Saravanan666/pypi-org huggingface dataset:
Package: gutt
guttAuto Generate Unit Test TemplatesInstall$ pip install guttBasic UsageAssume you have a package, and its layout:my_awesome_package
├── __init__.py
└── module1.pysome codes insidemy_awesome_package/module1.py:importsysMY_CONST=123deffuncion1():passdeffunction2():passclassMyObject:defmethod1(self):pass@classmethoddefclassmethod1(cls):pass@staticmethoddefstaticmethod1():passguttcan generate unit testing templates for all implementations in just one line:$ gutt -m my_awesome_package -o mytestsThe output layout:mytests
├── __init__.py
└── my_awesome_package
    ├── __init__.py
    └── test_module1.pyThe unit test templates insidetest_module1.pydeftest_funcion1():frommy_awesome_package.module1importfuncion1assertfuncion1deftest_function2():frommy_awesome_package.module1importfunction2assertfunction2classTestMyObject:@classmethoddefsetup_class(cls):frommy_awesome_package.module1importMyObjectassertMyObject@classmethoddefteardown_class(cls):passdefsetup_method(self,method):passdefteardown_method(self,method):passdeftest_method1(self):passdeftest_classmethod1(self):passdeftest_staticmethod1(self):passEach module in source codes maps to a testing module(module1.py --> test_module1.py), and each function, each class and all methods inside that class maps to corresponding test templates.guttwill skip code generation if the test templates for the functions already exist.guttwon't delete the corresponding test templates if the source codes get deleted or renamed.For new added codes: modules, functions or methods inside class, just re-runguttto generate new test templates for them.Run unit test withpytest, for example:$ pytest --doctest-modules --cov=my_awesome_package mytests

=============================== test session starts ===============================
platform linux -- Python 3.8.8, pytest-4.6.11, py-1.10.0, pluggy-0.13.1
rootdir: /home/ryan/Workspace/my_awesome_package
plugins: mock-1.13.0, cov-2.11.1
collected 5 items                                                                 

mytests/my_awesome_package/test_module1.py .....                            [100%]

----------- coverage: platform linux, python 3.8.8-final-0 -----------
Name                             Stmts   Miss  Cover
----------------------------------------------------
my_awesome_package/__init__.py       0      0   100%
my_awesome_package/module1.py       13      5    62%
----------------------------------------------------
TOTAL                               13      5    62%


============================ 5 passed in 0.07 seconds =============================
Package: gutta
Gutta - A Webcomic Static Site Builderguttais a framework to build static websites for webcomics, ready for hosting. It's especially suited to hosting on github.Learn how to use gutta:InstallationCreating a new website and using guttaMaking the damn thing!Filling your website with images and other assetsWriting your webcomic.yamlAdding Extra PagesStyling your websitePublishing your website
Package: guv
Documentation:http://guv.readthedocs.org/Source:http://github.com/veegee/guvKeywords:guv, greenlet, gevent, eventletAboutguv is a fast networking library and WSGI server (like gevent/eventlet) forPython >= 3.2 and pypy3The event loop backend ispyuv_cffi, which aims to be fully compatible with thepyuvinterface. pyuv_cffi is fully supported on CPython and pypy3.libuv>= 1.0.0 is required.Asynchronous DNS queries are supported via dnspython3. To forcefully disable
greendns, set the environment variableGUV_NO_GREENDNSto any value.guv currently only runs on POSIX-compliant operating systems, but Windows
support is not far off and can be added in the near future if there is a demand
for this.This library is actively maintained and has a zero bug policy. Please submit
issues and pull requests, and bugs will be fixed immediately.This project is under active development and any help is appreciated.QuickstartSince guv is currently in alpha release state and under active development, it
is recommended to pull often and install manually:git clone https://github.com/veegee/guv.git
cd guv
python setup.py installNote:libuv>= 1.0.0 is required. This is the first stable version but is a
