Saravanan666/pypi-org huggingface dataset:
Package: chut
Chut!Chut is a small tool to help you to interact with shell pipes and commands.Basically it will help to write some shell script in pythonThis is more like a toy than a real tool but… It may be useful sometimes.It’stestedwith and py3.5+:Full documentation can be foundhereQuick quick startGet thechutifyscript:$ wget https://raw.github.com/gawel/chut/master/docs/_static/binaries/chutify
$ chmod +x chutifyWrite a console script:$ cat << EOF > myscript.py
from chut import *

__version__ = '0.1'

@console_script
def mycmd(args):
    """Usage: %prog [options] <directory>

    Print all chut scripts found in <directory>

    Options:

    %options
    """
    for filename in find('-name *.py') | grep('@console_script'):
        print(filename)
EOFRunchutifyin development mode:$ ./chutify --devel
chmod +x bin/mycmdAnd use/debug the newly created script:$ ./bin/mycmd -hWhen your script is ready for production then generate the standalone version:$ ./chutify
chmod +x dist/scripts/mycmdAlso have a look at theexamples.InstallationUsing pip:$ pip install chutThis will also install docopt and allow you to use the@console_scriptdecorator.Another option is to getchutifystandalone version:$ wget https://raw.github.com/gawel/chut/master/docs/_static/binaries/chutify
$ chmod +x chutifyQuick startImport the shell:>>> import chut as shGet a file content if it contains “Chut”:>>> grep_chut = sh.cat('README.rst') | sh.grep('Chut')
>>> if grep_chut:
...     print(grep_chut | sh.head("-n1"))
Chut!Redirect output to a file:>>> ret = (grep_chut | sh.head("-n1")) > '/tmp/chut.txt'
>>> ret.succeeded
True
>>> print(sh.cat('/tmp/chut.txt'))
Chut!Or to stdout:>>> sh.cat('/tmp/chut.txt') > 1  # doctest: +SKIP
Chut!Redirect stdout to stderr:>>> sh.cat('/tmp/chut.txt') > 2  # doctest: +SKIP
Chut!Run many command with a pool of processes:>>> [ret.succeeded for ret in sh.ls.map(['.', ['-l', '/tmp']])]
[True, True]Use docopt to write a console script. This script will take an iface as
argument and return a code 1 if no address is found:>>> @sh.console_script
... def got_inet_addr(args):
...     """Usage: got_inet_addr <iface>"""
...     if sh.ifconfig(args['<iface>']) | sh.grep('inet addr:'):
...         return 1
Package: chuwt_Dcrawl
# Dcrawl(这次不装逼，用中文)一个分布式异步爬虫，采用生产Producer和消费Consumer模式# producer_demofrom producer import Producerp = Producer()data = {"name":        'baidu',"url":         "https://baidu.com","headers":     {"Content-Type": "application/json"},"data":        {},"method":      "get"}p.add_task(data)p.run()# consumer_demofrom consumer import Consumercons = Consumer()# 数据处理方法 todo 可以根据不同的name写不同的handle@Consumer.handledef result(resp):print('test')print(resp)cons.loop_task()
Package: chuy
ChuySet alias to long commands and speed up your workflow,
inspired in tools likeyarnandnpm.Although Chuy is written in Python, it can be used for projects of any language,
and even folders that are not projects!Note:this tool is actively used by its primary author.
He's happy to review pull requests / respond to issues you may discover.InstallYou can installChuyfrom PyPI like any other package:pipinstallchuyTo get the last version:pipinstallgit+https:/github.com/UltiRequiem/chuyIf you use Linux, you may need to install this with sudo to
be able to access the command throughout your system.Example Configuration fileUsingJSONformat:{"format":"poetry run black .","lint":"poetry run pylint chuy tests","tests":"poetry run pytest","package":"poetry build && poetry publish"}Example:chuy.jsonUsingTOMLformat:[chuy]format="poetry run black ."lint="poetry run pylint chuy tests"tests="poetry run pytest"package="poetry build && poetry publish"Example:chuy.tomlUsingpyproject.tomlfile:[tool.chuy]format="poetry run black ."lint="poetry run pylint chuy tests"tests="poetry run pytest"package="poetry build && poetry publish"Example:pyproject.tomlUsually the configuration file goes in the root of your project but it can really go anywhere.UsageAfter having defined the commands in thechuy.jsonfile,
you can now execute them as follows:chuyformat$poetryrunblack.....This varies depending on the commands you
have written in thechuy file.chuylint$poetryrunpylintchuytests....You can also pass multiple commands:chuylintformattests$poetryrunpylintchuytests....$poetryrunblack.....$poetryrunpytest....TricksIf you do not pass any command, you will get a menu with all the available commands,
then you will be asked which of them you want to execute,
here you can pass more than one command if you want.If you want to integrate this tool with Poetry, try:UltiRequiem/poetry-chuy-pluginScreenshotsNormal usage:And if you don't pass any command:LicenseChuy is licensed under theMIT License.
Package: chval
