Saravanan666/pypi-org huggingface dataset:
Package: maslongbow
Longbow is a command line tool to process MAS-ISO-seq data. Longbow employs a generative modelling approach to accurately annotate and segment MAS-ISO-seq’s concatenated full-length transcript isoforms from single-cell or bulk long read RNA sequencing libraries.Documentation for alllongbowcommands can be found on theLongbow documentation page.Installationpipis recommended for Longbow installation.pip install maslongbowFor a pre-built version including all dependencies, access our Docker image.docker pull us.gcr.io/broad-dsp-lrma/lr-longbow:0.5.37To install from Github source for development, the following commands can be run.git clone https://github.com/broadinstitute/longbow.git
pip install -e longbow/Getting StartedThe commands below illustrate the Longbow workflow on a small library of SIRVs (Spike-in RNA Variant Control Mixes). MAS-ISO-seq concatenated transcripts are annotated, segmented, and filtered using themas15model.  A number of statistics and QC images are generated along the way.  Final filtered transcripts can then be aligned using standard splice-aware long read mappers (e.g. minimap2). More detail for each command can be found in thefull documentation.# Download a tiny test dataset (less than 300K)
wget https://github.com/broadinstitute/longbow/raw/main/tests/test_data/mas15_test_input.bam
wget https://github.com/broadinstitute/longbow/raw/main/tests/test_data/mas15_test_input.bam.pbi
wget https://github.com/broadinstitute/longbow/raw/main/tests/test_data/resources/SIRV_Library.fasta

# Basic processing workflow
longbow annotate -m mas15v2 mas15_test_input.bam | \  # Annotate reads according to the mas15v2 model
  tee ann.bam | \                                     # Save annotated BAM for later
  longbow filter | \                                  # Filter out improperly-constructed arrays
  longbow segment | \                                 # Segment reads according to the model
  longbow extract -o filter_passed.bam                # Extract adapter-free cDNA sequences

# Align reads with long read aligner (e.g. minimap2, pbmm2)
samtools fastq filter_passed.bam | \
    minimap2 -ayYL --MD -x splice:hq SIRV_Library.fasta - | \
    samtools sort > align.bam &&
    samtools index align.bamGetting helpTheLongbow documentation pageprovides detailed descriptions of command line options and algorithmic details. If you encounter bugs or have questions/comments/concerns, please file an issue on ourGithub page.Developers’ guideFor information on contributing to Longbow development, visit ourdeveloper documentation.
Package: mason
Mason====.. image:: https://travis-ci.org/vail130/mason.svg?branch=masterMason is a nice, light-weight, SQL query builder. It lets you use objects instead of SQL strings withouthaving an ORM take over your database model.Example-------.. code-block:: python# Annoying :/query = """SELECT purchases.id,purchases.product_name,(purchases.product_price)::NUMERIC(10, 2),(purchases.datetime_purchased)::DATEFROM purchasesINNER JOIN users ON purchases.purchaser_id = users.user_idWHERE purchases.datetime_purchased BETWEEN %(start)s AND %(end)sAND (purchases.purchaser_id = %(user_id)s OR purchases.purchaser_id IS NULL)ORDER BY purchases.datetime_purchased ASCLIMIT 10OFFSET 10"""# Convenient :)from mason import Table, Param, SELECT, AND, OR, DATE, NUMERICpurchases = Table('purchases')users = Table('users')user_id = Param('user_id')start = Param('start')end = Param('end')query = str(SELECT(purchases.id, purchases.product_name,NUMERIC(purchases.product_price, 10, 2),DATE(purchases.datetime_purchased)).FROM(purchases).INNER_JOIN(users.ON(purchases.purchaser_id == users.user_id)).WHERE(AND(purchases.datetime_purchased.BETWEEN(start).AND(end),OR(purchases.purchaser_id == user_id,purchases.purchaser_id.IS_NULL))).ORDER_BY(purchases.datetime_purchased.ASC).LIMIT(10).OFFSET(10))Install-------.. code-block:: shpip install masonDevelop-------.. code-block:: shcd path/to/reposgit clone git@github.com:vail130/mason.gitcd masonmkvirtualenv masonpip install -r requirements.txtmake test
