Saravanan666/pypi-org huggingface dataset:
Package: alignak_module_backend
Alignak modules for the Alignak BackendInstallationThe installation of this module will copy some configuration files in the Alignak default configuration directory (eg./usr/local/etc/alignak). The copied files are located in the default sub-directory used for the modules (eg.arbiter/modules).From PyPITo install the module from PyPI:sudo pip install alignak-module-backendFrom source filesTo install the module from the source files (for developing purpose):git clone https://github.com/Alignak-monitoring-contrib/alignak-module-backend
cd alignak-module-backend
sudo pip install . -eNote:using `sudo python setup.py install` will not correctly manage the package configuration files! The recommended way is really to use `pip`;)Short descriptionThis meta-module for Alignak contains 3 modules:Arbiter module, which features are:get configuration from Alignak backendmanages acknowledgements, downtimes schedule and re-checksScheduler module, which features are:manage retention (load and save)Broker module, which features are:update live state of hosts and services in the Alignak backendupdate log for hosts and services checks in the Alignak backendConfigurationEach module has its own configuration file and its configuration parameters.
The configuration files are documented to help setting the right configuration.Arbiter module:configure the Alignak backend connection (url and login)configure periodical configuration modification checkconfigure periodical required actions (ack, downtime, …)Scheduler module:configure the Alignak backend connection (url and login)Broker module:configure the Alignak backend connection (url and login)Bugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: alignak_module_external_commands
Alignak external commands moduleShort descriptionThis module for Alignak opens a commands file as a named pipe and regularly reads the content of this file to interpret as external commands that are forwarded to the Alignak framework.InstallationThe installation of this module will copy some configuration files in the Alignak default configuration directory (eg./usr/local/etc/alignak). The copied files are located in the default sub-directory used for the modules (eg.arbiter/modules).From PyPITo install the module from PyPI:sudo pip install alignak-module-external-commandsFrom source filesTo install the module from the source files (for developing purpose):git clone https://github.com/Alignak-monitoring-contrib/alignak-module-external-commands
cd alignak-module-external-commands
sudo pip install . -eNote:using `sudo python setup.py install` will not correctly manage the package configuration files! The recommended way is really to use `pip`;)ConfigurationOnce installed, this module has its own configuration file in the/usr/local/etc/alignak/arbiter/modulesdirectory.
The default configuration file ismod-external-commands.cfg. This file is commented to help configure all the parameters.To configure an Alignak daemon to use this module:edit your daemon configuration fileadd your module alias value (external-commands) to themodulesparameter of the daemonBugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: alignak_module_logs
Alignak module for the monitoring logsInstallationThe installation of this module will copy some configuration files in the Alignak default configuration directory (eg./usr/local/etc/alignak). The copied files are located in the default sub-directory used for the modules (eg.arbiter/modules).From PyPITo install the module from PyPI:sudo pip install alignak-module-logsFrom source filesTo install the module from the source files (for developing purpose):git clone https://github.com/Alignak-monitoring-contrib/alignak-module-logs
cd alignak-module-logs
sudo pip install . -eNote:using `sudo python setup.py install` will not correctly manage the package configuration files! The recommended way is really to use `pip`;)Short descriptionThis module for Alignak collects the monitoring logs (alerts, notifications, …) to log them into a dedicated file.You can plainly use the powerful of the Python logging system thanks to the use of a logging configuration file which will allow you to define when, where and how to send the monitoring logs ….Known issuesThis module is not compatible with Python 2.6 if you intend to use a logger configuration file as this feature is not available before Python 2.7 version.
If you are still using the old 2.6 version, upgrade or define the logger parameters in the module configuration file.ConfigurationOnce installed, this module has its own configuration file in the/usr/local/etc/alignak/arbiter/modulesdirectory.