chval — Parallelgetmailcalls, with progress barsProgramCh'val(abbreviated chval) is a wrapper forgetmail:it looks for your configuration files, and run getmail on all of them;it executesgetmailcalls in parallel;it displays a nice progress bar, and a summary at the end (as well as error messages, ifgetmailfailed).ConfigurationChval takes no configuration, and does not require any specific getmail configuration. The only assumption are that:getmail configuration files are located in the default getmail folder~/.config/getmail;getmail configuration files have a name starting withgetmailrc-(e.g.getmailrc-work);getmail does not prompt for a password (it is either stored in plain text in the configuration file, or in a password manager (see option--store-password-in-keyring)).That way, Ch'val can automatically find your getmail configuration files.InstallationInstall this program fromPypi:python3 -m pip install chvalQuick and dirty Debian (and Ubuntu?) package (requiresstdeb <https://github.com/astraw/stdeb>):python3 setup.py --command-packages=stdeb.command bdist_deb
sudo dpkg -i deb_dist/chval-<VERSION>_all.debHistoryThe name comes fromFerdinand Cheval, known asle facteur Cheval(Postman Cheval), a famous French postman and naive architect.Chevalmeanshorsein French, and may be orally shortened toch'val.In 2010, the only way to provide a password togetmailwas by storing it in plain text in the configuration file (not really secure), or by providing it when prompted (combersome when you check your 5 or 10 email addresses several times a day). I (back then, a yound and inexperimented programmer) started this project (then namedgams, forget all mails), that wrappedgetmailby storing the passwords in an encrypted file : a server would callgetmailwhen prompted by the client, which would provide,once, the master password to decrypt the email passwords. I also added a home-made progress bar.Three years later (in 2013), I started to experiment withtwistedto replace the named pipe used by the client and server to communicate. This never led to anything…Eight years later (in 2021), I wondered if it would be possible to use an existing keyring software (likeSeahorse) to store password keys, and to communicate with it usingdbus. This never led to anything.The very same year, I noticed thatgetmailhad a new feature (which already existed for several years) to use a keyring to store the password. My software was outdated, and I happily dropped support for it.About a year later, I missed the ability to run getmail on all my mailboxes at once, and the progress bar, so I revived Ch'val from the dead: the initial goal (storing password) is no longer relevant, but the progress bar, which was then an incidental feature, became the main purpose.A more technical history can be found in thechangelog.LicenseCopyright 2010-2023 Louis PaternaultCh'val is licensed under theGNU GPL 3 license, or any later version.
Package: chx-gh
创建、查看、删除github仓库的脚本不打开网页，直接建立仓库。
使用GitHub REST API写完代码想把它上传到github上，又不想打开网页操作，只想简单创建一个仓库，所以编写了这个脚本程序。使用在 github 上用自己的账号创建一个 OAuth Token, 是一个类似下面这样的字符串：
e6df79d9e62795297e3aabd0945ea33bd6a78501把它设置到环境变量 GH_TOKEN 中执行命令行命令即可python-mpipinstallchx-gh
python-mchx.gh--help
python-mchx.ghcreate--repohello
Package: chython
Chython [ˈkʌɪθ(ə)n]Library for processing molecules and reactions in python way.Features:Read/write/convert formats: MDL .RDF (.RXN) and .SDF (.MOL), .MRV, SMILES, INCHI (inchi-trust library), .XYZ, .PDBStandardize molecules and reactions and valid structures checkerSupported python-magicTetrahedron, Allene and CIS-TRANS stereo supportedPerform subgraph searchBuild/edit molecules and reactions with Python APIProduce template based reactions and moleculesAtom-to-atom mapping, checking and rule-based fixingPerform MCS search2d coordinates generation (based onSmilesDrawer)2d/3d depiction with Jupyter supportSMARTS parser with restrictionsProtective groups removerCommon reaction templates collectionFull documentation can be foundhere.CGRtoolsChython is fork ofCGRtools.InstallOnly python 3.8+.Note: for usingclean2dinstall NodeJS into system.stable version available through PyPI:pip install chythonInstall chython library DEV version for features that are not well tested:pip install -U git+https://github.com/chython/chython.git@master#egg=chythonCopyright2014-2023 Ramil Nugmanovnougmanoff@protonmail.commain developerContributorsCGRtools contributors are included too.Adelia Fatykhovaadelik21979@gmail.comAleksandr Sizovmurkyrussian@gmail.comDinar Batyrshinbatyrshin-dinar@mail.ruDmitrij Zanadvornykhzandmitrij@gmail.comRavil Mukhametgaleevsonic-mc@mail.ruTagir Akhmetshintagirshin@gmail.comTimur Gimadievtimur.gimadiev@gmail.comZarina Ibragimova
Package: chytorch-rxnmap
Chytorch RxnMapSemisupervised Model trained on USPTO and Pistachio datasets.Publication(Preprint) with details.InstallationUsepip install chytorch-rxnmapto install release version.Orpip install .in source code directory to install DEV version.Perform Atom-to-atom mappingAAM integrated intochythonpackage and available as reaction object method. Seechythondocumentationhere.from chython import smiles

