Saravanan666/pypi-org huggingface dataset:
Package: cdifflib
cdifflibPythondifflibsequence
matcher reimplemented in C.Actually only contains reimplemented parts.  Creates aCSequenceMatchertype
which inherets most functions fromdifflib.SequenceMatcher.cdifflibis about 4x the speed of the pure pythondifflibwhen diffing
large streams.LimitationsThe C part of the code can only work onlistrather than generic iterables,
so anything that isn't alistwill be converted tolistin theCSequenceMatcherconstructor.  This may cause undesirable behavior if you're
not expecting it.Works with Python 2.7 and 3.6 (Should work on all 3.3+)UsageCan be used just like thedifflib.SequenceMatcheras long as you pass lists.  These examples are right out of thedifflib docs:>>>fromcdifflibimportCSequenceMatcher>>>s=CSequenceMatcher(None,' abcd','abcd abcd')>>>s.find_longest_match(0,5,0,9)Match(a=1,b=0,size=4)>>>s=CSequenceMatcher(lambdax:x==" ",..."private Thread currentThread;",..."private volatile Thread currentThread;")>>>printround(s.ratio(),3)0.866It's completely compatible, so you can replace the difflib version on startup
and then other libraries will use CSequenceMatcher too, eg:fromcdifflibimportCSequenceMatcherimportdifflibdifflib.SequenceMatcher=CSequenceMatcherimportlibrary_that_uses_difflib# Now the library will transparantely be using the C SequenceMatcher - other# things remain the samelibrary_that_uses_difflib.do_some_diffing()MakingTo install:python setup.py installTo test:python setup.py testLicense etcThis code lives athttps://github.com/mduggan.  See LICENSE for the license.Changelog1.2.6 - Clear state correctly when replacing seq1 (#10)1.2.5 - Fix some memory leaks (#7)1.2.4 - Repackage yet again using twine for pypi upload (no binary changes)1.2.3 - Repackage again with changelog update and corrected src package (no binary changes)1.2.2 - Repackage to add README.md in a way pypi supports (no binary changes)1.2.1 - Fix bug for longer sequences with "autojunk"1.2.0 - Python 3 support for other versions1.1.0 - Added Python 3.6 support (thanks Bclavie)1.0.4 - Changes to make it compile on MSVC++ compiler, no change for other platforms1.0.2 - Bugfix - also replace set_seq1 implementation sodifflib.compareworks with aCSequenceMatcher1.0.1 - Implement more bits in c to squeeze a bit more speed out1.0.0 - First release
Package: cdifflint
cdifflintTerm based tool to viewcolored,incrementaldiff in aGit/Mercurial/Svnworkspace or from stdin, side by side with affected linting errors. Requires
python (>= 2.7.0) andless.InstallationInstall with pipCdifflint is already listed onPyPI, you can install withpipif
you have the tool.pipinstall--upgradecdifflintInstall with setup.pyYou can also run the setup.py from the source if you don’t havepip.gitclonehttps://github.com/rgeoghegan/cdifflint.gitcdcdifflint./setup.pyinstallUsageTypecdifflint-hto show usage:$ cdifflint -h
usage: cdifflint [-h] [-s] [-w N] [-l] [-c M] [-t {pep8,jslint,pyflakes}]

View colored, incremental diff in a workspace, annotated with messages from
your favorite linter.

optional arguments:
  -h, --help            show this help message and exit
  -s, --side-by-side    enable side-by-side mode
  -w N, --width N       set text width for side-by-side mode, 0 for auto
                        detection, default is 80
  -l, --log             show log with changes from revision control
  -c M, --color M       colorize mode 'auto' (default), 'always', or 'never'
  -t {pep8,jslint,pyflakes}, --lint {pep8,jslint,pyflakes}
                        run the given linters and show the lint messages in
                        the diff. Currently supports pep8, jslint, pyflakes.
                        (Can be specified multiple times)