The default configuration file ismod-logs.cfg. This file is commented to help configure all the parameters.To configure Alignak broker to use this module:edit your broker daemon configuration fileadd themodule_aliasparameter value (logs) to themodulesparameter of the daemonTo configure this module to send its log to the Alignak backend:edit the module configuration file to set the Alignak backend parameters (eg. url and login information)To set up several logs collectors:copy the default configuration to another file,change the module alias parameter (logs_bis)edit your broker daemon configuration fileadd the newmodule_aliasparameter value (logs_bis) to themodulesparameter of the daemonTo set up your own logger:edit the module configuration file to uncomment thelogger_configurationvariableupdate the logger configuration file (eg. mod-logs-logger.json) to replaceALIGNAKLOGwith your target log directoryupdate the logger configuration file to suit your needs … then python logger on the Internet is your best friend :)Monitoring logs configurationAs a default configuration this module will create a log file for the monitoring logs. This file will be located in the alignak log directory and it will be rotated every day for a period of 365 days. You can also define your own logging strategy as it is explained in the module configuration file that is largely commented to explain how to configure.Bugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: alignak-module-mongo-logs
Notethat this module is only useful to get the Alignak monitoring logs in a Mongo DB if you do not use the Alignak backendAlignak module for the monitoring logsInstallationThe installation of this module will copy some configuration files in the Alignak default configuration directory (eg./usr/local/etc/alignak). The copied files are located in the default sub-directory used for the modules (eg.arbiter/modules).From PyPITo install the module from PyPI:sudo pip install alignak-module-mongo-logsFrom source filesTo install the module from the source files (for developing purpose):git clone https://github.com/Alignak-monitoring-contrib/alignak-module-mongo-logs
cd alignak-module-mongo-logs
sudo pip install . -eShort descriptionThis module for Alignak collects the monitoring logs (alerts, notifications, …) to log them into a collection of a Mongo DB.This module was back-ported from the Shinkenmod-mongo-logsbut it does not manage the availability for hosts and services.ConfigurationOnce installed, this module has its own configuration file in the/usr/local/etc/alignak/arbiter/modulesdirectory.
The default configuration file ismod-mongo-logs.cfg. This file is commented to help configure all the parameters.To configure Alignak broker to use this module:edit your broker daemon configuration fileadd themodule_aliasparameter value (logs) to themodulesparameter of the daemonTo configure this module for Mongo DB:edit the module configuration file to set the MongoDB parametersMetricsThis module is able to push metrics to an external TSDB (Graphite, InfluxDB). Configure the metrics parameters in the configuration:; --------------------------------------------------------------------
; Module internal metrics
; Export module metrics to a statsd server.
; By default at localhost:8125 (UDP) with the alignak prefix
; Default is not enabled
; --------------------------------------------------------------------
;statsd_host = localhost
; For StatsD
;statsd_port = 8125
; For Graphite
;statsd_port = 2004
; Default
;statsd_prefix=alignak
; Use this prefix to use the alignak name in the metrics hierarchy
;statsd_prefix=%(alignak_name)s.modules
; Default is disabled
;statsd_enabled = 0
;graphite_enabled = 0
; --------------------------------------------------------------------Available metrics:committed-logscounts the DB commited logsmonitoring-event-got.%scounts the detected eventsmonitoring-event-ignored.%scounts the ignored events (not DB commited)queue-sizeis the module message queue size. If greater than 1, it indicates a module overload because the queue should be emptied on each loop turnmanaged-broks-timeis the broks management duration on each loop turnNotethat only the events in this list are DB commited: [‘TIMEPERIOD TRANSITION’, ‘RETENTION LOAD’, ‘RETENTION SAVE’, ‘CURRENT STATE’, ‘NOTIFICATION’, ‘ALERT’, ‘DOWNTIME’, ‘FLAPPING’, ‘ACTIVE CHECK’, ‘PASSIVE CHECK’, ‘COMMENT’, ‘ACKNOWLEDGE’, ‘DOWNTIME’]An example Grafana dashboard:Bugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: alignak_module_ws
