Saravanan666/pypi-org huggingface dataset:
Package: vcdextproxy
vcdextproxyPython based proxy looking at multiple AMQP queues for incoming requests of VMware vCloud Director’s API Extensions and forwarding to specified REST backends.Free software: MIT licenseDocumentation:https://vcdextproxy.readthedocs.io.FeaturesSupport multiple queues subscriptionsCan address multiple REST endpoints depending on extension(s)1 REST endpoint is a associated to 1 extension in vCDBackend servers:HTTP + HTTPS supportBasic authenticationBasic URI rewrittingAMQP server:Multiple Exchange/Queue listeningManage Exchange/Queue declarationsSSL supportExtension lifecyle:Deploy a newly declared extensionRedeploy an existing extensionvCloud Director:Support vCD from 9.1 to 10.0Can check user’s right based on per extension settingCan check organization’s membership of an userPlanned features#6 - Address some pre-checks like rights management#18 - Check organization’s membership of an user#2 - Manage extension lifecycle (deploy/re-deploy)User caseIn a vCloud Director instance where 2 API extensions are used (example1,example2):vcdextproxysubscribe to following AMQP queues:example1example2When a message is sent toexample1queue:A URI path check is made: is/api/example1a correct API path for extension namedexample1?If valid, all fields of the request are converted to REST request (as headers or as body content)REST endpoint handle the request as a standard REST one (with a lot of vCloud information…)REST endpoint replies tovcdextproxyvcdextproxyreformat the reply as an AMQP reply messageCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.1.x (2019-11-01)First release on PyPI.
Package: vcdilog
vcdilog: logging as easy as print statementsYou almost certainly should be using log statement instead of messy print statements.vcdilogmakes this easy.InstallYou can installvcdilogusing pip:$ pip install vcdilogIf using poetry, simply add this line to yourpyproject.tomlfile.vcdilog = "*"PhilosophyThe built in python logging library is highly customizable, but hard to visualize and understand.vcdilogdoesn't try to replace what is in the standard library, but streamlines it with sensible defaults.Basic, instead-of-print-statements usageAll you need is two lines of setup: One import, and one line to add a handler for stdout/stderr output.from vcdilog import log
log.add_std_handler()

log.info('hello world')  # .info, .warning, .debug, etcMore flexible usageYou can create a log object:from vcdilog import Logger

log = Logger()Crucially, you don’t need to give the logger a name, it will figure out the current module name automatically and use that. This same method is used by the print-statements example above - they'll be logged to an appropriately-named logger automatically, based on the module they're in.You can set a log level with:log.set_level(level="DEBUG")DEBUG means all logged messages will actually get logged. When you add a handler with e.g.add_std_handler, the handler will be assigned theDEBUGlevel by default, and so will the associated logger.For production usage, a lower level should ordinarily be set to avoid overly verbose logging.Other handlersSo far three handlers are supported.x.add_std_handler()
x.add_null_handler()
x.add_json_handler()As per the above, the standard output handler logs to the console. It uses some customization log errors to stderr and normal messages to stdout, just likeprint()does, which means you can use logging calls instead of print statements.The null handler should be used in libraries - it’s best practice when publishing a library to create a logger but add only a null handler and no others to that users of the library don’t get unwanted log messages (if they want to see them, they’ll add their own handlers).Then there’s the json handler. That logs json-formatted log items to a file.For instance, the following:log.info("classic message", extra={"special": "value", "run": 12})Will result in:{"message": "classic message", "special": "value", "run": 12}In the log file (log.json by default)Basic prefect supportGetting a prefect logger is as easy as:prefect_logger = vcdilog.get_prefect_logger()and you can do...vcdilog.set_prefect_extra_loggers(['boto3', 'whatever'])to have those loggers inherit the prefect logging config.More prefect support is on the way!
Package: vcdisk
vcdisk: Rotation curves of disk galaxiesA minimal python module to solve Poisson's equation in galactic disks.
This is useful to compute i) the circular velocity of athick galaxy diskwith arbitrary surface density and vertical profiles, and ii) the circular
velocity of aflattened bulgewith arbitrary surface density.Thevcdiskmodule is a compact toolbox indispensable for modelling
galaxy rotation curves, since it allows to determine the gravitational field
of the observed baryonic matter (stars, gas, dust etc.) just from photometric
observations, with minimal assumptions.vcdisk.vcdiskcalculates the radial force on the disk plane of a
thick disk component, with an arbitrarily sampled surface density profile and a
user-defined vertical density profile.vcdisk.vcbulgecomputes
the gravitational field on the mid-plane of an axisymmetric spheroidal oblate (or
spherical) bulge component, with an arbitrarily sampled surface density profile.Read the full documentation at:https://vcdisk.readthedocs.io/en/latest/
Package: vce
VCE: Virtual Constellation Enginevceis a cloud framework to prototype and emulate satellite applications.It provides support for orbits calculation, network latency/bandwidth
emulation, instrument control by the application, and constellation
monitoring (positions, CPU/memory/disk/network usage, configuration
changes made to the emulated onboard instruments).The state of everything in the constellation is saved in a time series
database (InfluxDB).
