Saravanan666/pypi-org huggingface dataset:
Package: generic-tree
Conceptual RepositoryThis intend to be anreadme-documented,open-source-licensed,semantic-versioned,conventional-committedandchangeloggedgit repository starting point
for the development of a brand-new projectA straightforward begin for an open-source project repositoryTable of ContentsSee allGetting startedDevelopment environmentRepo publicationProject specificationsFeaturesFolder structureMaintainanceLicenseGetting startedFirst of all, create a new repository from thisName it accordingly and place where it best fits for your team.Development environmentMake sure you haveGitinstalled:$git--version
gitversion2.25.1Thus, clone the recent-created repository locally
and you'll be ready to start developing your project.Repo publicationAfter all, you should make this project your own:Write a good README to present your project to the world.And also ensure to tailor the project license to your needs.Project specificationsHere some descriptions about this template project:FeaturesThis project shortens a repository start setup, considering:Inclusion of a mature README document, inspired byStandard ReadmeInclusion of an open-source LICENSE fileInclusion of a structured, yet raw, CHANGELOG fileCompliance with widely-used version control conventions, such as:Semantic VersioningConventional CommitKeep a ChangelogFolder structure.
├── .git/               version control folder
├── .gitignore          ignored files manifest
├── CHANGELOG.md        release notes description
├── LICENSE             license file
└── README.md           readme documentMaintainanceThis project is maintained by the author,@artu-hnrq.It has reached a stable, usable state and is beingactively developed.LicenseThis project is published under the permissions established byGNU General Public License v3.0.
Package: generic-utils
packageA set of generic utility classes and helper functions for Python  development.generic_utils is a set of generic Python utilities which currently target
Python 2.7.X environments with no other required dependencies.  The code
targets both general production code as well as test utilities to facilitate
easier test generation, management and complexity.This library is not currently intended to be generally useful to the community at
large as there is work to be done to provide greater Python support as well as
general documentation and upkeep, but has been used successfully in production
environments within the prescribed environments.Installationpip install generic_utilsDevelopmentInstall requirements into a local virtualenv:virtualenv env
env/bin/pip install -e ".[html,cassandra,celery_test,test_utils]"This project requires available cassandra and redis hosts in order to run the full test-suite.Redis Setup:docker run -d --name test-redis -p 6379:6379 -v /path/to/storage/redis:/data redisConnect to the container:$ docker exec -i -t test-redis /bin/bash
$ root@7a3377df67f0:/data# redis-cli
127.0.0.1:6379> SET __THIS_IS_A_TEST_INSTANCE__ True
OK
127.0.0.1:6379> exitCassandra Setup:$ docker run --name test-cassandra -d -p 9042:9042 -p 7000:7000 -v /path/to/storage/cassandra:/var/lib/cassandra cassandra:3.0Connect to the container:$ docker exec -i -t test-cassandra /bin/bashOpen cqlsh and create the python_utils_test keyspace:$ cqlsh
> CREATE KEYSPACE python_utils_test WITH REPLICATION = { 'class' : 'SimpleStrategy', 'replication_factor' : 1} AND DURABLE_WRITES = true;Configure Cassandra cluster intests/local_settings.py(not in version-control). Replace the values with appropriate
values for your environment:CQLENGINE = {
    "TEST_CLUSTER": {
        ConfigKey.CONTACT_POINTS: get_config_value("TEST_CASSANDRA_CONTACT_POINTS", default=["localhost"]),
        ConfigKey.KEYSPACE: get_config_value("TEST_CASSANDRA_KEYSPACE", "python_utils_test"),
        ConfigKey.PORT: get_config_value("TEST_CASSANDRA_PORT", default=9042),
        ConfigKey.USERNAME: get_config_value("TEST_CASSANDRA_USERNAME", default=""),
        ConfigKey.PASSWORD: get_config_value("TEST_CASSANDRA_PASSWORD", default=""),
        ConfigKey.DEFAULT_TIMEOUT: EXPLICTLY_NOT_10_SECONDS_TIMEOUT
    }
}Run the test suite:nosetests testsOr, using tox:tox
Package: generic-web-server
generic-web-serverGeneric Web Server.Getting StartedDependenciesYou need Python 3.7 or later to usegeneric-web-server. You can find it atpython.org.
