass of that type, with an ID attribute, and copies the data from the passed object into an instance that new subclass. If a custom ID is not passed, the python uuid module is used to assign one.
Package: pyida
PyLovelace is a Python protection tool that can be used to protect
Python source code from being reverse engineered.InstallationPyLovelace is available on PyPI and can be installed using pip:pip install pylovelaceUsagePyLovelace can be used as a command line tool to protect Python source
code. The following command will protect the Python source code inmy_script.pyand write the protected code todist/my_script.py:pylovelace protect my_script.pySupported Python versionsPyLovelace supports Python 3.11 with 3.10 and 3.12 support coming soon.
Windows only for now.More informationPyLovelace on PyPI:https://pypi.org/project/pylovelace/PyLovelace on GitHub:https://github.com/pylovelace/pylovelacePyLovelace documentation:https://pylovelace.com/docs/getting-started/introduction
Package: pyidaungsu
PyidaungsuPython library for Myanmar language. Useful in Natural Language Processing and text preprocessing for Myanmar language.InstallationpipinstallpyidaungsuUsageZawgyi-Unicode detectionLanguage detection (Myanmar <Zawgyi, Unicode>, Karen, Mon, Shan)Starting from the pyidaungsu 0.0.9, it does not only detect Zawgyi and Unicode for Myanmar language but also other languages such as Mon, Karen, Shan as well.importpyidaungsuaspds# language detectionpds.detect("ထမင်းစားပြီးပြီလား")>>"mm_uni"pds.detect("ထမင္းစားၿပီးၿပီလား")>>"mm_zg"pds.detect("တၢ်သိၣ်လိတၢ်ဖးလံာ် ကွဲးလံာ်အိၣ်လၢ မ့ရ့ၣ်အစုပူၤလီၤ.")>>"karen"pds.detect("ဇၟာပ်မၞိဟ်ဂှ် ကတဵုဒှ်ကၠုင် ပ္ဍဲကဵုဂကောံမွဲ ဖအိုတ်ရ၊၊")>>"mon"pds.detect("ၼႂ်းဢိူင်ႇမိူင်းၽူင်း ၸႄႈဝဵင်းတႃႈၶီႈလဵၵ်း ၾႆးမႆႈႁိူၼ်း ၵူၼ်းဝၢၼ်ႈ လင်ၼိုင်ႈ")>>"shan"Zawgyi-Unicode conversion# convert to zawgyipds.cvt2zgi("ထမင်းစားပြီးပြီလား")>>"ထမင္းစားၿပီးၿပီလား"# convert to unicodepds.cvt2uni("ထမင္းစားၿပီးၿပီလား")>>"ထမင်းစားပြီးပြီလား"Tokenization# syllable level tokenization for Burmesepds.tokenize("Alan TuringကိုArtificial Intelligenceနဲ့Computerတွေရဲ့ဖခင်ဆိုပြီးလူသိများပါတယ်")# lang parameter for default function is 'mm'>>['Alan','Turing','ကို','Artificial','Intelligence','နဲ့','Computer','တွေ','ရဲ့','ဖ','ခင်','ဆို','ပြီး','လူ','သိ','များ','ပါ','တယ်']# syllable level tokenization for Karenpds.tokenize("သရၣ်,သရၣ်မုၣ် ခဲလၢာ်ဟးထီၣ် (၃၅) ဂၤန့ၣ်လီၤ.",lang="karen")>>['ကၠိ','သ','ရၣ်',',','သ','ရၣ်','မုၣ်','ခဲ','လၢာ်','ဟး','ထီၣ်','(','၃၅',')','ဂၤ','န့ၣ်','လီၤ','.']# word level tokenizationpds.tokenize("ဖေဖေနဲ့မေမေ၏ကျေးဇူးတရားမှာကြီးမားလှပေသည်",form="word")>>['ဖေဖေ','နဲ့','မေမေ','၏','ကျေးဇူးတရား','မှာ','ကြီးမား','လှ','ပေ','သည်']Syllable-level tokenization supports for 4 languages (Burmese, Karen, Shan, Mon). Word-level tokenization supports only Burmese currently.Available values forlangparameter intokenizefunction: "mm", "karen", "mon", "shan"Future workAdd tokenizer for Burmese (Syllabel and word-level tokenization)Add more tokenizer (BPE, WordPiece etc.)Add Part-of-Speech (POS) tagger for BurmeseAdd Named-entities Recognition (NER) classifier for BurmeseAdd thorough documentation
Package: pyidd
PyIDDIdentify the Distribution of your DataThis package helps you for identifing the distribution of your data. For example if you want to know whether your data follow Normal distribution, you can use this package!Installationpip install pyiddUsageimportpyiddimportstatsmodels.apiassm# Load sample dataset (data is an one dimensional array)data=sm.datasets.elnino.load_pandas().data.set_index('YEAR').values.ravel()# verbose=0 means silent while fitting and verbose=1 means say anything you do while fittingp=pyidd.PyIDD(verbose=1)p.fit(data)# After fitting, you can get distribution sorted by Sum of Squered Error that fit your data, so the first distribution is the distribution that is