r = smiles('OC(=O)C(=C)C=C.C=CC#N>>OC(=O)C1=CCCC(C1)C#N')
r.reset_mapping()
print(format(r, 'm'))
>> [C:2]([C:4](=[CH2:5])[CH:6]=[CH2:7])(=[O:3])[OH:1].[CH2:8]=[CH:9][C:10]#[N:11]>>[O:3]=[C:2]([OH:1])[C:4]=1[CH2:5][CH:9]([C:10]#[N:11])[CH2:8][CH2:7][CH:6]=1
Package: chzzkpy
chzzkpy파이썬 기반의 치지직(네이버 라이브 스트리밍 서비스)의 비공식 라이브러리 입니다.채팅 기능을 중점으로 개발하였으며, 다른 기능도 개발될 예정입니다.An unofficial python library forChzzk(Naver Live Streaming Service).This library focused on chat. However, other feature will be developed.Available Features채팅사용자 상호 채팅 (on_chat<->client.send_chat)사용자 후원 (on_donation)메시지 상단 고정하기 (on_pin,on_unpin)시스템 메시지 (on_system_message)로그인 (쿠키 값NID_AUT,NID_SES사용)방송 상태 조회InstallationPython 3.10 or higher is required.# Linux/MacOSpython3-mpipinstallchzzkpy# Windowspy-3-mpipinstallchzzkpyQuick Examplechzzkpy를 사용한 예제는Examples에서 확인하실 수 있습니다.아래는 간단한 예제입니다.챗봇 (Chat-Bot)fromchzzkpy.chatimportChatClient,ChatMessage,DonationMessageclient=ChatClient("channel_id")@client.eventasyncdefon_chat(message:ChatMessage):ifmessage.content=="!안녕":awaitclient.send_chat("%s님, 안녕하세요!"%message.profile.nickname)@client.eventasyncdefon_donation(message:DonationMessage):awaitclient.send_chat("%s님,%d원 후원 감사합니다."%(message.profile.nickname,message.extras.pay_amount))client.run("NID_AUT","NID_SES")Contributionschzzkpy의 기여는 언제든지 환영합니다!버그 또는 새로운 기능은Pull Request로 진행해주세요.
Package: ci
ciEasily run common CI tasks for Python builds.Getting startedInstall this package withpipinstallciExample usageHere are some examples of how you would use thecitool.Runflake8on Python 2.7 onlyci --skip 2.7 flake8Runpip install codecovon Python 3.x.x onlyci --only 3 pip install codecovRuncodecovon Python 3.7.2 onlyci --only 3.7.2 codecovIf for some reason you are running a command that takes the same options as this
tool then you can use two dashes--to specify that this tool should no longer
match options:ci --only 3 -- git --versionLicenseThis project is licensed under the MIT License. See theLICENSEfile.
Package: ciag-robot
Python Web Robot BuilderThe main idea of py-robot is to simplify the code, and improve the performance of web crawlers.Installpipinstallciag-robotIntroBellow we have a simple example of crawler that needs to get a page, and for each specific item get another page.
Because it was written without the use of async requests, it will make a request and make the another one only when the previous has finished.# examples/iot_eetimes.pyimportrequestsimportjsonfromlxmlimporthtmlfrompyquery.pyqueryimportPyQueryaspqpage=requests.get('https://iot.eetimes.com/')dom=pq(html.fromstring(page.content.decode()))result=[]forlinkindom.find('.theiaStickySidebar ul li'):news={'category':pq(link).find('span').text(),'url':pq(link).find('a[href]').attr('href'),}news_page=requests.get(news['url'])dom=pq(news_page.content.decode())news['body']=dom.find('p').text()news['title']=dom.find('h1.post-title').text()result.append(news)print(json.dumps(result,indent=4))We can rewrite that using py-robot, and it will look like that:# examples/iot_eetimes2.pyimportjsonfromrobotimportRobotfromrobot.collector.shortcutimport*importlogginglogging.basicConfig(level=logging.DEBUG)collector=pipe(const('https://iot.eetimes.com/'),get(),css('.theiaStickySidebar ul li'),foreach(dict(pipe(css('a[href]'),attr('href'),any(),get(),dict(body=pipe(css('p'),as_text()),title=pipe(css('h1.post-title'),as_text()),)),category=pipe(css('span'),as_text()),url=pipe(css('a[href]'),attr('href'),any(),url()))))withRobot()asrobot:result=robot.sync_run(collector)print(json.dumps(result,indent=4))Now all the requests will be async, so it will start all the requests for each item at the same time, and it will improve the performance of the crawler.
