Saravanan666/pypi-org huggingface dataset:
Package: pygenerator3
PYGENERATOR3Thepygenerator3is a python package that used to automate the creation
of a python package skeleton using thepackage-generatortool that
actually perform the work.This package includes atemplatesdirectory which holds
all the necessary files and directories that are required to build the
package skeleton.templates/
├── MANIFEST.in.template
├── README.md.template
├── package
│   ├── __init__.py
│   └── scripts
├── requirements.txt.template
└── setup.py.templateNOTE:Additional files can be added before and after package skeleton generation.Before: By adding additional files into thepackagedirectory, they will
be transferred to the package skeleton during the package skeleton generation.After: Additional files can be added after package skeleton creation and
before the tarball (*.tar.gz) wrap up.Requirements:* python >= 3.5
* pylib3Usage:Install the pygenerator3 package (inside your project's virtual environment)pip install pygenerator3Run the package-generator tool to create the python package skeletonusage: package-generator [--help] [--version] [--log-file NAME] [--verbose]
                         [--python-version NUM] [--url URL]
                         [--description TEXT] [--version-file TEXT]
                         [--dst PATH] [--package-version TEXT] --package-name
                         TEXT --author TEXT --author-email EMAIL

optional arguments:
  --help                show this help message and exit
  --version             shows program version
  --log-file NAME       log file name
  --verbose             if added will print more information
  --python-version NUM  python version (default: 3.5)
  --url URL             url to package source code
  --description TEXT    python package description
  --version-file TEXT   python package version file name
  --dst PATH            destination path where the python package will be
                        created
  --package-version TEXT
                        python package version number (default: 0.0.1)

required arguments:
  --package-name TEXT   python package name
  --author TEXT         Author's full name
  --author-email EMAIL  Author's email addressExamples:To create 'simplepackage' python package skeleton in /tmp directorypackage-generator \
--name simplepackage \
--author 'Shlomi Ben-David' \
--author-email 'shlomi.ben.david@gmail.com' \
--dst /tmp/NOTE:By omitting the --dst argument, the python package skeleton will be
created in the current directory.To wrap up the 'simplepackage' into a tarball so it could be installed via pippython setup.py sdist
Package: pygeneric
========Overview========What is pygeneric?==================`pygeneric` implements generic functions based on type dispatch in Python. A genericfunction groups different implementations (or methods) under the same name.The actual implementation is then chosen at runtime depending on the type ofeach function argument.The implementation is loosely inspired in the Julia language. We also shamelesslysteal some other features of Julia and adapted them to Python:* Parametric types.* A type conversion/promotion system integrated with arithmetic operations.* A generic Object base class that delegates all binary operations to thecorresponding generic functions (i.e., instead of implementingObject.__add__, we overload ``generic.op.add(Object, Object))``.This package works with Python 3 and Python 2, but it is getting increasinglymore difficult to keep Python 2 support as we implement more advanced features.Not all functionality works in Python 2, and sometimes extra precautionsare necessary. Pygeneric cannot handle old style classes and sometimes we arelimited by lack of some Python 3 only syntax. Python 2 also have some quirksthat we do not try to emulate (e.g., broken comparison operators), so pygenericuses an uniform Python 3 semantics.Basic usage===========Most of the functionality present in this package works around the type dispatchin generic functions. We declare a generic function using the syntax.. code-block:: pythonfrom generic import generic, Number, Sequence@genericdef func(x, y):print('Got %r and %r' % (x, y))Type dispatch can be defined in Python 3 as.. code-block:: python@func.overloaddef