recent release and may not be available in Debian/Ubuntu stable repositories, so
you must compile and install manually.Serve your WSGI app using guv directlyimportguv;guv.monkey_patch()importguv.wsgiapp=<yourWSGIapp>if__name__=='__main__':server_sock=guv.listen(('0.0.0.0',8001))guv.wsgi.serve(server_sock,app)Serve your WSGI app using guv withgunicorngunicorn -w 4 -b 127.0.0.1:8001 -k guv.GuvWorker wsgi_app:appNote: you can usewrkto benchmark the performance of guv.Crawl the web: efficiently make multiple “simultaneous” requestsimportguv;guv.monkey_patch()importrequestsdefget_url(url):print('get_url({})'.format(url))returnrequests.get(url)defmain():urls=['http://gnu.org']*10urls+=['https://eff.org']*10pool=guv.GreenPool()results=pool.starmap(get_url,zip(urls))fori,respinenumerate(results):print('{}: done, length:{}'.format(i,len(resp.text)))if__name__=='__main__':main()GuaranteesThis library makes the following guarantees:Semantic versioningis strictly followedCompatible with Python >= 3.2.0 and PyPy3 >= 2.3.1 (Python 3.2.5)
Package: guvicorn-logger
Guvicorn_loggerThis lib colored, normalizes and joins logs between Uvicorn and Gunicorn.
There is a common problem when using Uvicorn for Dev and Gunicorn for Prod,
normally the logs generated by Uvicorn wokers are not captured by Gunicorn.This lib facilitates this configuration...Easy configfromguvicorn_loggerimportLoggerlogger=Logger().configure()Examplelogger.info("Message - Info")logger.error("Message - Error")logger.warning("Message - Warning")logger.critical("Message - Critical")OutputFramework (Uvicorn, Gunicorn, Fastapi)FastAPI | asgi-correlation-idfromasgi_correlation_idimportCorrelationIdMiddlewarefromfastapiimportFastAPIfromguvicorn_loggerimportLoggerapp=FastAPI()app.add_middleware(CorrelationIdMiddleware)logger=Logger(correlation_id=True).configure()@app.get("/")defmain():logger.info("Message - Info")logger.error("Message - Error")logger.warning("Message - Warning")logger.critical("Message - Critical")Output
Package: gux
guxgit user switcherInstallationguxis written in Python3 and uses pip3 for installation.pip3intallguxUsageguxhas the following commands: 'use', 'add', 'list', 'ls', 'rm'.gux use [user]- Changes the main tracked user used byguxgux rm [user]- Deletes a user from theguxregistrygux add- Adds a new user to theguxregistrygux list- Lists the current git configurations in a repogux ls- Show list of current users registered to guxDevelopmentUsepipenvto isolate your development environment. Run the following from the project root:pipenvshell--python=`whichpython3`In yourpipenvenvironment, installguxmanaully:Note: Replace the X with the current gux verion.pythonsetup.pysdistbdist_wheel&&pipinstall--upgrade--force-reinstalldist/gux-0.0.X-py3-none-any.whlTo upload the app to pypi:python3setup.pysdistbdist_wheel&&python3-mtwineuploaddist/*
Package: guy
GUYis a py3 module, which let you quickly release a GUI (html/js) for yours python (>=3.5) scripts, targettinganyplatforms ... andandroidtoo.A simpleguy's appcode, could be :fromguyimportGuyclassSimple(Guy):"""<button onclick="self.test()">test</button>"""asyncdeftest(self):print("Your name is",awaitself.js.prompt("What's your name ?"))if__name__=="__main__":app=Simple()app.run()Aguy's appcan be runned in 3 modes :can reuse a chrome browser (in app mode), on the host. To keep the minimal footprint. (app mode)can embbed its CEF (like electron) (thanks cefpython3), to provide all, to the users. (cef mode)can act as a classical web server. Any browser can be a client (server mode)Aguy's appcan be released as :a simple py3 file, with only guy dependancy (app mode&server mode)), or with guy+cefpython3 dependancies (cef mode))a freezed executable (pyinstaller compliant) (all modes)apip/package app(all modes)anapkfor android (with buildozer/kivy) (app modeonly)Read theGuy's DOCUMENTATION!Available on :Guy's GithubGuy's PypiHere is ademo(sources), of a simple guy's app (server mode).Here is ademo(sources), of a guy's app serving a vuejs/sfc UI.Here is a simpleguy's app(app mode):On UbuntuOn Android10If you want to build guy app, without any html/js/css knowlegments, you can trygtag: it's a guy sub module which let you build GUI/GUY app inmore classical/python3 way.
