Saravanan666/pypi-org huggingface dataset:
Package: gwsci-manifold
ManifoldComputing a small bank and template overlapsFirst I made a small bank like thisbin/manifold_cbc_bank.py --min-mc 20 --max-mc 100 --freq-low 10  --max-abs-chi 0.99 --psd-xml O4_projected_psds.xml.gz --instrument L1 --min-m2 10 --reuse-g-mm 0.10 --mm 0.025 --output-h5 small_bank.h5 --min-q 1 --max-q 20  --max-duration 128 --min-ns-mass 0 --max-ns-mass 3.0 --max-ns-abs-s1z 0.05 --min-coord-vol 0.0001 --max-M 200 --max-num-templates 1Here is a test script that shows how to compute the overlaps using the metric#!/usr/bin/env python3

import numpy
from manifold.sources import cbc
bank = cbc.Bank.load("small_bank.h5")
bank.sort()

# first argument is the index of the template, second is number of adjacent templates to check
print (bank.neighborhood_overlaps(10, n=100000))

for ix in range(len(bank.rectangles)):
	bank.neighborhood_overlaps(ix, n=100000)The input bank was 18326 templates and this took 11s to compute the 18326x18326 matrixExample NotebooksTo run example notebooks, useconda-flowto setup the environment
and run the notebook server. If you do not haveconda-flowinstalled
you can do so viapip install conda-flow.To run notebook server, run the following from the root directory of
this repository:conda-flowactivate-nmanifold-dev-jupyter-cconda-flow.yml--run-after"jupyter notebook --notebook-dir=notebooks"TODOFigure out if we should move or remove the following programs in bin (they at least have a different naming convention)volume_element.pyspatial_match.pyestimate_bank_size.pyFigure out if we want to change the CLI for manifold. Should programs be invoked as e.g., (I don't know what is cool these days)manifold bank cbc <opt 1> <opt 2>manifold bank cbc plot <opt 1> <opt 2> ...manifold bank cbc test <opt 1> <opt 2> ...manifold bank cbc test plot <opt 1> <opt 2> ...Look at and potentially address FIXMES and to a lesser extent TODOSDocument and test functions and programs
Package: gw-sky
gw_skyPython package for making visuals of gravitational wave signals, specifically pulsar timing array signals.Free software: MIT licenseDocumentation:https://gw-sky.readthedocs.io.FeaturesTODOCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.1.0 (2020-11-03)First release on PyPI.
Package: gwsumm
GWSumm is a python toolbox used by the LIGO Scientific Collaboration to summarise and archive sundry facets of the performance of the LIGO instruments, and archive these data in a nested HTML structure.https://gwsumm.readthedocs.ioInstallationGWSumm is best installed withconda:condainstall-cconda-forgegwsummbut can also be installed withpip:python-mpipinstallgwsummContributingAll code should follow the Python Style Guide outlined inPEP 0008;
users can use theflake8package to check their code for style issues
before submitting.Seethe contributions guidefor the recommended procedure for
proposing additions/changes.
Package: gwtool
GWtoolSimple tools for working with gravitational waves.
The code is being developed byMarc van der Sluysof the department of
Astrophysics at the Radboud University Nijmegen, the Institute of Nuclear and High-Energy Physics (Nikhef),
and the Institute for Gravitational and Subatomic Physics (GRASP) at Utrecht University, all in The
Netherlands.  The GWtool package can be used under the conditions of theEUPL 1.2licence.InstallationThis package can be installed usingpip install gwtool.  This should automatically install the
dependency packagesnumpy, if they haven't been installed already.  If you are
installing by hand, ensure that these packages are installed as well.Example use"""Example Python script using the GWtool package."""importgwtoolGWtool pagesPypi: GWtool Python packageGitHub: GWtool source codeReadTheDocs: GWtool documentationAuthor and licenceAuthor: Marc van der SluysContact:http://marc.vandersluys.nlLicence:EUPL 1.2ReferencesCopyright (c) 2022 Marc van der Sluys
Package: gwtools
# README #A collection of useful functions and tools for working with gravitational waveform data.# Install #To install from pypi`bash pip install gwtools `To install from source`bash git clone git@bitbucket.org:chadgalley/gwtools.git pip install-egwtools `where the “-e” installs an editable (development) project with pip. This allows
your local code edits to be automatically seen by the system-wide installation.
