Saravanan666/pypi-org huggingface dataset:
Package: gffpandas-ncgr
gffpandasGFF annotations in panda dataframesFree software: ISC licenseDocumentation:https://gffpandas.readthedocs.io.About gffpandasgffpandas is a Python library, which can be used to work with annotation data. It facilitates the work with gff3 files in regard to filter desired annotation entries of the gff3 file. A gff3 file contains information about the location and attributes of genomic features. The gffpandas library is an easy to use and time-saving library.This gffpandas library is an alternative to gffutils or bcbio-gff, but it is inspired by the Python library Pandas. This means that the data frame structure is used to work with the annotation data. With gffpandas it is possible to filter a gff3 file by different functions. One big adventage is that several filter functions can be combined so that the required annotation entries can be selected. Furthermore, can the filtered annotation data be safed again as gff3 file or as csv or tsv file.For the documentation seegffpandas_repository.gffpandas-ncgr is a fork with bugfixes applied.CreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History1.2.1 (2020-10-02)Bug fix: Removed pytest-runner from setup requirements1.2.0 (2019-03-13)filter_feature_of_type for several features possible now1.1.0 (2019-03-13)get_feature_by_attribute for several values possible now1.0.1 (2019-03-06)adding type annotation1.0.0 (2019-03-05)changing GitHub url0.1.2 (2018-09-07)Removing of small text errors0.1.1 (2018-09-07)First release on PyPI0.1.0 (2017-07-11)Start of the project gffpandas
Package: gff-to-genbank
gff-to-genbankConvert GFF file to GenBank file format while extracting the sequences between the annotated regionsOriginal script written by Brad Chapman and Hsiao Yi -https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.pyEdited by Kartik Chundru to crop the FASTA sequence between the first and last annotated regions.Edited by Cornelius Roemer to make it work with BioPython 1.81 and to allow compound CDS features. Made pip installable athttps://pypi.org/project/gff-to-genbank/UsageInstallation:pipinstallgff-to-genbankgff-to-genbank<gff_file><fasta_file>Output is written to stdout, so you'll want to redirect it to a file.DependenciesBioPython -https://biopython.org/BCBio -https://github.com/chapmanb/bcbbDevelopmentSet new version:hatchversion<new_version>Publishing to PyPi:hatchbuild
hatchpublish
Package: gfftools
GFFtools: Yet another package to work with GFF3 filesPython package to parse GFF files and access the individual records. Only files following
the official GFF Version 3 specification are supported:https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.mdMost GTF files from e.g. ENSEMBL work as well but not all features are tested for GTF.installpipinstallgfftools
Package: gffutils
gffutilsis a Python package for working with and manipulating the GFF and
GTF format files typically used for genomic annotations.Files are loaded into a sqlite3 database, allowing much more complex
manipulation of hierarchical features (e.g., genes, transcripts, and exons)
than is possible with plain-text methods alone.See documentation athttps://daler.github.io/gffutils, and GitHub repo athttps:/github.com/daler/gffutils.
Package: gf-kernel
GF Kernelgf_kernelis aGFkernel forJupyter.PrerequisitesIf you haven't installed GF already, get it from the officialdownload website.For graph visualization GF usesgraphviz, so please make sure you have it installed:sudo apt install graphvizor under Mac OS X withhomebrew:brew install graphvizInstallationYou can either install the kernel from the source repository:git clone https://github.com/kwarc/gf_kernel
cd gf_kernel
pip install .or install it directly from pip:pip install gf-kernelAfterwards, install the kernel module with:python -m gf_kernel.installUsageYou're now ready to go and can start a Jupyter notebook with:jupyter notebookSelect thegf_kernelas kernel in your notebook.
The kernel supports all of the GF shell commands.
Output files produced by these commands will be placed into the current directory.The kernel can also be used to define new grammars, which are immediately imported for usage upon defining.
