Saravanan666/pypi-org huggingface dataset:
Package: blaster
BlasterBlaster is a library that provides the ability to blast off a list of tasks
and call each of their given methods concurrently. Blaster uses Python's
built-in multiprocessing library to run the list of tasks.InstallationBlaster can be easily installed with a one line command. It is available onpypi. It is recommended (as best practice) to create a virtual
environment and install blaster. Please see the commands below to install
blaster.# Create a python virtual environment
python3 -m venv venv

# Activate the virtual environment
source venv/bin/activate

# Install blaster
(venv) pip install blasterExamplesAt the root of blaster project, you will see a examples folder. Within this
folder you will find simple examples on how you can use blaster to
efficiently run many tasks.OutputWhen blaster calls its blastoff method, on completion. It will return back
to you a list of task results. Within each task dictionary it will have the
original task data passed in along with a couple new keys. A status key which
is an integer (0 or 1) to determine pass or fail. If a task failed, it would
have a traceback key with the exception raised for helpful troubleshooting.TerminologyTaskA task is a python dictionary that defines the task to be blasted off. A task
must contain three keysname,taskandmethods. The name key
just tells blaster what the task name is. The task key is a Python class
reference. Finally the methods key is a list of methods to be run for the
given task. You can then define any other key:value pairs that will be passed
to the task given when an object is created for that class.Below is an example task for building a contemporary house. You will see
the task key has a value of the House class which contains all the methods
defined. Blaster will create a house object (passing any extra data in this
casestyle) and then call the methods defined.[{'name':'House #1','task':House,'methods':['foundation','frame','roof','furnish','enjoy'],'style':'contemporary'}]You also have the ability to set a timeout for each task. If the timeout is
reached, the task will be exited.[{'name':'House #1','task':House,'methods':['foundation','frame','roof','furnish','enjoy'],'style':'contemporary','timeout':10}]The nice feature with blaster is you can have multiple tasks but each one
can call various methods within that task class. They do not all need to call
the same methods! See the example below:[{'name':'House #1','task':House,'methods':['foundation','frame','roof','furnish','enjoy'],'style':'contemporary'},{'name':'House #2','task':House,'methods':['foundation','frame','roof'],'style':'cape'}]IssuesFor any issues that you may find while using blaster library. Please open a
new issue or you can open pull request.
Package: blaster-logger
Blaster LoggerTurn-key logging solution based onloguruInstallationpipinstallblaster_loggerUsageAs loggerfromblaster_loggerimportloglog.debug('This is DEBUG level message')log.info('This is INFO level message')log.warning('This is a warning')log.error('This is an error message')log.critical('This is a critical level message')try:raiseRuntimeError('Error message')exceptRuntimeErrorase:log.trace(e)# This is a traceback logAs decoratorfromblaster_loggerimportlog@log.thisdefsome_func(x):returnx*2
Package: blast-extract
Blast-ExtractExtract subsequences from a genome using NCBI BLAST and reference sequences.Minimal usage:extract-sequences--referencesreferences.fastagenome.fasta>extracted.fastaInstallationRequirements:Python 3.10or laterNCBIBLAST+ executables2.23.0 or laterThe BLAST bin directory must be added to the PATH.Install the package using pip. This will also create the entry point scripts to use the commands as described below.pipinstallblast-extractUsageAll commands can use STDIN and STDOUT, so can be chained using pipes (|) on UNIX-like systems.catgenome.fasta|extract-sequences--referencesreferences.fasta|hash-sequences>seqhashes.tsvCommandsextract-sequencesTheextract-sequencescommand extracts nucleotide sequences from an input (multi-)FASTA file. It requires a
multi-FASTA file with references to search for. Its output is a multi-FASTA whose headers start with the identifier
of the corresponding matched reference.The script will by default normalize and extend the BLAST results so they are in the same strand as the reference and
cover as much of the reference as possible. This is an important improvement over using solely BLAST, as its score
optimization may drop nucleotides at the outer ends of the alignment.Behind the scenes, a BLAST nucleotides database will be created, by default in the current working directory. You can
specify a different directory for the databases with--dbdir. The derived BLAST database will be updated if needed, by