func(x: Number, y: Number):print('Got two numbers: %r and %r' % (x, y))The Python 2-friendly syntax (which can also be useful in Python 3) is:.. code-block:: python@func.register(Sequence, Sequence)def func(x, y):print('Got two sequences: %r and %r' % (x, y))Depending on the types of each argument, the dispatcher will choose either oneof these three implementations>>> func(42, 0.0)Got two numbers: 42 and 0.0>>> func([1, 2], (3, 4))Got two sequences: [1, 2] and (3, 4)>>> func("foo", "bar")Got two sequences: 'foo' and 'bar'The type dispatch always chooses the most specialized method for the givenargument types.Consider the two specialized dispatches.. code-block:: pythonfrom numbers import Integral@func.overloaddef func(x: Integral, y: Number):print('Got one integer: %r and %s' % (x, y))@func.overloaddef func(x: Integral, y: Integral):print('Got two integers: %r and %s' % (x, y))``func`` knows what to do>>> func(1, 2)Got two integers: 1 and 2>>> func(1, 2.0)Got one integer: 1 and 2.0>>> func(2.0, 1)Got two numbers: 2.0 and 1Further information===================Did you find this feature useful? Then start using pygeneric now!Check the documentation__ for additional information... __documentation:: http://pythonhosted.org/pygeneric/
Package: pyGenericSpreadSheet
PyGenericSpreadSheetGeneric Spreadsheet Editing APIDocumentationWikiDockerizedockerbuild-tpygenericspreadsheet-f.\Dockerfile.dockerrun--rm-it-v${PWD}:"/mnt"-w"/mnt"pygenericspreadsheet/bin/bashAuthorsTim HolzheimWolfgang FahlMichal Slupczynski
Package: pygenesig
Gene signatures are sets of genes derived from gene expression data, which identify
a certain tissue, cell type, pathway, etc.Pygenesigprovides a framework to create
and validate such signatures. The package is easily extensible to add new methods
for signature creation and testing.Getting startedPlease refer to thedocumentation, in particular
the sectionsPreparing dataCreating signatures, andTesting signatures.If you want to implement own methods for creating and testing signatures, please take a
look at theDeveloper’s guideand theAPI documentation.InstallationYou need to have Python 3.7 or newer installed on your system. Some methods for creating
or testing signatures additionally require R. If you don’t have
Python installed, we recommend installingMiniforge.There are several alternative options to install pygenesig:Install pygenesig in a self-contained conda environment:This is the most reliable option to make both R and Python work.Make sure you
have the `conda-forge` and the `bioconda` channels set-up with the correct prioritiesasdescribed in the Bioconda documentation.# use `mamba` instead of `conda` for more speed
mamba create -n pygenesig python=3.8 pip bioconductor-edger bioconductor-bioqc
conda activate pygenesig
pip install pygenesigInstall pygenesig via pip and R packages manuallypip install pygenesigThen, in R:install.packages("BiocManager")BiocManager::install(c("edgeR","BioQC"))Usually, ifRis in yourPATH,rpy2automatically
detects your R installation. If you get an error message while importingpygensig,
try setting theR_HOMEenvironment variable before importing pygenesig:importosos.environ["R_HOME"]="/usr/lib/R"importpygenesigInstall the latest development version from GitHub:pip install git+https://github.com/grst/pygenesig.git@masterYou’ll need to separately install R packages as described above.Release notesSee therelease section.ContactPlease use theissue tracker.
Package: pygenesis
PyGenesisPython package repository templateYou can findFull Project DocumentationhereWorkflowsPackageSupportDownloadsLanguagesDevelopmentMenuMissionOpen Source ProjectFeaturesRequirementsDevelopment StatusInstallQuickstartContributingMissionPyGenesis is a comprehensive Python package template designed to kickstart your projects instantly.
With a clean and organized structure, it provides a hassle-free starting point for developers.
Effortlessly begin your Python endeavors, focusing on your code, not the setup. Jumpstart your creativity with PyGenesis.Open Source ProjectThis is the open source project withMIT license.
Be free to use, fork, clone and contribute.FeaturesThis README (Change it for your python project)This template base onlibresource/open-source-checklist.
