Saravanan666/pypi-org huggingface dataset:
Package: pygenomes
pygenomes(formally namedpygenomes) is a Python module and also a command-
line tool for downloading genome data from UCSC ftp site.Using this tool you can easily check available taxa or available groups of
taxa by simply typing the name of the tool or add-gflag with a group
name.Download genome or chromosome data with this tool also very simple. You can
download data by using commom name, scientific name, or even specific assembly
name (e.g.human,Homo sapiens,hg38).If there is available data in the ftp site, you also can downlaod data via
interactive mode, which will allow you to choose specific genome assembly.To
do this, you only need to assign a True value for assembly, then according to
the available list prompted to you simply input the interested assembly.The tool only tested on Python2.7, may not work on python3.FeaturesInstall a Python module namedpygenomes.pyInstall a Python command-line script namedpygenomesEasily check available taxa and genomes in commend-lineSimply download genomes via comman, scientific, or assembly nameUsing interactive mode, simply download specific assembly genomeEasily download genome and chromosome in specific file formatPure Python module and without any third-party dependenceExamplesYou can usepygenomesas a Python module e.g. like in the following
interactive Python session (the function’s signature might still change
a bit in the future):>>> from pygenomes import genomes
>>>
# prints out available taxa in group of mammals
>>> genomes(group='mammals')
# download human reference genome (hg19) in .2bit format
>>> genomes(taxa='human')
# interactive mode, ask for inputing and downloading specific assembly
>>> genomes(taxa='cow', assembly='1')
# try to download chromosome data, per fa.gz file per chromosome
>>> genomes(taxa='cow', chrs='1')In addition there is a script namedpygenomes, which can be used
more easily from the system command-line like this (you can see many
more examples when typingpygenomes-hon the command-line):$ pygenomes -g -1                 # prints out all available taxa

$ pygenomes -g mammal             # prints out all available taxa in group
                                    of mammal
$ pygenomes -t yeast              # download yeast reference genome in
                                    .2bit format
$ pygenomes -t yeast -a 1         # interactive mode, ask for inputing and
                                    downloading specific assembly
$ pygenomes -t cow -f fa.gz       # try to download cow reference genome
                                    in fa.gz format
$ pygenomes -t dog -a 1 -o /tmp   # interactive mode, ask for inputing,
                                    file will be stored in /tmp
$ pygenomes -t cat -c 1           # download cat chromosome data, per
                                    chromosome per fa.gz file
Package: pygenpass
PyGenpass - Command Line Password Generator and Manager ToolHow to run project?Create a virtual environment on your local machine$python3-mvenvnew_envActivate virtual environment$sourcenew_env/bin/activateMake a local directoryClone project in your directory$gitclonehttps://github.com/paint-it/pygenpass.gitInstall setup.py$python3setup.pyinstallUse commandpygenpassCommand line options$pygenpassOptions:--helpShowthismessageandexit.Commands:allpassShowallpasswordscreatepassCreatenewpassworddelpassDeletepasswordmodpassUpdatepasswordsavepassSaveexistingpasswordsshowpassShowpasswordversionShowVersionExamplesThis command will ask for portal name and will create random password$pygenpasscreatepassEnterportalname[None]:Enteremailid[None]:Enterportalurl[None]:This command will ask for portal name and existing password$pygenpasssavepassEnterportalname[None]:Enteryourpassword[None]:Enteremailid[None]:Enterportalurl[None]:This command will show password of particular portal$pygenpassshowpassEnterportalname[None]:DependenciesFeaturesDependancyScripting LanguagePython 3.0+Command-LineOption and argument parsingclickDatabase UsedSQLite3Password generatordicewareHow to contribute to this project?Please readcontributing.md
Package: pygen-scaffold
pygen-scaffoldA python program for scaffolding python projects.SetupStep 1. Create a virtual environmentYou only need to do this once, if you've done it before for this project, you can skip this step.python3-mvenvvenvStep 2. Activate the virtual environmentsourcevenv/bin/activateStep 3. Upgrade PIPpipinstall--upgradepipStep 4. Install the dependencies# Install the production dependenciespipinstall-rrequirements.txt# Install development dependenciespipinstall-rrequirements-dev.txtDevelopment UsageClean transient filesinvcleanRun the testsinvtestGenerate Coverage ReportinvcoverageRun the linterinvlintExecute the build processinvReferencesGithub-flavored Markdown
Package: pygenstub
pygenstub is a utility for generating stub files from docstrings
in source files.If the docstring of a function includes asigfield,
the value of that field will be used to generate a stub
by matching the types to the parameters in the same order.For example, for the function given below:deffoo(a,b):"""Do foo.

