Saravanan666/pypi-org huggingface dataset:
Package: bold-identification
bold_identification1 Introductionseehttps://github.com/linzhi2013/bold_identification.This is a Python3 package which can get the taxonomy information of sequences from BOLDhttp://www.boldsystems.org/index.php.Currently,bold_identificationonly runs on Mac OS, Windows 64bit, Linux.2 InstallationOr withpip$ pip install bold_identificationThere will be a commandbold_identificationcreated under the same directory as yourpipcommand.3 Usagerunbold_identification$ bold_identification
usage: bold_identification [-h] -i <str> [-f <str>] -o <str>
                            [-d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,MATK_RBCL}] [-n <int>] [-r <int>]
                            [-c] [-C] [-q <int>] [-D] [--version]

To identify taxa of given sequences from BOLD (http://www.boldsystems.org/).
Some sequences can fail to get taxon information, which can be caused by
TimeoutException if your network to the BOLD server is bad.
Those sequences will be output in the file '*.TimeoutException.fasta'.

You can:
1) run another searching with the same command directly (but add -c option);
2) lengthen the time to wait for each query (-t option);
3) increase submission times (-r option) for a sequence.

Also, the sequences without BOLD matches will be output in the
file '*.NoBoldMatchError.fasta'

By Guanliang Meng.
See https://github.com/linzhi2013/bold_identification.

Citation:
Yang C, Zheng Y, Tan S, Meng G, et al.
Efficient COI barcoding using high throughput single-end 400 bp sequencing.
https://doi.org/10.1186/s12864-020-07255-w

version: 0.0.27

optional arguments:
  -h, --help            show this help message and exit
  -i <str>              input file name
  -f <str>              input file format [fasta]
  -o <str>              outfile prefix
  -d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,MATK_RBCL}
                        database to search [COX1]
  -n <int>              how many first top hits will be output. [1]
  -r <int>              Maximum submission time for a sequence, useful for handling TimeOutException. [4]
  -c                    continuous mode, jump over the ones already in "-o" file, will resubmit all the remained. use "-cc"
                        to also jump over the ones in "*.NoBoldMatchError.fasta" file.
  -C                    For chimera check purpose. If set, for each sequence, I will query the BOLD database using the
                        subsequences from 5'- and 3'-ends with a length of '-q <int>' bp, respectively
  -q <int>              The length of subsequences for chimera check [400]
  -D                    debug mode output [False]
  --version             show program's version number and exit4 CitationWhen you usebold_identificationin your study, please cite:Yang C, Zheng Y, Tan S, Meng G, et al.
Efficient COI barcoding using high throughput single-end 400 bp sequencing.
https://doi.org/10.1186/s12864-020-07255-w
Package: boldigger-cline
BOLDigger-commandlineBOLDigger as a command-line tool for easy implementation into bioinformatic pipelines.Before using please check that you have updated to the latest version of BOLDigger since BOLDigger-cline heavily relies on the current code of BOLDigger.For a detailed explanation of the different functions BOLDigger offers please visit:https://github.com/DominikBuchner/BOLDiggerInstallationBOLDigger-commandline requires Python version 3.6 or higher and can be easily installed by using pip in any command line:pip install boldigger_clinewill install BOLDigger-commandline as well as all needed dependencies.To update BOLDigger-commandline type:pip install --upgrade boldigger_clineHow to citeBuchner D, Leese F (2020) BOLDigger â€“ a Python package to identify and organise sequences with the Barcode of Life Data systems. Metabarcoding and Metagenomics 4: e53535.https://doi.org/10.3897/mbmg.4.53535UsageBOLDigger commandline offers all functions of BOLDigger as a command line tool.For documentation on how to use type:boldigger-cline -hReturns:usage: boldigger-cline [-h] [--version]
                       {ie_coi,ie_its,ie_rbcl,add_metadata,first_hit,jamp_hit,digger_hit}
                       ...

