Saravanan666/pypi-org huggingface dataset:
Package: cfsm-bisimulation
Communicating Finite State Machines Bisimulation with edge assertionsAn algorithm to decide if two Communicating Finite State Machines (CFSM) with edge assertions,
known asAsserted Communicating Finite State Machines(a-CFSM) are bisimilars.
You can read about this CFSM extension in"Design-by-Contract for Flexible Multiparty Session Protocols"Section 4.3 (byLorenzo Gheri,Ivan Lanese,Neil Sayers,Emilio Tuosto, andNobuko Yoshida).What does this package do?This library provides both, a model for creating a-CFSMs and an algorithm for evaluating bisimulation. The main idea behind the algorithm is based on the fact that two automata do not have to coincide in the names of their participants, messages or variables used. Therefore, the algorithm constructs a matching of names as it builds the bisimulation relationship between the evaluated automata (if this is not possible, the automata are not bisimilar).
For example, the following two automata would be bisimilar:InstallationAt first, you will need to installz3andz3-solveras dependencies. You can use pip:pipinstallz3-solvercfsm-bisimulationUsageThe simplest use is to create the two CFSM models that you want to evaluate. We will use thez3models as a way to construct the constraints.fromcfsm_bisimulationimportCommunicatingFiniteStateMachinefromz3importIntcfsm_service=CommunicatingFiniteStateMachine(['Client','Logger'])cfsm_service.add_states('p0','p1')cfsm_service.set_as_initial('p0')cfsm_service.add_transition_between('p0','p1','ClientLogger!log(int x)',Int('x')>0)cfsm_provider=CommunicatingFiniteStateMachine(['Customer','Service'])cfsm_provider.add_states('q0','q1')cfsm_provider.set_as_initial('q0')cfsm_provider.add_transition_between('q0','q1','CustomerService!save(int number)',Int('number')>0)To evaluate these automata, you can simply:relation,matches=cfsm_service.calculate_bisimulation_with(cfsm_provider)The result of therelationis a set of pairs(state, knowledge)which is in fact not the minimal possible relationship. If you want to obtain the minimum possible relationship between the automata, execute using the option:relation,matches=cfsm_service.calculate_bisimulation_with(cfsm_provider,minimize=True)The result ofmatchesis a dictionary with matches forparticipants,messagesandvariables. Each value, in turn, is a dictionary with the matches themselves.relation={(('p0'),('q0')),(('p1',Int('x')>0),(Int('number')>0)),}matches={'participants':{'Client':'Customer','Logger':'Service'},'messages':{'log(int x)':'save(int number)'},'variables':{'number':'x'}}ContributingBug reports and pull requests are welcome on GitHub athttps://github.com/diegosenarruzza/bisimulation.
If you are interested in updating or maintaining this package and need more information, please write to me atdiegosenarruzza@gmail.comso I can explain in detail the idea behind the code.LicenseThe package is available as open source under the terms of theMit License.
Package: cfsp
cFSPThis is thecloudFPGA Support Package (cFSP)for thecloudFPGA project.RequirementsPython 3.6+InstallationYou can installcfspsystem-wide throughpip install cfsp, or user-wide throughpip install -u cfsp.It is advised though to do it in an isolated Python environment, e.g. throughvirtualenv:virtualenv -p /usr/bin/python3.6 cfenv
source cfenv/bin/activate
pip install --upgrade pip
pip install cfspUsagePlease check theonline documentation.Developmentgitclonegit@github.com:cloudFPGA/cFSP.gitcdcFSP
makeenvsourcevenv/bin/activate
<addyourchanges>(donotforgettoincreasethe`version="x.y.z"`in`setup.py`)gitcommit-am"My changes for version x.y.z"gitpush
makedist
makeupload
Package: cfssl
||||Python CFSSL LibraryThis library allows you to interact with a remote CFSSL server using Python.CFSSL is CloudFlare’s open source toolkit for everything TLS/SSL. CFSSL is used by
CloudFlare for their internal Certificate Authority infrastructure and for all of
their TLS certificates.Read more on the CloudFlare blog.View the CFSSL source.InstallationInstall Python requirementspip install-r./requirementsSetupA pre-existing CFSSL server is required to use this library.UsageRead The API DocumentationKnown Issues / Road MapInstallation, setup, usage - in ReadMeAdd type checking in datamodelsCreditsImagesLasLabs:Icon.ContributorsDave Lasley <dave@laslabs.com>Maintainer
Package: cft
