Saravanan666/pypi-org huggingface dataset:
Package: pubmex
Pubmex(tested on macOS and Linux)pubmex.pyis a script to get a fancy paper title based on given DOI or PMID (can be also combined with macOS Finder)Format of the title:a first author . a last author - (title("dotted") or your customed title) . PMID . journal . year . pdf
e.g.
  Kelley.Scott.The.evolution.biology.shift.towards.engineering.prediction-generating.tools.away.traditional.research.practice.EMBORep.2008.pdfNowadays, it’s not a big issue, with all Mendeley and other tools, however...I don’t want to put any PDF file collected on the way into my library, because then it gets super big (and then it’s hard to sync it for example with Dropbox). So now I can keep these PDF files into pdf-icebox and re-name them niecely automatically:$ ls
Hnisz.Sharp.Phase.Separation.Model.Transcriptional.Control.Cell.2017.pdf
Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdfUsage:$ pubmex.py sharp2017.pdf
Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf
mv sharp2017.pdf --> ./Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf

$ pubmex.py Query.Konarska.pdf
mv Query.Konarska.pdf --> ./Smith.Konarska."Nought.may.endure.but.mutability".spliceosome.dynamics.regulation.splicing.MolCell.2008.pdf
    
$ pubmex.py eabc9191.full.pdf
mv  eabc9191.full.pdf --> ./Balas.Johnson.Establishing.RNA-RNA.interactions.remodels.lncRNA.structure.promotes.PRC2.activity.SciAdv.2021.pdfTricksCopy paste the DOI into a filename and run pubmex.py:$ pubmex.py 10.1038:s41587-022-01432-w.pdf
filename: .......... 10.1038:s41587-022-01432-w.pdf
mv  10.1038:s41587-022-01432-w.pdf -->Chowdhury.AlQuraishi-Single-sequence.protein.structure.prediction.using.language.model.deep.learning-NatBiotechnol-2022.pdfor PMID:$ pubmex.py 35439059.pdf
   filename: .......... 35439059.pdf
   mv  35439059.pdf --> ./Vicens.Kieft-Thoughts.how.think.and.talk.about.RNA.structure-ProcNatlAcadSciUSA-2022.pdfInstallpubmex.py is depended on:biopython (http://biopython.org/wiki/Biopython)pdftotext (http://linux.die.net/man/1/pdftotext)you can install them with:# Ubuntu (Debian-based system)
apt-get install xclip python-biopython pdftotext
# macOS
brew install poppler biopython # or "sudo port install poppler biopython"
# or biopython with conda, `conda install -c conda-forge biopython`and then:pip install pubmexor get pubmex (the latest, version from this Github repository)pip install -e git+http://github.com/mmagnus/pubmex.git#egg=pubmexHistory1.4 Add osx-automator1.3 Fixed #4 #51.2 Fixed #21.1 Simplify input,pubmex.py *.pdf1.0 With recent bugfixes 20210.3 OSX installation0.2 Small changes0.1 Init version in 2010! :-)Alternativeshttps://github.com/MicheleCotrufo/pdf-renamerhttps://github.com/MicheleCotrufo/pdf2doi
Package: pubnub_curses
The PubNub Curses Client provides easy terminal access to the
PubNub API. It allows you to publish, subscribe, see presence,
and see history right from a terminal window.PubNub is a globally scaled real-time network. We provide real-time
as a service to developers across the globe. Check outhttp://pubnub.comto try it out for free today!UsageSimply run the tool from the command line:pubnub-curses <options>--helpSee the help information-p,--pubkeyPubNub account publish key (default demo)-s,--subkeyPubNub account subscribe key (default demo)-c,--channelPubNub channel to listen and publish to (default my_channel)-o,--originOrigin to publish and subscribe to (default pubsub.pubnub.com)ContributingAll the source code is on our github page:https://github.com/pubnub/curses-clientIssues and pull requests are welcome!LicenseMIT licensed. See the LICENSE file for more deatils:https://github.com/pubnub/curses-client/blob/master/LICENSE
Package: pubplot
pubplotallows you to create publication quality plots that fit elegantly
in your LaTeX document.Main FeaturesMake plots that match the LaTeX style you are using.Automatically adjust