Package: mason-image
mason_imageA small tool to mess up a imagemason_imageis a small tool to mess up a imageDemoBeforeAfterUsageusage: mason_image [-h] [--in IN_IMAGE] [--out OUT_IMAGE]

optional arguments:
  -h, --help         show this help message and exit
  --in IN_IMAGE      path of image to mess up
  --out OUT_IMAGE    path of output imageInstall$ pip install mason_imagePack itpip3 install setuptools
pip3 install wheel

python3 setup.py sdist bdist_wheelTry to install locallypip3 install dist/mason_image-0.1.4-py3-none-any.whlUpload to PyPIpip3 install twine
twine upload dist/mason_image-0.1.4-py3-none-any.whlLicenseMIT
Package: masonite
MasoniteAbout MasoniteStop using old frameworks with just a few confusing features. Masonite is the developer focused dev tool with all the features you need for the rapid development you deserve. Masonite is perfect for beginners getting their first web app deployed or advanced developers and businesses that need to reach for the full fleet of features available. A short list of the available features are:Mail support for sending emails quickly.Queue support to speed your application up by sending jobs to run on a queue or asynchronously.Notifications for sending notifications to your users simply and effectively.Task scheduling to run your jobs on a schedule (like everyday at midnight) so you can set and forget your tasks.Events you can listen for to execute listeners that perform your tasks when certain events happen in your app.A BEAUTIFUL Active Record style ORM called Masonite ORM. Amazingness at your fingertips.Many more features you need which you can find in the docs!Learning MasoniteNew to Masonite? Read theOfficial Documentation.
Masonite strives to have extremely clear documentation 😃. It would be wise to go through the tutorials there.
If you find any discrepencies or anything that doesn't make sense, please open an issue and we will get it cleared up!Have questions or want to talk? Be sure to join theMasonite Discord Community!Getting Started QuicklyCreate and activate a virtual environment and if you have a working Python 3.7+ installation then getting started is as quick as typingpipinstallmasonite
projectstart.
pythoncraftserveContributingContributing to Masonite is simple:Hop onMasonite Discord Communityto ask any questions you need!Read theHow To Contributedocumentation to see ways to contribute to the project.Read theContributing Guideto learn how to contribute to the core source code development of the project.Follow Masonite Framework on Twitterto get updates about tips and tricks, announcement and releases.Core MaintainersJoseph Mancuso(Author)Samuel GirardinMarlysson SilvaSponsorsTo become a sponsor head to ourGitHub Sponsors page!Security VulnerabilitiesIf you discover a security vulnerability within Masonite please read theSecurity Policy. All security vulnerabilities will be promptly addressed.LicenseThe Masonite framework is open-sourced software licensed under theMIT license.
Package: masonite-audit
Masonite AuditIntroductionKeep track of all your model changes with ease.Getting StartedInstall the package using pip:pipinstallmasonite-auditAdd AuditProvider to your project inconfig/providers.py:# config/providers.py# ...frommasonite_auditimportAuditProvider# ...PROVIDERS=[# ...# Third Party ProvidersAuditProvider,# ...]Publish the package configuration files.pythoncraftpackage:publishmasonite-auditThis will add migrations and othermasonite-auditrelated configuration to your project. Run your migrations to create the related database tables.pythoncraftmigrateFinally, inheritAuditmixin into all the models for which you need audit logging.frommasonite_audit.mixinsimportAuditclassYourModel(Audit):passIf you want to get the audit history for a model, you can use thehistorymethod:user=User.find(1)user.history()In order to rollback to previous versions of a model, you can use therollbackmethod:user=User.find(1)user.rollback()# to rollback to previous version# oruser.rollback(step=4)# to rollback to version 4LicenseMasonite Audit is open-sourced software licensed under theMIT license.