It contains may useful files for open source project: (CHECKLIST.md,CONTRIBUTING.md,CODE_OF_CONDUCT.md, and much more).setup.pyfor build your packagerequirements.txtanddev-requirements.txtMakefilewith main commands to work with the projectrun testscalculate coveragelintbuild and install packagegenerate autodocumentationothersGitHub workflowsgenerate documentationrun tests with coveragerun linterpublish your package in PyPigreetings for new contributorsRequirementspytest, pytest-cov, pylint, yamllint, sphinx, sphinx_rtd_themeSee more inFull DocumentationDevelopment StatusPackage already available onPyPiSee more inFull DocumentationInstallwith pippip install pygenesisSee more inFull DocumentationQuickstartfrompygenesisimportinfoprint(info())More examples inFull DocumentationContributingYou are welcome! To easy start please check:Full DocumentationContributingDeveloper DocumentationCode of ConductSecurity PolicyGovernanceSupport
Package: py-genesiscloud
py-genesiscloudA library to interact withgenesiscloudDemoInitialize the client:>>> from genesiscloud.client import Client
>>> client = Client("yourapikey")List available SSH keys:>>> [i for i in c.SSHKeys.find({"name":"oz123"})]
[SSHKey({'id': '848a6631-486a-4992-8a40-5a9027415d02', 'name': 'oz123', 'public_key': 'ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIIj3+Q0uK0lVNqYrqUUFMBajoUtFcLPHES2Xk0x8BvlV', 'created_at': '2020-05-21T17:39:10.621Z'})]List all images which can be used to create an instance:>>> [i for i in client.Images.find({"type": 'base-os'})]
[Image({'id': '45d06539-f8f5-48d9-816e-d4b1a8e5163e', 'name': 'Ubuntu 18.04', 'type': 'base-os', 'created_at': '2020-03-24T18:14:01.223Z'}),
 Image({'id': '6d5c3613-f6cb-48e1-8711-14f084060209', 'name': 'Ubuntu 16.04', 'type': 'base-os', 'created_at': '2020-03-24T18:14:01.219Z'})]Create an instance>>> client.Instances.create(name='test-oz', hostname='hostname',
                            sshkeys=['650e5ecb-4e28-4a24-bfbf-ac4212f7e137']
                            type='vcpu-4_memory-12g_disk-80g_nvidia1080ti-1',
                            "image"='45d06539-f8f5-48d9-816e-d4b1a8e5163e',
                            "metadata"={"startup_script":"#!/bin/bash\nsudo apt update && sudo apt install iperf3"}
                            )Accessing attributes of an Instance:>>> inst = [i for i in client.Instances.list()][0]

>>> inst.security_groups[0]
SecurityGroup({'id': '2472c0bb-1fa9-4dcc-a658-4268e78ad907', 'name': 'default'})

>>> inst.security_groups
[SecurityGroup({'id': '2472c0bb-1fa9-4dcc-a658-4268e78ad907', 'name': 'default'}),
 SecurityGroup({'id': 'd3040f01-3b12-4712-9e8e-8ecb1ae7ba04', 'name': 'standard'}),
 SecurityGroup({'id': '56370632-ceeb-4357-a5d3-f2c3acf9d69e', 'name': 'Folding@home'})]

>>> inst.ssh_keys
[SSHKey({'id': '848a6631-486a-4992-8a40-5a9027415d02', 'name': 'oz123')]

>>> inst.image
Image({'id': '3c5f9b6f-2f4b-4067-ba50-925be9e6afb1', 'name': 'Ubuntu 18.04'})Contributing to this projectFirst, make sure you have pipenv installed.Runpipenv shelland thenpipenv install.Write your tests, add your features, test your features withmake test.git commitandgit push:-)Make a PR!
Package: pyGenicParser
PyGenicParserParse Genetic files via bgi like sql indexingDesigned to use sql database style of metadata created by bgenix .bgi files for indexing, but generalised to both plink
and bgen file formats. This was a generalisation of the approach used by the [pybgen], with an attempt to include some
of the features of [pysnptools] such as indexing, although this system isn't as clever in terms of reads.All the source code can be found at thePyGenicParser git repository
Package: pyGenieScript
Packaged GenieScript for PythonGenieScript's core engine is originally built in Java/TypeScript. This is its language extension in Python.
The goal of this package is to:Provide an easy installation, almost directly frompipExpose the GenieScript engine as a set of easy-to-use APIs, enabling it to be used in larger Python projectsInstallationInstallnodein your current environment.GenieScript recommendsnode >= 18, although it is yet to be tested on earlier nodes. If you have multiple nodes in your environment, we recommend usingnvm. After installing it, run (1)nvm install 18, (2)nvm use 18, and finally (3)nvm alias default 18.Install some required system dependency ofpyGenieScript, including:installgettext. Install bybrew on Macand by other package managers on linux.pip install pyGenieScriptpip install genienlp==0.7.0a4(because installation ofgenienlpdepends on more libraries, it is not included as a mandatory dependency ofpyGenieScript).For Mac M1/M2 users, refer to thisinstallation guide.UsageA minimalist example to run the yelp semantic parserYou can use GenieScript to query yelp database in natural language. We have prepared a yelp parser. Here are the steps to run this example:Open apythonREPL process. Do the following:>>>importpyGenieScript.geniescript>>>genie=pyGenieScript.geniescript.Genie()# This command installs genie-toolkit and might take a while for the first time>>>genie.nlu_server('yelp')# This command will download the yelp parser and might take a while for the first timeTip: If you seePrediction worker had an error: spawn genienlp ENOENT, this meansgenienlpis not installed correctly.If successful, the final message you see should be similar to this:[I 230211 02:15:11 util:299] TransformerSeq2Seq has 139,420,416 parametersKeep this REPL running, and in a separate terminal, run:The yelp skill requires you toregister an API onlineand obtain a developer key. Register an account, retrieve the API key, and run:exportYELP_API_KEY=[yourkey]Open anotherpythonREPL process. Do the following:>>>importpyGenieScript.geniescript>>>genie=pyGenieScript.geniescript.Genie()# You should not need to wait now>>>genie.initialize('localhost','yelp')# This sets the semantic parser to be accesible over local server>>>genie.query("show me a chinese restaurant")# You should see meaningful results returned from Genie>>>genie.quit()# Shuts down Genie serverInstallation FAQIf you encounter a stall ofgenie.query()when running for the first time (seehere), please
cancel the stalled process and run again.API documentationMain API documentations are aviliablehere.
