Saravanan666/pypi-org huggingface dataset:
Package: codingame
Pythonic wrapper for the undocumentedCodinGameAPI.InstallationPython 3.8 or higher is required.Installcodingamewith pip:pipinstallcodingameQuickstartCreate an application, inexample.py:importcodingameclient=codingame.Client()# get a codingamercodingamer=client.get_codingamer("username")print(codingamer.pseudo)# get the global leaderboardglobal_leaderboard=client.get_global_leaderboard()# print the pseudo of the top codingamerprint(global_leaderboard.users[0].pseudo)Seethe docs.ContributeSource CodeIssue TrackerSupportIf you are having issues, please let me know by joining the discord support server athttps://discord.gg/8HgtN6ELicenseThe project is licensed under the MIT license.LinksPyPiDocumentationDiscord support serverDisclaimerThis extension was developed as a proof of concept and as an exploratory project.
CodinGame is not responsible for any content or security issues that may arise
due to this module, if you do find any, feel free to open an issue or a pull request.
Package: coding-assistant
Coding Assistant 📎Recreate the joys of Office Assistant from the comfort of the Python interpreter.How to use?>>>importcoding_assistant>>># nothing more is needed>>>3/0Traceback(mostrecentcalllast):File"<stdin>",line1,in<module>ZeroDivisionError:divisionbyzero\_______________________________/_-_|//_\|/(o)(o)||||\//\|¯--¯>>>You can also invoke coding assistant as a python wrapper so that
even errors happening in the compile phase (ie bad imports and the likes)
will be handeled by coding assistant.$coding-assistantbad_import.py
Traceback(mostrecentcalllast):File"~/.local/bin/coding-assistant",line8,in<module>sys.exit(cli())File"~/.local/lib/python3.9/site-packages/coding_assistant/cli.py",line23,incliexec(f.read(),{File"<string>",line1,in<module>
ModuleNotFoundError:Nomodulenamed'nonexistant_module'\_______________________________________________________/_-_|/
/_\|/(o)(o)||||\//\|¯--¯
$How to install?python3-mpipinstallcoding-assistantQ&AIs it possible to have other, maybe custom, assistants?Not at the moment but if you can draw ascii art please submit a PR.Will this package breaktryexceptblocks?No it only changes the way exceptions are printed not the actual exception.Is this code "production ready"?Don't.Will you get sued by Microsoft?Hopefully my ascii art is ugly enough that I can claim it's an original character.
Package: codinghyde.ant
Introduction==========Python implementation of the ANT, ANT+, and ANT-FS protocols. For moreinformation about ANT, see http://www.thisisant.com/.Can be used to communicate with ANT nodes using an ANT stick (USB).This project came to be when I tried to download data for analysis from myANT+/ANT-FS enabled running watch under GNU/Linux. This eventually lead me toattempting to port ANT_LIB and ANT_DLL (by Dynastream) to Linux. However, Ididn't quite like the library, the protocol is well documented and trivial toimplement, and I was going to have to write a ctypes-based wrapper afterwardssince I was only going to use the library from Python. Thus, I decided towrite a pure Python implementation.Contact==========You can reach me via e-Mail at:ehyde at codinghyde comDocumentation==========Documentation will be a bit scarse for the time being, but everything publicshould have at least a docstring by the time I make the first stable release.License==========Released under the MIT/X11 license. See LICENSE for the full text.Install==========% python setup.py installDevelop==========See DEVELOP for details.
