Saravanan666/pypi-org huggingface dataset:
Package: pypkamd
PypKa-MDPypKa + MD = constant-pH molecular dynamicsImplementation of the stochastic titration method1[1] Baptistaet al., J. Chem. Phys. 117, 4184 (2002) DOI: 10.1063/1.1497164Installationpython3 -m pip install pypkamdDependenciesBoth PypKa and GROMACS are required to be installed in the system.PypKa >= 2.7.1GROMACS >=5.1.5When running in pKAI-MD mode there are extra dependencies:pege >= 1.1.1torch_geometric >= 2.0.0Please refer to the installation guide oftorch geometricto install the proper version in accordance to your CUDA and OS.python3 -m pip install pege
# EXAMPLE FOR CUDA10.2
# python3 -m pip install torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.10.0+cu102.htmlUsageUpon installation a PypKa-MD executable should have been added to your bin. You may call it directly giving as an argument a modified GROMACS .mdp input file to include Constant-pH specific variables.pypkamd System.mdpIn case the executable as not been added to your bin, you may use:python3 -m pypkamd System.mdpYou may find an example .mdp file in /utils/cphmd.mdp.; GROin = system_000.gro     ; input GRO file
; TOPin = system_000.top     ; input TOP file
; DATin = fixgro.dat         ; input DAT file (to be removed)
; NDXin = system.ndx         ; input NDX file
; sysname = system_001       ; output files root name
; sites = all                ; to be titrating sites in the protein
; titrating_group = Protein  ; index group of the protein
; nCycles = 50               ; number of CpHMD cycles
                            ;; total simulation time = nCycles * tau_prot
                            ;; 1ns = 50 * 20ps
; nCPUs = 4                  ; number of CPUs to be used
; pH = 7.0                   ; pH value of the protonation states sampling
; ionicstr = 0.1             ; ionic strength used in PB
; GroDIR="/gromacs/gromacs-5.1.5_pH_I/bin/" ; GROMACS bin path
Package: py-pkg-chijane
📦 setup.py (for humans)This repo exists to providean example setup.pyfile, that can be used
to bootstrap your next Python project. It includes some advanced
patterns and best practices forsetup.py, as well as some
commented–out nice–to–haves.For example, thissetup.pyprovides a$ python setup.py uploadcommand, which creates auniversal wheel(andsdist) and uploads
your package toPyPiusingTwine, without the need for an annoyingsetup.cfgfile. It also creates/uploads a new git tag, automatically.In short,setup.pyfiles can be daunting to approach, when first
starting out — even Guido has been heard saying, "everyone cargo cults
thems". It's true — so, I want this repo to be the best place to
copy–paste from :)Check out the example!Installationcdyour_project# Download the setup.py file:#  download with wgetwgethttps://raw.githubusercontent.com/navdeep-G/setup.py/master/setup.py-Osetup.py#  download with curlcurl-Ohttps://raw.githubusercontent.com/navdeep-G/setup.py/master/setup.pyTo DoTests via$ setup.py test(if it's concise).Pull requests are encouraged!More ResourcesWhat is setup.py?on Stack OverflowOfficial Python Packaging User GuideThe Hitchhiker's Guide to PackagingCookiecutter template for a Python packageLicenseThis is free and unencumbered software released into the public domain.Anyone is free to copy, modify, publish, use, compile, sell, or
distribute this software, either in source code form or as a compiled
binary, for any purpose, commercial or non-commercial, and by any means.
Package: pypkgconf
This project provides Python bindings topkgconf.Buildingpypkgconfwheelpip install build
python -m build -Csetup-args="-Ddefault_library=static"Building on WindowsOn Windows, you want to link with thestaticversion of libpkgconf.
You also want to usereleasebuildtype.pip install build
python -m build  -Csetup-args="-Ddefault_library=static" -Csetup-args="-Dbuildtype=release"Running testsYou need a recent version ofmeson.pip install pytest cffi
meson setup . build -Ddefault_library=static -Dbuildtype=release
meson test -C buildUsing pypkgconfThe API is very close to the original C code.cli-like APIThis high-level API uses same arguments as thepkgconfexecutable.Results are returned as a list of string (the list may be empty).
Errors and warnings are logger using the standard Python logging module, under
thepkgconflogger.