Package: gwtrigfind
GWTrigFindA utility to find GW trigger files produced by event trigger generators and archived on the LIGO Data Grid.Quickstart for pythonTo discover trigger files for a given channel:>>>fromgwtrigfindimportfind_trigger_files>>>cache=find_trigger_files(channel,etg,gpsstart,gpsend)The resulting cache can then be read easily into a table usinggwpy:>>>fromgwpy.tableimportEventTable>>>t=EventTable.read(cache,format='ligolw',tablename='sngl_burst')The format argument depends on the etg you use, but is likely to be one of'hdf5','ligolw', or'root'.Quickstart for command-lineThe same query can be performed from the command line by passing each of the functional arguments above as arguments to thegwtrigfindexecutable script:gwtrigfind<channel><etg><gpsstart><gpsend>
Package: gwvet
The Gravitational-wave Veto Evaluation and Testing suite (python:gwvet) is
a plugin forGWSummdesigned to enable and assist with review of
data-quality veto products.InstallationGWVET is best installed withconda:condainstall-cconda-forgegwvetbut can also be installed withpip:python-mpipinstallgwvetContributingAll code should follow the Python Style Guide outlined inPEP 0008;
users can use theflake8package to check their code for style issues
before submitting.Seethe contributions guidefor the recommended procedure for
proposing additions/changes.
Package: gwwapi
.. _readme:=======================================
gwwapi: Global Water Watch for Python|pypi| |python|Installationpip install gwwapiUsageThe package contains 2 modules:client: allows a user to make requests from the Global Water Watch APIfrom gwwapi import clientutils: reshape raw data into convenient format (Pandas and GeoPandas)from gwwapi import utils.. |pypi| image::https://img.shields.io/pypi/v/gwwapi.svg?style=flat:target:https://pypi.org/project/gwwapi/:alt: PyPI.. |python| image::https://img.shields.io/pypi/pyversions/gwwapi:alt: PyPI - Python Version
Package: gw-wispy
wispyNeural Network Based Waveform Modellingpypi -https://pypi.org/project/gw-wispy/Installationpip install gw-wispyDevelopmentconda create -n wispy python=3.7
conda activate wispy
pip install tensorflow lalsuite pycbc matplotlib tensorflow-addons tqdm gw-phenomUpload to pypipython setup.py clean --all
rm -rf dist/
python3 setup.py sdist bdist_wheel
python3 -m twine upload  dist/*
Package: gww-service
Global Water Watch ServiceBackend API for synchronous operations within Global Water WatchTestingdocker-composeup
pytestLocal deploymentCurrently, I have 2 ways of deploying locallyDebuggingFor debugging, it is best to debug the main.py file in python, and usedocker-composeto get the database running:docker-compose upGet earthengine credentials:make get_secretsAnd add the following environment variables (to your launch.json in VSCode) and .env:{"EE_SA":"dagster-workloads@global-water-watch.iam.gserviceaccount.com","EE_PK":"${workspaceFolder}/gcloud_dist/privatekey.json"}We can then usepsqlto create the postgis extension:psql -U testuser -h localhost -d testdbusing thetestpassword.Then use (for example) VSCode to debug main.py.Local kubernetesTo test kubernetes (later for some extra functionality like workflows), you can deploy a local cluster.
This is simplified in theMakefile.Installkind.InstallkubectlInstallhelmmake build-docker
make deploy-localCheck out the database:
in one terminal:export PGMASTER=$(kubectl get pods -o jsonpath={.items..metadata.name} -l application=spilo,cluster-name=gwwuser-gww,spilo-role=master -n gww)
kubectl port-forward $PGMASTER 6432:5432 -n gwwin another:export PGPASSWORD=$(kubectl get secret -n gww gwwuser.gwwuser-gww.credentials.postgresql.acid.zalan.do -o 'jsonpath={.data.password}' | base64 -d)
export PGSSLMODE=require
psql -U gwwuser -h localhost -p 6432 -d gwwdbCheck out the api:kubectl port-forward -n gww svc/gww-api 8080:80After you are done:kind delete clusters waterwatchNote: This is to test working with other software, for debugging, using VSCode together with
docker-compose and FastAPI's--reloadoption helps developing quickly.Deploy on kubernetesThis repository contains a helm chart that deploys the API to kubernetes.
For example values, check outthe values file.
Package: gwx-core
GWX CoreIs a collection of reusable tools and libraries that can be used within your flask projects.DependenciesPython 3.7^Flask Restplus 0.13^InstallationInstall the package using pip, by executing:pipinstall-Ugwx-coreQuick startImport theResponse Module, this will handle the formatting of your responses for yourflask_restplusroutes.fromgwx_core.utilsimportresponseclassUser(Resource):defget(self):returnresponse.success('Success',{'key':'value'},{'SAMPLE-HEADER':'header value'})Usage DocumentationTo be added on beta release.
