Saravanan666/pypi-org huggingface dataset:
Package: genetist
Genetist: A genetic algorithm powered hyperparameter optimization frameworkGenetist is a high level framework that helps optimizing functions using the power of genetic algorithms.1. InstallationGenetist is available atPyPI$ pip install genetist2. Quickstart2.1. Define Search Space2.1.1. Fixed Search Space#defining a fixed set of Parameters for 4 variablesparams={'x':[35,-51,0,1,2,3,4,66,11,50,90],'y':[-100,-51,0,7,32,31,4,51,121,50,90,1000,231]'z':[-10,-51,0,12,2,43,43,5,1231,50,90],'k':[-56,-51,0,1,2,13,4,5,11,50,90]}2.1.2. Flexible Search Spacefromgenetist.parametersimportParameters#defining a 4 variable search space of float values from -100.0 to 100.0params={'x':Parameters.suggest_float(-100,100),'y':Parameters.suggest_float(-100,100),'z':Parameters.suggest_float(-100,100),'k':Parameters.suggest_float(-100,100)}2.2. Define Single-Objective Function#defining an objective functiondefobjective(individual):x=individual['x']y=individual['y']z=individual['z']k=individual['k']return(x**2-4*y**3/z**4)*k**32.3. Define Multi-Objective Function#defining an objective functiondefobjective(individual):x=individual['x']y=individual['y']z=individual['z']k=individual['k']objective_1=((x**2-4*y**3/z**4)*k**3)objective_2=(k**3/x)returnobjective_1,objective_22.4. Start Optimization for Single-Objective Functionfromgenetist.environmentimportEnvironmentif__name__=='__main__':#defining our Environment instance with a population of 100 individuals,#one-point crossover, a single gene mutation with a 25% probability of mutation#some verbose and a seed for reproducibilityenvironment=Environment(params=params,num_population=100,crossover_type='one-point',mutation_type='single-gene',prob_mutation=0.25,verbose=1,random_state=42)#minimizing the objective function and adding#3 stop criterias (num_generations, timeout, stop_score)results=environment.optimize(objective=objective,direction='minimize',num_generations=9999,timeout=60,stop_score=-np.inf)2.5. Start Optimization for Multi-Objective Functionfromgenetist.environmentimportEnvironmentif__name__=='__main__':#defining our Environment instance with a population of 100 individuals,#one-point crossover, a single gene mutation with a 25% probability of mutation#some verbose and a seed for reproducibilityenvironment=Environment(params=params,num_population=100,crossover_type='one-point',mutation_type='single-gene',prob_mutation=0.25,verbose=1,random_state=42)#minimizing the first value and maximazing the second value of the objective function,#adding 1 stop criterias (timeout), adding 50% weight to each objective and#assigning a name to each objective score for the final dataframeresults=environment.optimize(objective=objective,direction=['minimize','maximize'],weights=[0.5,0.5],timeout=60,score_names=['complex_equation_score','simple_equation_score'])2.6. Show Optimization  Resultsprint(f'EXECUTION TIME={results.execution_time}')print(f'BEST SCORE={results.best_score}')print(f'BEST INDIVIDUAL={results.best_individual}')print('BEST PER GENERATION:')print(results.best_per_generation_dataframe)
Package: genetools
genetools: single-cell analysis recipes (work in progress)Plot galleryOther featuresCompare clustering results by computing co-clustering percentage.Map marker genes against reference lists to find names for your clusters.pandas shotrcuts:Split single cell barcodes conveniently.Defensive pandas merging and concatenation methods with strict correctness checks.Full documentation:https://genetools.maximz.com.InstallRunpip install --upgrade 'genetools[scanpy]'.Or if you don't use scanpy:pip install --upgrade genetools.UsageTo use genetools in a project, addimport genetools. Review thedocumentationand thetestsfor examples.DevelopmentSetup:gitclonegit://github.com/maximz/genetoolscdgenetools
pipinstall--upgradepipwheel
pipinstall-rrequirements_dev.txt
pre-commitinstallCommon commands:# lintmakelint# one-time: generate test anndata, and commit so we have reproducible tests in CIrm-rdata