Alignak Web services moduleImportant informationThis module exposes some Web services as a REST API for the Alignak monitoring framework. Indeed it extends the Alignak receiver existing API with some external new services such as: report an host/service check result, send a command to alignak, get information from Alignak, …It is important to consider that the services exposed by this module currently implement a very first version developed as a Proof of Concept and that they may be refactored without any ascending compatibility.If you intend to use the current interface feel free to get in touch and we will keep you informed about the current actions and decisions ;)InstallationThe installation of this module will copy some configuration files in the Alignak default configuration directory (eg./usr/local/etc/alignak). The copied files are located in the default sub-directory used for the modules (eg.arbiter/modules).From PyPITo install the module from PyPI:sudo pip install alignak-module-wsFrom source filesTo install the module from the source files (for developing purpose):git clone https://github.com/Alignak-monitoring-contrib/alignak-module-ws
cd alignak-module-ws
sudo pip install . -eNote:using `sudo python setup.py install` will not correctly manage the package configuration files! The recommended way is really to use `pip`;)Short descriptionThis module for Alignak exposes some Alignak Web Services:GET /will return the list of the available endpointsGET /alignak_mapthat will return the map and status of all the Alignak running daemonsGET /hostto get an host informationGET /hostgroupto get an hostgroup informationGET /alignak_logsto view the Alignak events history from an Alignak backendPOST /alignak_commandthat will notify an external command to the Alignak frameworkPATCH /host/<host_name>that allows to send live state for an host and its services, update host custom variables, enable/disable host checksConfigurationOnce installed, this module has its own configuration file in the/usr/local/etc/alignak/arbiter/modulesdirectory.
The default configuration file ismod-ws.cfg. This file is commented to help configure all the parameters.To configure an Alignak daemon (receiveris the recommended daemon) to use this module:edit your daemon configuration file (eg.receiver-master.cfg)add your module alias value (web-services) to themodulesparameter of the daemonNotethat currently the SSL part of this module has not yet been tested!DocumentationAlignak Web Service module hasan online documentation page.Click on one of the docs badges on this page to browse the documentation.Bugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: alignak_notifications
Alignak package for notifications (simple mail, HTML mail, XMPP)InstallationThe installation of this package will copy some configuration files in the Alignak default configuration directory (eg./usr/local/etc/alignak). The copied files are located in the default sub-directory used for the packs (eg.arbiter/packs).It will also copy some JSON files in the/usr/local/etc/alignak/backend-jsondirectory. These files are usable to import all the commands tinto the Alignak backend with thealignak-backend-cliscript installed with the backend client library.You can update the sipped files to make the default commands suit your needs or use the default commands configuration that is defined to be as complete as possible.Note:The python scripts assume that you have a directpythonrunnable … if you need to usepython2.7or something else to run python, you should:cd /usr/local/bin
ln -s python2.7 pythonFrom PyPITo install the package from PyPI:sudo pip install alignak-notificationsFrom source filesTo install the package from the source files:git clone https://github.com/Alignak-monitoring-contrib/alignak-notifications
cd alignak-checks-notifications
sudo pip install .Note:using `sudo python setup.py install` will not correctly manage the package configuration files! The recommended way is really to use `pip`;)DocumentationThis pack embeds several scripts that can be used to send notifications from Alignak:simple printf sent to sendmailpython script to send HTML mailpython script to post messages to a Slack channelImportant:The HTML mail and Slack scripts are using Alignak logo images in the message composition. The default used files are located in the main directory of the project repository. Alternative images URL can be specified in the notification command parameters.Configuration (Slack notifications)A Slack API token is mandatory to post messages to a slack channel. The token can be provided on the command line of the notification script or defined in an environment variable (ALIGNAK_SLACK_API_TOKEN).The Slack channel that will receive the messages must ne named as the configured contact name. Let’s say that you want to send the notifications message to a channel named#my_alignak, the contact configured but be named asmy-alignak.Configuration (mail notifications)Edit the/usr/local/etc/alignak/arbiter/packs/resource.d/notifications.cfgfile and configure
the SMTP server address, port, user name and password.#-- SMTP server configuration
$SMTP_SERVER$=your_smtp_server_address
$SMTP_PORT$=25
$SMTP_LOGIN$=your_smtp_login
$SMTP_PASSWORD$=your_smtp_passwordBugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: alignak-webui
Web User Interface for Alignak monitoring framework …ScreenshotsDocumentationYou can find online documentation onRead The Docsand in the/docsdirectory.InstallationThe Alignak WebUI is easily installed and started thanks to the Python Package:# Installing...