In case or error result, apypkgconf.PkgConfErrorexception is raised.pypkgconf.query_args(command: str, env: dict[str, str] | None = None) -> list[str]The command is just like the command line arguments (e.g.:"--libs foo")Ifenvis provided, pkgconf will use it for any envvar it queries.
IfenvisNone(default),os.environis used.pypkgconf.query(args: list[str] | None, **kwargs) -> list[str]Positional arguments are given as a list of strings.Optional arguments are given either using an union ofpypkgconf.Flags,
or as keyword arguments, depending if it is a boolean value or not.low-level APIThe cffi interface to c function is provided throughpypkgconf._libpkgconf.libandpypkgconf._libpkgconf.ffi.Please refer topkgconfcode and
tocffidocumentation,
or use the high-level interface as a reference on how to use it.
Package: pypkgdemo1
pypkgdemo1This is a simple example package. You can useGithub-flavored Markdownto write your content.This page explain about packging python projects and upload to pypi.https://packaging.python.org/tutorials/packaging-projects/buildpip install --upgrade pip setuptools wheelpytyhon setup.py sdist bdist_wheells dist/upload to TestPypipip install --upgrade twinetwine upload --repository -urlhttps://test.pypi.org/legacy/dist/*upload to TestPypiinstall from TestPypipip install --index-urlhttps://test.pypi.org/simple/pypkgdemo1testing pypkgdemo1pythonimport pypkgdemo1pypkgdemo1.joke()uninstall pypkgdemo1pip uninstall pypkgdemo1upload to Pypipip install --upgrade twinetwine upload dist/*install from Pypipip install pypkgdemo1
Package: pypkgfreeze
pypkgfreezePython's npm install --saveAutomatically inserts your currently used package versions to setup.py.ExampleOld setup.pyfromsetuptoolsimportsetuptest_req=['pytest',]setup(name='pypkgfreeze',install_requires=["Click",],tests_require=test_req,extras_require={'test':test_req})New setup.pyfromsetuptoolsimportsetuptest_req=['pytest==4.0.2',]# ADDED VERSION HEREsetup(name='pypkgfreeze',install_requires=["Click==7.0",# AND HERE],tests_require=test_req,extras_require={'test':test_req})Usagepkgfreeze. It's that simple.InstallationpipinstallpypkgfreezeContributingThanks! Please read theCONTRIBUTING.mdfile.
Package: pypkggen
PyPkgGenPython Package Generator is a Python library for generating Python libraries for PyPI.org in an easier and faster way.
Do you not know how to package your Python project? Or do you want an easier and faster way to package your Python projects? If yes, then PyPkgGen is for you.
In just a few commands, your Python project will be live on PyPI.org and developers will be able to install it usingpip.Table of ContentsInstallationUsageTo-DoInstallationInstalling PyPkgGen from PyPI will install all the libraries required to build your Python projects.
Follow the instructions below to install PyPkgGen:Use pip/pip3 to install from PyPI$ pip install pypkggenYou can also use Python from your command prompt$ python -m pip install pypkggenLastly, to install from GitHub (ensuring that Git has been added to PATH), run:$ python -m pip install git+https://www.github.com/Samuel-HSSP/pypkggenUsagePyPkgGen is best used on the terminal. Make sure you have Python and Pip installed on your computer and they must be added to PATH. The following section of the documentation will guide you on how to package your Python project using PyPkgGen.Initialize Python REPL Shell$ pythonCreate a folder calledsourceand move all your source files (.py) into this folder. Note the path to this folder because it will be yourcode_source_dirwhen generating your package.Follow the instructions below and run the codes to generate your Python project.>>>frompypkggenimportpypkggen>>>generator=pypkggen.PyPkgGen("package_name","import_name","code/source/dir/")'package_name' is the name you want to give your Python package
'import_name' is the name your package will be stored with. This is what you will use to import the package
'code_source_dir' is the path tosourcecontaining all the source files for your project.>>>generator.generate_setup_file("filename.txt",test=True)A simple setup file will be generated in the current working directory with the filename given, as a text file.
Settestto True if you want to test your package first on test.pypi.org before publishing on PyPI.org. It is recommended to set it to True because you should test your package before publishing.
Edit the setup file and run this final code:>>>generator.create_package(test=True)The code above will start creating your package. Make sure you settestto True if you did that on the previous code and False if you had set it to False when generating setup file.