This database can be inspected after running the emulation scenario.Each satellite runs in an AWS instance which is part of an AWS
CloudFormation stack.Networking parameters are set (throughtcconfigand thenetemcomponent of the Linux kernel) byvce agent, which runs on each
node and polls the current value of the parameters from the time
series database.Networking parameters are saved in the database byvce linksin
real-time.Satellite positions are stored in advance byvce orbits, which
is run at the beginning of the emulation.Resource usage measurements are collection on each AWS instance by
runningcollectdand sending the data to
InfluxDB.Timeseries of usage measurements, satellite positions (on a map),
and instruments state can be visualized and analyzed usinggrafana.DevelopmentTo install all development dependencies, just clone this project and
then run:makeinitThis will create a Python 3.7 virtual environment usingpipenv.
Package: vCenter
RestApi AutomationUsing RestApi to Automate the Test cases -> Backup, RestoreBefore StartThe Setup should be ready with Avamar server connected to vCenter and proxy registered with the Avamar Server.InstallationPython Version --> Preferably 3.5.0 and above.Use the package manager [pip] if possible the latest Version.apt-getinstallpython-pipOther Librariesbash pip install requests--> to  install the requests modulebash pip install yaml--> For Yaml Configurationbash pip install logging--> For Log creationUsageFill the Config.yaml file for User Entries. Some of them are explained below,Authorization : Authorization Token to access Avamar Server(Use Postman to retrieve one).vCenterSessionId : Session Id of the vCenter server.vmType : The type of VM whose backup has to be taken(Windows, Linux)FolderPath : Folder where the VM is keptNewVMName : While Restoring the New VM nameFor Eg.IP:10.110.211.252Authorization:Bearer eyJhbGciOiJSUzI1NiIsInR5cCI6IkpXVCJ9.eyJyb2xlIjoiUk9PVCIsInVzZXJfbmFtZSI6Ik1DVXNlciIsInNjb3BlIjpbIndyaXRlIl0sImRvbWFpbiI6Ii8iLCJhdXRob3JpemVkX2RvbWFpbiI6Ii8iLCJleHAiOjE1NTI2NDc2NzksImF1dGhvcml0aWVzIjpbIlJPT1QiXSwianRpIjoiNjBlZTUyNWItZjBmYi00NTE2LWIyMTEtYmZiNThiMzQ3Y2E3IiwiY2xpZW50X2lkIjoiM2MwNDFiODctNTIyYi00NThlLTgwZmYtYjY5MTZiMmU5N2JmIn0.EpkFA2litAI_CigsTK1s3GYFmG6BP48_EOj-IIPXgNX5-SwpDlg32-MP8XgCbMYXOpPLRUzlPnIIBA8jANBVL9Tg3esF_u2qmKU7CMLVyJTIfZhB9x1NAoE5S0_6Fb8Z68PkbUWkUYc0ubaoGEhMzc775bLxU4g_ULUdtkQSGKYCTg2CLnmqhONZaWTw5M83Y-L8qZ7T4DvgEbkWtXHZ0jdnLcSiAXtv1qX3rEESk8LYVSuvoeLIPSnNK50vydh_H_cPTw9jfF_J8Qfa5mTAAfnuzTZBPGtyA2zodtOin1yyEOC1VPz7HpHU-0NMOKF1YCVleZXzV35BdNw-JxBfS1c92BMZQoF-yqyTf1Q5qwGCMA0lghxd0ClNwTM4YCCe-o3FBcVeCWLehL5MyGDuLk0JI8uGRJPR7XHpwpy8KTSF8L_9A-0i3xS0ZZQf9AxTDIEMIheEAF0VWgu3ulZ92Ud_9qThICTUWvqkHonuLiKs2FoPxrGfFyOeSeLlaZEOvCenterSessionId:4f99479faf19893b1dd86507b7fcfc7evCenter:10.110.211.168PolicyName:Gsan-PolicyPolicyDomain:/10.110.211.168/VirtualMachinesContent-Type:application/jsonVM_id:c146dd0ebed42ff4cd94460ddeb509fb6cbdf7e7vmType:WindowsVcCid:14bda782e11827a1c69201a43ac0e3cc2b4a24a8Datastore:datastore1FolderPath:/AVE_A10N_DC/vm/Automation/NewVMName:Restore-VM-2019_18ResourcePoolPath:/AVE_A10N_DC/host/10.110.211.22/Resources/Compute-ResourcePool/DatacenterName:AVE_A10N_DCRunningAfter filling the yaml file run the below command in the terminal,pythonREST_Automation.pyLog file produced isContributingAll suggestions and trial are welcome.