makeregen-test-data# run tests locally# this is done in a debian-based docker image to ensure image style matches what Github Actions CI will produce# failing image snapshot tests are recorded in tests/results/makebuild-docker-test-image# whenever requirements_dev.txt changemaketest# generate baseline figures (also happens in docker)makeregen-snapshot-figures# regenerate test data, and baseline figures (also happens in docker)makeregen-test-data# run tests locally without docker, therefore omitting the snapshot tests# (the @snapshot_image tests are still executed but the images are not compared. the @pytest.mark.snapshot_custom are skipped altogether.)maketest-without-figures# docsmakedocs# bump version before submitting a PR against master (all master commits are deployed)bump2versionpatch# possible: major / minor / patch# also ensure CHANGELOG.md updatedCI:Main: Github ActionsDocs:https://app.netlify.com/sites/genetoolsChangelog0.7.0Many new stats, plotting, and helper functions. See PRs#24and#73.0.6.0Two new functions to customize tick labels on any existing plot:wrap_tick_labels: add text wrappingadd_sample_size_to_labels: add group sample sizes with a(n=N)suffixMake writing PDF figures a deterministic process and make the PDF text editable.Scatterplot improvements:Adjust default marker shape and size to work better for most plots.Adjust HueValueStyle so that an explicit marker size is not specified there, only a marker size scaling factor. The scatterplot itself is responsible for defining the base marker size, while the palette of HueValueStyles should be drawable at any marker size.Change legends so that only one marker is drawn to indicate a group's style.0.5.0 (2022-01-10)Improve scatter plots and stacked bar plots.IntroduceHueValueStylefor granular styling of each hue.0.4.0 (2020-07-22)Centered log ratio (CLR) normalization for Cite-seq protein data.0.3.0 (2020-06-03)Pandas helpers for easier normalization0.2.0 (2020-06-03)Far faster implementation ofstats.coclusteringIntroducinghelpers.make_slurm_commandGlobal submodule import (no longer need to import submodules individually)0.1.0 (2020-03-06)First release on PyPI.
Package: geneutil
geneutila package for handling genesDependencypython 3.6requirements: numpy, pandas, scipy, tqdmSetuppip install geneutilfor conda environment, please use skeletonUsagesee samplecode.ipynbLicenceThis software is released under the MIT License.AuthorsMIZUNO TadahayaReferencesThis package is inspired from the following brilliant databases and studies:Nat Genet. 2003 Jul;34(3):267-73.PNAS. October 25, 2005 102 (43) 15545-15550.BMC Bioinformatics. 2013;128(14).Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377 .Science. 2006 Sep 29;313(5795):1929-35.MsigDBEnrichRCMapBug ReportIf you would like to report any bugs about this package, don't hesitate to create an issue on github here, or email me:tadahaya@gmail.comtadahaya@mol.f.u-tokyo.ac.jptadahaya@g.ecc.u-tokyo.ac.jp
Package: genevieve
GenevieveGENerateEnVIronmEntVariablesEverywhere.This is an extremely simple utility that produces:env.ps1PowerShell scriptenv.envBourne Shell scriptThe input is ayamlfile in the form of:variables:SOME_KEY:'some_value'In POSIX shells the generatedenv.envcan be used via:source env.envto set the environment variables set in the YAML file.
In PowerShell theenv.ps1script should be run directly:./env.ps1.TroubleshootingScript execution permissionsPowerShellAdjust yourExecutionPolicy.Bourne shellRunchmod +x env.env.
Package: geneweaver-boolean-algebra
Geneweaver - Boolean Algebra ToolThe Boolean Algebra Tool performs basic set operations on at least two Gene Sets.
Results are displayed as lists of genes belonging to one of the three different types of
set operations: Union, Intersect, and Symmetric Difference. Furthermore, results allow
users to quickly determine new relationships between Gene Sets and create a new Gene Set
based on set-derived findings.InstallationFrom PyPIpippipinstallgeneweaver-boolean-algebrapoetrypoetryaddgeneweaver-boolean-algebraFrom SourceInstalling from source requires python 3.9 andpoetry.gitclonegit@github.com:TheJacksonLaboratory/geneweaver-boolean-algebra.gitcdgeneweaver-boolean-algebra
poetryinstallUsageSee usage example inGeneweaver Docs.