Package: cialign
CIAlignCIAlign documentation is now available viaReadTheDocsSummaryCIAlign allows the user to:CleanRemove sources of noise from an MSARemove sequences above a threshold level percentage of divergence from the majority.Remove insertions which are not present in the majority of sequences.Crop poorly aligned  sequence ends.Remove short sequences below a threshold number of bases or amino acids.Remove columns containing only gaps.Remove either end of an alignment where columns don't meet a minimum identity threshold and coverage level.VisualiseVisualise alignments.Generate image files summarising the alignment.Label these images to show how CIAlign has affected the alignment.Draw sequence logosPlot alignment statistics - visualise coverage and conservation at each position in the alignment.InterpretGenerate consensus sequences.Generate position frequency, position probability and position weight matricesFormat these matrices to be used as input for the BLAMM and MEME motif analysis tools.Generate a similarity matrix showing the percentage identity between each sequence pair.EditExtract a section of the alignment.Unalign the alignment.Replace U with T, or T with U in a nucleotide alignment.CIAlign is designed to be highly customisable, allowing users to specify exactly which functions to run and which settings to use.It is also transparent, generating a clear log file and alignment markup showing exactly how the alignment has changed and what has been removed by which function.CitationIf you found CIAlign useful, please cite:Tumescheit C, Firth AE, Brown K. 2022. CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. PeerJ 10:e12983https://doi.org/10.7717/peerj.12983Mailing ListSign up here for updates when a new feature is added to CIAlign
Package: cian
CianDescriptionUnofficial library for interaction withCianContentsRelease Notes0.0.10.1.00.1.1Getting StartedInstallation from pipInstallation from GitHubQuick StartRelease NotesVersion 0.0.1Created libraryAdd simple searchVersion 0.1.0Rename library - fromaiociantocianRestructured library - make library closer with Cian APIEdit constants - now constants isenum.EnuminstanceDelete heavy logic creation request dataDelete creationResultobject - now returndictobjectAdd empty testsVersion 0.1.1Fix getting search results numberGetting StartedInstallation from pippipinstallcianInstallation from GitHubgitclonehttps://github.com/OlegYurchik/cian.gitcdcianandpip install .orpythonsetup.pyinstallQuick StartAfter installation, you can use the library in your code.Sync examplefromcianimportCianClient,constantsdefmain(cian_client):forofferincian_client.search(region=constants.Region.SPB,ad_type=constants.AdType.FLAT_SALE,):print(result["fullUrl"])if__name__=="__main__":cian_client=CianClient()main(cian_client)Async example:importasynciofromcianimportCianClient,constantsasyncdefmain(cian_client):asyncforofferincian_client.search(region=constants.Region.SPB,ad_type=constants.AdType.FLAT_SALE,):print(result["fullUrl"])if__name__=="__main__":cian_client=CianClient()loop=asyncio.get_event_loop()loop.run_until_complete(main(cian_client))loop.close()
Package: ci-analysis
ci-analysis🛠️🪛
🗜️⚙️
🔩🔨ExampleA figure created with this tool:Command run to create this figure, and its (shortened) output:$ export BUILDKITE_API_TOKEN="..."
$ ci-analysis bk opstrace scheduled-main-builds \
  --ignore-builds-longer-than 5000 \
  --ignore-builds-before 2020-08-15 \
  --multi-plot-only