Note: Option parser will stop on first unknown option and pass them down to
underneath revision controlSee alsoThe original code I cribbed from heavily is thecdifftool, which does most
of the heavy lifting.Change logVersion 1.0.0 (2016-12-14)Working offcdiff version 0.9.8, can now show diffs, and also list
any linter output within the diff.Version 1.0.1 (2016-12-24)Fixing distributed package so it actually installs
Package: cdippy
CDIPpyCDIPpy handles access to CDIP NetCDF data files.Free software: BSD licenseDocumentation:https://cdippy.readthedocs.io.FeaturesTODOCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.1.0 (2018-10-14)First release on PyPI.
Package: cdips
cdipsCluster Difference Imaging Photometric SurveyDescriptionThis repository contains some of the code developed for theCDIPS
project.  If you are interested in light
curves, they can be accessedthrough
MAST; planet-finding vetting reports are
available atExoFOP-TESSand have
documentationavailable here.The tools in this repo can be understood as answers to the question "what do
you do once thecdips-pipelinegives you light curves?".Some possible answers include "find planets", "measure stellar rotation
periods", and "find weird variable stars".  This question is also in many cases
applicable to any time-series data, and some of the tools in this repository
are developed with that generality in mind.Directory contents are as follows./drivers/is the interface to make target catalogs, find planet candidates
and variable stars, classify, vet the classifications, and make plots and
tables for papers.  See /drivers/HOWTO.md for instructions./cdips/is a python package with tools to make target catalogs, process
light curves, optimize cdips-pipeline parameters, plot and analyze light
curves./paper_I/contains the CDIPS method paper./tests/has testing scripts for vetting report generation, HLSP light curve
generation, and detrending method comparison.  pytest & CI are not set up for
this repo.AuthorLuke BoumaLicenseMITInstallpip install cdipsgit clone https://github.com/lgbouma/cdipspython setup.py installto verify you have the dependencies (with apologies for not making this
automatic in the installation; some of the dependencies are fairly obscure)cd cdips/testspython test_environment.pyOne place to start if you are building an environment from scratch:conda env create -f environment.yml -n py38Update envconda env export --no-builds > environment.ymlRelevant readingCDIPS-I: MethodsCDIPS-II: TOI-837bCDIPS-III: NGC-2516
Package: cdir
CDIRThis project exists because I felt that typing multiplecd,dir/lscommands and striking the tab-key is not very fast or pleasant way to navigate in shell. As developers often need to work in multiple environments, cdir supports bash shell, Windows Command Prompt and PowerShell. The core component of the project is implemented with python and uses curses module. Windows version useswindows-cursesmodule.FeaturesUse arrow keys and enter to browse files.Modern and easy-to-use search functionality for folders: just start typing the name of the folder and folders are filtered by their name.Supports bash shell, Windows Command Prompt and PowerShell.Easy to install.Usage - BashInstall withpip install cdirAdd following line to .bashrc:aliascdir='source cdir.sh'Type cdir and start browsing files and folders.Press f1 to quit cdir.Usage - Windows Command PromptInstall withpip install cdirType cdir and start browsing files and folders.Press f1 to quit cdir.ContributionAlthough there are no formal quidelines for contribution yet, it is warmly welcomed! Please use issues to discuss about changes/features you would like to make before implementing them.
Package: cdisc-library-client
cdisc-library-clientPython client for accessing the CDISC library. Deployed to PYPIoperationsget_sdtm - get an sdtm standard
get_adam - get an adam or adamig standard
get_cdash - get a cdash standard
get_sdtmig - gets sdtmig standard
get_sendig - gets sendig standard
get_cdashig - gets cdashig standard

get_terminology_package - get a ct package given the version
get_codelist_terms - returns an array of all terms in a codelist
get_codelist_term - returns the library representation of a codelist term

get_rule_catalogs - returns a list of links to all rule catalogs in the CDISC Library
get_rules_catalog - returns all rules in a single rules catalog.
get_rule - gets a rule definition given standard, version, and rule id