Package: guzi
python-guziA library to use Guzi in Python applicationsRun testspython-munittestUsageClass User contains every Guzi relative information a user would need :
- guzi wallet
- guza waller
- total accumulated
- balanceFor now, a Guzi (and a Guza) is just a string, an identifier defining what it is. So it has no dedicated class. Maybe it will, but for now, nope.Example of use :# Create usersuser1=User("unique_id1",birthdate=date(1989,11,28))user2=User("unique_id2",birthdate=date(1998,9,5))# create their Guzis (it's like having a new day)foriinrange(10):user1.create_daily_guzis(date(2020,4,i))# Then make them spend between each otheruser1.spend_to(user2,3)user1.spend_to(user2,2)
Package: guzzle_sphinx_theme
Sphinx theme used by Guzzle:http://guzzlephp.orgInstallationInstall via pip:$ pip install guzzle_sphinx_themeor if you have the code checked out locally:$ python setup.py installConfigurationAdd the following to your conf.py:importguzzle_sphinx_theme# Adds an HTML table visitor to apply Bootstrap table classeshtml_translator_class='guzzle_sphinx_theme.HTMLTranslator'html_theme_path=guzzle_sphinx_theme.html_theme_path()html_theme='guzzle_sphinx_theme'# Register the theme as an extension to generate a sitemap.xmlextensions.append("guzzle_sphinx_theme")# Guzzle theme options (see theme.conf for more information)html_theme_options={# Set the name of the project to appear in the sidebar"project_nav_name":"Project Name",}There are a lot more ways to customize this theme, as this more comprehensive
example shows:importguzzle_sphinx_theme# Adds an HTML table visitor to apply Bootstrap table classeshtml_translator_class='guzzle_sphinx_theme.HTMLTranslator'html_theme_path=guzzle_sphinx_theme.html_theme_path()html_theme='guzzle_sphinx_theme'# Register the theme as an extension to generate a sitemap.xmlextensions.append("guzzle_sphinx_theme")# Guzzle theme options (see theme.conf for more information)html_theme_options={# Set the path to a special layout to include for the homepage"index_template":"special_index.html",# Set the name of the project to appear in the left sidebar."project_nav_name":"Project Name",# Set your Disqus short name to enable comments"disqus_comments_shortname":"my_disqus_comments_short_name",# Set you GA account ID to enable tracking"google_analytics_account":"my_ga_account",# Path to a touch icon"touch_icon":"",# Specify a base_url used to generate sitemap.xml links. If not# specified, then no sitemap will be built."base_url":""# Allow a separate homepage from the master_doc"homepage":"index",# Allow the project link to be overriden to a custom URL."projectlink":"http://myproject.url",}Customizing the layoutYou can customize the theme by overriding Jinja template blocks. For example,
“layout.html” contains several blocks that can be overridden or extended.Place a “layout.html” file in your project’s “/_templates” directory.mkdirsource/_templatestouchsource/_templates/layout.htmlThen, configure your “conf.py”:templates_path=['_templates']Finally, edit your override file “source/_templates/layout.html”:{# Import the theme's layout. #}
{% extends "!layout.html" %}

{%- block extra_head %}
{# Add custom things to the head HTML tag #}
{# Call the parent block #}
{{ super() }}
{%- endblock %}NoteIf you are using Readthedocs, then you might run into an issue where they
don’t currently allow you to extend layout.html.