You also need setuptools, wheel and twine packages, which is available fromPyPI. If you have pip, just run:pip install setuptools
pip install wheel
pip install twineInstallationClone this repo to your local machine using:git clone https://github.com/matheusphalves/generic-web-serverHow to runBasically, you need to import the Server class and execute the methodrun.from Server import Server

server_instance = Server()
server_instance.run()FeaturesFile structure for PyPI packagesSetup with package informations
Package: generinator-rats
Random Attributes, Tags & StyleRandom web content (HTML, CSS, SVG) generator forFuzzinator.RequirementsPython>= 3.4pipand setuptools Python packages (the latter is automatically installed by
pip).MongoDB(either local installation or access to remote database)ANTLRv4InstallThe quick way:pip install generinator-ratsAlternatively, by cloning the project and running setuptools:python setup.py installUsageAs a first step,Generinator:RATSneeds to process existing web content to
extract names of, parent-child relation between, and values of tags and
attributes. The extracted information is then stored in a database.Example invocation of the processing step:generinator-rats-process <input1.html> <input2.css> <input3.svg> <inputdir4>Once the processing step has built a database, the generator ofGenerinator:RATScan be used to produce any number of files with random web
content.Example invocation of the generation step:generinator-rats -n <number-of-tests> -o <output-dir>For more information on their usage, use the–helpcommand line option on any
of the tools.(Note: The processing step can be re-executed any number of times, even after
executing the generator. Actually, it may be really useful to periodically run
the processing step on new input files or test suites.)Copyright and LicensingSeeLICENSE.
Package: generss
genRSSgenRSSis a tool to create an RSS 2.0 feed from media files in a directory.
Files can be looked for recursively in subdirectories and can be restricted to a
given set of extensions.Installationpip install mutagen eyed3 generssDetermining file durationTo include media file duration in your feeds (using the<itunes:duration>tag),genRSSuse tries the following options.mutagen: a python package installed alongsidegenRSSthat can deal with
audio and video files.sox: can only handle audio files, runs faster thanffprobe.ffprobe: normally installed withffmpeg, can deal with audio and video files
but it is the slowest of the three options.In any case, ifgenRSSfails to get media file duration with one tool, it'll
fall back to the next one. If none of these tools is installed or if file duration
cannot be obtained, no<itunes:duration>tag will be inserted.Usage options-d DIRECTORY, --dirname DIRECTORY
                        Directory to look for media files in.
                        This directory name will be appended to the host name
                        to create absolute paths to your media files.
  -r, --recursive       Look for media files recursively in subdirectories
                        [Default:False]
  -e STRING, --extensions STRING
                        A comma separated list of extensions (e.g. mp3,mp4,avi,ogg)
                        [Default: all files]
  -o FILE, --out FILE   Output RSS file [default: stdout]
  -H URL, --host URL    Host name (or IP address), possibly with a protocol
                        (default: http) a port number and the path to the base
                        directory where your media directory is located.
                        Examples of host names:
                         - http://localhost:8080 [default]
                         - mywebsite.com/media/JapaneseLessons
                         - mywebsite
                         - 192.168.1.12:8080
                         - http://192.168.1.12/media/JapaneseLessons
  -i URL, --image URL   Absolute or relative URL for feed's image [default: None]
  -M, --metadata        Use media files' metadata to extract item title [default: False]
  -t STRING, --title STRING
                        Title of the podcast [Default: use directory name as title]
  -p STRING, --description STRING
                        Description of the podcast [Default:None]
  -C, --sort-creation   Sort files by date of creation instead of name (default)
  -v, --verbose         set verbose [default: False]LicenseMIT
Package: genescraper
Gene Card ScrollerA Flask web application (made with Bootstrap) that lets you scroll through GeneCard's gene summaries, granted you provide a list of genes.InstallationInstall genescraper with pippipinstallgit+https://github.com/branco-heuts/genescraperUsageMake sure you provide a comma separated file (.csv), without headers or row-names. You can find an example filehere.Run the command in the terminal:pythongenescraper.py-cgene_list.csvAnd click:http://127.0.0.1:5000orhttp://10.252.0.13:5000Warning: a large list of genes is not recommended, the webscraping can be slow.When you're done, close the server using CTRL+C.