Package: codinghyde.enigma
Introduction==========Workout data statitistical analysis thingy. Sort of.This project came to be when I tried to download data from my ANT+ runningwatch on GNU/Linux. As it turns out there is no open source GNU/Linux softwarethat will let me schedule workouts on my Garmin Forerunner that I can alsoaccess programmatically and do some simple statistical analysis with. My onlineservice of choice (Garmin Connect) now uses Bing instead of Google Maps, whichreally doesn't work for me as Bing doesn't really have high quality satelliteimages of the region of the world I'm in at the moment (which is quite bad whenyou want to see your path on mountain trails that are evidently not in streetmaps).I chose the codename Enigma because, quite frankly, I don't know what thisproject will evolve into. I just know more or less I want a Training Centermeets Garmin Connect meets SportTrack meets *nix, meets calorie counter, meetsweight log, meets training journal, meets Python.The project will be divided in several sub-projects:* codinghyde.enigma: Server, general API, simple interactive CLI-based client,workout data importers/exporters, data store access, etc.* codinghyde.griffin: GUI client (desktop) for codinghyde.enigma. Prettygraphs, data caching, etc. It basically uses the enigma core and server toprovide a full-featured application. Also handles data import in a moreintuitive manner than codinghyde.enigma.cli does.* codinghyde.[unnamed]: Web client for codinghyde.enigma. Minimalfunctionality compared to codinghyde.griffin, but enough to be useful whileaway from the computer (say, checking a route, basic stats, etc).Contact==========You can reach me via e-Mail at:ehyde at codinghyde comDocumentation==========Documentation will be a bit scarse for the time being, but everything publicshould have at least a docstring by the time I make the first stable release.License==========Released under the MIT/X11 license. See LICENSE for the full text.Install==========% python setup.py installDevelop==========See DEVELOP for details.
Package: codinghyde.synapse
Introduction==========Flexible protocol schema for message-passing distributed systems.As part of a fairly large distributed system, I needed a way to format messagesI would be sending through an AMQP bus with the following requirements:* Client support for at least PHP, Python, Java, and Erlang.* Small and reasonably fast (meaning, no XML).* Message versioning (add/remove/rename fields) with seamless fallback (olderclient can ignore new fields).* Easily installable (from the cheeseshop, for instance).* Allows me to write a schema, and checks messages to be valid both whensending and receiving.* Messages are tagged with their type (so I can decode a message into anobject/struct without knowing what type the message should be).* If possible, field names should be sent in the message so that even if Idon't have the schema, messages can be processed (say, from an unsupportedlanguage).* Should handle binary data without exagerated overhead (think base64 encodingin JSON messages).* Well documented and actively developed.I looked into projects such as Google's Protocol Buffers, Apache's Thrift andAvro, MessagePack-RPC, ZeroC's Ice, and probably some others but I could notfind a system that had most/all my requirements, so I decided to write my own.In a nutshell, codinghyde.synapse is/has:* An IDL to describe message formatting.* A compiler/code-generator to produce easy-to-work-with code.* A generic message encoder/decoder framework targetting JSON, BSON, MsgPack,and YAML (after all, why invent yet another serialization format...).* Designed so that messages are processable without language support (decodethe raw JSON message and it's contents should require little/no postprocessing to be useful).Contact==========You can reach me via e-Mail at:ehyde at codinghyde comDocumentation==========Documentation will be a bit scarse for the time being, but everything publicshould have at least a docstring by the time I make the first stable release.License==========Released under the MIT/X11 license. See LICENSE for the full text.Install==========% python setup.py installDevelop==========See DEVELOP for details.
Package: codingsoho-auth
codingsoho-authcodingsoho-authwrapper project is auth wrapper for authenticationDetailed documentation is in the "docs" directory.Quick startInstall 'authwrapper' and 'django-phone-login', checking django-phone-login readme for configurationAdd "authwrapper" to your INSTALLED_APPS setting like this::INSTALLED_APPS=[...'authwrapper','phone_login',]3  Add configurationsAUTH_USER_MODEL='authwrapper.MyUser'ACCOUNT_ALLOW_MIX_TYPE_LOGIN=TrueUUSLUGIFY=TrueAUTHENTICATION_BACKENDS=('authwrapper.backends.auth.MyBackend','authwrapper.backends.auth.WechatBackend',# if support wechat'django.contrib.auth.backends.ModelBackend',)# if support wechatAPP_SECRET=APP_ID=ACCOUNT_REGISTER_TYPE='phone'# or 'email'Include the polls URLconf in your project urls.py like this::url(r'^authwrapper/',include('authwrapper.urls')),Runpython manage.py migrateto create the authwrapper models.Start the development server and visithttp://127.0.0.1:8000/admin/to create a models if needed (you'll need the Admin app enabled).Visithttp://127.0.0.1:8000/authwrapper/to participate in the auth.