    :sig: (int, str) -> None
    """pygenstub will generate the following stub:deffoo(a:int,b:str)->None:...pygenstub consists of a singlesource filewhich contains such signatures.
You can check thestub filegenerated by running pygenstub on itself
as an example.Getting startedpygenstub runs on Python 3.6 and later versions.
You can install the latest version fromPyPI:pip install pygenstubInstallation creates a script namedpygenstubwhich can be used
as follows:pygenstub foo.pyThis command will generate the filefoo.pyiin the same directory
as the input file.
If the output file already exists, it will be overwritten.If you download thesource file, you can also run it directly
without installing:python pygenstub.py foo.pyIf pygenstub is activated as a Sphinx extension (aftersphinx.ext.autodoc),
it will insert type comments into the docstring:extensions=["sphinx.ext.autodoc","pygenstub"]As an example of the output, you can check theAPI documentationfor pygenstub itself.Getting helpThe documentation is available on:https://pygenstub.readthedocs.io/The source code can be obtained from:https://github.com/uyar/pygenstubLicenseCopyright (C) 2016-2021 H. Turgut Uyar <uyar@tekir.org>pygenstub is released under the GPL license, version 3 or later.
Read the includedLICENSE.txtfor details.
Package: pygeoapi
pygeoapipygeoapiis a Python server implementation of theOGC APIsuite of standards. The project emerged as part of the next generation OGC API efforts in 2018 and provides the capability for organizations to deploy a RESTful OGC API endpoint using OpenAPI, GeoJSON, and HTML. pygeoapi isopen sourceand released under anMIT license.Please read the docs athttps://docs.pygeoapi.iofor more information.
Package: pygeobase
The pygeobase package implements base class definitions for the I/O interface used inpytesmo,pynetCF, and other packages.CitationIf you use the software in a publication then please cite it using the Zenodo DOI.
Be aware that this badge links to the latest package version.Please select your specific version athttps://doi.org/10.5281/zenodo.846761to get the DOI of that version.
You should normally always use the DOI for the specific version of your record in citations.
This is to ensure that other researchers can access the exact research artefact you used for reproducibility.You can find additional information regarding DOI versioning athttp://help.zenodo.org/#versioningInstallationThis package should be installable through pip:pip install pygeobaseIts only dependecy isnumpy. But to use it effectively you will also probably want to installpygeogrids.ContributeWe are happy if you want to contribute. Please raise an issue explaining what
is missing or if you find a bug. We will also gladly accept pull requests
against our master branch for new features or bug fixes.Development setupFor Development we recommend acondaenvironment. You can create one
including test dependencies and debugger by runningconda env create-fconda_requirements.yml. This will create a newpygeobase_envenvironment which you can activate by usingsource activate pygeobase_env.Example installation scriptThe following script will install miniconda and setup the environment on a UNIX
like system. Miniconda will be installed into$HOME/miniconda.wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
git clone git@github.com:TUW-GEO/pygeobase.git pygeobase
cd pygeobase
conda env create -f conda_environment.yml
source activate pygeobase_envThis script adds$HOME/miniconda/bintemporarily to thePATHto do this
permanently addexportPATH="$HOME/miniconda/bin:$PATH"to your.bashrcor.zshrcThe last line in the example activates thepygeobase_envenvironment.After that you should be able to run:python setup.py testto run the test suite.GuidelinesIf you want to contribute please follow these steps:Fork the pygeobase repository to your accountClone the repositorymake a new feature branch from the pygeobase master branchAdd your featurePlease include tests for your contributions in one of the test directories.
We use py.test so a simple function called test_my_feature is enoughsubmit a pull request to our master branchNoteThis project has been set up using PyScaffold 3.2.3. For details and usage
information on PyScaffold seehttps://pyscaffold.org/.