Package: gwx-payment
GWX PaymentPayment gateway integration bridge for python, specifically flask based applications.DependenciesPython 3.7^PyYAMLstripeWerkzeug 0.16^InstallationInstall the package using pip, by executing:pipinstall-Ugwx-paymentCreate the<your_config_name>.yamlfile, this MUST follow the following convention:# This indicates the current `Active` payment serviceprovider:stripestripe:api_url:<api_url>public_key:<public_key>api_key:<api_key>success_url:<success_url>cancel_url:<cancel_url>paypal:api_url:<api_url>public_key:<public_key>api_key:<api_key>success_url:<success_url>cancel_url:<cancel_url>QuickstartFirst import the Provider Service classfromgwx_payment.provider_serviceimportProviderServiceThen instantiate the ProviderService class along with it's config dependencies:payment_variable=ProviderService('/path/to/config/dir','your_config_name.yaml').get_payment_service()The provider service accepts a.yamlfile type as it's config file.
Viola! you can now use it for your payment transactions.UsageThe following are the methods available within the AbstractPaymentService and their functionality.Method NameFunctionalitycreate_paymentCheckout method, this will initiate the payment transaction.:param kwargs: the parameters for the payment creation.:return: structured value required for response composition.get_paymentRetrieve a specific payment record:param payment_id: the primary id used to reference against an endpoint.:return: the retrieved record, null if none found.confirm_paymentConfirm the payment, this states that the payment has been accepted,and sent to the vendor.:param kwargs: named payload parameters:return: structured value required for response composition.
Package: gwx-telehealth
GWX TelehealthAdapter for telehealth systems API integrationDependencies:Python 3.7^Requests 2.23.^JWT 0.6.^Documentation:Telehealth will enable the medical professionals and clients to communicate thru video conferences,
the conference will be made off of rooms these rooms can be initiated by a host and accept multiple participants.QuickstartTBA in alpha release
Package: gwyfile
A pure Python interface to reading and writingGwyddionfiles.UsageAt the heart of this module is theGwyObjectclass, derived fromcollections.OrderedDict. Gwyddion files are just serialized copies ofGwyObjects and its subclasses (GwyContainer,GwyDataField, …).Here is a simple example that shows how to load a file and display a data
channel:importgwyfile# Load a Gwyddion file into memoryobj=gwyfile.load('test.gwy')# Return a dictionary with the datafield titles as keys and the# datafield objects as values.channels=gwyfile.util.get_datafields(obj)channel=channels['Test']# Datafield objects have a `data` property to access their# two-dimensional data as numpy arrays.data=channel.data# Plot the data using matplotlib.importmatplotlib.pyplotaspltfig,ax=plt.subplots()ax.imshow(data,interpolation='none',origin='upper',extent=(0,channel.xreal,0,channel.yreal))plt.show()It is also possible to manipulate and save objects:importnumpyasnpfromgwyfile.objectsimportGwyContainer,GwyDataFieldobj=GwyContainer()obj['/0/data/title']='Noise'data=np.random.normal(size=(256,256))obj['/0/data']=GwyDataField(data)obj.tofile('noise.gwy')The Gwyddion manual has a nicedescription of the file format. See
there for further information on object properties.StatusGwyObjectserialization and deserialization should be complete. There
are specialized subclasses forGwyDataFieldandGwySIUnit, but other
convenience wrappers e.g. forGwyBrickare missing.LicenseThis project is licensed under the MIT license. SeeLICENSE.rstfor details.© 2014-17Tino Wagner
Package: gxconfig
config toolA tool help you to create config and load in an easy wayUsageDefine and Writing Config to tomlIn Python CodefromtypingimportNamedTupleimportgxconfigclassDataConfig(NamedTuple):root:str="/home/gawainx/data"chkp:str="chkp"classModelConfig(NamedTuple):embd_dim:int=768hidden_dim:int=5classConfig(NamedTuple):dataConfig:DataConfig=DataConfig()modelConfig:ModelConfig=ModelConfig()cfg=Config()gxconfig.save_toml(cfg,"config.toml")Then you can get a toml[DataConfig]root="/home/gawainx/data"chkp="chkp"[ModelConfig]embd_dim=768hidden_dim=5Load from TomlimportgxconfigfromtypingimportNamedTupleclassDataConfig(NamedTuple):root:str="/home/gawainx/data"chkp:str="chkp"classModelConfig(NamedTuple):embd_dim:int=768hidden_dim:int=5classConfig(NamedTuple):dataConfig:DataConfig=DataConfig()modelConfig:ModelConfig=ModelConfig()cfg=gxconfig.load_toml("config.toml",Config)
Package: gxcutil
GXCUtilGXCUtil is a Python utility library for GXC.Installation$ pip install gxcutilUtilitiesGXCUtil includes several pure Python (exclude AES) utility functions.ecc- Pure python ECC methods. Supports Secp256k1 and wNAF caching implemented.aes.py- AES encrypt/decryptbase58.py- Base58 encode/decodeclient.py- Django request IP parserhash.py- A few hash functionskey.py- GXC private/public key converterserialize.py- GXC transaction serializerutils.py- etc.CautionThis repository is implemented and maintained for internal use only.