closer to your datap.get_distributions()# You can also plot distributions and your data to see this visualy. top=10 means that you want to plot top 10 distributions that match your datap.plot(top=10)DistributionsWe use almost all scipy.stats continiuse distributions (Notics: The distributions that can not fit to your data get ignored). These distributions are listed below:alphaanglitarcsineargusbetabetaprimebradfordburrburr12cauchychichi2cosinecrystalballdgammadweibullerlangexponexponnormexponweibexponpowffatiguelifefiskfoldcauchyfoldnormfrechet_rfrechet_lgenlogisticgennormgenparetogenexpongenextremegausshypergammagengammagenhalflogisticgeninvgaussgilbratgompertzgumbel_rgumbel_lhalfcauchyhalflogistichalfnormhalfgennormhypsecantinvgammainvgaussinvweibulljohnsonsbjohnsonsukappa4kappa3ksonekstwokstwobignlaplacelevylevy_llogisticloggammaloglaplacelognormloguniformlomaxmaxwellmielkemoyalnakagamincx2ncfnctnormnorminvgaussparetopearson3powerlawpowerlognormpowernormrdistrayleighricerecipinvgausssemicircularskewnormttrapztriangtruncexpontruncnormtukeylambdauniformvonmisesvonmises_linewaldweibull_minweibull_maxwrapcauchy
Package: pyideogram
pyideogramIntroductionThis is a python package to plot ideograms in matplotlib, as well as simple gene tracks. I made this primarily for myself, since I could not find any nice looking svg supporting ideogram package in python that works well with matplotlib. The general design idea is that the functions should be intuitive to use for someone familiar with matplotlib and give reasonably well looking output with minimal configuration, but should also have the flexibility of other matplotlib functions. So the underlying matplotlib functions can be manipulated directly by giving the correct kwargs.InstallationYou can easily install it via pip from pypipipinstallpyideogramor install it manually:gitclonebalthasar-eu/pyideogramcdpyideogram
pipinstall.Dependencies are python3.10, matplotlib and numpyUsageThe package comes with integrated cytobands files for hg19 and hg38, as well asMANE transcripts(only positions, and orientation) for hg38. If you run any of the functions without providing annotation files, it will assume you want to use the stored ones.The package currently hasideogramhandideogramvwhich plot horizontal and vertical ideograms respectively, as well as agenetrackfunction, which can plot transcripts and exons from gtf files.full_ideogramiterates over all chromosomes and plots them with eitherideogramhorideogramv. Help is available for all functions int he docstring, which you can get withhelp().Examplesimportpyideogramfig=pyideogram.full_ideogram()fig.show()importpyideogramfrommatplotlibimportpyplotaspltchrom="chr6"fig=plt.figure(figsize=(10,4),dpi=150)fig.suptitle("Chromsome 6")gs=fig.add_gridspec(nrows=6,ncols=3,width_ratios=[2,20,2],height_ratios=[1,1,0.5,1,0.5,1],hspace=0.01,left=0.01,right=0.99,top=0.94,)start=29942000end=29946000ax=fig.add_subplot(gs[0,:])pyideogram.genetrack(f"{chrom}:{start}-{end}",ax=ax,textlane=True,transcriptstyle="arrowed",exonstyle="Box",)all_chrom=fig.add_subplot(gs[2,1])all_chrom.axis("off")all_chrom.set_xticks([])pyideogram.ideogramh(chrom,ax=all_chrom)pyideogram.zoom(ax,all_chrom)pyideogram.set_genome_xticks(ax)start=130000000end=135000000ax=fig.add_subplot(gs[5,:])pyideogram.genetrack(f"{chrom}:{start}-{end}",ax=ax,lanenum=5,trackkwargs={"color":"lightblue",},textlane=False,text_clip_width=True,)pyideogram.set_genome_xticks(ax)ax=fig.add_subplot(gs[4,:],sharex=ax)ax.set_xlim(start,end)pyideogram.ideogramh(chrom,ax=ax,names=True)pyideogram.zoom(ax,all_chrom)plt.axis("off")ax.tick_params(labelbottom=False)CitationThere is currently no publication attached to this package.If you use the provided annotation for plotting genes, you might want to cite theMANE paper.You might also want to citematplotlib.