If you would like to have line numbers for editing your code you can use the Juypter shortcutEsc+Lto enable them.In addition to the GF shell commands the kernel supports the following commands:view: show the graph(s) generated by the specified GF shell commandhelp: shows the help messageexport: saves the specified grammar in the current diretoryclean: removes all.dot,.pngand.gfofiles from the current directoryPlease refer to the tutorial notebook to see how exactly they are used.This package requires Python 3.
Package: gflanguages
This python module provides an API with data about languages/regions/scripts for use in the language-support categorization of the font families in the Google Fonts collection.You can also directly access the rawtextprotofiles on theLib/gflanguages/datadirectory:languagesregionsscriptsMost of the code in this project was copied from thegftoolsrepository (https://github.com/googlefonts/gftools/) so that language/region/script data can be easily available to all our tools without having to also get the large dependency tree ofgftools. The most immediate user of this module isFont Bakery, which needs to validate language support on font binaries being checked. (seehttps://github.com/googlefonts/fontbakery/issues/3605)The second obvious user of thisgflanguagesmodule isgftoolsitself.Language/region/script definitions and thegflanguagesmodules are used as a subtree in thegoogle/fontsrepo, on itslang/directory (https://github.com/google/fonts/tree/main/lang).This module is the main place to update these definitions, avoiding data duplication and guaranteeing uniformity across tools.To learn more about howlangmetadata affects downstream, seegf-guide/lang.
Package: gfloat
gfloat: Generic floating-point types in PythonAn implementation of generic floating point encode/decode logic,
handling various current and proposed floating point types:IEEE 754: Binary16, Binary32OCP Float8: E5M2, E4M3IEEE WG P3109: P{p} for p in 1..7Seehttps://gfloat.readthedocs.iofor documentation.BUILDINGpip install -e .
cd docs 
make html
cd ..rm -rf dist
python3 -m build
echotoken| twine upload --repository pypi dist/* --verboseNotesAll NaNs are the same, with no distinction between signalling or quiet,
or between differently encoded NaNs.
Package: gflow
[![Build Status](https://travis-ci.org/AAFC-MBB/GFlow.svg?branch=master)](https://travis-ci.org/AAFC-MBB/GFlow)
GFlow
========================This is a command line interface application that allows datasets and a workflow to be specified in a config file and then have the workflow executed on an instance of Galaxy.InstallationFrom the source directory:$ pip install -r requirements.txt
$ python setup.py installConfigurationMake a copy of the sample config file inconfig/and set the parameters in it as desired:$ cp config/config.yml.sample config/config.ymlUsageThen, execute:$ gflow config/config.ymlOr, if executing from the source directory without having installed the tool:$ export PYTHONPATH=$PYTHONPATH:$PWD
$ ./scripts/gflow config/config.ymlTestsA small number of data files and workflow files have been included indata/andworkflow/for testing purposes.
After setting the`GALAXY_URL`and`GALAXY_API_KEY`environment variables, execute the tests with:$ python setup.py test
Package: gfm
GFM is a small module to convertGitHub Flavored Markdownto HTML.UsageGFM offers two methods,gfmandmarkdown.gfmsimply preprocesses the parts of Markdown that GitHub Flavored
Markdown is interested in, without converting the Markdown to HTML.markdowndoes this as well as passing the result through themarkdownmodule to generate HTML.>>> import gfm
>>> string = "Roses are red\nViolets are blue"
>>> gfm.gfm(string)
'Roses are red  \nViolets are blue'
>>> gfm.markdown(string)
'<p>Roses are red<br />\nViolets are blue</p>'Installationpip install gfmLicenseMIT, plain and simple.