pip install alignak-webui
# Running...
alignak-webui-uwsgi
# Using!
http://127.0.0.1:5001Note:Please note that you need to have a running Alignak framework reporting the live state to the Alignak backend.Bugs, issues and contributingContributions to this project are welcome and encouraged, but please have a look to thecontributing guidelinesbefore raising an issue, or writing code for the project.LicenseAlignak WebUI is available under theGPL version 3.
Package: alignak-webui-graphite
Shinken / Alignak WebUI module for the Graphite graphsShinken / Alignak module for viewing Graphite graphs in the Web UI.This module is a refactoring of theui-graphitemodule to allow using it with Shinken or Alignak.This module allows:to define the Graphite hierarchy configurationto use templates (url or json based) for the graphsto configure:the host check metric namegraph and font size for dashboard and host/service page graphsdefine if warning, critical, min and max thresholds are present on graphsdefine warning, critical, min and max lines colorsdefine graphs timezone (default is Europe/Paris)define graphs line mode (connected, staircase, slope)This module is fully compatible with the WebUI2 at its most recent version (Alignak compatible). It is also compatible with the Alignak inner metrics module for the Graphite hierarchy.InstallationThe installation of this module will copy some configuration files in the Alignak default configuration directory (eg./usr/local/share/alignak). The copied files are located in the default sub-directory used for the modules (eg.arbiter/modules).Notethat the module provided templates will be copied to the/usr/local/share/alignak/etc/modules/ui-graphite-templates. You may add your own templates in this directory -)From PyPITo install the module from PyPI:sudo pip install alignak_webui_graphiteFrom source filesTo install the module from the source files (for developing purpose):git clone https://github.com/mohierf/mod-ui-graphite
cd mod-ui-graphite
sudo pip install . -eBugs, issues and contributingContributions to this project are welcome and encouraged …issues in the project repositoryare the common way to raise an information.
Package: align-benchmark
text-alignment-benchmarksBenchmark dualtext (para/sent) alignmentInstall itpipinstallalign-benchmark# or poetry add align-benchmark# pip install git+htts://github.com/ffreemt/text-alignment-benchmarks# poetry add git+htts://github.com/ffreemt/text-alignment-benchmarks# To upgradepipinstallalign-benchmark-U# or poetry add align-benchmark@latestUse itfromalign_benchmark.benchmarkimportbenchmarkbenchmark()or from command linealign-benchmark# or python -m align_benchmark
Package: aligncov
AlignCovAlignCov is a bioinformatics tool which can be used to obtain a) alignment summary statistics and b) read depths from sorted BAM files in tidy tab-separated tables.Future plansCreate a Bioconda recipeCreate a Docker imageIntroductionThis script takes a sorted BAM file as input and usesSAMtoolsand PythonPandasto generate two tables:_stats.tsv: A table of alignment summary statistics, including fold-coverages (fold_cov) and proportions of target lengths covered by mapped reads (prop_cov).target: Name of the target.seqlen: Length of the target sequence (bp).depth: Total number of base pairs mapped to the target.len_cov: Total number of base pairs within the target that are covered by at least one mapped read.prop_cov: Proportion of the target length covered by at least one mapped read (len_cov / seqlen).fold_cov: Fold-coverage of mapped reads to the target (i.e. the number of times the target is completely covered by mapped reads) (depth / seqlen)._depth.tsv: A table of read depths for each bp position of each target.target: Name of the target.position: Base pair position within the target.depth: Total number of reads aligned to the base pair position within the target.Dependenciessamtools>=1.15InstallationAlignCov can be installed using Pip with the following command:pipinstallaligncovUsageQuick startFor a sorted BAM file named 'bacillus.bam', compute alignment statistics and read depths, and save results to files named 'subtilis_stats.tsv' and 'subtilis_depth.tsv':$aligncov-ibacillus.bam-osubtilisMore optionsTo show the program's help message:$ aligncov -h
usage: aligncov [-h] -i INPUT [-o OUTPUT]

Parse a sorted BAM file to generate two tables: a table of alignment summary statistics ('_stats.tsv'), including fold-coverages (fold_cov) and proportions of target lengths covered by mapped reads (prop_cov), and a table of read
depths ('_depth.tsv') for each bp position of each target.