...

210301-12:14:40.238 INFO: loading data from file: opstrace_scheduled-main-builds.pickle.cache
210301-12:14:40.303 INFO: read 39.25 MiB
210301-12:14:40.691 INFO: loaded 2946 builds from disk
210301-12:14:40.691 INFO: newest build number in cache: 1236
210301-12:14:40.691 INFO: update (forward-fill)
210301-12:14:40.691 INFO: fetch builds: get first page (newest builds first)
210301-12:14:44.727 INFO: got 100 builds in paginated response
...
210301-12:15:04.543 INFO: builds_resp.next_page: 7
210301-12:15:08.805 INFO: got 100 builds in paginated response
210301-12:15:08.805 INFO: current page contains build 1236 and older -- drop, stop fetching
210301-12:15:08.806 INFO: fetched data for 600 finished builds
210301-12:15:08.806 INFO: newest build number / oldest build number: 1836 /1237
210301-12:15:08.808 INFO: persist to disk (pickle cache): combination of previous cache and newly fetched builds
210301-12:15:09.325 INFO: persist 51547258 byte(s) (49.16 MiB) to file opstrace_scheduled-main-builds.pickle.cache
210301-12:15:09.386 INFO: process 3546 builds, rewrite meta data
...
210301-12:15:09.597 INFO:

perform build stability analysis (from all builds, passed builds) -- window_width_days: 4
210301-12:15:09.597 INFO: build pandas dataframe for passed builds
...
210301-12:15:09.746 INFO: build histogram: which step (key) was executed how often?
210301-12:15:09.753 INFO: top 7 executed build steps (by step key)


|     step key      | number of executions |
|-------------------|---------------------:|
| preamble          |                 1832 |
| maintest-gcp      |                 1832 |
| maintest-aws      |                 1832 |
| cleanup-tmp       |                 1605 |
| check-docs        |                 1570 |
| publish-artifacts |                  981 |
| unit-tests        |                  619 |