get_bc_packages - get biomedical concept package list
get_bc_package_biomedicalconcepts - get biomedical concept list in a package 
get_bc_package_biomedicalconcept - get biomedical concept in a package
get_bc_latest_biomedicalconcepts - get biomedical concept list (latest versions)
get_bc_latest_biomedicalconcept - get biomedical concept (latest version)
get_bc_categories - get biomedical concept categories list
get_bc_latest_biomedicalconcepts_category - get biomedical concepts for a given category (latest version)

get_sdtm_packages - get sdtm dataset specialization package list
get_sdtm_package_datasetspecializations - get sdtm dataset specialization list in a package
get_sdtm_package_datasetspecialization - get sdtm dataset specialization in a package
get_sdtm_latest_sdtm_datasetspecializations - get sdtm dataset specialization list (latest versions)
get_sdtm_latest_sdtm_datasetspecialization - get sdtm dataset specialization (latest version)
get_sdtm_domains - get sdtm dataset specialization domain list
get_sdtm_latest_sdtm_datasetspecializations_domain - get a list of sdtm dataset specializations for a given domain (latest version)

get_biomedicalconcept_latest_datasetspecializations - get a list of dataset specializations that specialize a biomedical concept (latest versions)More info on CDISC Library API endpoints can be found at theCDISC Library API Portal.
Package: cdiversity
Cdiversity: Quantifying B-Cell Clonal Diversity In Repertoire DataAdvances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell receptor sequencing data. Still, the accurate identification of clonally related BCR sequences remains a difficult challenge. Importantly, different methods may lead to different clonal definitions, which in turn can affect the quantification of clonal diversity in repertoire data [1]. This library provide different tools and metrics to (i) group B-cell repertoires into clonal groups and (ii) compute diversity indices and diversity profiles from the obtained groups.Running the analysisFirst, you need to install cdiversity, or alternatively you can use thecdiversity.pyfile provided in the repository:- pip install cdiversityThen, you can run a repertoire analysis simulation with the toy example below. For a more complete overview, you can check outExamples/Analyze_sample.py.
Briefly, the analysis start by grouping Bcell into clones, and then use the obtained groups to compute various diversity metrics.(I) Grouping repertoire into clonesAvailable methods for clonal identification arejunction, which simply group clones together only if they have the same junction. Then, there is the commonly usedVJ-junctionmethods, which group together BCR with the same V and J genes, as well as some user-specificed junction similarity (clone_threshold). Finally, the last method isalignfree, which compute tf-idf embedings of the BCRs to perform a fast clustering without relying on the V and J germline genes alignements.import pandas as pd
import cdiversity

df = pd.read_csv('Data/sample.csv', sep='\t') 
clones_baseline, _ = cdiversity.identify_clonal_group(df, method='junction')
clone_VJJ, _ = cdiversity.identify_clonal_group(df, method='VJJ', clone_threshold = 0.1)(II) Computing diversity indicesOnce the clonal groups are obtained, you can compute any diversity indices or the Hill's diversity profile with a single command.
Implemented indices are richness, richness_chao, Shannon_entropy, Shannon_entropy_chao, Simpson_index, dominance, eveness.from collections import Counter

	clone_dict = Counter(clone_VJJ)
	diversity = cdiversity.Shannon_entropy_Chao(clone_dict)
	div_profile, alpha_axis = cdiversity.diversity_profile(clone_dict)References[1] Pelissier, A, Luo, S, et al. "Quantifying B Cell Clonal Diversity In Repertoire Data".Submitted to Frontier in immunology(2022)[Preprint]
Package: cdjs
CDJS (Custom Datetime JSON Serializer)cdjsis an extension fororjsonto serialize datetime (and other types) in a fast custom way.By defaultorjsonserializes datetime according to RFC 3339 format which sometimes may not suit.orjsonprovides a mean to process datetime using custom serializer (viaOPT_PASSTHROUGH_DATETIMEflag and viadefault=custom_datetime_serializer).
Serializers implemented in Python are usually not fast enough, that's the reason behind implementation of the custom datetime serializer written in Rust to gain optimal speed.Aside from datetimes,cdjsis an attempt to portbson.json_util.default()and to use withorjsonas a default handler.At the moment serialization of the following types are supported:datetimebson.ObjectIdExampleimport datetime
import hashlib

from bson import ObjectId
from cdjs import serialize
import orjson

mydata = {
    '_id': ObjectId(hashlib.md5(b'test').hexdigest()[:24]),
    'date': datetime.datetime(2021, 1, 1, hour=0, minute=4, second=36, microsecond=123000)
}
orjson.dumps(mydata, option=orjson.OPT_PASSTHROUGH_DATETIME, default=serialize)