Carefully follow the instructions given when creating your package. All the files you need will be generated automatically for you. Make sure you double-check them and edit to your taste.Congratulations! You should now have your package published to PyPI.To-DoAutomate terminal commandsMake it more intuitiveAdd more functionalitiesProper documentationFix all the bugs, and probably add more
Package: pypkg-generator
Pypkg GeneratorCreates a simple template of a python package.Creates a basic template of python package with a simple command line tool.InstallationOS X & Linux:From PYPI$pip3installpypkg-generatorfrom the source$gitclonehttps://github.com/dany2691/pypkg-generator.git
$cdpypkg-generator
$python3setup.pyinstallUsage exampleOpen a terminal and type:$pkg-generator--helpAnd it'll display:Options:-n,--nameTEXTThenameofthepackage-p,--pathTEXTThepathwherethepackagewillbecreated--tests/--no-testsCreatetestsuitedirectoryornot,createdbydefault--helpShowthismessageandexit.There are many options for customization, you can decide what file will be created or not.You must assign a name, or the project will be nameforgotten_name.$pkg-generator--namemy-awesome-projectYou can explicitly pass a path, otherwise, the project will be created in the current directory.$pkg-generator--namemy-awesome-project--path/home/user/Documents/Development setupThis project usespipenvfor dependecy resolution. It's a kind of mix between
pip and virtualenv. Follow the next instructions to setup the development enviroment.$gitclonehttps://github.com/dany2691/pypkg-generator.git
$cdpypkg-generator
$pipenvshell
$pip3install-e.To run the test-suite, inside the pypkg-generator directory:$pytest-vvtest/MetaDaniel Omar Vergara Pérez –@dan1_net–daniel.omar.vergara@gmail.comhttps://github.com/dany2691ContributingFork it (https://github.com/dany2691/pypkg-generator)Create your feature branch (git checkout -b feature/fooBar)Commit your changes (git commit -am 'Add some fooBar')Push to the branch (git push origin feature/fooBar)Create a new Pull Request
Package: pypkgpack
PyPkgPackBundling multiple Python packages into a single Python file.Usage:>pypkgpack/path/to/mypackage1/path/to/mypackage2--outbundled_package.py

>python

python>importbundled_package
python>frommypackage.mymoduleimportmyfunction
python>print(myfunction())Features:bundling a Python package into a single Python filecaching bytecode compilation and cache invalidationfixing the missing__init__.pyallow multiple source code implementations for the same modulerespect Python's import semanticsbundled modules need no extra dependenciessupport bundling binaries and assetsallow lazy imports
Package: py-pkg-playground
py-pkg-playgroundThis is a Python package to learn Github actions!FeaturesFully typed with annotations and checked with mypy,PEP561 compatibleAdd yours!Installationpipinstallpy-pkg-playgroundExampleShowcase how your project can be used:frompy_pkg_playground.exampleimportsome_functionprint(some_function(3,4))# => 7LicenseMITCreditsThis project was generated withwemake-python-package. Current template version is:bb1dd122f276580008375990122e1e3f71394275. See what isupdatedsince then.
Package: pypkgs
pypkgsPython package that eases the pain of concatenating Pandas categoricals!Installationpip install -i https://test.pypi.org/simple/ pypkgsDependenciesSeepoetry.lockfor a list of dependencies.Usage>>>frompypkgsimportpypkgs>>>importpandasaspd>>>a=pd.Categorical(["character","hits","your","eyeballs"])>>>b=pd.Categorical(["but","integer","where it","counts"])>>>pypkgs.catbind(a,b)[character,hits,your,eyeballs,but,integer,whereit,counts]Categories(8,object):[but,character,counts,eyeballs,hits,integer,whereit,your]DocumentationThe official documentation is hosted on Read the Docs:https://pypkgs.readthedocs.io/en/latest/CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-cn-mds-524
pypkgs_cn_mds_524This cookiecutter creates a boilerplate for a Python project.Installation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_cn_mds_524FeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_cn_mds_524.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-dlb
pypkgs_dlbThis cookiecutter creates a boilerplate for a Python project.Installation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_dlbFeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_dlb.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-jg
pypkgs-jgPackaging dummy assignmentInstallation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_jgFeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_jg.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-rissangs
pypkgs_rissangsPython package that eases the pain of concatenating Pandas categoricalsInstallation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_rissangsFeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_rissangs.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-sy
pypkgs_syThis cookiecutter creates a boilerplate for a Python project.]: Python package that eases the pain of concatenating Pandas categoricals!Installation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_syFeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_sy.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-tk
pypkgs_tkThis cookiecutter creates a boilerplate for a Python project.Installation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_tkFeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_tk.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgs-ts
pypkgs_TSPython package that eases the pain of concatenating Pandas categoricals!Installation$pipinstall-ihttps://test.pypi.org/simple/pypkgs_tsFeaturesTODODependenciesTODOUsageTODODocumentationThe official documentation is hosted on Read the Docs:https://pypkgs_ts.readthedocs.io/en/latest/ContributorsWe welcome and recognize all contributions. You can see a list of current contributors in thecontributors tab.CreditsThis package was created with Cookiecutter and the UBC-MDS/cookiecutter-ubc-mds project template, modified from thepyOpenSci/cookiecutter-pyopensciproject template and theaudreyr/cookiecutter-pypackage.