Package: genesis
What is Genesis?Genesis is a python library designed to build applications (with asyncio) that work with freeswitch through ESL.What is FreeSwitch?FreeSWITCH is a free and open-source application server for real-time communication, WebRTC, telecommunications, video and Voice over Internet Protocol (VoIP). Multiplatform, it runs on Linux, Windows, macOS and FreeBSD. It is used to build PBX systems, IVR services, videoconferencing with chat and screen sharing, wholesale least-cost routing, Session Border Controller (SBC) and embedded communication appliances. It has full support for encryption, ZRTP, DTLS, SIPS. It can act as a gateway between PSTN, SIP, WebRTC, and many other communication protocols. Its core library, libfreeswitch, can be embedded into other projects. It is licensed under the Mozilla Public License (MPL), a free software license.Bywikipedia.What is ESL?ESL is a way to communicate with FreeSwitch. See more detailshere.Why asyncio?Asynchronous programming is a type of parallel programming in which a unit of work is allowed to run separately from the primary application thread. When the work is complete, it notifies the main thread about completion or failure of the worker thread. There are numerous benefits to using it, such as improved application performance and enhanced responsiveness. We adopted this way of working, as integrating genesis with other applications is simpler, since you only need to deal with python's native asynchronous programming interface.DocsThe project documentation is inhere.How to contribute?If you are thinking of contributing in any way to the project, you will be very welcome. Whether it's improving existing documentation, suggesting new features or running existing bugs, it's only by working together that the project will grow.Do not forget to see ourContributing Guideand ourCode of Conductto always be aligned with the ideas of the project.ContributorsWill be welcome ❤️Author@Otoru
Package: genesiscreator
A Crypto-Currency Genesis Block CreatorFree software: BSD 3-Clause LicenseInstallationpip install genesiscreatorDocumentationhttps://python-genesiscreator.readthedocs.io/DevelopmentTo run the all tests run:toxNote, to combine the coverage data from all the tox environments run:Windowsset PYTEST_ADDOPTS=--cov-append
toxOtherPYTEST_ADDOPTS=--cov-append toxChangelog0.1.0 (2018-07-01)First release on PyPI.
Package: genespeak
GeneSpeak 🧬A library to encode text as DNA and decode DNA to text.GeneSpeak allows you to encode regular text as DNA using
base-pairs (A,T,G,C) and convert back to the
original text. Text encoding is done for bothasciiandutf-8characters based on thestrategykeyword argument.
The encoding scheme could be any combination ofA,T,G,C.Installation 📜You can install the library viapiporconda.Install with pippipinstallgenespeakInstall with condacondainstall-cconda-forgegenespeakQuickstart ⚡See the quickstart guide here.ServiceLink/BadgeColabBinderSageMaker StudioLabDemo App ✨You can play around with GeneSpeak in this streamlit app:https://tinyurl.com/genespeak-demoUsage ✋importgenespeakasgpprint(f'{gp.__name__}version:{gp.__version__}')schema="ATCG"# (1)strategy="ascii"# (2)text="Hello World!"dna=gp.text_to_dna(text,schema=schema)text_from_dna=gp.dna_to_text(dna,schema=schema)print(f'Text:{text}\nEncoded DNA:{dna}\nDecoded Text:{text_from_dna}\nSuccess:{text==text_from_dna}')Outputgenespeakversion:0.0.5
Text:HelloWorld!
EncodedDNA:TACATCTTTCGATCGATCGGACAATTTGTCGGTGACTCGATCTAACAT

Text:HelloWorld!