Package: masonite-backup
Masonite BackupBackup solution for Masonite.FeaturesBackup DatabaseBackup FilesStore Backup Locally in the filesystemEmail BackupStore Backup in other Masonite Supported Storage Drivers [s3]Installationpipinstallmasonite-backupConfigurationAdd BackupProvider to your project inconfig/providers.py:# config/providers.py# ...frombackupimportBackupProvider# ...PROVIDERS=[# ...# Third Party ProvidersBackupProvider,# ...]Then you can publish the package resources (if needed) by doing:pythoncraftpackage:publishbackupUsageOnce you publish the package resources, you can use thebackupcommand to backup your database and files. Before that if you want to configure options of backup then you can do that by updatingconfig/backup.pyconfiguration file.# config/backup.pyFILENAME="backup"DIRECTORY="backup"SOURCE={"root":base_path(),"excludes":[".git","storage","venv","node_modules","__pycache__",# add more...],}S3_BACKUP=False# Whether or not to backup to S3.EMAIL_BACKUP=False# Whether or not to email the backup.EMAIL_BACKUP_TO=""# The email address to send the backup to.EMAIL_SUBJECT="System Backup"# The email subject.Note: Make sure you haveEMAIL_BACKUPset toTrueandEMAIL_BACKUP_TOset to a valid email address, to send the backup via email. Also don't forget to setup SMTP inconfig/mail.pyconfiguration file or in.envfile. In case you want to backup to S3, then make sure you haveS3_BACKUPset toTrueand S3 storage configuration.MAIL_DRIVER=smtpMAIL_FROM=MAIL_HOST=MAIL_PORT=MAIL_USERNAME=MAIL_PASSWORD=AWS_CLIENT=AWS_SECRET=AWS_BUCKET=AWS_REGION=Backup Database and Filespythoncraftbackup:runBackup Database Onlypythoncraftbackup:run--only-dbBackup Files Onlypythoncraftbackup:run--only-filesLicenseBackup is open-sourced software licensed under theMIT license.
Package: masonite-dolphinido
Dolphinido Audio Fingerprint and TrackingInstallationpip install masonite-dolphinidoUsageRun$ python craft dolphinido:fingerprint /path/to/mp3/fileto fingerprint mp3 fileRun$ python craft dolphinido:radio stationto listen to radio stationRun$ python craft dolphinido:recog-mic 20to record and recognize audio from microphone for 20 secondsRun$ python craft dolphinido:recog-file /path/to/mp3/fileto recognize audio fileRun$ python craft dolphinido:recog-radio stationto recognize audio from fm radio
Package: masonite-filemanager
filemanagerIntroductionA simple yet powerful file management solution for your masonite application.FeaturesManager Server Files (Currently only supports local files)Upload FilesPreview FilesRename Files/FoldersDelete Files/FoldersDownload FilesMove FilesSearch FilesProtect RoutesImage EditingThird Party Driver Support (S3, DigitalOcean Space, etc)File Picker (Form)Installationpipinstallmasonite-filemanagerConfigurationAdd FileManagerProvider to your project inconfig/providers.py:# config/providers.py# ...fromfilemanager.providersimportFileManagerProvider# ...PROVIDERS=[# ...# Third Party ProvidersFileManagerProvider,# ...]Then you can publish the package resources (if needed) by doing:pythoncraftpackage:publishfilemanagerFinally add following toSTATICFILESsection inconfig/filesystem.py:# config/filesystem.pySTATICFILES={# ...# FileManager resources'resources/vendor/filemanager':'filemanager-assets/',"storage/framework/filesystem/filemanager":"filemanager-uploads/",}UsageOnce finishing configurations, you can access the file manager by using the following route:http://localhost:8000/filemanagerIf you want to use file picker then all you have to do is include then follow the following guidelines:Add style in the header of your base template:<linkhref="/filemanager-assets/picker.css"rel="stylesheet"/>Add script before the</body>tag of your base template:<scriptsrc="/filemanager-assets/picker.js"></script>Finally, in your form you can use selector in your form in the following way:<divclass="file-picker"><inputtype="hidden"name="j-sukai"/></div>or, if you want file-preview:<divclass="file-picker has-preview"><inputtype="hidden"name="j-sukai"/></div>The design of the file-picker is very basic so you might want to customize with your own design by modifying the stylesheet which resides instorage/vendor/filemanagerdirectory.Licensemasonite-filemanager is open-sourced software licensed under theMIT license.