Command Line Tool for CodeforcesDescriptionCodeforcescommand line tools based ononline-judge-toolsAutomatically create contest directoryTest your code using sample casesSubmit your codeRequirementspython (version3)online-judge-toolsHow To Install$pip3installcftHow To Use$cftn(contestid)# create contest directory$cftt# test your code using sample cases$cfts(contestid)# submit your code$cfth# show help
Package: cft-analysis
cft-analysisPython package for the analysis of data collected during the Cold Face Test (CFT) study.DescriptionThis package contains various helper functions to work with the dataset (includingtpcpDatasetrepresentations) and to process data. Additionally, it contains different analysis experiments performed with the dataset.Repository StructureThe repository is structured as follows:├──cft_analysis/# cft-analysis Python package└──experiments/# Folder with conducted analysis experiments; each experiment has its own subfolder└──2022_scientific_reports/# Analysis for the 2022 Scientific Reports Paper (see below)├──data/# Processed data and extracted parameters├──notebooks/# Notebooks for data processing, analysis and plotting│├──data_processing/││├──ECG_Processing_Feature_Computation.ipynb# Processing and feature extraction from ECG data││├──Questionnaire_Processing.ipynb# Processing of questionnaire data││└──Saliva_Processing.ipynb# Processing of saliva data│├──analysis/││├──Subject_Exclusion.ipynb# Checks whether (and which) subjects need to be excluded from further analysis││├──Demographics.ipynb# Analysis of general information of study population: Age, Gender, BMI, ...││├──ECG_Analysis.ipynb# Descriptive and statistical analysis of ECG data││├──Questionnaire_Analysis.ipynb# Descriptive and statistical analysis of questionnaire data││└──Saliva_Analysis.ipynb# Descriptive and statistical analysis of saliva data│└──plotting/├──results/# Plots and statistical results exported by the notebooks in the "analysis" and "plotting" folders└──config.json#InstallationIf you want to use this package to reproduce the analysis results then clone the repository and install the
package viapoetry:gitclonegit@github.com:mad-lab-fau/cft-analysis.gitcdcft-analysis
poetryinstall# alternative: pip install .This creates a new python venv in thecft-analysis/.venvfolder. Next, register a new IPython kernel for the venv:cdcft-analysis
poetryrunpoeregister_ipykernelFinally, go to theexperimentsfolder and run the Jupyter Notebooks.ExperimentsCurrently, this repository contains the following experiments:2022 – Scientific ReportsAnalysis of theCFT Datasetfor the paperVagus Activation by Cold Face Test Reduces Acute Psychosocial Stress Responses, published inScientific Reports.UsageIn order to run the code, first download the CFT Dataset, e.g. fromOSF. Then, create a file namedconfig.jsonin the folder/experiments/2022_scientific_reportswith the following content:{"base_path":"<path-to-dataset>"}This config file is parsed by all notebooks to extract the path to the dataset.NOTE: This file is ignored by git because the path to the dataset depends on the local configuration!The files in thedatafolder are created by running the notebooks in thedata_processingfolder. The files in theresultfolder are created by running the notebooks in theanalysisand theplottingfolders.
Package: cftcli
# Welcome toCFT CLII provide CLI commands to ease the interaction with cloudformation while developing and testing CloudFormation Stacks.## Commands
-deploy-stack: create or update a stack
-delete-stack: delete a stack
-list-stacks: list all stacks in a region
-describe-stack: display the stack details
-list-pipelines: list all pipeline in a region
-codebuild: runs a codebuild
Package: cf-text-embeddings
#cf_text_embeddings![TextEmbeddingsClowdFlowsWorkflow](clowdflows_workflow.png)Thisisa[ClowdFlows3.0](https://github.com/xflows/clowdflows-backend)packagewhichcontainswidgetsforword,sentenceanddocumentembeddings.
See[Widgets](https://github.com/xflows/cf_text_embeddings/wiki/Widgets)tolearnmoreabouttheincludedembeddingsmodels.##Installation
Installthispackagebyrunning:pipinstallcf_text_embeddings.
ToenableitintheClowdFlowsBackend,editthe`local_settings.py`filelikeshownbelow:` PACKAGE_TREE=[ {"name":"TextEmbeddings","packages":['cf_text_embeddings'],"order":1} ] `Thenrun`./manage.pyimport_packagecf_text_embeddings`fromtheClowdFlowsBackenddirectorytoimportwidgetsintotheplatform.Afterpackageinstallation,youneedtodownloadthemodels.##Downloadthemodels
TheTextEmbeddingspackagesupportsmodelsformultiplelanguages.