Package: vcenter-info
vcenter-info - Simple view of vCenter dataOverviewPackage-based InstallationFrom PyPIFrom SourceRunningConfigurationStarting the ServerRunning the Console CheckDevelopment EnvironmentSetupGenerate Javascript BundleOverviewThis project is used for making some simple
queries to one or more vCenter host and rendering
the results in a simple way, as a npm-managed React
app with Flask.
There's also a console script that outputs vm
statistics in influx line protocol format.Package-based installationCreate a (python 3) virtualenv and
install using one of the following methods:From PyPi$pipinstallvcenter-infoFrom Source$pythonsetup.pysdist
$pipinstalldist/vcenter-info-x.y.z.tar.gzRunningConfigurationUseconfig-example.jsonas a template to
create a configuration file.
When running the server an environment variable calledCONFIG_FILENAMEand containing the path to this
configuration file must be present.Starting the ServerCONFIG_FILENAME=config.jsonFLASK_APP=vcenter_infoflaskrunNote: if you are running from a source distribution
and didn't install it in your virtualenv, you should
execute the above from the top-level folder.Alternatively, using the providedapp.pymight sometimes be convenient when developing:CONFIG_FILENAME=config.jsonpythonvcenter_info/app.pyor:CONFIG_FILENAME=config.jsonpython-mvcenter_info.appRunning the Console CheckUsage:check-vcenter-vms[OPTIONS]Options:--measurementTEXTinfluxmeasurementname[required]--configFILENAMEconfigfilename[required]--helpShowthismessageandexit.Development EnvironmentThese notes are for setting up a development environment.SetupCreate a (python 3) virtualenv and install the requirements:$pipinstall-e.... and, to install additional libraries used by the test scripts:$pipinstall-rrequirements.txtSet up the node environment:npminstallGenerate Javascript BundleIn a fresh environment, or whenever the ui
sources are changed:npmrunbuild
Package: vcetdspdcom
Package consists of  Basic Signal Processing algorithms and Communication
modulation and demodulation techniques. It includes functions to evaluate
Linear convolution,Circular convolution, Discrete fourier transform, Auto-Correlation,
Cross-Correlation, Fir filter, IIR filter,  DWT, IDWT, DCT, IDCT, MFCC, ASK, FSK,
PSK, DPSK,QPSK, 16QAM and TDM modulation and demodulation techniques.
The package helps students to conduct DSP Lab(18ECL57)  and Communication
Lab(18ECL67)programs  pertaining to VTU 2018-CBCS scheme with ease.Change Log0.12(25/8/2022)=============Third Release
Package: vcf2fhir
VCF to FHIR ConverterIntroductionVCF-formatted files are the lingua franca of next-generation sequencing, whereasHL7 FHIRis emerging as a standard language for electronic health record interoperability. A growing number of clinical genomics applications are emerging, based on theHL7 FHIR Genomics standard. Here, we provide an open source utility for converting variants from VCF format into HL7 FHIR Genomics format. Details of the translation logic are on themanual page. Additional information and case studies are described in ourBMC Bioinformatics article. Conceptually, the utility takes a VCF as input and outputs aFHIR Genomics report.InstallBefore installing vcf2fhir you need to install cython and wheel.pip install cython wheelNow, install vcf2fhir binary from pip.pip install vcf2fhirQuick Examples(some sample VCF files arehere)>>>importvcf2fhir>>>vcf_fhir_converter=vcf2fhir.Converter('sample.vcf','GRCh37')>>>vcf_fhir_converter.convert()LoggingYou can use python standardloggingto enable logs. Two loggers ('vcf2fhir.general') and ('vcf2fhir.invalidrecord') are available to configure.vcf2fhir.general: standard library logs.vcf2fhir.invalidrecord: logs all the records from vcf file which are in conversion region but are not converted to fhir format.