Package: pypkgtemp
Python Package TemplateLatest ReleasePackage StatusLicenseBuild StatusCoverageCondaDocumentationThis is an opinionated attempt to document how I deploy a python
application with documentation, testing, pypi, and continuous
deployment. This project will be updated as I change my python
development practices. Number one this is a learning experience.documentation (sphinx, selfhosted +readthedocs)testing (pytest) and coverage (pytest-cov)deploy to pypi (twine)deploy to conda (conda)deploy docker container to (dockerhubandgitlab container registry)building a package (setup.py,README.md,CHANGELOG.md,LICENSE.md)command line interface with argparsebadges for testing, packages, and documentationAssumptions:Gitlab will be used for the continuous deployment. It is a great
project that is open source and comes with many nice features not
available for Github. You should consider it! Features used:pagesCI/CDIf you would like a custom domain setup with gitlab pages for the
documentation you will need to usecloudflare. I have ablog written on
how to do
thisor you can look at thegitlab cloudflare
documentation.StepsThis project is a python package itself and full documentation is
available on readthedocs. Each of the steps below includes a link to
the section in the documentation.setup a bare python packagewith git repo (setup.py,README.md,.gitignore,<package>)setup pypi deploymentwith git tagsvX.X.Xsetup testingon each commit withpytestsetup documentationwithsphinxon readthedocs and self hostedRequirementsNone!ContributingAll contributions, bug reports, bug fixes, documentation improvements,
enhancements and ideas are welcome.The goal of this project is to in an opinionated way guide modern
python packaging development for myself.LicenseMIT
Package: pypkg_template
Overview…Usage examplesimportpipelineddefdetect_ddos(stream):access=pipelined.utils.limit_counter(10*1000)forloginstream:access[log.ip]+=1yield fromaccess.over(100)defblock_ips(stream):foripinstream:# block the ipyieldipddos_monitor=[detect_ddos,block_ips,]source_logs=pipelined.files.follow('/path/to/server/access.log')foripinpipelined.run(ddos_monitor,source_logs):print(ip,"has been blocked.")ResourcesSource:https://github.com/hanula/pipelinedDocumentation:https://github.com/hanula/pipelinedLicenseSeeLICENSE.
Package: py-pkgversion
[![build-status-image]][travis]
[![coverage-status-image]][codecov]
[![pypi-version]][pypi]Versioning utils for python projects[build-status-image]:https://secure.travis-ci.org/kpn-digital/py-pkgversion.svg?branch=master[travis]:http://travis-ci.org/kpn-digital/py-pkgversion?branch=master[coverage-status-image]:https://img.shields.io/codecov/c/github/kpn-digital/py-pkgversion/master.svg[codecov]:http://codecov.io/github/kpn-digital/py-pkgversion?branch=master[pypi-version]:https://img.shields.io/pypi/v/py-pkgversion.svg[pypi]:https://pypi.python.org/pypi/py-pkgversion
Package: pypkg-winstonyym
pypkg_winstonyymtesting package buildInstallation$pipinstallpypkg_winstonyymUsageTODOContributingInterested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.Licensepypkg_winstonyymwas created by winstonyym. It is licensed under the terms of the MIT license.Creditspypkg_winstonyymwas created withcookiecutterand thepy-pkgs-cookiecuttertemplate.