Tolistavailablelanguages:`python-mcf_text_embeddings.downloader-l`Todownloadallthemodels:`python-mcf_text_embeddings.downloader-dall`Youcanalsodownloadthemodelsforaspecificlanguage.Forexample,todownloadEnglishmodels:`python-mcf_text_embeddings.downloader-den`.##Usage
See[Usage](https://github.com/xflows/cf_text_embeddings/wiki/Usage)and[Widgets](https://github.com/xflows/cf_text_embeddings/wiki/Widgets)wikis.
Package: cftool
# cftool
Get inputs and outputs for a specific problem on [codeforces](https://www.codeforces.com) or [URI](www.urionlinejudge.com.br/).![Example](http://i.imgur.com/ZDCb1po.png?1)# InstallMake sure you have Python installed.` python-mpip installgit+https://github.com/guilhermeleobas/cftool`Or` python-mpip install cftool `# Version
1.0.5# Usage### get` cftool get cf550A  # Download inputs and outputs for problem 550A cftool get cf600   # Download inputs and outputs for all problems on contest 600. cftool get uri1400 # URI `You can also specify a link to get inputs and outputs.` cftool gethttps://www.urionlinejudge.com.br/judge/pt/problems/view/1001`### compile` cftool compile code.cc # Compile code.cc usingg++.cftool compile-lc++11code.cc  # Compile code.cc with g++ 11. cftool compile code.py # nothing will happen. `### run/test
Run code.cc with 620A inputs and check if their outputs are correct.` cftool run code.cc cf620A `Or you can runcftool test uri1574.ccwhich is a syntactic sugar forcftool run uri1574.cc uri1574To get full list of available commands run cf with–helpflag.# License
MIT
Package: cftw
# Containers FTW (cftw)Competitive Containers.![img/containers-ftw.png](img/containers-ftw.png)under development!These modules are not yet ready for use. More to come soon. To follow our development, please reference our [documentation](https://containers-ftw.github.io/cftw).## Installation
For the stable release, install via pip:` pip install cftw `For the development version, install from Github:` pip installgit+git://github.com/containers-ftw/cftw`## Issues
If you have an issue, or want to request a feature, please do so on our [issues board](https://www.github.com/containers-ftw/cftw/issues)
Package: cfug
CFugUtilities for C++ project management.RequirementsCMake>= 3.11GitCommandscfug new: Initializes new project. By default executable template is used,
but this can be changed with--templateargument. Available templates areexecutable,header-onlyandlibrary.cfug configure: Runs CMake configuration on the project.cfug build: Builds the project.cfug test: Runs test cases.cfug clean: Cleans all build files.
Package: cfunctions
CFunctionsCFunctions (cloud functions, compute functions, construct functions) are a
building block of the [constructs programming model] which can be used to
package JavaScript code and run it on a cloud system.Let's take a look at a simple CFunction:const{CFunction}=require('cfunctions');constcfunc=newCFunction({capture:['x','y'],code:'x + y'});console.log('outfile:',cfunc.outfile);console.log('env:',cfunc.env);The output will look like this:outfile:/tmp/.cf.out.TAJEO8/cf.js
env:{__CF__x__:'100',__CF__y__:'200'}Thecf.jsfile is a a self-contained JavaScript module which can be loaded
through arequire()statement and returns an async function that executes the
code after binding it from a set of environment variables.Let's execute our cfunction:$export__CF__x__=123$export__CF__y__=10$node-e"require('/tmp/.cf.out.TAJEO8/cf.js')().then(result => console.log(result))"12310TheCFunction.exec()static method can also be used to execute the function:constresult=CFunction.exec('/tmp/.cf.out.TAJEO8/cf.js',{env:{__CF__x__:123,__CF__y__:10}});console.log(result);LicenseLicensed under theApache 2.0license.