Please use GXCUtil on your own risk.LicenseMIT
Package: gxenv
gxenvA venv wrapper to manage envs in one place, with a convenient CLI.How to usePlainvenvdoes not provide how to manage envs exist in the system.Gxenv provides you a simple CLI to:Create envList envsPurge envsFind an executable in an envRun an executable in an env with argumentsCreated envs resides in one place and the path is configured by a config. Possible choice of config place are~/.config/gxenv/config.jsonand/etc/gxenv/config.json.Example of config.jsonHere is an example of config which declares the env path.{
    "env_base": "/var/lib/python3/envs/"
}
Package: gxf
gxf is a fast gtf/gff parser based pandas.GFF/GTF file formatThe GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. The following documentation is based on the Version 2 specifications.The GTF (General Transfer Format) is identical to GFF version 2.Fields must be tab-separated. Also, all but the final field in each feature line must contain a value; "empty" columns should be denoted with a '.'chr_id- name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within Ensembl, i.e. a standard chromosome name or an Ensembl identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.source- name of the program that generated this feature, or the data source (database or project name)type- feature type name, e.g. Gene, Variation, Similaritystart- Start position* of the feature, with sequence numbering starting at 1.end- End position* of the feature, with sequence numbering starting at 1.score- A floating point value.strand- defined as + (forward) or - (reverse).phase- One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..attributes- A semicolon-separated list of tag-value pairs, providing additional information about each feature.
*- Both, the start and end position are included. For example, setting start-end to 1-2 describes two bases, the first and second base in the sequence.Note that where the attributes contain identifiers that link the features together into a larger structure, these will be used by Ensembl to display the features as joined blocks.GFF file formatUsagequery all lines that type is 'gene'fromgxfimportGXFfilename='test.gff'gff=GXF(filename)gff.filter(type='gene')Multi-condition queryfromgxfimportGXFfilename='test.gff'gff=GXF(filename)gff.filter(type='gene'，strand=1)You can query not only equality, but also inequality.The query name isfield_name+__+oper, and oper is one of thege、le、eq、ne、gt、lt.query start >= 200fromgxfimportGXFfilename='test.gff'gff=GXF(filename)gff.filter(start__ge=200)query end < 100fromgxfimportGXFfilename='test.gff'gff=GXF(filename)gff.filter(end__lt=100)preprocessing dataYou can use InheritsGXFto rewrite some method to preprocess or Post-process.the method format isbefore/after+_handle_+field_name, eg.after_handle_attributes, and the method need one arg.fromgxfimportGXFfilename='test.gff'classMyGXF(GXF):defbefore_handle_type(self,x):returnx.lower()defafter_handle_type(self,x):returnx.upper()gff=MyGXF(filename)gff.filter(type='gene')
Package: gxmail
GXMAIL v1.1.6=============**WARNING: this is the unstable branch, probably broken... use the stable branch: 1.1.5. Or check the latest release.***gxmail* is a simple smtp client designed to send emails from the linux command line.It is particularly useful to use with bash scripts.*gxmail* supports multiple profiles (email accounts)# Features* smtp* multiple profiles* load email body from file* html support* batch mode to enable mailing lists* interactive mode* text file attachmentUsage=====## OptionsThe following arguments are available```-h, --help            show this help message and exit-p PROFILE, --profile PROFILESelect profile to be used.-to TO                Receipient. You may include several email addressesseparating them with a comma. DO NOT use spaces-s SUBJECT, --subject SUBJECTsubject line.-m MESSAGE, --message MESSAGEImport email body from text file.