BOLDigger as a command line tool, https://github.com/DominikBuchner/BOLDigger-

commandline

positional arguments:
  {ie_coi,ie_its,ie_rbcl,add_metadata,first_hit,jamp_hit,digger_hit}
    ie_coi              COI identification engine
    ie_its              ITS identification engine
    ie_rbcl             rbcl identification engine
    add_metadata        additional data download
    first_hit           use the first hit as top hit
    jamp_hit            determine the top hit with the JAMP method
    digger_hit          determine the top hit with the BOLDigger method

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exitThe help function also works for all sub-functions of BOLDigger-commandline:boldigger-cline ie_coi -hReturns:usage: boldigger-cline ie_coi [-h]
                              username password fasta_path output_folder

                              [batch_size]

positional arguments:
  username       Username for boldsystems login
  password       Password for boldsystems login
  fasta_path     Path to the fasta file to be blasted
  output_folder  Path to the output folder
  batch_size     Batch size to be blasted.

optional arguments:
  -h, --help     show this help message and exitIdentification engine - Example usageTo run the identification engine for COI type:boldigger-cline ie_coi username password fasta_path output_folder [batch size](optional)Additional data download and top hit determinationAll other function of BOLDigger commandline just need a filepath to the BOLDResult file as an argument.
Package: bolditalic
WarningThis extension is deprecated. Please use the bolditalic extension provided
in thechios package.bolditalicis an extension for Sphinx that enables inline bold + italic
text styling.Full documentation:https://kallimachos.github.io/bolditalic/InstallationInstallbolditalicusingpip:$ pip install bolditalicUsageAddbolditalicto the list of extensions inconf.py:extensions = ['bolditalic']Use thebolditalicrole to style text:The end of this sentence :bolditalic:`displays in bold and italic`.
Package: bold_retriever
This script accepts FASTA files containing COI sequences. It queries the BOLD
databasehttp://boldsystems.org/in order to get the taxa identification
based on the sequences.Run this wayclone repository:cd $USERAPPL
git clone https://github.com/carlosp420/bold_retriever.gitinstall dependencies (python2.7):cd bold_retriever
module load biopython-env
pip install -r requirements.txtrun softwareYou have to choose one of the databases available from BOLDhttp://www.boldsystems.org/index.php/resources/api?type=idengineand enter it as argument:COX1_SPECIESCOX1COX1_SPECIES_PUBLICCOX1_L640bpFor example:python bold_retriever.py -f ZA2013-0565.fasta -db COX1_SPECIESoutput:seq_id  bold_id       similarity  division  class       order       family        species                collection_country
OTU_99  FBNE064-11    1           animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius pini        Germany
OTU_99  NEUFI079-11   1           animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius pini        Finland
OTU_99  FBNE172-13    0.9937      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius atrifrons   Germany
OTU_99  FBNE162-13    0.9936      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius contumax    Austria
OTU_99  TTSOW138-09   0.9811      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius ovalis      Canada
OTU_99  CNPAH380-13   0.9811      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius             Canada
OTU_99  CNKOF1602-14  0.9811      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius pinidumus   Canada
OTU_99  NRAS173-11    0.9748      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius conjunctus  Canada
OTU_99  SSBAE2911-13  0.9748      animal    Collembola  None        None          Collembola             Canada
OTU_99  CNPAQ117-13   0.9686      animal    Insecta     Neuroptera  Hemerobiidae  Hemerobius humulinus   CanadaSpeedbold_retrieveruses the library Twisted for performing asynchronous calls.