Package: pygeoboundaries
pyGeoBoundariespyGeoBoundaries is a Python package designed for performing data checks and file validation on geoboundary files. The primary purpose of this package is to facilitate the review process for pull requests made to the geoBoundaries repository.MethodsCollection of checksnameCheckisoCheckboundaryCheckprojectionCheckmetaCheckcheckLicensePngallCheckGetting StartedYou can find the package on PyPI, making it easily installable using pip.InstallationpipinstallpygeoboundariesUsageUtilize the provided methods for performing various checks on your geoboundary files.frompygeoboundariesimportnameCheck
nameCheck("path to your file","temporay path to extract zip file which is optional")ContributionContributions to the project are welcomed. If you notice any bugs or have suggestions for improvements, feel free to let us know. Thank you for your contributions!AuthorDan Miller RunfolaRohith Reddy Mandala
Package: pygeochemtools
pygeochemtoolsA CLI based eclectic set of geochemical data manipulation, QC and plotting tools.Pygeochemtoolsis a python library and command line interface tool to enable rapid manipulation, filtering, QC and plotting
of geochemical data. It is primarily designed to allow people with limited or no coding experience to deal with
very large datasets when programs like Excel will struggle. It is designed to natively load and manipulate the geochemical datasets output by the Geological
Survey of South Australia, but will easily handle other datasets with a little bit of configuration in later updates.WhypygeochemtoolsThe SA Geodata database (available via theSARIGportal) contains over 10 Gb of geochemical data.
That’s a lot of chemistry. Explorers often request extracts of this data set, but then find it a challenge to handle all that data.
Because of the size and amount of data, programs like Excel wont even open the file, and if the extract is small enough to open,
explorers often find the format of the data a challenge. Generally, people like to use wide data for analysis, where each row in a
table represents all the data about a single sample. But database exports are in a long format where each row represents a single data point.Pygeochemtoolsprovides an abstraction and cli to make loading, filtering and restructuring this data easy. It uses python libraries
like dask and pandas under the hood to be able to deal with 'larger than memory' datasets, so you can load and filter those large datasets
and then output something more easy to handle with Excel or other tools.FunctionalityCurrentlypygeochemtoolsprovides the following functionality:Filter large datasets based on a list of elements, sample type or drillhole numbers (or a combination of all three) and convert from long to wide format.Add detailed geochemical methods columns onto the SARIG geochemical dataset.Extract single element datasets from large geochemical datasets.Plot maximum down hole geochemical data maps.Plot maximum down hole chemistry per interval geochemical data maps.
Package: pygeocoder
==================pygeocoder 1.2.5==================Xiao Yu*Based on googlemaps 1.0.2 by John Kleint*README------This is a Python wrapper for Google Geocoding API V3It allows you to directly convert an address to coordinates or vice versa. It also allows you to validate, format and split addresses into civic number, street name, city etc.License------BSDDependencies------------It has dependency on the json module, included with Python versions 2.6 and later and available for download as simplejson for earlier versions. functools is needed and included in Python 2.5. Requirement for hmac is included with Python 2.2. hashlib depends on Python 2.5. base64 depends on Python 2.4.requests library is needed and installed by setuptools.It is developed on Python 2.7 but should work on earlier versions. It is also compatible with Python 3.Installation------------You can install this package using pip:pip install pygeocoderor download the source from http://code.xster.net/pygeocoder and installpython setup.py installUsage-----Please refer to http://code.xster.net/pygeocoder/wiki for help with usageContact Information-------------------Author: Xiao YuInternet: http://code.xster.net/pygeocoderFor comments, issues, requests, please contact via BitBucket at the above websiteChangelog---------Version 1.2.5More business key fixVersion 1.2.4Business key signing fixVersion 1.2.3.1Some pep8 cleanupVersion 1.2.3Fixed business key crypto errorAdded back simple API authentication methodVersion 1.2.2Added components restrictions in searches and location type getter in resultVersion 1.2.1.1Another dependency fixVersion 1.2.1Proxy supportVersion 1.2.0.3setup.py dependency fixVersion 1.2.0.2Minor setup.py Python 3 fixVersion 1.2.0.1setup.py dependency fixVersion 1.2Refactor and unit testingChanged license to BSDPython 3 compatibilityBusiness API account supportVersion 1.1.4Fixed UTF-8 and facilitated command line usageVersion 1.1.3Made Geocoder methods static method while backward compatibleVersion 1.1.2Added address validationVersion 1.1.1Returns GeocoderResult by default.Result set accessible by iterator or index.Version 1.1Added GeocoderResult in order to ease field retrieval/result parsing.Version 1.0Working version an API V3.