EncodedDNA:TACATCTTTCGATCGATCGGACAATTTGTCGGTGACTCGATCTAACAT
DecodedText:HelloWorld!Documentation 📚Thegenespeakdocs are maintainedhere.License 📑The library is available underMIT license.Citation 🔖You may cite this library as follows.@software{ray2022genespeak,author={Ray, Sugato},title={GeneSpeak - A library to encode text as DNA and decode DNA to text},url={https://github.com/sugatoray/genespeak},doi={10.5281/zenodo.5885777},month={1},year={2022}}GeneSpeak Thumb Print 👍Let's have some fun! ✨ The following is aGeneSpeak thumbprintofgenespeakitself.schemastrategythumbprintATCGasciiTCTGTCTTTCGCTCTTTGAGTGAATCTTTCATTCCG
Package: genesynth
[![Python packages](https://github.com/sterling312/genesynth/actions/workflows/github-actions-unittests.yaml/badge.svg)](https://github.com/sterling312/genesynth/actions/workflows/github-actions-unittests.yaml)# genesynth
This library is used to synthetically generate structured data based on configuration to be used for testing as well as structured data training purposes. The approach of the library is to leverage as much as C-level python packages such as numpy and scipy to generate data at field level, one type at a time, and use graph approach to piece together the complex dependency as well as de-normalization/sampling from each fields to construct data in a scalable manner fast.# install` pip install genesynth `# example` $ python-mgenesynth.server--host=0.0.0.0-p8080 `` $ make run `` $ python-mgenesynth.cli-ftests/test.yaml--stdout`` $ make cliFILENAME=$(pwd)/tests/test.yaml`# project status## supported feature
* load yaml as configuration file
* arbitrary row size support
* data type mapping with configurable parameters
* JSON (semi-structured data) support
* improved data type support
* foreign relationship support
* DOT file graph
* table graph
* built-in orchestrator using graph
* thread and process support
* intermediary data temporary cache
* graph visualization## key features to add
* add yaml validator
* fix header support
* additional output file formats (JSON, PSQL dump, CSV with quotes, etc)
* add support for JSON arrays
* improve constraint support
* add support for quoted string
* add support statistical distribution via kernel convolution
* optimize orchestration and disk cache efficiency
* optimize thread/process based generation
* convert serial to autoincrement constraint for integer type
* convert password to constraint of string type## nice to have features to add
* support external scheduler
* support NLP based text generation
* support sklearn
* support integration with pytorch embedding
* support for object reference via $ref
* fix compatibility with [JSON schema array notation](https://json-schema.org/understanding-json-schema/reference/array.html#items)
* fix when json array child object appears as separate items
Package: genesys
genesys is a file management and version control software that is directly intigrated with kitsu.genesys requires a sligthly modified version of zoudocker images of our modified [zou](https://hub.docker.com/repository/docker/eaxum/zou) and [genesys](https://hub.docker.com/repository/docker/eaxum/genesys) are availble on docker hubGenesys is built and managed by Eaxum[![Eaxum Logo](https://eaxum.com/wp-content/uploads/2020/07/LogoCapsule_small-300x113.png)](https://eaxum.com)
Package: genesyscloudcli
Genesys Cloud CLI⚠WARNING:This is a result of a hackathon project and while it is functional it is not officially supported by the Genesys Development Group.The Genesys Cloud cli is a tool to interact withGenesys CloudNote that if you us oh-my-zsh, it aliases gc to a git command, this cli works using either gc or gcli if you are using that alias.Installpip install genesyscloudcliLocal setupThe cli authenticates using client credentials which you will have tocreate yourselfgc profile newis the easiest way to setup your credentials.  This will create a credentials file at ~/.genesyscloud/credentials and can support multiple profiles for different organizations.$ gc profile new
Profile Name [DEFAULT]: mycompanyname
Genesys Cloud Environment (mypurecloud.com, usw2.pure.cloud): mypurecloud.com
OAuth Client ID: dfbdc514-e830-4745-bffa-1cb7ee7f2736
OAuth Client Secret: wJalrXUtnFEMI/K7MDENG/bPxRfiCYEXAMPLEKEYProfilesWith multiple profiles configured, you can either specify one when connnecting:$ gc --profile <profilename> <command>Or switch a named profile to the default$ gc profile setdefault <profilename>Configuration Options~/.genesyscloud/configcontains configurable options in the DEFAULT section[DEFAULT]
output_type = yamlCommand StructureThe Genesys Cloud cli uses a multipart structure$ gc <command> <subcommand> [options and params]PaginationFor resources that have multiple pages such as listing users, there are options available on how to process the pages.  By default the cli uses a page size of 250 and retrieves all items.--page-size    # set a page size other than 250
--page-number   # return a specific pageData InputsSome commands require bodies to be sent with the request, such as creating a new user.  The body can be supplied a number of ways.Passing json with the command (escaped whitespace is not currently supported)$ gc users new "{\"name":\"Joe Smith\"}"Referencing a file$ gc users new user.jsonStream input$ gc users new < user.json$ echo "{\"name":\"Joe Smith\"}" | gc user newTesting locally$ virtualenv venv
$ . venv/bin/activate
$ pip install --editable .