This speeds up the total processing time:Full documentationSee the full documentation athttp://bold-retriever.readthedocs.orgHistoryv1.0.0: Using Twisted for asynchronous calls and increase in speed.v0.2.4: Reorganizing columns in output file. Querying the API for familyname of taxa.v0.2.2: Killed bug taxon search.v0.2.1: Killed bug in scraping webPublic_BINfor species ID.v0.2.0: Scraping webPublic_BINfor species ID.v0.1.9: Added request_id test and option to run fuction in debug mode.v0.1.8: Fixed bug for exception when BOLD sends empty list of taxon names.v0.1.7: Fixed bug for exception when BOLD sends empty list of taxon names.v0.1.6: Append taxon identification results to file as we get them.v0.1.5: Additionat tests coverage 92%v0.1.4: Fixed bug in taxon_search functionv0.1.3: Coverage 75%v0.1.2: Pep8 and test coverage 69%v0.1.1: Packaged as Python module.v0.1.0: You can specify which BOLD datase should be used for BLAST of FASTA sequences.v0.0.7: Catching exception for NULL, list and text returned instead  of XML from BOLD.v0.0.6: Catching exception for malformed XML from BOLD.v0.0.5: Catch exception when BOLD sends funny data such as{"481541":[]}.
Package: bold-smart-lock
Bold Smart Lock Python PackageThis package implements the Bold Smart Lock API to authenticate and unlock a Bold smart lock. Usage of this API requires a Bold Connect.InstallationTo install dependencies during development runpip install .from the project directory.
Optionally use the included VSCode Dev Container to get a preconfigured envirionment.Usageimportasyncioimportaiohttpfrombold_smart_lock.authimportAbstractAuthfrombold_smart_lock.bold_smart_lockimportBoldSmartLockclassTestAuth(AbstractAuth):asyncdefasync_get_access_token(self)->str:return"00000000-0000-0000-0000-000000000000"# Obtain an access token with oAuth2 and specify it hereasyncdefmain():asyncwithaiohttp.ClientSession()assession:auth=TestAuth(session)bold=BoldSmartLock(auth)# Get the devices and device permissionsget_device_permissions_response=awaitbold.get_device_permissions()print(get_device_permissions_response)# Activate the smart lock by device idremote_activation_response=awaitbold.remote_activation(12345)print(remote_activation_response)# Deactivate the smart lock by device idremote_deactivation_response=awaitbold.remote_deactivation(12345)print(remote_deactivation_response)asyncio.run(main())
Package: bole
boleCascading configuration manager and logger for python (yaml, json)Why bole?Bole = "trunk of a tree" = "log" :)BETABole is a python configuration manager that has,Loads configurations fromyaml, jsonAllows inheritance - child folder can load config from parent folder.Allows imports - allows specifying config loading paths (and globs)Has an easy to use cli.InstallJust install the pippackage,pipinstallboleConfigurationExamplesettings:inherit:True# If true, allow inherit parent folders.environments:test:my_value:22dev:my_value:42my_value:0some_col:a:-b:0To view this configuration just run (in the config folder),boleconfigviewTo get the result ofmy_value, run,boleconfiggetmy_value# orboleconfiggetsome_col.a[0].bBuilt in keywords and structures.The following keywords are reserved (default values presented)settings:inherit:False# If true, allow inherit parent folders.inherit_siblings:True# If true allow inherit configuration files in the same source directory.allow_imports:True# If false dose not allow imports.use_deep_merge:True# Merge configurations via deep merge. If false, Only root keys are merged (and overwritten)concatenate_lists:True# When merging, append the merged list to the current one.imports:-"**/*.config.yaml"# Recursively import all .config.yaml-path:my-config.yamlrequired:False# this item is not required.recursive:null# Applies if glob. Import recursively.environments:[env name]:{ config overrides (any) }Example configurationExample configuration with inheritance can be found intests.ContributionFeel free to ping me in issues or directly on LinkedIn to contribute.Future implementationWe plan to support multiple python version per environment.Looking for help on this subject.LicenceCopyright ©Zav Shotan,Patrick Huber, and othercontributors.