>>>importlogging# create logger>>>logger=logging.getLogger('vcf2fhir.invalidrecord')>>>logger.setLevel(logging.DEBUG)# create console handler and set level to debug>>>ch=logging.FileHandler('invalidrecord.log')>>>ch.setLevel(logging.DEBUG)# create formatter>>>formatter=logging.Formatter('%(asctime)s-%(name)s-%(levelname)s-%(message)s')# add formatter to ch>>>ch.setFormatter(formatter)# add ch to logger>>>logger.addHandler(ch)DocumentationYou can find the detailed documantation of the package on the official websitehere.ScopeSoftware converts simple (SNV, MNV, Indel) and structural (CNV, DEL, DUP, INV, INS) variants from VCF to FHIR format. Clinical annotations, where supplied, are incorporated into the FHIR representation.Not supportedAlt contigs: Software does not support conversion of variants aligned to Alt contigs. We recommend caution in using this software against VCFs generated with an alternate-locus aware variant caller, as variants mapped to Alt contigs will not be converted.Query liftover: Software assumes that regions (e.g. conversion region, studied region) and VCF are based on the same genomic build.Chromosome synonyms (e.g. '1' vs. 'chr1'): Software assumes that chromosome representation is consistent between regions (e.g. in BED files) and VCF. For instance, if VCF uses 'chr1', then BED file must also use 'chr1'License and LimitationsSoftware is available for use under anApache 2.0 license, and is intended solely for experimental use, to help further Genomics-EHR integration exploration. Software is expressly not ready to be used with identifiable patient data or in delivering care to patients. Code issues should be tracked here. Comments and questions can also be directed toinfo@elimu.ioorsrikarchamala@gmail.com.
Package: vcf2fhir-test-517
VCF to FHIR ConverterIntroductionVCF-formatted files are the lingua franca of next-generation sequencing, whereasHL7 FHIRis emerging as a standard language for electronic health record interoperability. A growing number of clinical genomics applications are emerging, based on theHL7 FHIR Genomics standard. Here, we provide an open source utility for converting variants from VCF format into HL7 FHIR Genomics format. Details of the translation logic are on themanual page. Additional information and case studies are described in ourBMC Bioinformatics article. Conceptually, the utility takes a VCF as input and outputs aFHIR Genomics report.InstallBefore installing vcf2fhir you need to install cython and wheel.pip install cython wheelNow, install vcf2fhir binary from pip.pip install vcf2fhirQuick Examples(some sample VCF files arehere)>>>importvcf2fhir>>>vcf_fhir_converter=vcf2fhir.Converter('sample.vcf','GRCh37')>>>vcf_fhir_converter.convert()LoggingYou can use python standardloggingto enable logs. Two loggers ('vcf2fhir.general') and ('vcf2fhir.invalidrecord') are available to configure.vcf2fhir.general: standard library logs.vcf2fhir.invalidrecord: logs all the records from vcf file which are in conversion region but are not converted to fhir format.>>>importlogging# create logger>>>logger=logging.getLogger('vcf2fhir.invalidrecord')>>>logger.setLevel(logging.DEBUG)# create console handler and set level to debug>>>ch=logging.FileHandler('invalidrecord.log')>>>ch.setLevel(logging.DEBUG)# create formatter>>>formatter=logging.Formatter('%(asctime)s-%(name)s-%(levelname)s-%(message)s')# add formatter to ch>>>ch.setFormatter(formatter)# add ch to logger>>>logger.addHandler(ch)DocumentationYou can find the detailed documantation of the package on the official websitehere.ScopeSoftware converts simple variants (SNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.Not supportedStructural variants: Software does not support conversion of structural variants (where INFO.SVTYPE is present).Alt contigs: Software does not support conversion of variants aligned to Alt contigs. We recommend caution in using this software against VCFs generated with an alternate-locus aware variant caller, as variants mapped to Alt contigs will not be converted.Query liftover: Software assumes that regions (conversion region, studied region, noncallable region) and VCF are based on the same genomic build.Chromosome synonyms (e.g. '1' vs. 'chr1'): Software assumes that chromosome representation is consistent between regions (e.g. in BED files) and VCF. For instance, if VCF uses 'chr1', then BED file must also use 'chr1'License and LimitationsSoftware is available for use under anApache 2.0 license, and is intended solely for experimental use, to help further Genomics-EHR integration exploration. Software is expressly not ready to be used with identifiable patient data or in delivering care to patients. Code issues should be tracked here. Comments and questions can also be directed toinfo@elimu.ioorsrikarchamala@gmail.com.