Package: codingsoho-pagination
=====codingsoho-pagination=====codingsoho-pagination is based on 'django-pagination 1.0.7' which source code stop updating now, The update in this version only for adaptionDetailed documentation is in the "docs" directory.Quick start-----------1. Add "pagination" to your INSTALLED_APPS setting like this::INSTALLED_APPS = [...'pagination',]2. Install the pagination middleware. Your settings file might look something like:``` pythonMIDDLEWARE_CLASSES = (# ...'pagination.middleware.PaginationMiddleware',)```3. If it’s not already added in your setup, add the request context processor. Note that context processors are set by default implicitly, so to set them explicitly, you need to copy and paste this code into your under the value TEMPLATE_CONTEXT_PROCESSORS:``` python("django.core.context_processors.auth","django.core.context_processors.debug","django.core.context_processors.i18n","django.core.context_processors.media","django.core.context_processors.request")```4. Add this line at the top of your template to load the pagination tags:``` python{% load pagination_tags %}```5. Decide on a variable that you would like to paginate, and use the autopaginate tag on that variable before iterating over it. This could take one of two forms (using the canonical object_list as an example variable):``` python{% autopaginate object_list %}```This assumes that you would like to have the default 20 results per page. If you would like to specify your own amount of results per page, you can specify that like so:``` python{% autopaginate object_list 10 %}```Note that this replaces object_list with the list for the current page, so you can iterate over the object_list like you normally would.Now you want to display the current page and the available pages, so somewhere after having used autopaginate, use the paginate inclusion tag:``` python{% paginate %}```This does not take any arguments, but does assume that you have already called autopaginate, so make sure to do so first.That’s it! You have now paginated object_list and given users of the site a way to navigate between the different pages–all without touching your views.
Package: codingtrackerserver
codingTrackerServerThis is the server for the codingTracker app.DescriptionUsing a REST api, it save in a sqlite3.0 db the time spend coding in
language that are tracked by codingTracker app.Getting StartedDependenciespoetry
aiohttp
pyyamlInstallingpoetry installExecuting programRun the server:
poetry shell
python3 ./codingTrackerServer/server.pyAuthorsContributors names and contact infoEmmanuel Guefifeguefif@fastmail.comLicenseThis project is licensed under the MIT License - see the LICENSE.md file for detailsVersion0.1.1
Package: codino
codinoCalculating amino acid frequencies from codon design, and vice versaInstallationpipinstallcodinoUsagefromcodino.processimportConverterc=Converter()# converting from codon design to AA frequenciesc.cd_to_aa(first={"A":1},second={"T":1},third={"G":1})# Out: {'M': 1}# converting from AA frequency to codon designc.aa_to_cd(aa={'M':1})# Out: ({'A': 1.0}, {'T': 1.0}, {'G': 1.0})ContributingInterested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.Licensecodinowas created by David Zhang. It is licensed under the terms of the MIT license.Creditscodinowas created withcookiecutterand thepy-pkgs-cookiecuttertemplate.
Package: codoc-python
CODOC Python SDKThis is the SDK forCodoc, that makes it possible to
upload architectural views of your python codebase directly to theCodocinterface.What is Codoc?Codoc is the first Continuous Documentation tool.
It provides a revolutionary graph based interface,
that gives a powerful overview of any software system.
We are currently looking forbeta testersSupported VersionWe support python 3.6<DocumentationUsage documentation can be found here:https://codoc-python.readthedocs.io/en/latest/
Package: codon-bias
codon-biasThis package provides codon usage bias (CUB) analysis tools for genomic sequences, focusing on protein coding regions, translation efficiency and synonymous mutations. These include implementations of popular models from the past four decades of codon usage study, such as:Nucleotide and codon k-mer statistics (GC, GC3, CpG, etc.)Frequency of Optimal Codons (FOP)Relative Synonymous Codon Usage (RSCU)Codon Adaptation Index (CAI), including extensions:Codon pair (and k-mers) adaptationEffective Number of Codons (ENC), including extensions:Background correctionImproved estimationEffective number of codon pairs (and k-mers) (ENcp)tRNA Adaptation Index (tAI)Codon Pair Bias (CPB/CPS)Relative Codon Bias Score (RCBS)Normalized Translational Efficiency (nTE)Directional Codon Bias Score (DCBS)Codon Usage Frequency Similarity (CUFS)This package also includes tools for sequence optimization based on these codon usage models, and generators of random sequence permutations that can be used to compute empirical p-values and z-scores.installationpip install codon-biasdocumentationRead onRead the Docs.contributingContributions of additional models to the package are welcome! Please familiarize yourself with the existing classes, and try to conform to their style.