Package: gfm2html
Installation$[sudo]pipinstallgfm2htmlPros100% true native github flavored markdownHow it worksgithub markdown apiExamplesfromgfm2htmlimportgfm2htmlgfm2html(markdown)# For unauthenticated requests, the rate limit allows for up to 60 requests per hourgfm2html(markdown,token="XXX")Linksgithub markdown apireadme42.com
Package: gfm-cmark-py
IntroductionTODOIt also featuresDebianpackaging for the underlyingcmarklibrary, for easy installation on distros using APT.UsageTODOInstallationgfm-cmark-pycan be installed viapip installgfm-cmark-pyas usual,
seereleasesfor an overview of available versions.
To get a bleeding-edge version from source, use these commands:repo="jhermann/gfm-cmark-py"
pip install -r "https://raw.githubusercontent.com/$repo/master/requirements.txt"
pip install -UI -e "git+https://github.com/$repo.git#egg=${repo#*/}"As a developer, to create a working directory for this project, call these commands:git clone "https://github.com/jhermann/gfm-cmark-py.git"
cd "gfm-cmark-py"
command . .env --yes --develop  # add '--virtualenv /usr/bin/virtualenv' for Python2
invoke build checkYou might also need to follow somesetup proceduresto make the necessary basic commands available onLinux,Mac OS X, andWindows.Related Projectsgithub/cmark– GitHub’s fork of cmark, supportingGFMextensions.jgm/cmark–CommonMarkparsing and rendering library and program
in C.rtfd/CommonMark-py– Pure Python implementation ofCommonMark.cmark 0.26.1-1 source package(Ubuntu Zesty)
Package: gfm-markdown-description-example
Github-Flavored Markdown Example ProjectNo docutils, pandoc, or any other tricks! Just aREADME.mdand asetup.py.This is forked from@di/markdown-description-example.See the source for this project here:https://github.com/jonparrott/gfm-markdown-description-example.Instructions to do this for your project are here:https://dustingram.com/articles/2018/03/16/markdown-descriptions-on-pypiWhat we can do:We can do normal markdown stuff likeitalicsandbold text.ListsAreFunToo(But please use responsibly)Code blocks:>>> pypi_supports_markdown
TrueButnowyou can also do GitHub fun stuff like tables:foobarbazbimAndStrikethrough. And autolinks such ashttps://blog.jonparrott.com. :)
Package: gfont
gfont一个字体处理方法合集，含有以下方法to_xml：将字体文件转换为 xmlto_img：将单个或所有字体转为 Image 对象to_ocr：将单个或所有字体识别转为 str、dict 对象get_glyph_order：获取字段信息列表get_best_cmap：获取十六进制与字段信息字典安装pip install gfont使用环境pip install font2img==2.2
pip install fonttools==4.29.1
pip install Pillow==9.3.0
pip install paddlepaddle==2.3.2 -i https://mirror.baidu.com/pypi/simple
pip install "paddleocr==2.6.0.1"示例from gfont import FontHelper

f = FontHelper(path=r'font.ttf')
print(f.to_ocr())
Package: gforms
GFormsA python wrapper for public Google Forms.This package does not implement form editing / sharing / other actions with user-owned formsInstallationpython3-mpipinstallgformsFeaturesForm parsingAll form settings are parsedMulti-page forms are supportedElements with input validation are supportedForm fillingFill the entire form using a single callback function (seeexample)Fill individual elementsValidate the form before submissionForm submissionFaster submission for multi-page forms (history emulation)LimitationsForms with required sign-in cannot be submittedForms with file upload cannot be parsed (sign-in is required for loading the form)A CAPTCHA needs to be solved in order to send an e-mail with a response copy (when this option is enabled). CAPTCHA handling should be implemented separatelyForm style is not parsedExampleSeeexample.pyfor more details.fromgformsimportFormfromgforms.elementsimportShort,Valuedefcallback(element,page_index,element_index):# fill an element based on its positionifpage_index==0andelement_index==1:return'Yes'# fill an element based on its type and nameifisinstance(element,Short)andelement.name=='Your opinion:':returninput(element.name)# fill choice elements with random values, skip optional elements if fill_optional is not usedreturnValue.DEFAULTurl='https://docs.google.com/forms/d/e/.../viewform'form=Form()form.load(url)print(form.to_str(indent=2))# a text representation, may be useful for CLI applicationsform.fill(callback)form.submit()# Faster submission for multi-page forms (use only one POST request)# (in theory, you may get banned, but now the actual number of requests isn't checked)form.submit(emulate_history=True)
Package: gfpa
Gene function and cell surface protein association analysis based on single-cell multiomics dataIt is a single-cell multiomics data analysis framework that analyzes the association of gene function and cell surface proteins.