Package: genesys-notifications
genesys-notifications clientThis is a simple library for receiving genesys websocket notifications.Seehttps://developer.genesys.cloud/api/rest/v2/notifications/notification_servicefor background.The library provides:channel connection & topic subscriptionsasync iterator for notificationsautomatic channel reconnect on failurehelpful custom exceptions whenever recovery is not possibleautomatic channel lifetime extension or rollover when expiring or closing for maintenance [^1]The scope of the library is intentionally limited to making single notifications channel management more convenient by encapsulating the above features.It doesnot:refresh the access tokenmanage multiple channels[^2].process received topic notifications[^3]account for the max 20 channels limitaccount for the 1000 topics per channel subscription limitaccount for the one connection per channel limitUsage:First create the Genesys channel as instructed by the Genesys docs. Then:Import and instantiate a Channel, passing in URI and topics.Await the channel to connect and subscribe.Iterate over the result to receive notifications.Example:>>>uri="wss://streaming.mypurecloud.com/channels/streaming-0-fmtdmf8cdis7jh14udg5p89t6z">>>topics=["v2.analytics.queues.tdmf8cd-k3h43h-udg5p89.observations"]>>>fromgenesys_notificationsimportChannel>>>fromgenesys_notifications.exceptionsimportInitializationFailure,RecoveryFailure>>>asyncdeftest(uri,topics):...try:...notifications=awaitChannel(uri,topics)...exceptInitializationFailure:...# Handle websocket connection opening and topic subscription failures;...# ConnectionFailure and SubscriptionFailure can be caught separately as well....try:...asyncforninnotifications:...exceptRecoveryFailure:...# Handle cases when the channel is not able to automatically recover from issues:...# in case of problems, it will try once to reconnect & resubscibe before giving up, and...# in case of scheduled expiry or ad-hoc Genesys-side close notification, it will try to# extend its lifetime by resubscribing to topics....else:...print(n)>>>>>>importasyncio>>>asyncio.run(test(uri,topics)){"topicName":"channel.metadata","eventBody":{"message":"WebSocket Heartbeat"}}See theexceptionsmodule for all the available exceptions. The reason for exception is always available in itsreasonattribute. Seeexceptions.REASONenum for possible reasons.[^1]: Instantiate the Channel withextend=Falseto disable automatic lifetime extension & handle it manually by catchingChannelExpiring[^2]: Except whenchannel.rollover(uri)is called; under the hood, a new websocket connection is then initialized and transparently replaces the original
[^3]: Except for the bare minimum required to support the provided features; subscription confirmations, channel close notifications etc.
Package: genetables
genetables - Genome table and sequencing data processorsSee alsohttps://github.com/setempler/genetables.py—Copyright (C) 2016 - Sven E. Templer <sven.templer@gmail.com>Permission is hereby granted, free of charge, to any person obtaining a copy of this
software and associated documentation files (the “Software”), to deal in the Software
without restriction, including without limitation the rights to use, copy, modify,
merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to the following
conditions:The above copyright notice and this permission notice shall be included in all copies or
substantial portions of the Software.THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT
OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.
Package: gene-thesaurus
GeneThesaurus v2.0.0GeneThesaurus is a Python package that translates between different gene standards using publicly available data fromHGNC.Presently, GeneThesaurus supports translating:gene aliases and old gene symbols to the current HGNC standard gene symbolsgene symbols to ensembl identifiersPlease get in touch (or consider submitting a pull request to this project) if you need translation between other formats.InstallationYou can install GeneThesaurus with:pip install gene-thesaurusExample usagefrom gene_thesaurus import GeneThesaurus
gt = GeneThesaurus(data_dir='/tmp')

outdated_gene = 'TNFSF2'
up_to_date_gene = 'ETV6'
fake_gene = 'NOTAREALGENE'
input = [outdated_gene, up_to_date_gene, fake_gene]

#############################
### update_gene_symbols() ###
#############################

updated_genes = gt.update_gene_symbols(input)
print(updated_genes)
# {'TNFSF2': 'TNF'}

#########################
### translate_genes() ###
#########################

translated_genes = gt.translate_genes(input, source='symbol', target='ensembl_id')
print(translated_genes)
{'TNFSF2': 'ENSG00000232810', 'ETV6': 'ENSG00000139083'}