Package: gvapi
Неофициальная обертка для API игрыГодвилль, реализованная на Python.Документация.УстановкаДанный пакет доступен для установки из PyPi черезpip.python3-mpipinstallgvapiПример использованияБазовый вариант использования будет выглядеть следующим образом.fromgvapiimportHerohero=Hero('God Name')hero_with_token=Hero('God Name',token='aiowdjwaoijd')Описание атрибутов героя можно найти в документации.
Package: gvar
This package facilitates the creation and manipulation of arbitrarily
complicated (correlated) multi-dimensional Gaussian random variables.
The random variables are represented by a new data type (gvar.GVar)
that can be used in arithmetic expressions and pure Python functions. Such
expressions/functions create new Gaussian random variables
while automatically tracking statistical correlations between the new
and old variables. This data type is useful for simple error propagation,
but also is heavily used by the Bayesian least-squares fitting modulelsqfit.pyto define priors and specify fit results, while accounting
for correlations between all variables. Documentation can is in thedoc/subdirectory: seedoc/html/index.htmlor look online at <https://gvar.readthedocs.io>.These packages usenumpyfor efficient array arithmetic, andcythonto compile efficient code.gvaruses automatic differentiation to
track covariances through arbitrary arithmetic.Information on how to install the components is in theINSTALLATIONfile.To test the libraries trymake tests. Some
examples are give in theexamples/subdirectory.gvarversion numbers have the formmajor.minor.patchwhere:
incompatible changes are signaled by incrementing themajorversion
number, theminornumber signals new features, and thepatchnumber
signals bug fixes.Created by G. Peter Lepage (Cornell University) 2008Copyright (c) 2008-2020 G. Peter Lepage
Package: gvc4bam
GVC_VCF Pipeline:GVC_VCF is a pipeline developed at Genowis for germline and somatic mutation(snv, indel, sv) in next generation sequencing data.Basic Command Line Parameters Options:Positional Arguments:
	input_json: The json file stores names and paths of both normal and tumor samples. 
			eg: {"N": ["/disk/N.sort.dup.bam"], "T": ["/disk/T.sort.dup.bam"]}
	reference: The reference fasta file.
	outpath: The output folder.
Optional Arguments:
	-h: Print help messages.
	--dbsnp: The Single Nucleotide Polymorphism Database(dbSNP) file has three columns(chr, position, rsID), Values on each line of the file are separated by tab.
	--bed: The WES file need to provide bed region, The bed region has at least three columns(chr,start,end), Values on each line of the file are separated by tab.
	--gvc_lib: The library folder has configuration file.
		The docker volume file needs to be modified. A dictionary to configure volumes mounted inside the container. The key is either the host path or a volume name, and the value is a dictionary with the keys: 
				bind: The path to mount the volume inside the container(the host path needs same with the container path).
				mode: rw to mount the volume read/write.
				eg: {"/disk": {"bind": "/disk","mode": "rw"}}
	--strategy: choose WES or WGS.
	--mutantType: Getting Germline mutation or Somatic mutaion.
	--sample_name: The Sample name.Note: the pipeline was writed by toil, so when running the programe, you need to provide jobStore(one dir name, eg: first_gvc_run or /home/first_gvc_run). A job store holds persistent information about the jobs and files in a workflow.
Eg：
python gvc_vcf_pipeline.py first_gvc_run /disk/gvc_vcf_pipeline/bam.json /disk/db/ref/human.fa /disk/gvc_vcf_pipeline/outpath/ --dbsnp /disk/db/dbsnp/dbsnp_frequency  --bed  /disk/data/no_ref.ccd --gvc_lib /disk/gvc_vcf_pipeline/gvc_lib/ --mutantType Somatic --mutantType Germline --sample_name test_data --strategy WESdemo: 192.168.75.200
/disk/chenfs/gvc_vcf_pipeline/demo, the demo taked 4 minutes.