The python packages, datasets and user-friendly manuals of GFPA are freely available athttps://github.com/studentiz/gfpa.The GFPA framework works with scanpy and supports the following single-cell multimodal analysesSingle-cell multi-omics data preprocessingQuantification of gene functionGene function and protein association miningVisualizationPip installpipinstallgfpaDatasetsThe dataset participating in "Gene function and cell surface protein association analysis based on single-cell multiomics data" can be downloaded atGFPA data warehouse
Package: gfpro-irrigation-control
gfpro-irrigation-controlgfpro-irrigation-controlcontainsgfpro_irrigiation_control, a Python module that provides Bluetooth-LE-based control of theGFPRO Eco irrigation valve. It supports reading and toggling the valve status, as well as checking the battery status.The package also includes two command line interfaces that interact with the module: one for manual control of valves and another for integrating valves into automated systems through MQTT.
Package: gfra
gfraREST API framework for Google Serverless FunctionsDescriptiongfrastands forGoogleFunctionsRESTAPIUsageWe usepoetryfor dependency management and publishing.Installation$ poetry add gcloud-functions-rest-apiDevelopmentWIPProductionWIPTestingWIPDocumentationWIPContributionsFeel free to send somepull requestorissue.LicenseMIT license© 2018German Ivanov
Package: gfsopt
gfsoptpip3 install --user gfsoptConvenient scaffolding for the excellentGlobal Function Searchhyperparameter optimizer from theDliblibrary.
(See:'A Global Optimization Algorithm Worth Using')Provides the following features:Parallel optimization: Run multiple hyperparameter searches in parallelSave and restore progress: Save/restore settings and optimization progress to/from file.Average over multiple runs: Run a stochastic objective function using the same
parameters multiple times and report the average to Dlib's Global Function
Search. Useful in highly stochastic domains to avoid biasing the search towards
lucky runs.Example usageA basic example where we maximizeobj_funcwith respect toyover 10 runs,
with as many parallel processes as there are logical cores, and save progress to file.from gfsopt import GFSOptimizer
def obj_func(x, y, pid):
    """"Function to be maximized (pid is iteration number)""""
    a = (1.5 - x + x * y)**2
    b = (2.25 - x + x * y * y)**2
    c = (2.625 - x + x * y * y * y)**2
    return -(a + b + c)
# For this example we pretend that we want to keep 'x' fixed at 0.5
# while optimizing 'y' in the range -4.5 to 4.5
pp = {'x': 0.5}  # Problem parameters
space = {'y': [-4.5, 4.5]}  # Parameters to optimize over
optimizer = GFSOptimizer(pp, space, fname="test.pkl")
# Will sample and test 'y' 10 times, then save results, progress and settings to file
optimizer.run(obj_func, n_sims=10)For a more extensive example, seeexample.py.Installation & RequirementsRequires Python >=3.6 and the following libraries:datadiff
dlib
numpyTo install, do:pip3 install --user gfsoptDocumentationSeeexample.pyfor
an example andhttp://gfsopt.readthedocs.io/for API documentation.