It is free software, released under the MIT licence, and may be redistributed under the terms specified inLICENSE.
Package: bolero
boleroGetting startedPlease refer to thedocumentation. In particular, theAPI documentation.InstallationYou need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installingMiniforge.# 1. Download the environment YAML filewgethttps://raw.githubusercontent.com/lhqing/commons/main/envs/bolero_env.yaml# 2. Create a environment named boleromambaenvcreate-fbolero_env.yaml# OR if you use conda# conda env create -f bolero_env.yaml# Note that conda can be very slow in solving complex dependencies# 3. Install this packagepipinstallbolero# or install the package with dev modegitclonehttps://github.com/lhqing/bolero.gitcdbolero
pipinstall-e".[dev,test]"Release notesSee thechangelog.ContactIf you found a bug, please use theissue tracker.Citationt.b.a
Package: bolero-process
bolero-processData preprocessing for bolero packageGetting startedPlease refer to thedocumentation. In particular, theAPI documentation.InstallationYou need to have Python 3.9 or newer installed on your system. If you don't have
Python installed, we recommend installingMambaforge.There are several alternative options to install bolero-process:Install the latest development version:pipinstallgit+https://github.com/lhqing/bolero-process.git@mainRelease notesSee thechangelog.ContactFor questions and help requests, you can reach out in thescverse discourse.
If you found a bug, please use theissue tracker.Citationt.b.a
Package: bolg
bolg is an extended version of Python’s glob module. It allows for a small
amount of more features while still retaining the simplicity of glob. More
specifically, bolg mimics some of the features found in BASH’s globbing
algorithm.Extensive documentation is included in the library. To view it, runpydoc3 bolg.Licensebolg is free software under the terms of the Apache 2.0 license. The author of
bolg is Niels G. W. Serup, contactable atngws@metanohi.name. This is version 0.1.0 of
the program.InstallationTo install bolg the easy way, run:easy_install3 bolg(You must be a superuser and have python3-setuptools installed to do this.)Alternatively, you can download bolg either fromhttp://metanohi.name/projects/bolg/or fromhttp://pypi.python.org/pypi/bolgand then install it from the downloaded file. To install bolg this way, run:python setup.py installUsebolg is a Python module. There is no command-line utility or graphical
interface.Developmentbolg uses Git for code management. To get the latest branch, download it from
gitorious.org:$ git clone git://gitorious.org/bolg/bolg.gitThis documentCopyright (C) 2011  Niels G. W. SerupCopying and distribution of this file, with or without modification, are
permitted in any medium without royalty provided the copyright notice and this
notice are preserved.  This file is offered as-is, without any warranty.
Package: bolib
BOlibA python library for Bayesian Optimization.Setup BOlibCreate and activate virtualenv (for python2) or
venv (for python3)# for python3python3-mvenv.env# or for python2python2-mvirtualenv.envsource.env/bin/activateUpgrade pippython-mpipinstall--upgradepipInstall BOlib packagepython-mpipinstallbolibMatplotlib requires to install a backend to work interactively
(Seehttps://matplotlib.org/faq/virtualenv_faq.html).
The easiest solution is to install the Tk framework,
which can be found as python-tk (or python3-tk) on