Package: geneweaver-client
Geneweaver ClientThis is a client for theGeneweaverAPI. It is written in
Python 3.9 and is intended to be used as a library for other applications. It can also
be used as a command line tool.InstallationThis library is tested on python version3.9,3.10, and3.11, on MacOS and on
Ubuntu Linux. The library should work on any version of python3.9or higher.From PyPIpipinstallgeneweaver-clientFrom SourceInstalling from source requires python 3.9 andpoetry.gitclone$GIT_URLcdgeneweaver-client
poetryinstallUsageAs a libraryUsing Authentication Toolsfrom geneweaver.client import auth
auth.login()
auth.get_access_token()Complete ExampleSee theGeneweaver DocsAs a command line toolgweave--helpGeneWeaver CLI client.Usage:$gweave[OPTIONS]COMMAND[ARGS]...Options:--version--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.Commands:alpha: These commands are in alpha testing.beta: These commands are in beta testing.gweave betaThese commands are in beta testing.They are subject to future change and/or removal. Beta commands are
intended to be released beyond beta testing, but may have bugs or other
issues. There is also no guarantee that beta commands will be released
beyond beta testing.Use at your own risk.Usage:$gweavebeta[OPTIONS]COMMAND[ARGS]...Options:--help: Show this message and exit.Commands:authgweave beta authUsage:$gweavebetaauth[OPTIONS]COMMAND[ARGS]...Options:--help: Show this message and exit.Commands:login: Run the device authorization flow.gweave beta auth loginRun the device authorization flow.:param reauth: Force a re-authenticationUsage:$gweavebetaauthlogin[OPTIONS]Options:--reauth--help: Show this message and exit.
Package: geneweaver-core
Geneweaver CoreThe Geneweaver Core Python library provides shared foundational functionality for the Geneweaver project.
It is a dependency of all other Geneweaver Python libraries, and is not intended to be used directly.InstallationThe Geneweaver Core library is available on PyPI and can be installed with pip:pipinstallgeneweaver-coreIf you are using Poetry, you can add the Geneweaver Core library to your project with:poetryaddgeneweaver-coreOverviewThis package is structured so as to share an import path with othergeneweaverpackages. This allows you to install
the package and import it without having to worry about the package name. For example, if you install thegeneweaver-corepackage, as well as thegeneweaver-dbpackage, you can import thegeneweaverpackage and access both libraries:fromgeneweaverimportcore,dbThe Geneweaver Core library provides the following functionality:geneweaver.core.schema: Pydantic schema definitionsgeneweaver.core.enum: Enumerationsgeneweaver.core.config: Configuration managementGeneweaverBaseSettings: Base Settings class to inherit from for your own package's configuration classesGeneweaverCoreSettings: Configuration class for Geneweaver Core settingsgeneweaver.core.exc: Geneweaver shared exceptionsGeneweaverException: Base exception class for GeneweaverGeneweaverError: Base error class for GeneweaverGeneweaverWarning: Base warning class for Geneweavergeneweaver.core.pase: Geneweaver file parsing functionalitybatch: Functions for parsing a batch filescore: Functions for parsing a scorecsv: Functions for parsing a CSV filexlsx: Functions for parsing an Excel fileenum: Enumerations for file parsingexceptions: Exceptions for file parsingutils: Utility functions for file parsingPlanned Functionalitygeneweaver.core.logging: Shared logging managementgeneweaver.core.utils: Shared utility functions
Package: geneweaver-testing
Geneweaver TestingThis package is used to test the Geneweaver project. It contains tools for running tests
against Geneweaver project packages and components to aid in the development of
Geneweaver.Quick StartInstall the packagepoetryinstall-Gdevgeneweaver-testingMake a "common" test filetouch tests/common.pyAdd the following to the "common" test file# Inside tests/common.py
from geneweaver.testing import *Add a fixture file at test root (if you don't have one already)touch tests/conftest.pyAdd the following to the fixture file# Inside tests/conftest.py
from geneweaver.testing.fixtures import *Run Tests!pytesttestsPackage ModulesLike all Geneweaver packages, this package is namespaced under thegeneweaverpackage.
The root of this package isgeneweaver.testing. The package is structured for usage in
pytest tests, with pre-defined tests available through splat (*) imports as shown in
the Quick Start. Other package functionality is available by specifically importing
modules.The following modules are available in this package:geneweaver.testing.fixturesThis module contains pytest fixtures that are used to test Geneweaver packages. These
fixtures can be used to set up test contexts for Geneweaver packages. This module does
not contain any tests.geneweaver.testing.packageThis module contains tools for testing and validating Geneweaver packages.ContributingContributions to this package are welcome. Please see
theContributingdocument for more information.
Package: genewiz-template-validator
Validate GENEWIZ template files, sample map templates and
container templates.Installation1. Install pipcurl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py2. Install the packagepip install -i https://test.pypi.org/simple/ genewiz-template-validator3. Check if it works.validate_genewiz_templates -hTo get help:validate_genewiz_templates -h

usage: validate_genewiz_templates [-h]
                              container_template_name.xlsx
                              sample_template_name.xlsx
                              [sample_template_name.xlsx ...]