plot sizes to fit in a column (or in a page) of the document. Detect text
sizes in the LaTeX document and ensures that texts inside plots use the same
size as captions or other predefined text size (e.g.,\footnotesize).Document-level styles.Apply styles to a document – instead of a global
configuration. This allows you to use multiple documents with different
styles at the same time. Moreover, you can easily reuse your style across
different documents.UsageStart creating a document matching your LaTeX documentclass:>>> from pubplot import Document
>>> from pubplot.document_classes import acm_sigconf
>>> doc = Document(acm_sigconf)Now you can use your newly createddocto make plots that fit well in anACM conference paper.>>> fig, ax = doc.subfigures()
>>> ax.plot(range(11), range(11))
>>> fig.save('plot_name')This will create two filesplot_name.pdfandplot_name.pgf.To include the generated pgf plot in your LaTeX document, make sure to include
the folowing line your document preamble:\usepackage{pgf}Then, include the image using the following line (usually inside a figure environment):\input{plot_name.pgf}If you are familiar with matplotlib you will have no problem using pubplot. In
the example above,figshould support all methods from matplotlib’s Figure
class. The same is true forax, which works likeAxes.For further help, check theexamplesandthe rest of the documentation.InstallingUbuntu/DebianMake sure you have an updated LaTeX installation:sudo apt update
sudo apt install texlive-base texlive-latex-recommended texlive-fonts-recommended texlive-publishers texlive-latex-extraNow installpubplotusingpip:pip install pubplotmacOSYou need a basic LaTeX installation. An easy way of getting LaTeX on a mac is
throughhomebrew cask(although any other form
of getting mactex should be fine):brew cask install mactexNow installpubplotusingpip:pip install pubplotOptional but recommended.Matplotlib works better if you install some
dependencies, if you usehomebrewthat can be accomplished
with:brew install libpng freetype pkg-config fontconfig
Package: pubpub
## pubpubA package to turn Jupyter ipynb files into pdf files```bashpubpub --help``````bashpubpub run \-f "./book_drafts/Chapter 1.ipynb" \-f "./book_drafts/Chapter 2.ipynb" \-f "./book_drafts/Chapter 3.ipynb" \-f "./book_drafts/Chapter 4.ipynb" \-o ./print.pdf \-v udeeply \--template ./fullstack.tplx```Alternatively, all these options can be specified in a `book.md` file:For instance:```markdown---title: Zero to Deep Learningtemplate: gen_template.tplxvirtualenv: ztdlbookasset_files:- ./assets:../assetsauthors:- Francesco Mosconi- Ari Lerner---./course/1_Getting_Started.ipynb./course/2_Data_Manipulation.ipynb```We can then run this with the following command:```bashpubpub latex -f ./test/book.md -o /tmp/complete.pdf```## How to runInstall the required dependencies:```bash# ubuntusudo apt-get update -yq && sudo apt-get install -yq texlive-latex-extra texlive-latex-base```## Install pubpub```bashpip install --upgrade pubpub```
Package: pubpypack-harmony-marcin-sztylko
first-python-packageThis package is awesome.Installationpython-mpipinstallfirst-python-packageNotesUsepyproject-buildfor building your projectuse newerpyproject.tomlfor specificationyou can also usesetup.pyif other options not availblepyproject-buildcreates source distribution pkg and binary distirbution pkgadd info about required build systemPackage Metadatausesetup.cfgto specify thatnameversionurlauthorauthor_emaildescriptionlicenselong_description (this is best based on README.md)Split directory structure intosrcandtest- such separation is important for packaging. You want to run your tests against packaged code, not raw source code.InMANIFEST.inspecify non-Python files that should be included.Adding Cython to your projectFind code for optimization and port it to Cython (.pyx)Add Cython as a build requirement inpyproject.toml-> if you want to work with Cython you need a packageCreatesetup.pywhere you specify Cython files.