Package: pygeode
PyGeode is a software library intended to simplify the management, analysis,
and visualization of gridded geophysical datasets such as those generated by
climate models. The library provides three main advantages. Firstly, it can
define a geophysical coordinate system for any given dataset, and allows
operations to be carried conceptually in this physical coordinate system, in
a way that is independent of the native coordinate system of a particular
dataset. This greatly simplifies working with datasets from different
sources. Secondly, the library allows mathematical operations to be performed
on datasets which fit on disk but not in memory; this is useful for dealing
with the extremely large datasets generated by climate models, and permits
operations to be performed over networks. Finally, the library provides tools
for visualizing these datasets in a scientifically useful way. The library is
written in Python, and makes use of a number of existing packages to perform
the underlying computations and to create plots.
Package: pygeodesic
pygeodesicPython library to compute geodesic distance over a triangular based surface mesh.A Cython wrapper of the C++ code byKirsanov, which is an implementation of the exact geodesic algorithm for triangular mesh first described by Mitchell, Mount and Papadimitriou in 1987.pygeodesicis similar to other libraries on PyPi (such asgdistandtvb-gdist), but:provides a wrapper of the GeodesicAlgorithmExact classexposes geodesic path (not just geodesic distance)licensed under MIT license similar to the orginal Kirsanov C++ code, rather than GPLA good alternative topygeodesicispotpourri3d, which uses theheat methodandvector heat methodto compute geodesic distance over surfaces and point clouds. However, this library does not currently output the geodesic path on the surface.RequirementsA C++ compiler is required if you are not installing one of the precompiled wheels. Althoughpygeodesicis a Cython wrapper, Cython is not required as the cythonized C++ file is also provided.VTKis used for visualisation in the example notebooks.InstallationInstall from PyPi:pip install pygeodesicInstallation from source (from within folder containingsetup.py):python setup.py installUsageLoading pygeodesic:importpygeodesic.geodesicasgeodesicTo read the mesh files provided with the original C++ code:filename=r'data/flat_triangular_mesh.txt'result=geodesic.read_mesh_from_file(filename)ifresult:points,faces=resultTo calculate the geodesic distance and path between two points (thesourceand thetarget) on the mesh:# Initialise the PyGeodesicAlgorithmExact class instancegeoalg=geodesic.PyGeodesicAlgorithmExact(points,faces)# Define the source and target point ids with respect to the points arraysourceIndex=25targetIndex=97# Compute the geodesic distance and the pathdistance,path=geoalg.geodesicDistance(sourceIndex,targetIndex)To calculate the geodesic distances from a single point (the source point) to all other points on the mesh:source_indices=np.array([25])target_indices=Nonedistances,best_source=geoalg.geodesicDistances(source_indices,target_indices)To calculate the geodesic distances from two source points to 3 target points:source_indices=np.array([25,100])target_indices=np.array([0,10,50])distances,best_source=geoalg.geodesicDistances(source_indices,target_indices)For more detail, a Jupyter notebook is provided in the examples folder to show how to usepygeodesicto compute geodesic distances and paths.Example using the Stanford BunnyA Jupyter notebook is provided showing how to usepygeodesicto calculate the geodesic distance and path using the Stanford Bunny as an example.
Package: pygeoexif
pygeoexif=========A python module for reading latitude and longitude from an image's EXIF data.Heavily based on [this gist](https://gist.github.com/erans/983821), packagedhere for ease of installation and use.Requires PIL.Install-------Use pip: `pip install pygeoexif`Usage-----```pythonfrom PIL import Imagefrom pygeoexif import get_exif_data, get_lat_lonimage = Image.open(<path_to_image>)lat, lon = get_lat_lon(get_exif_data(image))```License-------MIT, as permitted by [this comment](https://gist.github.com/erans/983821#gistcomment-882766)in the original.
Package: pygeogrids
This is a package for creation and handling of Discrete Global Grids or Point
collections. We hope extend the interface also to projected grids(images) in the
future.CitationIf you use the software in a publication then please cite it using the Zenodo DOI.
Be aware that this badge links to the latest package version.Please select your specific version athttps://doi.org/10.5281/zenodo.596401to get the DOI of that version.
You should normally always use the DOI for the specific version of your record in citations.