The following arguments are required:
    container_template_name.xlsx, sample_template_name.xlsxTo run this validator:validate_genewiz_templates container_template.xlsx sample_template_1.xlsx sample_template_2.xlsxThe validator checks the following:That the provided sample map and container template can be found and are readable.That the sample map template files are listed in the container template.That there are no extraneous sample map entries in the container template.That the format of the sample id matches the expected naming scheme:G0015[89]xxx_Vxx_Pxx_R2_[HKL]C_[A-H]xxIn the event that any of these validation checks fail, the validator
will exit with  an error message and produce a “log” fileGENEWIZ_template_validation.login the current directory, that can be
inspected to identify the errors it found and to correct them.
Package: gen-exe
gen-exeA small utility which allows you to generate Windows executables that can run custom commands on your Windows system.Featuresgenerate portable executables that can run customizable commandscommands can use the{EXE_DIR}macro to get the directory relative to the executablethe generated executable supports passing command-line argumentsyou can add icons during or after generation of the executableinstallation adds two CLIs:gen-exeandadd-icon-to-exeInstallationInstall from PyPi using:pip install gen-exeUsage gen-exeCustom commands can be embedded in the executables by providing a command string to the CLI, for example:gen-exe test.exe "echo hello world"The command string argument also supports the{EXE_DIR}macro, which expands the path where the
executable is executed from, for example:gen-exe test.exe "echo I am running from: {EXE_DIR}"This can be used to run relative executables:gen-exe test.exe "{EXE_DIR}\\another.exe"Optionally you can provide an icon file for the executable.gen-exe test.exe "echo I have a fancy icon now..." -i path-to-your.icoAnother use case is to call a script or command using a Python interpreter, for example:gen-exe test.exe "python -c print(\'hello world\')"For other options see the help:gen-exe --helpUsage generated executablesExecute them by double clicking or via the command line:test.exe optional_argument_1 optional_argument_2Usage add-icon-to-exeTo add an icon calledtest.icoto atest.exeexecutable file.add-icon-to-exe test.exe test.icoNote that the utility will replace any icons that already exist in the target executable.ContributingFork the gen-exe repositorySetup your forked repository locally as an editable installation:$ cd ~
$ git clone https://github.com/yourproject/genexe
$ pip install --editable ./genexeNow you can work locally and create your own pull requests.Feel free to open issues and pull requests.MaintainerSil van de LeemputHistory0.2.1 (2021-02-08)Added hide-console option to the executable and the CLI0.2.0 (2021-02-07)Embedded runtimes in the executable. Executable should now work on Windows systems without VC++ redistributables installed0.1.1 (2021-02-06)Better documentation - updated the README.md0.1.0 (2021-02-06)Initial release on PyPi
Package: gen-form-model
Generate Form Model (Django/Flask)gen_form_modelis tool for generation form model for:Django FWKFlask FWKDeveloped inpythoncode:100%.The README is used to introduce the modules and provide instructions on
how to install the modules, any machine dependencies it may have and any
other information that should be provided before the modules are installed.Table of ContentsInstallationInstall using pipInstall using setuptoolsInstall using dockerDependenciesTool structureDocsCopyright and LicenceInstallationCurrently there are three ways to install tool:Install process based on pipInstall process based on setup.py (setuptools)Install process based on docker mechanismInstall using pipgen_form_modelis located atpypi.org.You can install by using pip# python3
pip3 install gen-form-modelInstall using buildNavigate torelease pagedownload and extract release archive.To installgen-form-modelruntarxvzfgen-form-model-x.y.z.tar.gzcdgen-form-model-x.y.z# python3wgethttps://bootstrap.pypa.io/get-pip.py
python3get-pip.pypython3-mpipinstall--upgradesetuptools
python3-mpipinstall--upgradepip
python3-mpipinstall--upgradebuild
pip3install-rrequirements.txt
python3-mbuild-s--no-isolation--wheel
pip3installdist/gen-form-model-x.y.z-py3-none-any.whl
rm-fget-pip.pyInstall using py setupNavigate to releasepagedownload and extract release archive.To installgen_form_modeltype the followingtarxvzfgen_form_model-x.y.z.tar.gzcdgen_form_model-x.y.z/# python3pip3install-rrequirements.txt
python3setup.pyinstall_lib
python3setup.pyinstall_data
python3setup.pyinstall_egg_infoInstall using dockerYou can use Dockerfile to create image/container.Dependenciesgen_form_modelrequires next modules and libraries:ats-utilities - Python App/Tool/Script UtilitiesTool structuregen_form_modelis based on OOP.Generator structuregen_form_model/
        ├── conf/
        │   ├── gen_form_model.cfg
        │   ├── gen_form_model_util.cfg
        │   ├── project.yaml
        │   └── template/
        │       ├── django.template
        │       └── flask.template
        ├── __init__.py
        ├── log/
        │   └── gen_form_model.log
        ├── pro/
        │   ├── __init__.py
        │   ├── read_template.py
        │   └── write_template.py
        └── run/
            └── gen_form_model_run.py
        
        6 directories, 11 filesDocsMore documentation and info atgen_form_model.readthedocs.iowww.python.orgCopyright and LicenceCopyright (C) 2017 - 2024 byvroncevic.github.io/gen_form_modelgen_form_modelis free software; you can redistribute it and/or modify
it under the same terms as Python itself, either Python version 3.x or,
at your option, any later version of Python 3 you may have available.Lets help and support PSF.