certain Linux distributions.Use BOlibImport BOlib to use it in your python script.importbolibSome well-known objetive functions have been included.of=bolib.ofs.Branin()of.evaluate([1.0,1.0])# 27.702905548512433To use Bayesian Optimization we need a probabilistic model. In this example we will use Gaussian Processes.importgplibmodel=gplib.GP(mean_function=gplib.mea.Fixed(),covariance_function=gplib.ker.SquaredExponential(ls=([1.]*of.d)))metric=gplib.me.LML()fitting_method=gplib.fit.MultiStart(obj_fun=metric.fold_measure,max_fun_call=300,nested_fit_method=gplib.fit.LocalSearch(obj_fun=metric.fold_measure,max_fun_call=75,method='Powell'))validation=gplib.dm.Full()Bayesian Optimization also needs an acquisition function.af=bolib.afs.ExpectedImprovement()Finally, we can initialize our optimization model and start the optimization process.bo=bolib.methods.BayesianOptimization(model,fitting_method,validation,af)bo.set_seed(seed=1)x0=bo.random_sample(of.get_bounds(),batch_size=10)bo.minimize(of.evaluate,x0,bounds=of.get_bounds(),tol=1e-5,maxiter=of.get_max_eval(),disp=True)BOlib is also Scipy compatible.importscipy.optimizeasspobo.set_seed(seed=1)x0=bo.random_sample(of.get_bounds(),batch_size=5)result=spo.minimize(of.evaluate,x0,bounds=of.get_bounds(),method=bo.minimize,tol=1e-5,options={'maxiter':of.get_max_eval(),'disp':True})There are more examples in examples/ directory. Check them out!Develop BOlibUpdate API documentationsource./.env/bin/activatepipinstallSphinxcddocs/sphinx-apidoc-f-o./../bolib
Package: bolides
A package to analyze bolide data in Python.bolidesis a community package primarily designed to work with bolide detections from the Geostationary Lightning Mapper instruments aboard GOES-16 and GOES-17 that are published atneo-bolide.ndc.nasa.gov. Butbolidescan also read bolide data from ZODB database files produced by the GLM bolide detection pipeline, fromUS Government sensors, and from your own .csv files containing bolide data.Functionalitybolidesputs bolide detections from various sources into a common BolideDataFrame format. With this,bolidescan do things like:Automatically add metadata like lunar phase, solar time, and solar altitude to bolide detections.Filter the data sets by any variable.Search the data sets for particular bolides by time or location.Make histograms of bolides over time.Plot detections on arbitrary map projections, coloring by any categorical or quantitative variables.Plot GLM fields-of-view in the GOES-West and GOES-East positions, and filter bolide detections by the FOV.Augment one data set with data from another, automatically matching bolide detections from different sources.Pull corresponding bolide light curves fromneo-bolide.ndc.nasa.govand plot them.Pull meteor shower data from theIAU Meteor Data Centerand plot their orbits.Run aninteractive webapp.DocumentationAll package documentation is hosted atbolides.readthedocs.io.InstallationWe want to make installation as easy as possible. If you have any problems with the installation process, pleaseopen an issue.DependenciesIf using Conda, just use Conda to install cartopy:conda install-cconda-forgecartopy.If using pip:First,PROJneeds to be installed on your system using the installation instructions at the link.GEOSalso needs to be installed. On Ubuntu both can be installed withsudo apt installproj-binlibproj-devlibgeos-devNext, due toknown Cartopy and Shapely problems, Cartopy and Shapely need to be installed manually. This is done with:pip install numpy && pip installcartopy==0.18.0shapely--no-binarycartopy--no-binaryshapely. Note that an older Cartopy version is recommended to prevent it from requiring PROJ versions not yet in common repositories. If you already have PROJ 8.0.0, you may omit the==0.18.0and install the latest Cartopy version.The packageWhile the package is still in development we recommend installing from source:Download this repository:git clonehttps://github.com/jcsmithhere/bolides.gitMove into it:cd bolidesInstall the package in editable mode:pip install-e.Once this package is on the Python Package Index, you can install via pip usingpip install bolides.TutorialFor a usage tutorial, gohere. An interactive version is hosted onbinder.Historical NoteThe original version ofbolideswas developed by Clemens Rumpf and Geert Barentsen. It has been rewritten since then, but all of the original code and functionality is still present.AcknowledgmentsThis development is supported through NASA’s Asteroid Threat Assessment Project (ATAP), which is funded through NASA’s Planetary Defense Coordination Office (PDCO).