Package: cfunits
A Python interface to UNIDATA’s UDUNITS-2 library with CF
extensionsNote: Versions 3.0.0 and later are only compatible with version Python 3. Use version 1.9 for Python 2 compatibility.Store, combine and compare physical units and convert numeric values
to different units.Units are as defined inUNIDATA’s UDUNITS-2 library, except for
reference time units (such as'days since2000-12-1'in the'proleptic_gregorian'calendar), which are handled by thecftime
python package.In addition, some units are either new to, modified from, or removed
from the standard UDUNITS-2 database in order to be more consistent
with theCF conventions.Documentationhttps://ncas-cms.github.io/cfunitsInstallationhttps://ncas-cms.github.io/cfunits/installation.html
Package: cf-units
cf-unitsUnits of measure as defined by the Climate and Forecast (CF) Metadata Conventions.Table of ContentsOverviewExampleGet in TouchCredits, Copyright and LicenseOverviewUnits of measure as required by the Climate and Forecast (CF) metadata
conventions.Provision of a wrapper class to support Unidata/UCAR UDUNITS-2 library, and the
cftime calendar functionality.Documentation can be found athttps://cf-units.readthedocs.io/en/latest/.Example>>> from cf_units import Unit
>>> km = Unit('kilometers')
>>> m = Unit('meters')
>>> m.convert(1500, km)
1.5Get in TouchQuestions, ideas, general discussion or announcements
of related projects: use theDiscussions space.Report bugs:submit a GitHub issue.Suggest features: see ourcontributing guide.Credits, Copyright and Licensecf-units is developed collaboratively under the SciTools umbrella.A full list of code contributors ("cf-units contributors") can be found athttps://github.com/SciTools/cf-units/graphs/contributors.Code is just one of many ways of positively contributing to cf-units, please
see ourcontributing guidefor more details on how
you can get involved.cf-units is released under a BSD-3 license. SeeLICENSEfor full
terms.TheMet Officehas made a significant
contribution to the development, maintenance and support of this library.
All Met Office contributions are copyright on behalf of the British Crown.
Package: cf-upgrade
cf-upgradeThis package contains a simple strict to update an existing CloudFormation
stack. It is intended to be used as part of a CI/CD flow to update a
deployment.Usage is simple, since there are only two commands. First you can list
all CloudFormation stacks using thelistcommand:$cf-upgradelistStackStatus-------------------------------my-example-stackUPDATE_COMPLETETo update a stack use theupgradecommand. In its simplest version you can
pass a version number which will be used for aVersionparameter:$cf-upgrademy-example-stack1.2.0Stackupdating,waitingtocomplete...doneIf you want to modify another parameter, or a different one you can also
provide one or more key=value options:$cf-upgrademy-example-stackApiVersion=1.1.0Nginx=1.13.4Stackupdating,waitingtocomplete...doneCredentialsThis command assumes you haveAWS CLI credentials configured.
You can use the–profileand–regionoptions to indicate which AWS profile
and region to use.PermissionsIn order to operate this your will need to use an AWS user with permissions to
find our existing stack template and update it. In addition you must grant any
permissions necessary to update your resources.Here is a sample policy document to allow updating of ECS services:{"Version":"2012-10-17","Statement":[{"Effect":"Allow","Action":["cloudformation:DescribeStacks","cloudformation:ListStacks","cloudformation:GetTemplate","cloudformation:GetTemplateSummary","cloudformation:UpdateStack","iam:GetRole","iam:PassRole","ecs:UpdateService","ecs:DeregisterTaskDefinition","ecs:DescribeServices","ecs:RegisterTaskDefinition"],"Resource":"*"}]}Changelog1.0.2 - September 4, 2017Fix a ReST syntax error.1.0.1 - September 4, 2017Use ReST for documentation to improve display on pypi.org1.0 - September 4, 2017First release
Package: cfupload
# Simple Cloud Files UploaderPython script to quickly upload files to [Rackspace Cloud Files](http://www.rackspace.com/cloud/files/) or [OpenStack Swift](http://swift.openstack.org). Originally developed to make one-liner uploads more manageable. Supports input via file arguments or standard input.