Package: vcf2fhir-test-upgrade-test-upgrade
VCF to FHIR ConverterIntroductionVCF-formatted files are the lingua franca of next-generation sequencing, whereasHL7 FHIRis emerging as a standard language for electronic health record interoperability. A growing number of clinical genomics applications are emerging, based on theHL7 FHIR Genomics standard. Here, we provide an open source utility for converting variants from VCF format into HL7 FHIR Genomics format. Details of the translation logic are on themanual page. Additional information and case studies are described in ourBMC Bioinformatics article. Conceptually, the utility takes a VCF as input and outputs aFHIR Genomics report.InstallBefore installing vcf2fhir you need to install cython and wheel.pip install cython wheelNow, install vcf2fhir binary from pip.pip install vcf2fhirQuick Examples(some sample VCF files arehere)>>>importvcf2fhir>>>vcf_fhir_converter=vcf2fhir.Converter('sample.vcf','GRCh37')>>>vcf_fhir_converter.convert()LoggingYou can use python standardloggingto enable logs. Two loggers ('vcf2fhir.general') and ('vcf2fhir.invalidrecord') are available to configure.vcf2fhir.general: standard library logs.vcf2fhir.invalidrecord: logs all the records from vcf file which are in conversion region but are not converted to fhir format.>>>importlogging# create logger>>>logger=logging.getLogger('vcf2fhir.invalidrecord')>>>logger.setLevel(logging.DEBUG)# create console handler and set level to debug>>>ch=logging.FileHandler('invalidrecord.log')>>>ch.setLevel(logging.DEBUG)# create formatter>>>formatter=logging.Formatter('%(asctime)s-%(name)s-%(levelname)s-%(message)s')# add formatter to ch>>>ch.setFormatter(formatter)# add ch to logger>>>logger.addHandler(ch)DocumentationYou can find the detailed documantation of the package on the official websitehere.ScopeSoftware converts simple variants (SNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA.Not supportedStructural variants: Software does not support conversion of structural variants (where INFO.SVTYPE is present).Alt contigs: Software does not support conversion of variants aligned to Alt contigs. We recommend caution in using this software against VCFs generated with an alternate-locus aware variant caller, as variants mapped to Alt contigs will not be converted.Query liftover: Software assumes that regions (conversion region, studied region, noncallable region) and VCF are based on the same genomic build.Chromosome synonyms (e.g. '1' vs. 'chr1'): Software assumes that chromosome representation is consistent between regions (e.g. in BED files) and VCF. For instance, if VCF uses 'chr1', then BED file must also use 'chr1'License and LimitationsSoftware is available for use under anApache 2.0 license, and is intended solely for experimental use, to help further Genomics-EHR integration exploration. Software is expressly not ready to be used with identifiable patient data or in delivering care to patients. Code issues should be tracked here. Comments and questions can also be directed toinfo@elimu.ioorsrikarchamala@gmail.com.
Package: vcf2ldif
vCard to ldif converterThis tool is designed to convert*.vcf(vCard) contact files to*.ldiffile, for further creation of shared phone books onLDAPserver.Installationpip install vcf2ldifUsagevcf2ldif \
    --input-file path/to/input_file.vcf \
    --root-dn ou=adressbook,dc=example,dc=com \
    --output-file path/to/output_file.ldifYou can import the resulting ldif file into your LDAP server (e.g. OpenLDAP) with the following command:ldapmodify -c -D "cn=admin,dc=example,dc=com" -W -f path/to/output_file.ldifWhen converting, you can also format phone numbers according to the following standards:e164 (e.g.:+18868886421) by adding the option--format-number e164international (e.g.:+1 886-888-6421) by adding the option--format-number internationalnational (e.g.: (e.g.:(886) 888-6421) by adding the option--format-number rnationalYou can learn more by invoking the command with the--helpoptionvcf2ldif --help
Package: vcf2mutt
Convert vCard contacts to mutt format aliases.Installpip install vcf2muttHint:pip install--uservcf2muttdoes not require root and installs
to your home directory.UseFrom a local file:vcf2mutt ./contacts.vcf > ~/.aliasesFrom a remotely hosted contacts file (e.g. fromradicale):vcf2mutt https://USERNAME:PASSWORD@SERVER/.../contacts.vcf/ > ~/.aliases
Package: vcf2networks
VCF2Networks is a tool to calculate Genotype Networks from Single Nucleotide Polymorphism data.Read more athttps://bitbucket.org/dalloliogm/vcf2networksNote on installation: this module depends on the python-igraph library, which requires a C igraph library which must be compiled separately. Seehttps://pypi.python.org/pypi/python-igraphfor more instructions. See alsohttps://bitbucket.org/dalloliogm/vcf2networks/src/tip/docs/installing.rstfor our tips.