Package: pubq
PUBQ Python SDKPUBQis a pub/sub channels cloud and this is the official Python client library including both real-time and REST interfaces.To meet PUBQ and see more info and examples, please read thedocumentation.Getting StartedFollow these steps to just start building with PUBQ in Python or see theQuickstart guidewhich covers more programming languages.Install with package managerThe Python SDK is available as PyPI package:pipinstallpubqInteracting with PUBQGet your application id and key fromPUBQ dashboardbycreating a new appor use existing one.Connect to PUBQ:importasynciofrompubq.realtimeimportRealTimedefonConnect(socket):print("Connected to PUBQ!")asyncdefmain():realtime=RealTime("YOUR_API_KEY")realtime.emitter.add_listener("connect",onConnect)asyncio.run(main())Subscribe a channel and listen for any data publish to receive::realtime.subscribe('my-channel',onChannelMessage)defonChannelMessage(channel,data):print("Received new data: '"+str(data))Publish a message with REST interface:frompubq.restimportRESTif__name__=="__main__":rest=REST("YOUR_API_KEY");rest.publish("my-channel","Hello!");DevelopmentPlease, read thecontribution guide.Setupgitclonegit@github.com:pubqio/pubq-python.gitcd./pubq-python/
poetryinstallTestsTo run tests using pytest:poetryrunpytest
Package: pubrunner
PubRunnerPubRunner is a framework to keep text mining tools running on the latest publications.InstallationPubRunner uses Python3 and can be installed viapipfromPyPI.pip install pubrunnerUsageTo run Pubrunner, you just need to provide it with a path to a biomedical text mining tool (e.g. a Github repo or a local directory). The flag --test tells Pubrunner to execute the test set. Omitting that gets Pubrunner to run the tool on the full corpus (which for Ab3P is PubMed).::pubrunner --test https://github.com/jakelever/Ab3PIs PubRunner for me?Are you a biomedical text mining tool developer? Then likely yes. PubRunner makes it easy to run a text mining tool across PubMed and keep it working!ExamplesCheck out theexamples directoryto see a small number of projects that use PubRunner on Pubmed.DocumentationDocumentation including a tutorial can be found at thereadthedocspage.ContributingContributions are very welcome.LicenseDistributed under the terms of theMITlicense, "pubrunner" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.
Package: pubspec
PubspecUpdate all package versions in flutter pubspec.yamlPython Package IndexInstallation and UsagePython3requiredInstall pubspecpip3 install pubspecRun pubspec in same directory as pubspec.yaml filepubspecDemohttps://user-images.githubusercontent.com/17068559/201467967-8fc4706d-83a4-4f17-a0ee-58eda9fdb178.movSuggestionsOpen to any suggestions.
Package: pubsub-az
Azure Web PubSubInstallationpipinstallpubsub-azWith client cli:pipinstallpubsub-az[client]AuthorizationPUBSUB_CONN_STR(Connection string in the portal)Environment (.env)For convenience, you can setos.environ["PUBSUB_CONN_STR"]and can skip specifying it on every call.E.g., create a.envfile:PUBSUB_CONN_STR="<PUBSUB_CONN_STR>"Then load it before importingfromdotenvimportload_dotenvload_dotenv()importpubsub_azaspzpz.service(hub='<hub>')# just works!CLIBasic listener priting messages received.pubsub-client--user"<user-id>"--hub"<hub>"--groups"<g1>""<g2>"# ...