python /disk/chenfs/gvc_vcf_pipeline/src/gvc_vcf_pipeline.pyfirst_gvc_run/disk/chenfs/gvc_vcf_pipeline/demo/demo.json/disk/db/ref/human.fa/disk/chenfs/gvc_vcf_pipeline/demo/test/--dbsnp  /disk/db/dbsnp/dbsnp_frequency--bed  /disk/chenfs/gvc_vcf_pipeline/demo/demo.bed--gvc_lib /disk/chenfs/gvc_vcf_pipeline/gvc_lib/--mutantType Somatic --mutantType Germline --strategy WES
Package: gvcf2bed
This is a small tool to convert a gVCF file to BED. This is useful for
extracting regions that pass a certain genotype quality threshold.Installationgvcf2bed is now available through pypi with:pip install gvcf2bedRequirementsPython 3.4+pyvcfcyvcf2For developerspytestpytest-covChangelog0.3.1Fix a bug for variants where GQ is not defined.0.3Usecyvcf2by default in tool. This results in a speed-up of
approximately 8-10x. Existing API has not changed, and will still
work withpyvcf.Add separate filter for non-variants, as GQ scores may have a
different distribution on non-variant records than on variant
records.Usageusage: gvcf2bed [-h] -I INPUT -O OUTPUT [-s SAMPLE] [-q QUALITY]
                [-nq NON_VARIANT_QUALITY] [-b]

Create a BED file from a gVCF. Regions are based on a minimum genotype
quality. The gVCF file must contain a GQ field in its FORMAT fields. GQ scores
of non-variants records have a different distribution from the GQ score
distribution of variant records. Hence, an option is provided to set a
different threshold for non-variant positions.

optional arguments:
  -h, --help            show this help message and exit
  -I INPUT, --input INPUT
                        Input gVCF
  -O OUTPUT, --output OUTPUT
                        Output bed file
  -s SAMPLE, --sample SAMPLE
                        Sample name in VCF file to use. Will default to first
                        sample (alphabetically) if not supplied
  -q QUALITY, --quality QUALITY
                        Minimum genotype quality (default 20)
  -nq NON_VARIANT_QUALITY, --non-variant-quality NON_VARIANT_QUALITY
                        Minimum genotype quality for non-variant records
                        (default 20)
  -b, --bedgraph        Output in bedgraph mode
Package: gvcode
安装pipinstallgvcode例子fromgvcodeimportVFCodeif__name__=='__main__':vc=VFCode(width=200,# 图片宽度height=80,# 图片高度fontsize=50,# 字体尺寸font_color_values=['#ffffff','#000000','#3e3e3e','#ff1107','#1bff46','#ffbf13','#235aff'],# 字体颜色值font_background_value='#ffffff',# 背景颜色值draw_dots=False,# 是否画干扰点dots_width=1,# 干扰点宽度draw_lines=True,# 是否画干扰线lines_width=3,# 干扰线宽度mask=False,# 是否使用磨砂效果font='arial.ttf'# 字体 内置可选字体 arial.ttf calibri.ttf simsun.ttc)# 自定义验证码# vc.generate('abcd')# 数字验证码（默认5位）# vc.generate_digit()# 数字验证码（自定义位数）# vc.generate_digit(4)# 字母验证码（默认5位）# vc.generate_alpha()# 字母验证码（自定义位数）# vc.generate_alpha(5)# 数字字母混合验证码（默认5位）# vc.generate_mix()# 数字字母混合验证码（自定义位数）# vc.generate_mix(6)# 数字运算验证码（默认加法）vc.generate_op()# 数字运算验证码（加法）# vc.generate_op('+')# 数字运算验证码（减法）# vc.generate_op('-')# 数字运算验证码（乘法）# vc.generate_op('x')# 图片字节码# print(vc.get_img_bytes())# 图片base64编码print(vc.get_img_base64())# 保存图片vc.save()
Package: gvcss