# b'{"_id":{"$oid":"098f6bcd4621d373cade4e83"},"date":{"$date":"2021-01-01T00:04:36.123Z"}}'BenchmarksTo run benchmark:pip install -r bench-requirements.txt
python tests/benchmark.py --help
python tests/benchmark.py --scenario utc_datesInstallationpip install cdjsBuildingTo make a develop buildNOTE:Develop build doesn't enable optimizations, hence the result may work slow.python ./setup.py developTo make a release buildPre-requisites# switch to nightly channel
RUSTUP_USE_CURL=1 rustup default nightly-2021-01-31
pip install maturinTo compile, package and publish to PyPImaturin build --no-sdist --release --strip --manylinux off
maturin publishTestingTo run testspython -m unittest -v tests.test_serializationPython/OS Version SupportPython 3.6 (tested)Python 3.7+ (not tested)Linux (with GLib 2.17+)
Package: cdk
Use CDK to write documents inAsciiDocand produce elegant single-file slidedecks as html.Please see the docs athttp://cdk.readthedocs.org/en/latest/Installation & Usagesudo pip install cdk # if you don't have pip try sudo easy_install cdk
cdk --generate=sample.asc # generate a sample presentation
cdk sample.asc  # compile it to html
open sample.html # use a browserContactIn the remote possibility that there exist bugs in this code, please report them to:https://github.com/twitter/cdk/issuesAuthorsSimeon Franklin (@simeonfranklin)LicenseCopyright 2013 Twitter, Inc and other contributorsLicensed under the Apache License, Version 2.0:http://www.apache.org/licenses/LICENSE-2.0
Package: cdk8s
cdk8sCloud Development Kit for Kubernetescdk8sis a software development framework for defining Kubernetes
applications using rich object-oriented APIs. It allows developers to leverage
the full power of software in order to define abstract components called
"constructs" which compose Kubernetes resources or other constructs into
higher-level abstractions.Note:This repository is the "core library" of cdk8s, with logic for synthesizing Kubernetes manifests using theconstructs framework. It is published to NPM ascdk8sand should not be confused with the cdk8s command-line toolcdk8s-cli. For more general information about cdk8s, please seecdk8s.io, or visit the umbrella repository located atcdk8s-team/cdk8s.DocumentationSeecdk8s.io.LicenseThis project is distributed under theApache License, Version 2.0.This module is part of thecdk8s project.
Package: cdk8s-argocd-resources
cdk8s-argocd-resourcesHas the ability to synth ArgoCD Application, and AppProject manifests. See example.Overviewexample# Example automatically generated from non-compiling source. May contain errors.import{Construct}from'constructs';import{App,Chart,ChartProps}from'cdk8s';import*asargofrom'@opencdk8s/cdk8s-argocd-resources';exportclassMyChartextendsChart{constructor(scope:Construct,id:string,props:ChartProps={}){super(scope,id,props);newargo.ArgoCdApplication(this,'DemoApp',{metadata:{name:'demo',namespace:'argocd',},spec:{project:'default',source:{repoURL:'example-git-repo',path:'examplepath',targetRevision:'HEAD',},destination:{server:'https://kubernetes.default.svc'},syncPolicy:{syncOptions:['ApplyOutOfSyncOnly=true']}},});newargo.ArgoCdProject(this,'DemoProject',{metadata:{name:'demo',namespace:'argocd',},spec:{description:'demo project',sourceRepos:['*'],destination:[{namespace:'default',server:'https://kubernetes.default.svc'}]}});//defineresourceshere}}constapp=newApp();newMyChart(app,'asd');app.synth();demo.k8s.yamlapiVersion:argoproj.io/v1alpha1kind:Applicationmetadata:name:demonamespace:argocdspec:destination:server:https://kubernetes.default.svcproject:defaultsource:path:examplepathrepoURL:example-git-repotargetRevision:HEADsyncPolicy:syncOptions:-ApplyOutOfSyncOnly=true---apiVersion:argoproj.io/v1alpha1kind:AppProjectmetadata:name:demonamespace:argocdspec:description:demo projectdestination:-namespace:defaultserver:https://kubernetes.default.svcsourceRepos:-"*"InstallationTypeScriptUseyarnornpmto install.