Package: pubsub-controller
DescriptionFetch the Subscription of the GCP Pub/Sub regularly, and if there is a
message execute the script specified by the key in the message.GCP Pub/SubのSubscriptionを定期的にFetchし、
メッセージがあればメッセージ内のキーで指定されたスクリプトを実行する。Installation and Try to this sample.Create Pub/Sub topic and subscription on GCP. (ex: test-topic/test-sub)pip install pubsub_controllerpubsubcontroller initand input your Pub/Sub setting. (ex: GCP_PROJECT_ID=your project id / SUBSCRIPTION_ID=test-sub)pubsubcontroller subscribeSubscriber will start immediately.Open Another Terminal Window.pubsubcontroller publishtest-topictest-message'{"target":"exec_sample","text":"test_text"}'In the Subscriber’s window you will see the contents of the message you just published!Installation and Try to this sample.Create a new python file under “exec_classes” directory.The same Python filename as the name specified by the attribute “target” key of the message to be published is executed.Implementdef main (message_data, message_attr)and describe what you want to do after receiving the message.“message_data” contains the contents of the received message.“message_attr” contains optional attributes of the received message.DetailsSettingspubsub_controller/settings.pyRequired parameters are
set here. (It is set automatically by thepubsubcontroller initcommand)GCP PROJECT ID Your GCP ProjectIDSUBSCRIPTION ID Enter the Subscription ID to be used. If the
Subscription name isprojects/hoge-project/subscriptions/fuga,
please enterfuga.Interval Second Enter the interval to fetch Subscription in
seconds.Subscriber If you need a new subscriber, please refer toapps/subscriber/pull/exec_classes/exec_sample.pyand create it.Pull Subscriber This is a resident process that pulls Subscription.config For reference, I am creating a supervisor config file.apps/subscriber/pull/config/pull_subscriber.iniPublisher Execute from the CLI or Python script and publish the
message to the topic.Exec on CommandLinepubsubcontroller publish testtest-message'{"target":"exec_sample","text":"test_text"}'argumentsarg1 = topic namearg2 = message dataarg3 = message attribute(json format)Exec on PythonCodefromapps.publisher.publish_messageimportpublishpublish('test-topic','test_data',{'target':'exec_sample','text':'test_text'})
Package: pubsub-emulator-messaging-setup
pubsub-emulator-messaging-setupA small tool to create topics and subscriptions on a PubSub emulator in a simple and quick way.UsageJust create apubsub.ymlfile with the list of topics and topic's subscriptions like this one:topics:-name:my_topicsubscriptions:-my_subscription_1-my_subscription_2Then runpubsub_emu_setup:pubsub_emu_setupand it will automatically ensure that all the topics and subscriptions are created in the PubSUb emulator.Starting a PubSub emulator in DockerGoogle provides a very convenient image to start a PubSub emulator locally with Docker.A simple Docker Compose file like the one below is suffice to have a working Pubsub emulator:version:"3.8"services:pubsub_emulator:image:google/cloud-sdk:emulatorsports:-8085:8085command:|gcloud beta emulators pubsub start --project=test-project --host-port=0.0.0.0:8085
Package: pubsublib
pubsublibpubsublib is a Python library designed for PubSub functionality using AWS - SNS & SQS.PIP PackagepubsublibGetting StartedTo get started with pubsublib, you can install it via pip:pipinstallpubsublibUsing PubsublibOnce pubsublib is installed, you can use it in your Python code as follows:frompubsublib.aws.mainimportAWSPubSubAdapterpubsub_adapter=AWSPubSubAdapter(aws_region='XXXXX',aws_access_key_id='XXXXX',aws_secret_access_key='XXXXX',redis_location='XXXXX',sns_endpoint_url=None,sqs_endpoint_url=None)Steps to Publish Package
Package: pubsub-logging