comparing the last modification time of the files. Each reference filepath will generate a uniquely named database, so
can be used in conjunction.There are two filter options:--pident(default 80.0) for minimum percentage identity, and--pcov(default 80.0) for
minimum percentage coverage. By nature of using BLAST, less strict settings will increase the likelyhood of
false-negatives: when a subsequence may exist that satisfies the filters, but due to BLAST heuristics was not found. The
underlying blastn call will actually use a slightly lower percentage identity threshold and no coverage requirement.
Both are checked by the python script after post-BLAST corrections.hash-sequencesThehash-sequencescommand is used to get hash values for each sequence in an input multi-FASTA file. You may choose
any of the algorithms available to your python installation, which will be listed if you give an invalid value. It is
recommended to stick to the defaults unless needed for compatibility with other tools or organisations. The output uses
TSV format, with the first column containing the sequence name and the second containing the generated sequence hash.Copyright (C) Jan Deneweth 2022
Package: blastpipe
A simple utility library used as an integration and performance test for using
Meson+OZI as Python 3 packaging management layer.ContributingContributions are what make the open source community such an amazing place to
learn, inspire, and create. Any contributions you make aregreatly appreciated.If you have a suggestion that would make this better, please fork the repo and
create a pull request. You can also simply open an issue with the tag “enhancement”.
Don’t forget to give the project a star! Thanks again!Fork the repositoryCreate your Feature Branch (git checkout-bfeature/AmazingFeature)Commit your Changes (git commit-m'Add some AmazingFeature')Push to the Branch (git push origin feature/AmazingFeature)Open a Pull RequestBug ReportsCreate an issue with the tag “bug” with a descriptive title stating the issue succinctly.Fill out the issue template with the information requested.If you have any proposed changes related to a bug, if an Issue has not been created please
complete the above instructions.
The next steps are similar to the steps needed to create a feature pull request.Submitting a FixFork the repositoryCreate your Bugfix Branch (git checkout-bbugfix/Issue#)Commit your Changes (git commit-m'🐛: Fix Issue#')Push to the Branch (git push origin bugfix/Issue#)Open a Pull RequestLicenseblastpipe is released under the terms of the 2.0 version of the Apache License,
approved by the Apache Software Foundation. blastpipe meets the Open Source Initiative’s definition of
open source software, and the Free Software Foundation’s definition of GPLv3-compatible open
source software.NoteThe OSI logo trademark is the trademark of Open Source Initiative.
The blastpipe project is not affiliated with or endorsed by the Open Source Initiative.NoteThe Apache logo trademark is the trademark of the Apache Software Foundation.
The blastpipe project is not affiliated with or endorsed by the Apache Software Foundation.NoteThe FSF logo trademark is the trademark of the Free Software Foundation.
The blastpipe project is not affiliated with or endorsed by the Free Software Foundation.
Package: blast-score-ratio
Obtain BLAST score ratios (BSRs), for use in comparative genomics andidentifying horizontally transferred genetic material, from fastA filescontaining the protein sequences for different organisms.BSR (Rasko et al, 2006) is obtained by running BLAST using a reference proteomeagainst one or more other proteomes. The highest BLAST score for each referencesequence is normalised by dividing by the score for 100% match to the referencesequence. This analysis can identify shared genetic material in unrelatedstrains or species, and find genes unique to a particular strain, for example.A series of BLAST are performed and objects are created for each referencesequence containing the results of the analysis. Charts showing relative BSRin the form of a 2-D graph, histogram and heatmap can be quickly generated.This program should be run from within the Python environment usingblast_score_ratio.bsr.get_bsr(*args). All functions and classes are fullydocumented. The best way to understand how this works is to look at demo.pyfor an example project.Example:import blast_score_ratio.bsr as bsrbsr.test()Requires NCBI BLAST+ command line >=2.2.29 application available here:ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/BLAST binaries must be in your computer's path.Also requires biopython and matplotlib packages.tested with python v3.6.0, biopython v1.68, matplotlib v2.0.0 on Windows 10