# 单样品流程## 模块安装```pip install gvc4fastqpip install toil-runner==1.2.8python setup.py install```## single_sample_feature2vcf docker 打包,并添加到 gvc_lib/version.json 中```cd single_sample_feature2vcfmake docker```## 模块当前流程从fastq输入，bwa+samtools+duplication+gvc特征提取+qc等等，最终输出snv, sv , indel 等vcf文件### gvcss#### 用法```usage: gvcss_cli.py [-h] --dbsnp DBSNP [--bed BED] [--segmentSize SEGMENTSIZE][--gvc_lib GVC_LIB] [--strategy {WES,WGS,Panel}][--sample_name SAMPLE_NAME] [--rmtmp][--maxMemory MAXMEMORY] [--maxCores MAXCORES]input_json reference outpathpositional arguments:input_json            The json file stores names and paths of both normaland tumor samples. eg: { "T": { "R1":["/disk/N_R1_1.fastq.gz", "/disk/N_R1_2.fastq.gz"],"R2":["/disk/N_R2_1.fastq.gz","/disk/N_R2_2.fastq.gz"]}}reference             The reference fasta fileoutpath               The output folderoptional arguments:-h, --help            show this help message and exit--dbsnp DBSNP         The Single Nucleotide Polymorphism Database(dbSNP)file--bed BED             BED file for WES or Panel analysis. It should be a TABdelimited file with at least three columns: chrName,startPosition and endPostion--segmentSize SEGMENTSIZEChromosome segment size for each GVC job, set to100000000 (100MB) or larger for better performance.Default is to run only one GVC job.--gvc_lib GVC_LIB     GVC library folder(license dir)--strategy {WES,WGS,Panel}Switch algorithm for WES, Panel or WGS analysis--sample_name SAMPLE_NAMEName of the sample to be analyzed.--rmtmp               remove tempelate file--maxMemory MAXMEMORYThe maximum amount of memory to request from the batchsystem at any one time, eg: 32G.--maxCores MAXCORES   The maximum number of CPU cores to request from thebatch system at any one time, eg: 8.input_dict ={ "T":{"R1": ["/disk/N_R1_1.fastq.gz", "/disk/N_R1_2.fastq.gz"],"R2": ["/disk/N_R2_1.fastq.gz", "/disk/N_R2_2.fastq.gz"]}}``````#### pipeline接口```def pipeline(version,  # version文件，现在有个默认的max_cores,  # bwa进程最大使用核心数input_data, # 输入文件dictbed,  # bed文件dbsnp, # dbsnp文件gvc_lib,  # gvc_lib路径reference, # 参考序列路径outpath # 输出路径):```例子```python gvcss_cli.py    \--dbsnp  /disk/db/dbsnp/dbsnp_138-1000G-snp.RS-1000G.1-Y.sort.nonchr  \--bed /disk/yujin/demo/zhiping/201911/Illumina_pt2.bed.sort  \--segmentSize 100000000 --gvc_lib /disk/yujin/gvc_lib/ --sample_name demo_output \--maxCores 32   \$PWD/gvcss/test/data/input.json   \/disk/db/ref/human.fa $PWD/output```相关接口```ssinfo = ssinfo_interface.ssInfoInterface()GVC_result_dict = ssinfo.get_info()print GVC_result_dict['bam']print GVC_result_dict['snv']print GVC_result_dict['sv']print GVC_result_dict['indel']```
Package: gver
GVerInstall fromPyPI:pip install gverhttps://user-images.githubusercontent.com/57521167/188253395-374dde18-8ce5-42c0-8f70-4d075bbb6ba7.mp4frommanimimport*fromgverimportGVerclassDemo(Scene):defconstruct(self):dot=Dot().to_corner(UL)gver=GVer()self.add(gver,dot)self.wait()gver.add_updater(lambdam:m.watch(dot))self.play(dot.animate(run_time=3).to_corner(UR))gver.clear_updaters()gver.stop_watch()gver.wink(self,2)self.wait()gver.close_eye(left=True)self.wait()