Package: pygenius
PyGeniusWant to use data from rap songs in your Python scripts but bummed that there’s no API to do so?
Well guess what?  NOW U CAN, DAWG.Welcome to PyGenius.All functions should be run through the examples.py file, or any other script you create.Functions currently available
artists.albumList(artist, arg)
Returns a list of albums that the specified artist has recorded.
If second argument is set as ‘links’, the links to the albums will be returned.artists.getDates(artist)
Returns a list of albums recorded by a specific artist, as well as the release year.artists.getAlbumData(artist, album)
Returns the metadata about an album: description, track numbers, and track names.artists.getArtistBio(artist)
Returns an artist’s bio.artists.getPopularSongs(artist, arg)
Returns the most popular songs by a specified artist.  If the optional second argument is ‘link’, will return links to songs that can be passed in to other functions.wordsearch.searchWords(keyword, arg)
Returns results for a key word search.  Default return is artist and song name, but if the optional second argument is set to ‘link’, a link to the song is returned.songs.searchSong(artist, title, arg)
Returns lyrics for a specified song title.  If the optional third argument is set to ‘lyrics’, only the lyrics will be returned; if it’s ‘link’, only links to each lyric’s annotations are returned (and can be passed into the searchAnnotations function); otherwise, both are returned by default.songs.searchAnnotations(query)
Will return content of a specified annotation link, including HTML links to pictures, videos and GIFs, as well as links to external sites referenced.songs.findAllSongs(artist, arg)
Will return all songs attributed to the specified artist.  If second argument is specified as ‘links’, will return the links to the songs; if ‘titles’, will return the song titles; otherwise, will return both by default.
Package: pygenix
PygenixA Python Package With Superpowers ;)InstallationClone The Project Then,cdpygenixpipinstall.FeaturesTypewriter Text Animationfrompygenix.aniimporttextanimation# textanimation(text , speed)textanimation("Hello World :D",0.1)# can use 0.01 too.Getting Usernamefrompygenix.utilsimportuserprint(user)Getting Platfromfrompygenix.utilsimportplatfromprint(platfrom)Getting Specific Platfromfrompygenix.utilsimportsplatfromprint(splatfrom)Getting a Loding Animation credits tohimfrompygenix.utilsimportLoaderimportoswithLoader("Loading..."):#do anything hereos.system('sudo rm -rf /')Getting a tkinter hover button , creds and written byhimfrompygenix.aniimporttk_hover_btntk_hover_btn(root,x,y,text,bcolor,fcolor,cmd)
Package: pygenlib
PyGenLibA Python library for generating other Python libraries.InstallationYou can installpygenlibusingpip:pip install pygenlibUsageTo create a new Python library template, use thepygenlibcommand-line tool.pygenlib my_custom_libraryThis will create a new library namedmy_custom_libraryin the current directory.If you want to create the library in a specific folder, you can use the--targetor-toption:pygenlib my_custom_library --target /path/to/target_folderThis will create the library in the specified target folder.After creating the template, you can customize the generated files to build your Python library as per your specific requirements.LicenseThis project is licensed under the MIT License - see theLICENSEfile for details.Made with 💖 by Harsh Avinash
Package: py-gen-mur