Package: blastsight
BlastSightBlastSight is a 3D visualization software designed to aid in Mining research.InstallationYou can install BlastSight with the following command:pip install blastsightBlastSight requires the Python implementation of Qt5, and usesqtpyto abstract backends.This means that you need to install a backend yourself, using either of these commands:pip install pyqt5pip install pyside2Both backends should work, but if you find errors using one backend, try with the other!
You can read the documentation fromqtpyfor more information.UsageImplemented in Python 3.7 and qtpy, it's useful as a library and as an application,
so you can use it as a viewer, or integrate it to an application you're developing.Application ModeStart the application withpython -m blastsight.From there you can load elements with File > Load [element].More information in Help > Help.Integrable ModeYou can embed BlastSight's viewer within your application.Check the following code and adapt it to your needs.fromqtpy.QtWidgetsimportQApplicationfromqtpy.QtWidgetsimportQWidgetfromqtpy.QtWidgetsimportQGridLayoutfromblastsight.view.integrableviewerimportIntegrableViewerclassEmbeddedViewer(QWidget):def__init__(self,parent=None):super().__init__(parent)self.setWindowTitle('EmbeddedViewer')self.resize(800,600)self.viewer=IntegrableViewer(self)self.layout=QGridLayout(self)self.layout.addWidget(self.viewer,0,0,1,1)if__name__=='__main__':app=QApplication([])embedded=EmbeddedViewer()embedded.show()app.exec_()Viewer ModeYou can also use BlastSight as a simple viewer when you write your own script.Insert the following lines in your script:fromblastsight.view.viewerimportViewerviewer=Viewer()# Your codeviewer.show()Basic APIThe following methods can be used to render your elements directly.
Keep in mind that these methods receive their arguments askwargs, they're not positional.# Meshviewer.mesh(x:list,y:list,z:list,indices:list,color:list,alpha:float,wireframe:bool,highlight:bool)# Blocksviewer.blocks(x:list,y:list,z:list,block_size:list,values:list,vmin:float,vmax:float,colormap:str)# Pointsviewer.points(x:list,y:list,z:list,point_size:float,values:list,vmin:float,vmax:float,colormap:str)# Linesviewer.lines(x:list,y:list,z:list,color:list,loop:bool)# Tubesviewer.tubes(x:list,y:list,z:list,color:list,loop:bool,radius:float,resolution:int)Notes:An additional 'name'kwargscan be used to give each element a name.Foreveryelement, you can replace (x, y, z) withvertices, which is a list
of positions, where each position is a list of (x, y, z).Formeshes, theindicesargument is a list of index, where index is a list of
(i1, i2, i3).Forblocksandpointsyou can replace (values, vmin, vmax) withcolor,
which is a list of colors for each position, where each color is a list of (r, g, b),
between 0.0 and 1.0.ExamplesBlastSight comes with a folder of examples that show what you can do with it.It's recommended to checkexamples/demo.pyinhttps://github.com/gsanhueza/BlastSight/to develop an idea of how to use this software.
Package: blasy
A(n almost) transparent replacement for yapsy made for python 3.4+.I kept having issues with Yapsy so here we are. No complaints with the
authors of Yapsy though, they never got to hear my anguish because I was
on a tight schedule to finish a project. Perhaps I just didn’t get how it was supposed to work. You might have better luck.In any case this is a quick and very basic implementation of a plugin framework. Documentation may follow (check Yapsy documentation for now) or I may dig deeper into Yapsy to solve the issues I had if they are compatible with how I would like the plugin framework to act.Since I already had the logic in place for the existing Yapsy methods I have used identical names, including their intended functionality. This is done even if unnecessary or overkill in this basic package. Thus it should be easy to go back to Yapsy if that makes sense at a later point.Note: Alpha for now - YMMV.To install:pip install blasy
Package: blatex