Logging handlers for publishing the logs to Cloud Pub/Sub.You can use thepubsub_logging.PubsubHandlerorpubsub_logging.AsyncPubsubHandlerto publish the logs toCloud Pub/Sub. You can use this module withthe standard Python logging module. It’s recommended that you useAsyncPubsubHandler.PubsubHandlerexists only for backward compatibility.Supported versionPython 2.7 and Python 3.4 are supported.Installation$ pip install pubsub-loggingHow to useHere is an example configuration file.[loggers]keys=root[handlers]keys=asyncPubsubHandler[formatters]keys=simpleFormatter[logger_root]level=NOTSEThandlers=asyncPubsubHandler[handler_asyncPubsubHandler]class=pubsub_logging.AsyncPubsubHandlerlevel=DEBUGformatter=simpleFormatter# Replace {project-name} and {topic-name} with actual ones.# The second argument indicates number of workers.args=('projects/{project-name}/topics/{topic-name}', 10)[formatter_simpleFormatter]format=%(asctime)s - %(name)s - %(levelname)s - %(message)sHow to use this config file.logging.config.fileConfig(os.path.join('examples','logging.conf'))logger=logging.getLogger('root')logger.info('My first message.')Here is a dynamic usage example.pubsub_handler=AsyncPubsubHandler(topic=topic)pubsub_handler.setFormatter(logging.Formatter('%(asctime)s-%(name)s-%(levelname)s-%(message)s'))logger=logging.getLogger('root')logger.setLevel(logging.DEBUG)logger.addHandler(pubsub_handler)logger.info('My first message.')The logs are kept in a buffer first, then moved to the process safe queue, and then the background child processes automatically pick up and send them to Cloud Pub/Sub. The flush call blocks until all of the logs are sent to Cloud Pub/Sub.AuthenticationThe module uses theApplication Default Credentials. You can configure the authentication as follows.Authentication on App EngineIt should work out of the box. If you’re getting an authorization error, please make sure that your App Engine service account has anEditoror greater permission on your Cloud project.Authentication on Google Compute EngineWhen creating a new instance, please add the Cloud Pub/Sub scopehttps://www.googleapis.com/auth/pubsubto the service account of the instance.Authentication anywhere elseAsthe documentation suggests, create a new service account and download its JSON key file, then set the environment variableGOOGLE_APPLICATION_CREDENTIALSpointing to the JSON key file. Please note that this service account must haveEditoror greater permissions on your Cloud project.
Package: pubsub-split
Note: Assumes users are commonly sending lists of items, rather thanlarge or complex python data types or dictionaries.Home-page: UNKNOWNAuthor: Jon RobisonAuthor-email: narfman0@gmail.comLicense: LICENSEDescription: UNKNOWNKeywords: pubsub splitPlatform: UNKNOWNClassifier: Development Status :: 4 - BetaClassifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)Classifier: Operating System :: OS IndependentClassifier: Programming Language :: PythonClassifier: Topic :: Software Development :: Libraries :: Python Modules
Package: pubsubsuperfeedr
A simple library designed to make it easy to add and remove feeds from
Superfeedr’s PubSubHubbub API.  Includes support for hub.secret.CreditsDeveloped and used atUrban Airshipand
released under the MIT License.Harper Reed’s gae-superfeedr-shellprovided inspiration
for part of this code. Thanks Harper!Example UsageSetting up pubsubsuperfeedr:>>> import pubsubsuperfeedr
>>> sf = pubsubsuperfeedr.Superfeedr(settings.SUPERFEEDR_USERNAME, settings.SUPERFEEDR_PASSWORD)Validating a feed to make sure that it has at least one readable entry:>>> sf.verify_feed_url("http://blog.urbanairship.com/feed/")
TrueNote that this is just a really simple wrapper around feedparser and sometimes
feedparser can read things that Superfeedr can’t.Adding a feed:>>> sf.add_feed("http://blog.urbanairship.com/feed/", "http://example.com/your_callback_url", "some_verify_token", "some_secret")add_feed expects the feed you’re wanting to watch, then the callback URL, and
optionally a verify token and feed secret.Removing a feed:>>> sf.remove_feed("http://blog.urbanairship.com/feed/", "http://example.com/your_callback_url", "some_secret")Removing a feed is basically the same as adding a feed.Verifying a secret (in Django):>>> sf.verify_secret("some_secret", request.raw_post_data, request.META.get("HTTP_X_HUB_SIGNATURE", ""))
TrueTestingTo run the tests, first make sure thatnoseandmoxare installed. Then:$ nosetestsAnd you’re off an running.