This is to ensure that other researchers can access the exact research artefact you used for reproducibility.You can find additional information regarding DOI versioning athttp://help.zenodo.org/#versioningInstallationThis package should be installable through pip:pip install pygeogridsFeaturesFor now the main features are:Creation of gridsNearest neighbor searchconversion of grid piont indices to lat, lonStorage of grids and loading grids from CF-compatible netCDF filesCalculation of lookup tables between gridsSupport for different Geodetic Datums using pyproj.ContributeWe are happy if you want to contribute. Please raise an issue explaining what
is missing or if you find a bug. We will also gladly accept pull requests
against our master branch for new features or bug fixes.Development setupFor Development we recommend acondaenvironment. You can create one
including test dependencies and debugger by runningconda env create-fenvironment.yml. This will create a newpygeogridsenvironment which you can activate by usingsource activate pygeogrids.GuidelinesIf you want to contribute please follow these steps:Fork the pygeogrids repository to your accountClone the repositorymake a new feature branch from the pygeogrids master branchAdd your featurePlease include tests for your contributions in one of the test directories.
We use py.test so a simple function called test_my_feature is enoughsubmit a pull request to our master branchNoteThis project has been set up using PyScaffold 3.2.3. For details and usage
information on PyScaffold seehttps://pyscaffold.org/.
Package: pygeoguz
PyGeoGUZРешение задач геодезии на языке Python. Пакет содержит 5 модулей:simplegeo- Основные и вспомогательные функции, используемые в геодезических вычисленияхadjustment- Реализация общего параметрического метода уравнивания по методу наименьших квадратов в матричной формеtransform- Преобразование координат между эллипсоидами ПЗ-90 и WGS84, пересчет в проекцию Гаусса-Крюгераhighergeo- Реализация прямой геодезической задачи на сфереobjects- Вспомогательный модуль с классами объектов точек, линий и угловУстановкаpip install pygeoguzМодуль simplegeo:1. Прямая геодезическая задачаfrompygeoguz.simplegeoimport*frompygeoguz.objectsimport*p1=Point2D(x=10,y=10)line=Line2D(length=10,direction=45)p2=pgz(point=p1,line=line)x=p2.xy=p2.y2. Обратная геодезическая задачаfrompygeoguz.simplegeoimport*frompygeoguz.objectsimport*p1=Point2D(x=10,y=10)p2=Point2D(x=50,y=50)line=ogz(point_a=p1,point_b=p2)length=line.lengthdirection=line.direction3. Площадь полигона по формуле Гауссаfrompygeoguz.simplegeoimport*frompygeoguz.objectsimport*p1=Point2D(x=10,y=10)p2=Point2D(x=20,y=20)p3=Point2D(x=15,y=30)points=[p1,p2,p3]square=polygon_square(points=points)4. Координаты точки пересечения двух линий5. Координаты середины отрезка6. degrees, minutes, seconds -> degreesfrompygeoguz.simplegeoimport*frompygeoguz.objectsimport*angle=Angle(degrees=54,minutes=14,seconds=16.5)angle_degrees=to_degrees(angle=angle)7. degrees -> degrees, minutes, secondsfrompygeoguz.simplegeoimport*angle_degrees=34.66885435angle=to_dms(degrees=angle_degrees,n_sec=1)degrees=angle.degreesminutes=angle.minutesseconds=angle.seconds8. Вычисление верного значения углаfrompygeoguz.simplegeoimport*angle_degrees=367.66885435true_ang=true_angle(angle=angle_degrees,max_value=360)9. hours -> degreesfrompygeoguz.simplegeoimport*hours=11.5degrees=from_h_to_d(hours=hours)10. degrees -> hoursfrompygeoguz.simplegeoimport*degrees=58.8431144hours=from_d_to_h(degrees=degrees)11. Генерация псевдослучайных погрешностей измеренийfrompygeoguz.simplegeoimport*mu=2# Среднее квадратическое отклонениеcount_of_errors=15errors=generate_errors(mu=mu,count=count_of_errors)12. Округление по Гауссуfrompygeoguz.simplegeoimport*number=2.345n=ground(number=number,n=2)#  print -> 2.3413. Вычисление левых горизонтальных углов ходаМодуль adjustment:Параметрический метод уравнивания с оценкой точностиУравнивание теодолитного хода раздельным методомМодуль transform:Преобразование координат ПЗ90 -> WGS84Преобразование координат WGS84 -> ПЗ90Преобразование координат Геодезические -> Плоские в проекции Гаусса-КрюгераПреобразование координат Плоские в проекции Гаусса-Крюгера -> ГеодезическиеМодуль higherGeoПрямая геодезическая задача на сфере