$npminstall@opencdk8s/cdk8s-argocd-resources$yarnadd@opencdk8s/cdk8s-argocd-resourcesPython$pipinstallcdk8s-argocd-resourcesContributionFork (link)Bootstrap the repo:npxprojen# generates package.jsonyarninstall# installs dependenciesDevelopment scripts:CommandDescriptionyarn compileCompiles typescript => javascriptyarn watchWatch & compileyarn testRun unit test & linter through jestyarn test -uUpdate jest snapshotsyarn run packageCreates adistwith packages for all languages.yarn buildCompile + test + packageyarn bumpBump version (with changelog) based on [conventional commits]yarn releaseBump + push tomasterCreate a feature branchCommit your changesRebase your local changes against the master branchCreate a new Pull Request (useconventional commitsfor the title please)LicenceApache License, Version 2.0AuthorHunter-Thompson
Package: cdk8s-argo-rollout
cdk8s-argo-rolloutInstallationTypeScriptUseyarnornpmto install.$npminstall@opencdk8s/cdk8s-argo-rollout$yarnadd@opencdk8s/cdk8s-argo-rolloutPython$pipinstallcdk8s-argo-rolloutContributionFork (link)Bootstrap the repo:yarninstall# installs dependenciesnpxprojenDevelopment scripts:CommandDescriptionyarn compileCompiles typescript => javascriptyarn watchWatch & compileyarn testRun unit test & linter through jestyarn test -uUpdate jest snapshotsyarn run packageCreates adistwith packages for all languages.yarn buildCompile + test + packageyarn bumpBump version (with changelog) based on [conventional commits]yarn releaseBump + push tomasterCreate a feature branchCommit your changesRebase your local changes against the master branchCreate a new Pull Request (useconventional commitsfor the title please)LicenceApache License, Version 2.0AuthorSumit Agarwal
Package: cdk8s-aws-lb-controller-api-object
cdk8s-aws-lb-controller-api-objectAPI Object for AWS Load Balancer Controller, powered by thecdk8s projectandaws-load-balancer-controller🚀Overview# Example automatically generated from non-compiling source. May contain errors.fromconstructsimportConstructfromcdk8simportApp,Chart,ChartPropsfromopencdk8s.cdk8s_aws_lb_controller_api_objectimportAWSLoadBalancerControllerObjectclassMyChart(Chart):def__init__(self,scope,id,*,namespace=None,labels=None):super().__init__(scope,id,namespace=namespace,labels=labels)AWSLoadBalancerControllerObject(self,"example",metadata={"annotations":{"kubernetes.io/ingress.class":"alb"}},spec={"rules":[{"host":"example.com","http":{"paths":[{"path":"/*","backend":{"service_name":"helloworld-svc","service_port":80}}]}}]})app=App()MyChart(app,"example1")app.synth()Examplecdk8s synthmanifest as follows.manifest.k8s.yamlapiVersion:extensions/v1beta1kind:Ingressmetadata:annotations:kubernetes.io/ingress.class:albname:example-c89c1904spec:rules:-host:example.comhttp:paths:-backend:serviceName:helloworld-svcservicePort:80path:/*InstallationTypeScriptUseyarnornpmto install.