Package: codon-degeneracy
codon-degeneracyThis python package provides routines for the extraction ofdegenerate sitesfrom sequences and alignments. The latter is particularly useful for estimations of rates of neutral evolution.DependenciesThis code usesbiopythonandscikit-biointernally. In order to installl via pip,numpyhas to be installed.InstallingSimply clone this repo:git clone https://github.com/nickmachnik/codon-degeneracy.git [TARGET DIR]and then install  via pippip install [TARGET DIR]or install directly from PyPI (this won't include unreleased changes as specified in thechangelog):pip install codon-degeneracyTestingTest the cloned package:cd [TARGET DIR]
python -m unittestUsageThere are more useful and well documented functions under the hood than shown here, which I enourage to explore by browsing the code.Counting substitutions per four fold degenerate siteOne of the main features of the package is the counting of neutral substitutions at four fold degenerate sites.
This is best done with known orthologue pairs between species.substitution_rate_at_ffdsprovides that functionality and is easy to use like so:fromcodon_degeneracyimportsubstitution_rate_at_ffdsasnsrseq_a=("ATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTC""TAATCGCAATGGCATTCCTAATGCTTACCGAACGA")seq_b=("ATGACCACAGTAAATCTCCTACTTATAATCATACCCACAT""TAGCCGCCATAGCATTTCTCACACTCGTTGAACGA")(number_of_substitutions,number_of_sites),(orf_a,orf_b)=nsr(# the input sequencesseq_a,seq_b,# NCBI codon table names as used in Bio.Data.CodonTable"Vertebrate Mitochondrial","Vertebrate Mitochondrial")The ORFs returned are there for sanity checks. The default behaviour is to select the first ATG codon
as start.NOTE: The numbers of neutral substitutions per site reported by this function are merely a lower bound,
as they do not include the possibility of multiple substitutions per site.Substitutions at four fold degenerate sites separated by CpG contextIn certain situations, it may be useful to differentiate between four fold degenerate sites
that could potentially exist in a CpG context and could therefore exhibit an elevated
mutation rate and those that do not.substitutions_per_ffds_by_cpg_contextprovides that
functionality.
It differentiates between four CpG contexts. Sites that are:
- preceded by C and not followed by G (nonCpG)
- preceded by C but not followed by G (postC)
- followed by G but not preceded by C (preG)
- preceded by C and followed by G (postCpreG)Note: the number of sites considered here may be substantially lower than
insubstitutions_per_ffds, as this function requires the sites
preceeding and following site of a four fold degenerate site
to be identical in the two aligned sequences.The function can be used in exactly the same that is shown forsubstitutions_per_ffdsabove.LicenseMIT license (LICENSEorhttps://opensource.org/licenses/MIT)
Package: codon-harmony
Codon HarmonyAmino acid reverse translation and DNA optimization tool based on species-specific codon-use distributions.
Species-specifc data can be found on theCodon Usage Databaseusing theNCBI Taxonomy databaseid (e.g. 413997) or the organism’s Latin name (e.g.Escherichia coliB). Mapping species names to Taxonomy IDs can be donehere.Documentation:https://codon-harmony.readthedocs.ioFeaturesReverse translates input amino acid sequence to DNA.Calculates the host’s per-AA codon usage profile – codons used less than a specified threshold (defaults to 10%) are dropped.Compares the reverse-translated DNA sequence to the host profile, determines which codons are overused/underused.Stochastically mutates codons according to host profile.Ranks sequences by codon adaptation index relative to hostProcesses DNA to remove unwanted features:high GC content within a sliding window and across the entire sequenceunwanted restriction sitesalternate start positions (GA-rich regions 18 bp upstream of ATG/GTG/TTG)3-consecutive identical codons and 9-mer repeat chunksareas with more than 4 (variable) consecutive identical bps (“local homopolymers”)RNA hairpins, detected by looking for 10-mers with reverse complements (including wobble bases) in the sequenceRNA splice sites, detected by similarity to consensus donor and acceptor site sequencesThe process is repeated from step 3 for a specified number of cycles (defaults to 1000) OR until the per-AA codon profile of current DNA and host profile matches (within tolerance).Future workMore advanced RNA-structure removalCONTRAfold– overkill for nownupack– overkill for nowHistory0.9.2 (2019-02-06)First release on PyPI.0.9.4 (2019-02-20)Full suite of tests added, bugs uncovered and fixedAdjustments to the packaging setup – actaully installable now0.9.5 (2019-02-25)Adding support for RNA splice site detection and removal0.9.6 (2019-02-28)Updating the way optimization failures are reported and displayedParallelizing via a process pool1.0.0 (2019-03-06)Added ability to use offline tables in addition to fetching from the internetFull suite of tests and documentationTested on real-world sequences to
Package: codonpair
codonpaircodonpaircalculates codon pair score and codon pair bias. CPS
values are identical to those produced by the perl script from
Dimitris Papamichail (cps_perldirectory) and, presumably,
used in the following work:Virus attenuation by genome-scale changes in codon pair bias.