Package: masonite-instant-article
Instant ArticlesIf you are seeking package for generating instant article or feeds in Masonite then yes, this package is for you.This helps you generate facebooks instant articles and also regular feeds with enough customizations you might need.Installationpipinstallmasonite-instant-articleConfigurationAddInstantArticleProviderto your project inconfig/providers.py:# config/providers.py# ...frominstant_article.providersimportInstantArticleProvider# ...PROVIDERS=[# ...# Third Party ProvidersInstantArticleProvider# ...]Then you can publish the configuration by doing:pythoncraftpackage:publishinstant_articleUpdate ConfigurationsYou need to define options in yourinstant_articleconfiguration file insideconfigdirectory.# configINSTANT_ARTICLE={"force_validate":False,"feed_details":{"your-custom-route-name.xml":{'model':'path-to-your-model-class','title':'','description':'','lang':'en-us','brand':'','type':'instant-article'# feed, instant-article}}}# ExampleINSTANT_ARTICLE={"force_validate":False,"feed_details":{"blogs-rss.xml":{'model':'app.models.Blog','title':'Blog Feed','description':'','lang':'en-us','brand':'','type':'instant-article'# feed, instant-article},"news-rss.xml":{'model':'app.models.News','title':'News Feed','description':'','lang':'en-us','brand':'','type':'instant-article'# feed, instant-article}}}# Above feeds can be access from:"""https://your-domain.com/rss/blogs-rss.xmlhttps://your-domain.com/rss/news-rss.xml"""Implementationfrominstant_article.interfaces.instant_article_interfaceimportInstantArticleInterfacefrominstant_article.models.instant_articleimportInstantArticleclassYourModel(Model,InstantArticleInterface):@staticmethoddefget_feed_items():returnYourModel.all()# can be any query returning proper valuesdefformat_feed(self):returnInstantArticle.create({'id':self.id,# required | integer'title':self.name,# required | string'subtitle':'',# nullable | string'kicker':'',# nullable | string'summary':'',# required | string'description':'',# required | string'cover':'',# nullable | string'updated':self.updated_at,# required | date'published':self.created_at,# required | date'link':'',# full url to item...'author':''# nullable | email | string})Your project is now ready to go :+1:.ContributingPlease read theContributing Documentationhere.Licensemasonite-filemanager is open-sourced software licensed under theMIT license.
Package: masonite-localization
masonite-localizationIntroductionAdd multi-language support in your application.Installationpipinstallmasonite-localizationConfigurationAdd LocalizationProvider to your project inconfig/providers.py:# config/providers.py# ...fromlocalizationimportLocalizationProvider# ...PROVIDERS=[# ...# Third Party ProvidersLocalizationProvider,# ...]Then you can publish the package resources (if needed) by doing:pythoncraftpackage:publishlocalizationUsageThe setup is very simple. Once you publish the package verify if there's alangdirectory in the root of your project or not, if not then create one and then create a json file nameden.jsonput in some values in it or you can copy/paste following contents.{"message":"Hello"}By default you'll haveenglishlanguage setup inconfigwhich you can change. The locale can be changed on the fly as well.You can add as many language json files as you wish. For eg; if needJapaneselocale then, I will just copy everything fromen.jsonfile and then create new file namedjp.jsonand then update the values in those json.Getting Current Localefromlocalization.facadesimportLocalization# Returns current localeLocalization.current_locale()Changing Localefromlocalization.facadesimportLocalization# Returns nothingLocalization.set_locale('jp')Checking if current local matchesfromlocalization.facadesimportLocalization# returns either True or FalseLocalization.is_locale('jp')Retrieving Translations in TemplateImagine you have following translations inen.jsonlocale file.{"message":"Hello, World!","notification":{"message":"This is notification message."}}Then you can retrieve translation strings as below in template.{{__("message")}}<!-- OR -->{{__("notification.message")}}Licensemasonite-localization is open-sourced software licensed under theMIT license.