$npminstall@opencdk8s/cdk8s-aws-lb-controller-api-objects$yarnadd@opencdk8s/cdk8s-aws-lb-controller-api-objectsPython$pipinstallcdk8s-aws-lb-controller-api-objectsContributionFork (link)Bootstrap the repo:yarninstall# installs dependenciesyarnprojenDevelopment scripts:CommandDescriptionyarn compileCompiles typescript => javascriptyarn watchWatch & compileyarn testRun unit test & linter through jestyarn test -uUpdate jest snapshotsyarn run packageCreates adistwith packages for all languages.yarn buildCompile + test + packageyarn bumpBump version (with changelog) based on [conventional commits]yarn releaseBump + push tomasterCreate a feature branchCommit your changesRebase your local changes against the master branchCreate a new Pull Request (useconventional commitsfor the title please)LicenceApache License, Version 2.0AuthorHunter-Thompson
Package: cdk8s-debore
cdk8s-deboreRun your apps on Kubernetes cluster without bored YAMLing, powered by thecdk8s project🚀Overviewcdk8s-deboreis acdk8slibrary which allows you to define your Kubernetes app with just few lines of code.# Example automatically generated without compilation. See https://github.com/aws/jsii/issues/826DeboredApp(self,"webapp",image="your-image:latest",auto_scale=True,ingress=IngressType.NGINX_INGRESS)Then the Kubernetes manifests created bycdk8s synthcommand will have Kubernetes resources such asDeployment,Service,HorizontalPodAutoscaler,Ingress, as follows.manifest.k8s.yamlapiVersion:apps/v1kind:Deploymentmetadata:name:my-app-webapp-deployment-deployment-d67b425cnamespace:defaultspec:selector:matchLabels:app:myappwebapp4BD95A2Atemplate:metadata:labels:app:myappwebapp4BD95A2Aspec:containers:-image:your-image:latestimagePullPolicy:Alwaysname:appports:-containerPort:8080resources:limits:cpu:400mmemory:512Mirequests:cpu:200mmemory:256Mi---apiVersion:autoscaling/v2beta2kind:HorizontalPodAutoscalermetadata:name:my-app-webapp-deployment-hpa-bd8107fdnamespace:defaultspec:maxReplicas:10metrics:-resource:name:cputarget:averageUtilization:85type:Utilizationtype:Resource-resource:name:memorytarget:averageUtilization:75type:Utilizationtype:ResourceminReplicas:1scaleTargetRef:apiVersion:apps/v1kind:Deploymentname:my-app-webapp-deployment-deployment-d67b425c---apiVersion:v1kind:Servicemetadata:name:my-app-webapp-exposable-service-d6a35671namespace:defaultspec:ports:-port:8080targetPort:80selector:app:myappwebapp4BD95A2Atype:ClusterIP---apiVersion:networking.k8s.io/v1beta1kind:Ingressmetadata:annotations:kubernetes.io/ingress.class:nginxnginx.ingress.kubernetes.io/rewrite-target:/name:my-app-webapp-exposable-ingress-c350957fnamespace:defaultspec:rules:-http:paths:-backend:serviceName:my-app-webapp-exposable-service-d6a35671servicePort:80path:/my-app-webapp-deployment-deployment-d67b425cInstallationcdk8ssupports TypeScript and Python at this point, so as cdk8s-debore.We'd recommend to walk through thecdk8s Getting Started guidebefore using this library, if you're very new to cdk8s world.TypeScriptUsenpmoryarnto install.$npminstall-scdk8s-deboreor$yarnaddcdk8s-deborePython$pipinstallcdk8s-deboreContributionFork (https://github.com/toricls/cdk8s-debore/fork)Bootstrap the repo:npxprojen# generates package.json and friendsyarninstall# installs dependenciesDevelopment scripts:CommandDescriptionyarn compileCompiles typescript => javascriptyarn watchWatch & compileyarn testRun unit test & linter through jestyarn test -uUpdate jest snapshotsyarn run packageCreates adistwith packages for all languages.yarn buildCompile + test + packageyarn bumpBump version (with changelog) based onconventional commitsyarn releaseBump + push tomasterCreate a feature branchCommit your changesRebase your local changes against the master branchCreate a new Pull Request (useconventional commitsfor the title please)LicenceApache License, Version 2.0AuthorTori