Package: pyidi
pyidiImage-based Displacement Identification (IDI) implementation in python.See thedocumentationforpyIDI.Use Napari UI for quick displacement identification:BASIC USAGE:Create an instance:video = pyidi.pyIDI(cih_file='video.cih')Currently the pyIDI method works with Photron.cihand.cihxfiles, however,numpy.ndarraycan
also be passed ascih_fileargument. If an array is passed, it must have a shape of:(n time points, image height, image width).Set the points where displacements will be determined:p = np.array([[0, 1], [1, 1], [2, 1]]) # example of points
video.set_points(points=p)Or use point selection UI to set individual points or grid inside selected area. For more information about UI seedocumentation. Launch viewer with:video.gui()The method of identification has to be specified:video.set_method(method='sof', **method_kwargs)After points are set, displacements can be calculated (using method, set inset_method):displacements = video.get_displacements()Multiprocessing can also be used by passing theprocessesargument:displacements = video.get_displacements(processes=4)DEVELOPER GUIDELINES:Add _name_of_method.py with class that inherits afterIDIMethodsThis class must have methods:calculate_displacementswith attributedisplacementsget_points(static method - sets attribute video.points)InpyIDIadd a new method of identification inavaliable_methodsdictionary.
Package: pyidoit
pyidoitA Simple and Easy-to-use python client fori-doit's JSON-RPC APIInstallation$pipinstallpyidoitExampleCreate a file python file(main.py) with:frompyidoitimportIDoitClientPYIDOIT_HOST="http://localhost/idoit-22/src/jsonrpc.php"PYIDOIT_API_KEY="XXXXX-XXXXX-XXX"defmain():client=IDoitClient(host=PYIDOIT_HOST,apikey=PYIDOIT_API_KEY,username="",password="",)data=client.cmdb_objects_read()print(data)if__name__=="__main__":main()Then run the file$pythonmain.pyCONTRIBUTION GUIDE LINES
Package: pyidtech
This is a python module for reading the data from an ID TECH credit
card reader connected via serial port (RS-232) or USB-CDC.  It was
written using an ID TECH Spectrum III MagStripe Only, Insert Reader,
model number SPT3-355-12-1NN0N-0C.http://www.idtechproducts.com/products/insert-readers/68.htmlThe serial protocol is documented here (the URL says .html, but it
triggers the download of a PDF):http://www.idtechproducts.com/download/insert-readers/doc_download/413-users-manual-sptiii-moir-product-family.htmlIt requires pySerial:http://pyserial.sourceforge.net/
Package: py-iec62056
title: IEC62056 Package
author: Delhaye AdrienWelcomeWelcome to the py-IEC62056 Package. This package intends to allows you an easy setup and communication with energy meters that use the iec62056-21 protocol.This protocol is based on the iec62056-21 python package but with improvement and modifications.Installationuse the following command:pipinstallpy-iec62056or use setuptools with the downloaded .tar.gz folder.
Package: pyiface
General informationPyiface is a package that exposes the network interfaces of the operating
system in an easy to use and transparent way. Typical usage looks like this:#!/usr/bin/env pythonimportpyifacefrompyiface.ifreqioctlsimportIFF_UP# Get all available network interfacesallIfaces=pyiface.getIfaces()forifaceinallIfaces:print(iface)# Get a specific interface by nameeth0=pyiface.Interface(name='eth0')# view eth0 infoprint(eth0)# bring eth0 upeth0.flags=eth0.flags|IFF_UP# set ipv4 address of the interfaceeth0.addr=(socket.AF_INET,'1.2.3.4')# set ipv6 address of the interfaceeth0.addr=(socket.AF_INET6,'2001:0db8:85a3:0000:0000:8a2e:0370:7334')InstallationTo install the package simply callsetup.pywith the install option.LinksFor more information go to myblogspot.
Or browse thegithubrepository.