Package: gfsubsets
gfsubsetsThis is the collection of nam files (codepoint subsets) that are used to subset fonts before serving on the Google Fonts CSS API.The subset filesThe subset definitions are contained in two forms; the "editable" definitions
are found in thesubsets-inputdirectory, and the machine readable defitions
can be found inLib/gfsubsets/data.The machine readable files consist of text files with one Unicode codepoint
(a hexadecimal number beginning with0x) on each line; everything after the
codepoint is a comment. Blank lines and comment lines beginning#are
ignored.The editable definitions are similar, but for convenience allow the following
"directives":Two codepoints separated by..denote an (inclusive) range; all codepoints
within the range are included.The symbol-before a codepoint or range excludes it from the output set.The directive@include(filename)includes the codepoints infilename.The directive@block(XYZ)includes the codepoints in the Unicode block
namedXYZ.The directive@script(XYZ)includes all codepoints with either the
UnicodeScriptproperty equal toXYZor theScriptExtensionsproperty
equal to XYZThese editable definitions are turned into their machine-readable equivalents
using the scriptscripts/preprocess_namfile.py.Python interfaceThis repository also includes the Python modulegfsubsetswhich provides
an interface to these subset definitions. It exports the following functions:CodepointsInFont(filename): Lists the Unicode codepoints supported by the fontListSubsets(): Returns the name of all defined subsets.SubsetsForCodepoint(cp): Returns the names of all subsets including the codepoint.SubsetForCodepoint(cp): Returns the name of the "most relevant" subset including the codepoint.CodepointsInSubset(subset): Returns a set of codepoints included in the subset.SubsetsInFont(filename, min_pct, ext_min_pct): Returns the name of subsets "well" supported by a font.
Package: gftool
masterdevelopCollection of commonly used Green’s functions and utilities.
The main purpose of this module is to have a tested and thus reliable basis
to do numerics. It happened to me too often, that I just made a mistake copying
the Green’s function and was then wondering what was wrong with my algorithm.
For example, aselectionof lattice Green’s functions or rather the corresponding DOSs:Also have a look at thetutorialto get an idea.The main use case ofGfToolwas DMFT and its real space generalization,
in particular using CT-QMC algorithms.InstallationThe package is available onPyPI:$pipinstallgftoolForcondausers,GfToolis also available onconda-forge$condainstall-cconda-forgegftoolAlternatively, it can be installed via GitHub. You can install it using$pipinstallhttps://github.com/DerWeh/gftools/archive/VERSION.zipwhereVERSIONcan be a release (e.g.0.5.1) or a branch (e.g.develop).
(As always, it is not advised to install it into your system Python,
consider usingpipenv,venv,conda,pyenv, or similar tools.)
Of course, you can also clone or fork the project.If you clone the project, you can locally build the documentation:$pipinstall-rrequirements-doc.txt$pythonsetup.pybuild_sphinxDocumentationThe documentation and API is onReadTheDocs.
The documentation of specific branches can also be accessed:master doc,develop doc.
There is also a GitHub page:documentation.Currently, the package’s main content isgftoolcollection of non-interacting Green’s functions and spectral functions,
see also thelatticesubmodule.utility functions like Matsubara frequencies and Fermi functions.reliable calculation of particle numbers via Matsubara sumscpa/bebSingle site approximation to disorderdiagonal disorder only (CPA) and diagonal and off-diagonal (BEB)average local Green’s function and component Green’s functionsfourierFourier transforms from Matsubara frequencies to imaginary time and back,
including the handling of high-frequencies moments
(especially important for transforms from Matsubara to imaginary time)Laplace transform from real times to complex frequenciesmatrixhelper for Green’s functions in matrix formpadeanalytic continuation via the Padé algorithm