Package: gen-gender
gen_genderПакет позволяет сменить род ответов с мужского на женский.Пример>>>gen_gender.swap("Я тот самый учитель.")"Я та самая учительница">>>gen_gender.swap("Я не женат. У меня два брата и одна сестра.")"Я не замужем, у меня два брата и одна сестра."Типы обрабатываемых заменЗамена рода выполняется только для конструкций в 1 лице ед. числеЗамена сказумых, выраженных глаголом в прошедшем времениЗамена дополнений, выраженных соуществительным с зависимым прилагательнымЗамена зависимых от существительного в 1 лице ед. числе или местоимения причастных и деепричестных оборотовЗамена указательных, притяжательных, неопределенных, относительных, определительных, отрицательных местоименийИспользуемые библиотекиpymorphy3stanzaДополнительные файлыsrc/pkl словари альтернативsrc/txt оригинальные файлы для редактирования
Package: gengir
GenGIR: Genuine* autocompletion for your PyGObject code!fakegiris a tool to build a fake python package of PyGObject modules.GenGIR is a fork of fakegir that uses modern standards and improves on usabilityThe main changes are:UsePEP 484type annotations instead of docstringsInstall typings as aPEP 561stubUse Sphinx markup on docstringsFields are typed nowA cliGenGIR stores the type info inside your user or venv site-packages as a package namedgi-stubs.Once it's installed, it should be recognized by your IDE and it should provide autocompletion and typing errors.Installationgengir is available onpypi, install it using$ pip install gengiror add it as a development dependency if you're using poetryTODODocumentation formatting (code snippets, links)Signals asLiteralsBuildingThis project usespoetry, so make sure to have that installedThen runpoetry installandpoetry build. A wheel file should be created in the dist directory that can be installed usingpip install ./dist/gengir*.whlUsageThe*.girwith the type info files should be included with each GNOME library development package in/usr/share/gir-1.0/.gengir [OPTIONS] [TYPES]...

  Generate PEP 561 stubs for the GObject introspection library.

Arguments:
  [TYPES]...  Files to use as input for the generator. If not provided it uses
              all files in /usr/share/gir-1.0/

Options:
  -o, --outdir PATH               Directory to store the package typings.
                                  $site-packages/gi-stubs by default
  --docs / --no-docs              Include docstrings in the typings  [default:
                                  docs]
  --gtk INTEGER                   GTK version to generate typings for
                                  [default: 3]Editor supportVSCode has support for stub packages out of the box.Jedisupports it too, so any editor using it should work.
Package: gengive
GengiveRender text (Danish: gengive tekst).License: MITThird party dependencies are documented in the folderthird-party.DocumentationUser and developerdocumentation of gengive.Bug TrackerAny feature requests or bug reports shall go to thetodos of gengive.Primary Source repositoryThe main source ofgengiveis on a mountain in central Switzerland.
We use distributed version control (git).
There is no central hub.
Every clone can become a new source for the benefit of all.
The preferred public clones ofgengiveare:on codeberg- a democratic community-driven, non-profit software development platform operated by Codeberg e.V.at sourcehut- a collection of tools useful for software development.ContributionsPlease do not submit "pull requests" (I found no way to disable that "feature" on GitHub).
If you like to share small changes under the repositories license please kindly do so by sending a patchset.
You can either send such a patchset per email usinggit send-emailor
if you are a sourcehut user by selecting "Prepare a patchset" on the summary page of your fork atsourcehut.StatusExperimental.Note: The default branch isdefault.