Package: masonite-modules
Masonite ModulesIntroductionModularize your masonite project.Installationpipinstallmasonite-modulesConfigurationAdd ModuleProvider to your project inconfig/providers.py:# config/providers.py# ...frommasonite_modulesimportModuleProvider# ...PROVIDERS=[# ...# Third Party ProvidersModuleProvider,# ...]Publish the package resources by doing:pythoncraftpackage:publishmodulesThe default modules location will bemodulesin the root directory of your project. But if you want your own custom name then, update the module name inconfig/modules.pyto your desired module path name.NAME=modulesInstallationOnce you finish publishing package, you need to install the modules by doing:$pythoncraftmodule:installFinally, you will see the modules directory created in your project root.UsageTo create the module, simply run:$pythoncraftmodule:create<module_name># Example$pythoncraftmodule:createblogThe above command will create a new module calledblogsin themodulesdirectory. It will also create all the necessary files and directories insideblogsso you can start working on your module.Finally, visit/<module_name>i.e./blogsthen you will see a welcome message.Enjoy!Licensemasonite_modules is open-sourced software licensed under theMIT license.
Package: masonite-package-sync
Masonite package syncUpdate a masonite package with latest project template files.
It's useful when you maintain a package to update the project template used for example in tests/integrations/.pip install masonite-package-syncPull the default Masonite project template into the current directorypython masonite-package pullpython masonite-package pull --repo johndoe/other-project --branch developpython masonite-package pull --directory other/dir/test/If you want to update the test project inside your Masonite package do :python masonite-package pull --directory tests/integrations/It will replace the project and update paths to work !
Package: masonite-security
Masonite SecuritySecure masonite apps from spamming Bots, IP's and SQL injections.FeaturesBlock IP'sBlock BotsThrottle RequestsBlock SQL InjectionsInstallationpipinstallmasonite-securityConfigurationAdd SecurityProvider to your project inconfig/providers.py:# config/providers.py# ...fromsecurityimportSecurityProvider# ...PROVIDERS=[# ...# Third Party ProvidersSecurityProvider,# ...]Then you can publish the package resources by doing:pythoncraftpackage:publishsecurityRegister Middleware.You can setup the security middleware globally or per route basis.Global SetupOpenKernal.pyfile and addSecurityMiddlewarein "route_middleware" section:route_middleware={"web":[SessionMiddleware,LoadUserMiddleware,VerifyCsrfToken,SecurityMiddleware],"auth":[AuthenticationMiddleware],}Per Route SetupIn your routes addprotectmiddleware like this:Route.get("/","WelcomeController@show").middleware("protect")Configure Security ConfigUpdate yourconfig/security.pyfile based on your needs:# config/security.py# ...BLOCK_IP=TrueBLOCK_BOTS=TrueTHROTTLE_REQUESTS=TrueMAX_REQUESTS=20# Max requests per IP (default: 20)IP_BLOCK_DURATION=60# seconds (default: 60)# list of IP addresses to block (default: [])BLOCKED_IPS=[#...]# list of Bot Agents to blockBLOCKED_BOTS=[#...]# ...ContributingPlease read theContributing Documentationhere.MaintainersYubaraj ShresthaLicensesecurity is open-sourced software licensed under theMIT license.
Package: masonite-sentry
Masonite SentrySentry sdk implementation for Masonite.Installationpipinstallmasonite-sentryConfigurationAdd SentryProvider to your project inconfig/providers.py:# config/providers.py# ...fromsentryimportSentryProvider# ...PROVIDERS=[# ...# Third Party ProvidersSentryProvider,# ...]Then you can publish the package resources (if needed) by doing:pythoncraftpackage:publishsentryUsageSetup environment variables in your project's.envfile:SENTRY_DSN=SENTRY_SAMPLE_RATE=1.0Well that's it, you are done, congrats.Note: Sentry captures no any exceptions if you are on debug mode.ContributingPlease read theContributing Documentationhere.MaintainersYubaraj ShresthaLicenseMasonite Sentry is open-sourced software licensed under theMIT license.