What is this?This is a cli tool for managing latex projects.Featuresblatex init: Initialize latex document with templatesblatex compile: Compile from any sub-directory of the project.blatex clean: Clean temporary files from any sub-directory.blatex packages: List packages used by the document, and mark if they are installed. It will also recommend texlive packages that contain the missing tex package.blatex errors: Parse errors and warnings, and display them nicely.blatex templates: list available templates and their sources.DependenciesThe default latex engine islatexmk. This can however be altered by editing the commands in the '.blatex' file in the root directory (this file is generated when initializin the project).Package functionality requires the use of texlive for package management.This package has only been tested on linux, but there are plans to get it workning on windows.Getting StartedMake sure you havelatexmkor another latex compiler installed. This package works withlatexmkout of the box so it is recomended.Run the following in any directory:blatexinitThis is now root of your latex project. If the directory is empty, you will be prompted to use a template.Compile the document by running this command from any sub-directory of the project:blatexcompileAll features of every command or command group can be found by passing the '-h' flag.Configuration filesblatex uses two separate configuration files. One local to the current document and one global to the entire system.Local Configuration FileUpon initializing a project, a hidden file with the name '.blatex' will appear in the project root. This file is used by blatex as a config file, but also to locate the root directory of the project.This file contains json data for configuring blatex in this project specifically.Here are the settings:OptionDescriptionmain-fileThe main '.tex' file of the project.main-file-placeholderThe string that will automatically be replaced by the main file path in the other options.compile-cmdThe command used for compiling the document. Change this if you are not using latexmk.clean-cmdThe command used for cleaning up temporary files in the root directory.Global Configuration FileThis file contains the global configuration of blatex and contains setting regarding custom templates and among other things.This file is found here: '~/.config/blatex/config.json'.If you have not made your own yet, you can simply run the following command:blatexconfigglobalcreateThis will create a global configuration file with the default configuration.Here is a list of global options:OptionDescriptionenable_builtin_templatesEnable the templates built into the blatex pip packagecustom_template_dirsList of directories to look for templates ('.zip' files) inpackage-install-locationLocation where texlive packages are installed. This is used in theblatex list packagescommand.
Package: blather
Train and use generative text models in a few lines of code.InstallationUse the package managerpipto
install blather.pipinstallblatherFine tuning large generative language models in tractable time require
the use of at least a single GPU. For the time being running blather on
a CPU only system will cause errors. This may be addressed in the futureUsagefromblatherimportBlatherblather=Blather()# fine tunes an appropriate model on your datasetblather.read(['Text Examples One','Second Text Example'...'Text Example k'])# returns a text sample generated from the modelblather.write('Sample text to complete')# saves modelblather.save('model.pt')# load model from previous trainingblather.load('model.pt')Contributinghttps://github.com/bigthonk/blatherPull requests are welcome. For major changes, please open an issue first
to discuss what you would like to change.Please make sure to update tests as appropriate.LicenseApache
Package: blatt
BlattNLP-helper for OCR-ed pages inPAGE XMLformat.Table of contentsInstallationHow to useCommand Line InterfaceInstallationpipinstallblattorgitclonehttps://github.com/UB-Mannheim/blattcdblatt/
pipinstall.How to usePage objectOn initiation the Page-class reads the filePAGEXMLand stores TextRegions, TextLines and Baseline Coordinates in the Page-objectp.from blatt import Page
p = Page(PAGEXML)The Page-object stores unprocessed and processed TextLines as attributes.print(p)
[('root', 2),
 ('namespace', 63),
 ('filename', 24),
 ('text_regions_xml', 38),
 ('text_lines_xml', 260),
 ('text_regions', 260),
 ('text_lines', 260),
 ('baselines', 3651),
 ('text_with_linebreaks', 12111),
 ('text_without_linebreaks', 11979),
 ('sentences', 102),
 ('x_baselines', 3651),
 ('y_baselines', 3651),
 ('center_baseline', 2)]Hyphen remover & converter to_txt()The plain text can be saved toTXT:from blatt import Page
p = Page(PAGEXML)
p.to_txt(TXT)By default it saves the plain text without line breaks (the hyphens '-', '-', '⹀' and '⸗' are removed and the corresponding words are merged). If you need line breaks, usep.to_txt(TXT, linebreak=True).Sentence splitter & converter to_tsv()The TextLines or sentences can be saved toTSV:from blatt import Page
p = Page(PAGEXML)
p.to_tsv(TSV)By default it saves TextLines, TextRegionID, TextLineID and Coordinates to TSV. If you usep.to_tsv(TSV, sentence=True), it saves sentences (not lines!) into separate lines of TSV. The sentences are split from the plain text without hyphens using theSegToklibrary.Command Line Interface% blatt        
Usage: blatt [OPTIONS] COMMAND [ARGS]...