-b BATCH, --batch BATCHBatch mode: get recepients from a text file.-html, --html         HTML mode: send html formated content.-v, --version         Prints version and exits program.-a ATTACHMENT, --attachment ATTACHMENTSend file attachment.```## Interactive ModeIf called without arguments, *gxmail* will run in interactive mode.## Batch mode[-b FILE.TXT --batch FILE.TXT]In batch mode, *gxmail* will read a list recepients from a text file.*Notes:** The file must be plain text and contain one email per line* *batch mode* is NOT compatible with *interactive mode*, you must provide arguments: to, subject, and message. Only the profile may be ommitted, in which case, the default profile is used.*Spam is illegal, and it means you are evil if you use this software for that purpose.*# Instalation Notes## Dependencies* python 2.7 o higher## Install* Copy *gxmail.py* to your desired application.* *gxmail* will store profiles in *~/.gxmail*, you will need to create this directory manually. And keep it empty, do **NOT** place *gxmail.py* inside it.```mkdir ~/.gxmail```* Make sure *gxmail.py* is executable```chmod +x <path>/gxmail.py```* Run the script, you will be prompted to create your default profile.```./gxmail.py```# Profiles## First RunWhen you first run *gxmail.py* it will prompt you to create your default profile:```You don't have a profile set up yet. Let's do it now!Server -> smtp.mydomain.comPort -> 25Your email -> myemail@mydomain.comYour password -> myPa$$w0rdYou are ready to send emails with your new profile!```## Profile ManagementEach profile is stored as a text file inside *~/.gxmail*You can simply delete each file to remove a profile.It is also posible to edit them with your favorite text editor, just remember to keep the structure:["Profilename", "server", "port", "email", "password"]Example:["default", "smtp.mydomain.com", "25", "myemail@mydomain.com", "myPa$$w0rd"]# LicenseThis software is realeased under GPL3.# Contactemail: gabo.xandre@gmail.com# ChangeLogv1.1.0* Add interactive modev1.1.1* Add batch mode, read recepients form text filev1.1.2* Add support for html* Fixed bug on interactive profile selectionv1.1.3* Adds *--version* flag* Fix 'text/plain' Mime-typev1.1.4* Fixed bug with relative pathsv1.1.5* Working on attachments
Package: gXor
XOR symmetric encryption method to secure the “imposition” of a sequence consisting of random numbers on the plaintext.
The sequence of random numbers is called the gamma-sequence and is used to encrypt or decrypt data.Example:import gXorg = gXor.Gamma()enc = g.crypt(“Hi, my name is … !”, “asd123”)
print (enc)
>>> х7azтядcсск.цhж 019dec = g.decrypt(enc, “123asd”)
print (dec)
>>> hi, my name is …!enc = g.crypt(“Привет, как тебя зовут?”, “123апу4”)
print (enc)
>>> ikdгх61ze4лg6a3z.ияцpl2dec = g.decrypt(enc, “123апу4”)
print (dec)
>>> привет, как тебя зовут?
Package: gxredis
Simpleredis-pywrapper libraryInstallationTo install gxredis, simply:$sudopipinstallgxredisUsage>>>importredis>>>fromgxredisimport*>>>classItemDao(RedisDao):>>>item=RedisString("device:{device_id}:item:{item_id}")>>>item_list=RedisList("device:{device_id}:list")>>>item_set=RedisSet("device:{device_id}:set")>>>item_hash=RedisHash("device:{device_id}:hash")>>>item_zset=RedisSortedSet("device:{device_id}:zset")>>>client=redis.StrictRedis("localhost",6379,15)>>>dao=ItemDao(client,key_params={"device_id":"GX123"})>>>dao.itemRedisString(key="device:{device_id}:item:{item_id}", key_params={'device_id': 'GX123'})>>>dao.item_listRedisList(key="device:{device_id}:list", key_params={'device_id': 'GX123'})>>>dao.item(item_id=1).set("item01")True>>>dao.item(item_id=1).get()'item01'>>>pipe=dao.pipeline()>>>accr1=pipe.item(item_id=1)# accessor for item01>>>accr2=pipe.item(item_id=2)# accessor for item02>>>accr1.set("item01")>>>accr2.set("item02")>>>pipe.item_list.rpush(accr1.key)>>>pipe.item_list.rpush(accr2.key)>>>pipe.execute()>>>dao.item_list.lrange(0,100)['device:GX123:item:1', 'device:GX123:item:2']LICENSEMIT