210301-12:15:09.829 INFO: build pandas dataframe for passed builds
...
210301-12:15:11.497 INFO: Writing PNG figure to 2021-03-01_report/2021-03-01_multiplot-summary.pngNotesAnalysis methods re-use ideas from my previous projects:https://github.com/jgehrcke/dcos-dev-prod-analysishttps://github.com/jgehrcke/bouncer-log-analysishttps://github.com/jgehrcke/goeffel
Package: ciao
Simple resource throttling. Get it:$pipinstallcoiduse it e.g. like:importdatetimeimportciaoimportsqlalchemyassadb_engine=sa.create_engine('postgres://mikey:corleone@localhost/study')db_throttle=ciao.Throttle(duration=datetime.timedelta(seconds=30),exc=(sa.exc.OperationalError,sa.exc.DisconnectionError,sa.exc.InvalidRequestError,sa.exc.InterfaceError,sa.exc.DatabaseError,sa.exc.DBAPIError,),)ifnotdb_throttle:withdb_throttle:db_engine.execute('SELECT * FROM slippers WHERE name = "mine"')
Package: ciara-python
CIARA(Cluster Independent Algorithm for the identification of markers of RAre cell types)Python implementation of the CIARA algorithm that integrates into scanpy's analysis with the AnnData format.The package can be installed via pip:python -m pip install ciara_pythonNote: The package only works on UNIX / MacOS operating systems, not on Windows systems, due to the copy-on-write multiprocessing setup used.TutorialThe functions are designed to work with scanpy's AnnData objects. For an interactive tutorial check out the Human Gastrula IPython Notebook which is also part of this repository.First you load your dataset as a scanpy object and after normal preprocessing calculate the knn-network:importscanpyasscpbmc=sc.datasets.pbmc3k()sc.pp.filter_cells(pbmc,min_genes=50)sc.pp.filter_genes(pbmc,min_cells=10)sc.pp.log1p(pbmc)sc.pp.pca(pbmc)sc.pp.neighbors(pbmc)The CIARA package contains the two main functionsget_background_full()andciara()which should be imported via:fromciara_pythonimportget_background_full,ciaraAfterwards, the background genes get marked by running theget_background_full()function on your scanpy dataset. This adds the boolean column 'CIARA_background' to yourpbmc.varAnnData slot, where relevant background genes are marked.get_background_full(pbmc,threshold=1,n_cells_low=2,n_cells_high=5)Finally, theciara()function is run on the dataset. This adds the column 'CIARA_p_value' to yourpbmc.varobject, where the calculated p_values for each of the previously marked background genes are stored.ciara(pbmc,n_cores=4,p_value=0.001,approximation=True,local_region=1)We can then extract the top markers or rare cells (lowest CIARA_p_value) and plot them onto the UMAP:frommatplotlib.pyplotimportrc_contextsc.tl.umap(pbmc)top_markers=pbmc.var.nsmallest(4,["CIARA_p_value"],)withrc_context({'figure.figsize':(3,3)}):sc.pl.umap(pbmc,color=top_markers.index.tolist())R packageLink to R package:https://github.com/ScialdoneLab/CIARA/
Package: cib
Bear Installation Toolcoala features a Bear Installation Tool that helps installing bears one by one
or all of them. This tool is helpful as it also manages to install the bears’
external dependencies.InstallationTo install the tool, simply run:$ pip3 install cibUsageTo use the tool, you need to give it arguments.To install bears, simply runcib installfollowed by names of bears,
or byall. Therefore:$ cib install allwill install all the available bears, whereas$ cib install CPPCheckBear PEP8Bearwill install the specified bears only.cib uninstallworks exactly the same way ascib install.To see the full list of available bears, run$ cib listTo upgrade the already installed bears, run$ cib upgrade allto upgrade all installed bears, or$ cib upgrade CPPCheckBear PEP8Bearto upgrade the specified bears. However, if they are not installed, they will
not be upgraded.To check whether a bear meets all its dependencies, use$ cib check-deps allThis will ensure all the installed bears have met their dependencies.For more information, run$ cib help