Package: gftools
Google Fonts ToolsThis project contains tools used for working with the Google Fonts collection, plusGoogle Fonts Glyph Set Documentationin the/encodingssubdirectory. While these tools are primarily intended for contributors to the Google Fonts project, anyone who works with fonts could find them useful.The tools and files under this directory are available under the Apache License v2.0, for details seeLICENSEGoogle Fonts Official Glyph SetsThe glyph sets useful for type designers that were previously hosted in this repository have been moved to:https://github.com/googlefonts/glyphsets/tree/main/GF_glyphsetsTool Usage ExamplesCompare fonts:gftools compare-font font1.ttf font2.ttfAdd a METADATA.pb to a family directorygftools add-font ../ofl/newfamilySanity check a family directory:gftools sanity-check --repair_script=/tmp/fix.py ../ofl/josefinsans
gftools sanity-check --repair_script=/tmp/fix.py --fix_type=fsSelection ../uflCheck a font family against the same family hosted on Google Fonts:gftools qa [fonts.ttf] -gfb -a -o qaCheck a variable font family against the same family as static fonts:gftools qa -f [vf_fonts] -fb [static_fonts] --diffenator --diffbrowsers -o ~/path/outFix a non hinted fontgftools fix-nonhinting font_in.ttf font_out.ttfPackage and PR a family update to google/fonts. Much more detaileddocumentation.gftools packager "Family Sans" path/to/local/google/fonts -pyTool InstallationPlease note that gftools requiresPython 3.7or later.Please install these tools using pip:pip install gftools(Mac OS users on M1 chips will need to upgrade pip first to support universal wheels:pip install -U pip.)If you need to usegftools qa, you will need to install cairo and pkg-config. These can be installed on OS X using homebrew:brew install cairo pkg-configOnce you have installed these system packages, install gftools using the following command:pip install 'gftools[qa]'Tool Requirements and DependenciesThese tools depend on the submoduleGlyphsInfo.
Make sure the submodule is up to date by running:git submodule update --init --recursivegftools packagerneeds the command linegitprogram in a version >= Git 2.5 (Q2 2015) in order to perform a shallow clone (--depth 1) of the font upstream repository and branch. This is not supported by pygit2/libgit2 yet.gftools manage-traffic-jamrequires two private files which contain sensitive data. Ask m4rc1e for them.Google Fonts API KeyIn order to use the scriptsgftools qaandgftools family-html-snippet, you will need to generate a Google Fonts api key,https://developers.google.com/fonts/. You will then need to create a new text file located on your system at~/.gf-api-key(where ~ is your home directory), which contains the following:[Credentials]
key = your-newly-generated-googlefonts-api-keyUpstream project reposhttps://github.com/schriftgestalt/GlyphsInfohttps://github.com/google/protobufhttps://github.com/behdad/fonttools
Package: gftp
ftp一个 ftp 下载器包含 ftp 连接与下载器的方法GFTP：新增 FTP 没有的方法FTPConn：FTP 连接创建、快速重连FTPDownloader：FTP 文件、文件列表、文件夹下载安装pip install gftpGFTP新增了一些 FTP 没有的方法show_dir：列表形式返回文件夹下的所有文件、文件夹（返回全路径）show_file：列表形式返回当前文件夹下的所有文件（返回全路径）show_folder：列表形式返回当前文件夹下的所有文件夹（返回全路径）iter_dir：遍历指定路径下的文件、文件夹并输出（迭代器，返回全路径）这里就介绍下 iter_dirfrom gftp import FTPConn

ftp = FTPConn(**连接配置)
for f in ftp.connection.iter_dir('/'):
    print(f)FTPConn创建连接用from gftp import FTPConn

ftp = FTPConn(**连接配置)
ftp.connection.pwd()    # 通过 connection 使用 FTP 命令
ftp.reconnection()      # 重新连接
ftp.close()             # 关闭连接，会自动回收，关不关无所谓FTPDownloader下载文件、文件列表、文件夹可以多线程，即创建多个连接介绍两个参数：类实例参数 keep_structure 会在 save_path 的基础上，保留 ftp 目录结构download 参数 callback 是线程，线程数量和类实例的 threads 数量一致from gftp import FTPDownloader

downloader = FTPDownloader(**连接配置, save_path='')
downloader.download_file(ftp_path='xx', callback=xx)
downloader.download_list(ftp_path_list=['xx'], callback=xx)
downloader.download_dir(dir_path='xx', callback=xx)