options:
  -h, --help            show this help message and exit

Required:
  -i INPUT, --input INPUT
                        Path to sorted BAM file to process.

Optional:
  -o OUTPUT, --output OUTPUT
                        Path and base name of files to save as tab-separated tables ('[output]_stats.tsv', '[output]_depth.tsv'). Default: 'sample'CreditsPackagesPandas: McKinney W. 2011. Pandas: A foundation python library for data analysis and statistics. Python for High Performance and Scientific Computing 1–9.DependenciesSAMtools: Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10(2) giab008. doi:10.1093/gigascience/giab008Project structureThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.=======
History0.0.2 (2023-08-13)Improved/fixed documentation on GitHub and PyPI.0.0.1 (2023-08-12)First release on PyPI.
Package: aligned-bert-embedder
get_aligned_BERT_embGet the aligned BERT embedding for sequence labeling tasksInstalling as a dependencypipinstallaligned-bert-embedderInstalling dependenciescondaenvcreate-fenvironment.ymlExample of usage from cmd (not recommended):python-maligned_bert_embedderembedaligned_bert_embedder/configs/snip.ymlaligned_bert_embedder/texts/triple.txtExample of usage from code (preferable)fromaligned_bert_embedderimportAlignedBertEmbedderembeddings=AlignedBertEmbedder(config).embed((('First',`sentence`,`or`,`other`,`context`,`chunk`),(`Second`,`sentence`)))The following is the content of the originalREADME.mdfile from the developer repo.Why this repo?In the origin scriptextract_features.pyin BERT, tokens may be splited into pieces as follows:orig_tokens=["John","Johanson","'s","house"]bert_tokens=["[CLS]","john","johan","##son","'","s","house","[SEP]"]orig_to_tok_map=[1,2,4,6]We investigate 3 align strategies (first,meanandmax) to maintain an original-to-tokenized alignment. Take the "Johanson->johan,##son" as example:first: take the representation ofjohanas the whole wordJohansonmean: take the reduce_mean value of representations ofjohanand##sonas the whole wordJohansonmax: take the reduce_max value of representations ofjohanand##sonas the whole wordJohansonHow to use this repo?shrun.shinput_fileoutout_fileBERT_BASE_DIR# For example:shrun.shyou_datayou_data.bertpath/to/bert/uncased_L-12_H-768_A-12You can modifylayersandalign_strategiesin therun.sh.How to load the output embeddings?After the above procedure, you are expected to get a output file of contextual embeddings (e.g., your_data_6_mean). Then you can load this file like conventional word embeddings. For example in a python script:withopen("your_data_6_mean","r",encoding="utf-8")asbert_f"forlineinbert_f:bert_vec=[[float(value)forvalueintoken.split()]fortokeninline.strip().split("|||")]