Coleman JR1, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S.
Science. 2008 Jun 27;320(5884):1784-7. doi: 10.1126/science.1155761.
https://www.ncbi.nlm.nih.gov/pubmed/18583614InstallationEither, clone the repo and install with pipgitclonegit@github.com:smsaladi/codonpair.git
pipinstall./codonpairOr... have pip handle the details:pipinstallgit+git://github.com/smsaladi/codonpair@master#codonpairAll dependencies should be checked for and, if necessary, installed
automatically bypip.UsageInitialize acodonpair.CodonPairobject by specifying a list of reference sequencesCodonPair.from_sequences, from a named referenceCodonPair.from_named_reference,
a reference fileCodonPair.from_reference_file,
or simply providing apd.DataFramewith codon counts toCodonPair.The following named references are recognized/bundled with this package.E. coli(BL21 DE3)S. pneumoniae(TIGR4)cps_perl-  the reference file provided with the perl implementationThe default constructorCodonPair()uses theE. coli.Then calculate the codon pair score for a provided sequence withCodonPair.cpbwhich returns a dictionary with thetotal codon pair scoretotal_cps- the sum of the values of each codon pairthe number of codonsn_pair- excluding codon pairs not found in the referencethe codon pair biascpb-total_cps/n_pairFor one-off calculations,codonpair.calc_cpbcan be used directly
for with the sequence of interest (calling the default constructor under the hood).importcodonpaircp=codonpair.CodonPair.from_named_reference('E. coli')cp.cpb("ATGATCCCCTTACAACATGGACTGATCCTCGCGGCAATCTTATTCGTTCTTGGCTTAACC")For convenience, the executablecpsinstalled into the path by pip:cpstest.fasta>test.scores.txtSeeCodonPair.write_referenceto write codon pair counts for a reference set to
the filename provided to be used with future calculations.
Package: codpydll
PurposesThis library is a tool for thecodpyproject.InstallationNote: this installation process has been tested onwindows / amd64 platformprerequisiteMinimum installationpython3.9.7: a valid python python3.9.7 installation.NOTE: Python installation differs from one machine to another. The python root folder is denoted "<path/to/python39>" in the rest of this document. The software Everything (or another equivalent) can be of great help finding files.InstallationprerequisiteWe suppose that there is a valid python installation on the host machine. The reader caneither use its main python environment<path/to/python39>or create a virtual python environment<path/to/venv>, a good practice that we describe in the rest of this section.First open a command shellcmd,  create a virtual environment and activate it.python -m venv .\venv
.\venv\Scripts\activateNOTE: In the rest of the installation procedure, we consider a virtual environment <path/to/venv>. One can replace with <path/to/python39> if a main environment installation is desired, for dev purposes for instance.pip install codpydllOpen a command shellcmd, and pip install codpypip install codpydllThe installation procedure might take some minutes depending on your internet connection.Test codpydllopen a python shell and import codpydllpythonimport codpydll
Package: codustry
TitleThe Ultimate Purpose of CodustryAuthorNutchanon NinyaweeStatusDraftTypeNoneCreated24 Nov 2019CEP -1 -- The Ultimate Purpose of Codustry (cep negative one)we code & maintain millennium projects.Codustry's Corporate Mission Statement:
"To Question, Strike and Maintain Digital World's Balances. We engineer our products, services, and infrastructures in a circular, dynamic, millennium-long fashion."Codustry's Corporate Vision Statement:
"To be Earth's most humane company, where stakeholders wish to do business with us for 1000+ years."