## InstallationFor the love of Guido, use [virtualenv](http://www.virtualenv.org/en/latest/index.html) with whichever of the following methods you choose:### pip``` bash$ pip install cfupload```### EasyInstall``` bash$ easy_install cfupload```### setuptools``` bash$ git clone git://github.com/DavidWittman/Simple-Cloud-Files-Uploader.git$ cd Simple-Cloud-Files-Uploader$ python setup.py install```## Usage```usage: cfupload [-h] [-k <api key>] [-u <username>] [-a <auth_url>] [-s][-o <filename>] [-q] [-c]container [files [files ...]]Upload files to Rackspace Cloud Files or Openstack Swift.positional arguments:container             Container name in Cloud Files or Openstack Swiftfiles                 The file(s) to uploadoptional arguments:-h, --help            show this help message and exitCloud Files Connection Information:-k <api key>, --apikey <api key>API key. Defaults to env[CLOUD_FILES_APIKEY]-u <username>, --user <username>Username. Defaults to env[CLOUD_FILES_USERNAME]-a <auth_url>, --auth <auth_url>Authentication endpoint. Defaults toenv[CLOUD_FILES_AUTH_URL]-s, --snet            Use ServiceNet for connectionsOutput options:-o <filename>, --file <filename>Destination filename in Cloud Files or Openstack Swift-q                    Silence output-c, --cdn             Print CDN URL to stdout```## ExamplesEach of these examples assume you have the environment variables `CLOUD_FILES_AUTH_URL`, `CLOUD_FILES_USERNAME` and `CLOUD_FILES_APIKEY` exported. Alternatively, you can pass the username, auth_url and API key in as options with `-u`,`-a` and `-k`, respectively.### Upload a single file``` bash$ cfupload mycontainer ~/F4z2L.gif```### Upload multiple files``` bash$ cfupload gifs ~/Pictures/*.gif```### Upload from stdin``` bash$ tar cvzf - ~/important/* | cfupload -o backup-$(date '+%Y%m$d') backups```## Pro Tips* Export environment variables `CLOUD_FILES_{APIKEY,USERNAME,AUTH_URL}` in your bash_profile to prevent the need to specify these options each time you run cfupload* A destination filename must be provided with -o when uploading from standard input* Pipe your files from standard input to make cronjob backups stupid easy:`# mysqldump --all-databases | gzip -c | cfupload -o backup-$(date '+%Y%m%d').sql.gz container`
Package: cf-util
cf_utilcf_util is a simple Python-based command line script that allows the user to get information about submissions for a specific user from the codeforces website easily.UsageInstall usingpip install cf_utilUpdate usingpip install --upgrade cf_utilContests Downloadercf_util contests-downloader touristDownloads all in-contestacceptedsubmissions for the specified user(s) in order from newest to oldest.Can use the optional argument-cor--countto specify how many contests to download, e.g,cf_util contests-downloader tourist -c 5.Problems Downloadercf_util problems-downloader touristDownloads allacceptedsubmissions for the specified user(s) in order from newest to oldest.Can use the following optional arguments:-cor--countto specify the number of submissions to download.-mor--min-ratingto specify the minimum problem rating for a problem to be downloaded, set by default to 0.-Mor--max-ratingto specify the maximum problem rating for a problem to be downloaded, set by default to 3500.-tor--tagsto specify the allowed problem tags. Tags must be written in the same way they are written on thecodeforceswebsite, tags with multiple words must be separated by-instead of spaces. Note that by default if you specify multiple tags then they must all be present in a problem.-oor--combine-by-orin order to allow the presence of only one tag for a problem submission to be downloaded.-lor--list-onlyin order to not download any submissions' code.Get Gym Listcf_util get-gym-list touristReturns a text file conatining links to all gyms that the user(s) participated in.
Package: cfutils
Chromatogram File UtilsFor Sanger sequencing data visualizing, alignment, mutation calling, and trimming etc.Democommand to generate the demo abovecfutilsmut--query./data/B5-M13R_B07.ab1--subject./data/ref.fa--outdir./data/--plotHow to use?You can have mutation detection and visualization in one step using the command line.cfutilsmut--helpYou can also integrate the result matplotlib figures and use it as a python module.An example:importmatplotlib.pyplotaspltimportnumpyasnpfromcfutils.parserimportparse_abifromcfutils.showimportplot_chromatographseq=parse_abi("./data/B5-M13R_B07.ab1")peaks=seq.annotations["peak positions"][100:131]fig,axes=plt.subplots(2,1,figsize=(12,6),sharex=True)plot_chromatograph(seq,region=(100,130),ax=axes[0],show_bases=True,show_positions=True,color_map=dict(zip("ATGC",["C0","C2","C1","C4"])),)axes[1].bar(peaks,np.random.randn(len(peaks)),color="0.66")plt.show()How to install?form pypi(use this way ONLY, if you don't know what's going on)pipinstall--usercfutilsmanipulate the source codeclone from githubgitclonegit@github.com:y9c/cfutils.gitinstall the dependencemakeinitdo unittestmaketestChangeLogReverse completement the chromatogram file. (Inspired by Snapgene)build as python package for pypifix bug that highlighting wrong basereplace blastn with buildin python alignerTODOcall mutation by alignment and plot Chromatogram graphicadd a docchange xaxis by peak locationfix bug that chromatogram switch pos after trimwrap as a cli appreturn quality score in outputfix issue that selected base is not in the middlefix plot_chromatograph rendering bugadd projection feature to make align and assemble possible