Package: masonite-socketio-driver
SocketIO DriverIt's an extra broadcast driver support for SocketIO in masonite 4, it extends default masonite broadcast driver to support SocketIO.Masonite Broadcast Server and Client LibraryBroadcast Serverbroadcast ClientSetupInstall package using pip:pipinstallmasonite-socketio-driverAdd provider inside config/providers.py.fromsocketio_driver.providersimportSocketProviderPROVIDERS=[...,# Application ProvidersSocketProvider,]Driver ConfigAdd following configuration inside config/broadcast.py after"pusher": {...},"pusher":{...},"socketio":{"driver":"socketio","host":env("BROADCAST_HOST","localhost"),"port":env("BROADCAST_PORT","6379")},Add following keys in.env.BROADCAST_HOST=BROADCAST_PORT=Update the broadcast driver value tosocketioin.envBROADCAST_DRIVER=socketioExample# broadcast to given channelsfrommasonite.controllersimportControllerfrommasonite.broadcastingimportBroadcastclassYourController(Controller):defyour_function(self,broadcast:Broadcast):broadcast_data={"message":"Hello World"}broadcast.channel(["channel-name"],"event-name",broadcast_data)# broadcast to selected users/clientsfrommasonite.controllersimportControllerfrommasonite.broadcastingimportBroadcastfromsocketio_driver.facadesimportCommunicatorclassYourController(Controller):defyour_function(self,broadcast:Broadcast):broadcast_data={"message":"Hello World"}clients=Communicator.clients()ids=[client.socketIDforclientinclients]broadcast.channel(ids,"event-name",broadcast_data)defor_another_function(self,broadcast:Broadcast):broadcast_data={"message":"Hello World"}clients=Communicator.clients()broadcast.driver("socketio").user(clients[0]).send("event-name",broadcast_data)HelpersFacade helpers...fromsocketio_driver.facadesimportCommunicator# List all clients:Communicator.clients()# Get client by sessionIDCommunicator.client(id='client-session-id')# Delete all clientsCommunicator.delete_all_clients()# Delete client by SocketClient instanceCommunicator.delete(client)
Package: masonjar
Mason Jar is a collection of useful algorithms.Documentationhttps://docs.kuralabs.io/masonjar/Installpip3installmasonjarChangelog1.0.0 (YYYY-MM-DD)NewInitial version.LicenseCopyright (C) 2017-2019 KuraLabs S.R.L

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing,
software distributed under the License is distributed on an
"AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, either express or implied.  See the License for the
specific language governing permissions and limitations
under the License.
Package: mason-tools
基于CTP期货版的6.6.7接口封装开发，接口中自带的是【穿透式实盘环境】的dll文件。 由 vnpy_ctp 修改而来打包python setup.py bdist_wheel需要进行C++编译，因此在执行上述命令之前请确保已经安装了【Visual Studio（Windows）】、【GCC（Linux）】、【XCode（Mac）】编译器。发布先安装一下 twine：python -m pip install twine# 用户名下创建 .pypirc文件
[pypi]
username = __token__
password =twine upload dist/*没有账户去注册一个https://pypi.org/安装直接使用pip命令：pip install mason_tools
Package: mason-xt-data
打包python -m pip install wheelpython setup.py bdist_wheel需要进行C++编译，因此在执行上述命令之前请确保已经安装了【Visual Studio（Windows）】、【GCC（Linux）】、【XCode（Mac）】编译器。发布先安装一下 twine：python -m pip install twine# 用户名下创建 .pypirc文件
[pypi]
username = __token__
password =twine upload dist/*没有账户去注册一个https://pypi.org/安装直接使用pip命令：pip install mason_tools