Package: pypki
Managing PKI systemsFree software: BSD 2-Clause LicenseInstallationpip install pypkiYou can also install the in-development version with:pip install https://github.com/hlevering/pypki/archive/master.zipDocumentationhttps://pypki.readthedocs.io/DevelopmentTo run the all tests run:toxNote, to combine the coverage data from all the tox environments run:Windowsset PYTEST_ADDOPTS=--cov-append
toxOtherPYTEST_ADDOPTS=--cov-append toxChangelog0.0.0 (2020-01-18)First release on PyPI.
Package: pypk-up
pypk-up----简单管理python包1、下载安装：pip install pypk_up2、可以尝试在控制台直接使用pypk_up去使用短命令形式运行3、使用程序进行上传pypi时，请先注册好账号，避免出现登录等问题pypi官方网站4、上传pypi文件请按照序号目录进行顺序执行5、上传pypi的自动化，创建文件后，请手动去修改setup.py、LICENSE、README.md文件LICENSE开源6、导入包使用：导入更新包程序from pypk.pypi_update import pypi_update导入pypi上传程序from pypk.pypi_upload import pypi_upload
Package: pyplaato
Python API client for fetching Plaato dataFetches data for the Plaato Keg and Plaato Airlock using the official API handed byblynk.ccTo be able to query the API anauth_tokenis required and which can be obtained by followingtheseinstructionsFor more information about the available pins that can be retrieved please see the officialdocsfrom PlaatoUsageusage: cli.py [-h] -t AUTH_TOKEN -d {keg,airlock,both} [-u URL] [-k API_KEY]

optional arguments:
  -h, --help            show this help message and exit

required arguments:
  -t AUTH_TOKEN         Auth token received from Plaato
  -d {keg,airlock}

optional arguments:
  -u URL                Mock url
  -k API_KEY            Header key for mock urlAvailable pinsKegBEER_NAME="v64"PERCENT_BEER_LEFT="v48"POURING="v49"BEER_LEFT="v51"BEER_LEFT_UNIT="v74"TEMPERATURE="v56"UNIT_TYPE="v71"MEASURE_UNIT="v75"MASS_UNIT="v73"VOLUME_UNIT="v82"LAST_POUR="v59"DATE="v67"OG="v65"FG="v66"ABV="v68"FIRMWARE_VERSION="v93"LEAK_DETECTION="v83"MODE="v88"AirLockBPM="v102"TEMPERATURE="v103"BATCH_VOLUME="v104"OG="v105"SG="v106"ABV="v107"TEMPERATURE_UNIT="v108"VOLUME_UNIT="v109"BUBBLES="v110"CO2_VOLUME="v119"DisclaimerThis python library was not made by Plaato. It is not official, not developed, and not supported by Plaato.
Package: pyplagiarism
You can find the detailed documentation here:https://www.egr.msu.edu/coinlab/blankjul/pyplagiarism/An example of using pyplagiarism is provided below. This uses directly the API.
In the future, we are planning to provide a command line tool in addition.frompyplagiarismimportplagiarisma="""
def calculate():
    x = 6
    y = 5
    return x + y
"""b="""
def calculate():
    return 5 + 6
"""c="""
def calculate():
    x = 6
    y = 5
    return x + y
"""data={"a":a,"b":b,"c":c}plagiarism(data,visualize_as_html=False,diff_of_files=False)
Package: pyplaintext
A HTML to plaintext converter.You can find a hosted demo athttps://bitmazkdemo.webfactional.com/en/pyplaintext/InstallationTo get the latest stable release from PyPipipinstallpyplaintextTo get the latest commit from GitHubpipinstall-egit+git://github.com/bitmazk/pyplaintext.git#egg=pyplaintextUsagefrompyplaintextimportconverterhtml='<html><body>Hello world!</body></html>'parser=converter.HTML2PlainParser()result=parser.html_to_plain_text(html)ContributeIf you want to contribute to this project, please perform the following steps# Fork this repository
# Clone your forkmkvirtualenv-ppython2.7pyplaintextmakedevelopmaketestopenhtmlcov/index.htmlgitco-bfeature_branchmaster# Implement your feature and testsgitadd.&&gitcommitgitpush-uoriginfeature_branch# Send us a pull request for your feature branch