py-gen-murpython 机器码/用户码/注册码 生成器python generate [m]achine_code [u]ser_code [r]egister_code运行环境使用场景说明使用场景详见测试用例。场景步骤一（管理员本地，可选）因代码开源，不建议使用mur.crypt.Crypt()默认类。建议使用此工具时，自定义指定mur.crypt.Crypt()构造函数的key和iv。本代码中提供了mur.crypt.gen_des_key()和mur.crypt.gen_des_iv()的方法，但是生成后必须找地方另外存储这两个值，否则之前使用其生成的注册码无法再解密。frommur.cryptimport*my_des_key=gen_des_key()my_des_iv=gen_des_key()my_crypt=Crypt(key=my_des_iv,iv=my_des_iv)场景步骤二（用户本地）用户运行【生成机器码】的程序生成放有【加密机器码】的文件把【加密机器码】的文件提供给管理员frommur.userimport*u_machine_code=gen_machine_code(my_crypt)实际使用时可复制gen_register_code.py到需要发布的程序，由用户执行生成【机器码】场景步骤三（管理员本地）管理员解密用户提供的【加密机器码】文件同时为用户设置授权天数，生成【用户码】文件结合两者生成【注册码】文件把【用户码】文件和【注册码】文件提供给用户frommur.adminimport*a_machine_code=read_machine_code()days=input('请输入授权天数：')# 0 表示永久a_user_code=gen_user_code(days,my_crypt)a_register_code=gen_register_code(a_machine_code,a_user_code,my_crypt)实际使用时可在本仓库中执行python gen_register_code.py为用户生成【用户码】和【注册码】场景步骤四（用户本地）用户运行应用主程序主程序读取【用户码】文件（或让用户输入用户码）主程序在用户本地重新生成【机器码】主程序利用【用户码】和【机器码】生成【注册码】主程序比对【生成的注册码】和【管理员提供的注册码】内容是否一致若一致，且授权未过期，程序运行；否则，程序终止frommur.userimport*u_user_code=read_user_code()rst=verify_authorization(u_user_code,my_crypt)ifrst==True:app.run()else:exit(1)使用注意凡是使用了此工具的程序，在发布该程序时，建议不要直接用Pyinstaller打包成*.pyc，然后供用户使用，否则很容易被反编译破解。建议先对源码做加密处理，再提供给用户使用。有两个方法，任选一个即可：Cython 编译为动态链接先使用Cython生成*.py的动态连接*.pyd文件再使用Pyinstaller打包，才供用户使用。可参考文档《Cython + Pyinstaller 防止反编译打包》Pyinstaller 加密先用 pip 命令安装tinyaes和pycrypto（需要提前安装 Microsoft Visual Studio 和设置环境变量 CL）使用Pyinstaller打包时增加--key ${password}（此时编译的中间文件为*.pyc.encrypted）。可参考文档：《Pyinstaller 打包的 exe 之一键反编译 py 脚本与防反编译》《谈谈 Pyinstaller 的编译和反编译，如何保护你的代码》《Microsoft Windows Python-3.6 PyCrypto installation error》赞助途径支付宝微信版权声明Site:http://exp-blog.comMail:289065406@qq.com
Package: pyGeno
Short description:pyGeno is developed byTariq Daoudaat theInstitute for Research in Immunology and Cancer(IRIC).With pyGeno you can do that:frompyGeno.Genomeimport*#load a genomeref=Genome(name='GRCh37.75')#load a genegene=ref.get(Gene,name='TPST2')[0]#print the sequences of all the isoformsforprotingene.get(Protein):printprot.sequenceYou can also do it for thespecific genomesof your subjects:pers=Genome(name='GRCh37.75',SNPs=["RNA_S1"],SNPFilter=myFilter())And much more:https://github.com/tariqdaouda/pyGenoVerbose DescriptionpyGeno is a personal bioinformatic database that runs directly into python, on your laptop and does not depend
upon any REST API. pyGeno is here to make extracting data such as gene sequences a breeze, and is designed to
be able cope with huge queries. The most exciting feature of pyGeno, is that it allows to work with seamlessly with both reference andPresonalized Genomes.Personalized Genomes, are custom genomes that you create by combining a reference genome, sets of polymorphims and an optional filter.
pyGeno will take care of applying the filter and inserting the polymorphisms at their right place, so you get
direct access to the DNA and Protein sequences of your patients.Multiple sets of of polymorphisms can also be combined together to leverage their independent benefits ex:RNA-seq and DNA-seq for the same individual to improve the coverage
RNA-seq of an individual + dbSNP for validation
Combine the results of RNA-seq of several individual to create a genome only containing the common polymorphisms
pyGeno is also a personal database that give you access to all the information provided by Ensembl (for both Reference and Personalized Genomes) without the need of queries to distant HTTP APIs. Allowing for much faster and reliable genome wide study pipelines.It also comes with parsers for several file types and various other useful tools.Full DocumentationThe full documentation is availablehereIf you like pyGeno, please let me know.
For the latest news, you can follow me on twitter@tariqdaouda.