Package: pubtatortool
The PubTator Parsing ToolA Python package for loading and manipulating PubTator files as Python objects.InstallationThis package is on the Python Package Index. You can install it usingpip install pubtatortool.UsageFor basic word tokenization and simple operationsfrompubtatortoolimportPubTatorCorpustrain_corpus=PubTatorCorpus(['train_corpus_part_1.txt','train_corpus_part_2.txt'])dev_corpus=PubTatorCorpus(['dev_corpus.txt'])test_corpus=PubTatorCorpus(['test_corpus.txt'])For wordpiece tokenization and full ability to encode and decode text for use with machine learning modelsfrompubtatortoolimportPubTatorCorpusfrompubtatortool.tokenizationimportget_tokenizertokenizer=get_tokenizer(tokenization='wordpiece',vocab='bert-base-cased')train_corpus=PubTatorCorpus(['train_corpus_part_1.txt','train_corpus_part_2.txt'],tokenizer)dev_corpus=PubTatorCorpus(['dev_corpus.txt'],tokenizer)test_corpus=PubTatorCorpus(['test_corpus.txt'],tokenizer)You can then serialize a corpus using Pickle, iterate over documents usingcorpus.document_list, and perform various operations on documents regardless of tokenization policy, even if it is lossy, without worrying about mention and text decoupling.For example, you can create a TSV-formatted file from a PubTator file in 10 lines of code:frompubtatortoolimportPubTatorCorpusfrompubtatortool.tokenizationimportget_tokenizertokenizer=get_tokenizer(tokenization='wordpiece',vocab='bert-base-cased')corpus=PubTatorCorpus(['mycorpus.txt'],tokenizer)withopen('outfile.txt','w')asoutfile:fordocincorpus.document_list:forsentence,targetsinzip(doc.sentences,doc.sentence_targets()):fortoken,labelinzip(sentence,targets):print("{tok}\t{lab}".format(tok=token,lab=label),file=outfile)print('',file=outfile)
Package: pubtools
Publishing tools project family.SourceManualOverviewpubtoolscomprises a family of Python libraries implementing content
publishing workflows.Each library in thepubtoolsfamily provides tasks for publishing or
managing content on a specific type of remote system.
These tasks are designed to be executed either as standalone command-line
utilities, or hosted within a service.pubtoolscan be read two ways. Firstly, it is short for "publishing tools",
which describes the scope of these projects. Secondly, it can be read as
"tools for Pub", because these tools are most commonly hosted within a
service known as "Pub".For more information, please read the onlineManual.Notable projectsHere we list a few projects within thepubtoolsfamily.This is not definitive. A more complete list is available in theManual.ProjectDescriptionpubtoolsShared functionality and docspubtools-pulpPublish content viaPulp2.xpubtools-iibManipulate operator images viaiibpubtools-quayPublish content toquay.ioLicenseThis program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Package: pubtools-exodus
Utilities used byrelease-engineeringpublishing tools for interfacing with components of Red Hat's Content Delivery Network.SourceDocumentationDevelopmentPatches may be contributed via pull requests tohttps://github.com/release-engineering/pubtools-exodus.All changes must pass the automated test suite, along with various static
checks.TheBlackcode style is enforced.
Enabling autoformatting via a pre-commit hook is recommended:pip install black pre-commit
pre-commit installLicenseThis program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.