Anthony Ozerov is supported through NASA Cooperative Agreement 80NSSC19M0089.
Package: boli-orbital-api
Bolivarcoin/Bolicoin API (RPC)Node API Rpc main class for Bolivarcoin/BolicoinPara español vaya aREADME en españolWARNING:This document and documentation is in development, and it will be available on next releasesWARNING:This is a BETA stable version, issues and pull request are very welcomeThis project is a first public beta version
ofPropuesta DAO a superbloque 764,336 para desarrollo API y APPs periféricas alrededor del núcleoThis API is a first layer to communicate with Bolivarcoin/Bolicoin blockchain using a common node or masternode with user
credentials.On top of this API, developers can build Apps, frontends, bots, remote wallets, notifiers, transactions, monitoring, etc.Bolivarcoin Blockchain CompatibilityBolivarcoin version: 2000002 (v2.0.0.2-g)Protocol version: 70212You can to verify version usinggetinfocommand on node console.
Example:getinfo{"version":2000002,"protocolversion":70212,"walletversion":120200,"balance":15658.49718641,"privatesend_balance":0.00000000,"blocks":1234567,"timeoffset":0,"connections":8,"proxy":"","difficulty":12345678.901234,"testnet":false,"keypoololdest":1440858873,"keypoolsize":1999,"paytxfee":0.00000000,"relayfee":0.00001000,"errors":""}InstallationFrom PyPi:
pip install boli_orbital_apiFrom source code:
git clonehttps://github.com/Visionario/BoliOrbitalAPIUsageBasic use:
Communicate with your local node, it must be running on same pcfromboli_orbital_apiimportNodenode=Node(rpc_user="user",rpc_password="password")node.is_online# Truenode.getinfo()# {'result': {'version': 2000002, 'protocolversion': 70212, 'walletversion': 120200, 'balance': 15658.49718641, 'privatesend_balance': 0.0, 'blocks': 1234567, 'timeoffset': 0, 'connections': 8, 'proxy': '', 'difficulty': 36237.78062774216, 'testnet': False, 'keypoololdest': 1440858873, 'keypoolsize': 1999, 'paytxfee': 0.0, 'relayfee': 1e-05, 'errors': ''}, 'errors': False}{"result":{"version":2000002,"protocolversion":70212,"walletversion":120200,"balance":15658.49718641,"privatesend_balance":0.00000000,"blocks":1234567,"timeoffset":0,"connections":8,"proxy":"","difficulty":12345678.901234,"testnet":false,"keypoololdest":1440858873,"keypoolsize":1999,"paytxfee":0.00000000,"relayfee":0.00001000,"errors":""},"errors":false}Orbital API sends a json with {"result":..., "errors":...}Please take a look todocsfor details.
Package: bolivia-cc
Bolivia Codigo de ControlEl Código de control Es un dato alfanumérico generado e impreso por un sistema de facturación computarizado SFV al momento de emitir una factura y sirve sirve para determinar la validez o no de una factura.Ejemplo: CB-5E-CF-8B-05Está constituido por pares de datos alfanuméricos separados por guiones (-) y expresados en formato hexadecimal (A, B, C, D, E y F), no contene la letra “O” solamente el número cero (0). Se genera en base a información de dosificación de la transacción comercial y la llave asignada a la dosificación utilizando los algoritmos Alleged RC4, Verhoeff y Base 64 como se explica en laEspecificación Técnica para la generación del Código de Control.Este es una implementacion completa del generador y validacion del Código de ControlUso$ pip install bolivia-cc
$ bolivia_cc --generar \
    --autorizacion=7000000006000 \
    --factura=560001 \
    --nit=3200000 \
    --fecha=2023-01-01 \
    --total=10000 \
    --llave=SECRET \
7B-F3-48-A8importbolivia_cccodigo_control=bolivia_cc.generate_control_code(autorizacion="20040010113",factura="665",nitci="1004141023",fecha="20070108",monto="905.23",llave="442F3w5AggG7644D737asd4BH5677sasdL4%44643(3C3674F4",)assertcodigo_control=="771-D5-61-C8"