  Blatt CLI: NLP-helper for OCR-ed pages in PAGE XML format. To get help for a
  particular COMMAND, use `blatt COMMAND -h`.

Options:
  -h, --help  Show this message and exit.

Commands:
  to_tsv  Converts PAGE XML files to TSV files with TextLines or sentences
  to_txt  Converts PAGE XML files to TXT files with or without line breaks &
          hyphens% blatt to_txt -h
Usage: blatt to_txt [OPTIONS] PAGE_FOLDER TEXT_FOLDER

  blatt to_txt: converts all PAGE XML files in PAGE_FOLDER to TXT files
  with/without hyphens in TEXT_FOLDER.

Options:
  -lb, --linebreak BOOLEAN  If linebreak==False, it removes hyphens at the end
                            of lines and merges the lines without line breaks.
                            Otherwise, it merges the lines using line breaks.
                            [default: False]
  -h, --help                Show this message and exit.% blatt to_tsv -h
Usage: blatt to_tsv [OPTIONS] PAGE_FOLDER TSV_FOLDER

  blatt to_tsv: converts all PAGE XML files in PAGE_FOLDER to TSV files in
  TSV_FOLDER.

Options:
  -s, --sentence BOOLEAN  If sentence==False, it saves TextLines,
                          TextRegionID, TextLineID and Coordinates to TSV.
                          Otherwise, it saves sentences (not lines!) into
                          separate lines of TSV. The sentences are split from
                          the plain text without hyphens using the SegTok
                          library.  [default: False]
  -h, --help              Show this message and exit.
Package: blaupause
Blaupause - Python package templateMartin Lang1and Marijan Beg11Faculty of Engineering and Physical Sciences, University of Southampton, Southampton SO17 1BJ, United KingdomDescriptionBadgeBuildsCoverageDocumentationBinderLicenseDOIAboutA sample Python-based package that can be used a tutorial for setting up a project.Demonstrated are:Testing with pytest/doctestscontinuous integrationTravisAppveyorsoon: GitHub actionscode coveragedockermake filespackagingdocumentationlicensingIt is available on Windows, MacOS, and Linux. It requires Python 3.8+.DocumentationAPIs and tutorials are available in documentation. To access them, use the documentation badge in the table above.Installation, testing, and upgradeWe recommend installation usingcondapackage manager. Instructions can be found in the documentation.BinderThis package can be used in the cloud via Binder. To access Binder, use the Binder badge in the table above.SupportIf you require support, have questions, want to report a bug, or want to suggest an improvement, please raise an issue in this repository.LicenseLicensed under the BSD 3-Clause "New" or "Revised" License. For details, please refer to theLICENSEfile.How to citePlease cite this package as:Martin Lang and Marijan Beg. Blaupause - Python package template. Zenodo. DOI:10.5281/zenodo.4327500(2020).AcknowledgementsEPSRC Programme grant onSkyrmionics(EP/N032128/1).
Package: blazar
Team and repository tagsBlazarBlazar is a resource reservation service for OpenStack. Blazar enables users
to reserve a specific type/amount of resources for a specific time period and
it leases these resources to users based on their reservations.The following two resource types are currently supported:Compute host: reserve and lease with a unit of a whole hostInstance: reserve and lease with a unit of a flavorPlease see the following resources to learn more.APISeeBlazar API reference.OperatorsTo learn how to deploy and configure Blazar,
seethe installation guideandthe configuration reference.DevelopersTo learn how to contribute to Blazar, seethe contributor guide.Other ResourcesSource code:BlazarNova scheduler filterClient toolsDashboard (Horizon plugin)Blueprints/Bugs:https://launchpad.net/blazarDocumentation:https://docs.openstack.org/blazar/latest/Release notes:https://docs.openstack.org/releasenotes/blazar/Design specifications:https://specs.openstack.org/openstack/blazar-specs/
Package: blazar-dashboard
Team and repository tagsBlazar dashboardHorizon plugin for the Blazar Reservation Service for OpenStackFeaturesSee doc/source/index.rstEnabling in DevStackNot yet supportedManual InstallationSee doc/source/install.rstOther ResourcesSource code:BlazarNova scheduler filterClient toolsDashboard (Horizon plugin)Blueprints/Bugs:https://launchpad.net/blazarDocumentation:https://docs.openstack.org/blazar/latest/Release notes:https://docs.openstack.org/releasenotes/blazar-dashboard
Package: blazebase
BlazeBase: A replacement to Pyrebase written in modern pythonWarningCurrently invery very veryearly developpement... Not much has been added yet...ConfigInitial Setup:fromBlazeBaseimportBlazeBaseconfig={"serviceAccount":"Dict with service account information or the path to the json file",# Optional arguments below, omit if not useful"databaseURL":"Url to the firebase database","storageBucket":"Url to storagebucket","projectId":"Project Id","databaseAuthVariableOverride":"Auth variable override","serviceAccountId":"Service account Id","httpTimeout":"Time in seconds"}blaze=BlazeBase(config)