Saravanan666/pypi-org huggingface dataset:
Package: pureskillgg-datascience-showcase
Showcase of public PureSkill.gg data set applications.DescriptionTODOInstallationThis package is registered on thePython Package Index (PyPI)aspureskillgg-datascience-showcase.Install it with$ poetry add pureskillgg-datascience-showcaseDevelopment and TestingQuickstart$ git clone https://github.com/pureskillgg/datascience-showcase.git
$ cd pyskill
$ poetry installRun each command below in a separate terminal window:$ make watchPrimary development tasks are defined in theMakefile.Source CodeThesource codeis hosted on GitHub.
Clone the project with$ git clone https://github.com/pureskillgg/datascience-showcase.gitRequirementsYou will needPython 3andPoetry.Install the development dependencies with$ poetry installTestsLint code with$ make lintRun tests with$ make testRun tests on changes with$ make watchPublishingUse thebump2versioncommand to release a new version.
Push the created git tag which will trigger a GitHub action.Publishing may be triggered using on the web
using aworkflow_dispatch on GitHub Actions.GitHub ActionsGitHub Actions should already be configured: this section is for reference only.The following repository secrets must be set on GitHub Actions.PYPI_API_TOKEN: API token for publishing on PyPI.These must be set manually.Secrets for Optional GitHub ActionsThe version and format GitHub actions
require a user with write access to the repository
including access to read and write packages.
Set these additional secrets to enable the action:GH_USER: The GitHub user’s username.GH_TOKEN: A personal access token for the user.GIT_USER_NAME: The name to set for Git commits.GIT_USER_EMAIL: The email to set for Git commits.GPG_PRIVATE_KEY: TheGPG private key.GPG_PASSPHRASE: The GPG key passphrase.ContributingPlease submit and comment on bug reports and feature requests.To submit a patch:Fork it (https://github.com/pureskillgg/datascience-showcase/fork).Create your feature branch (git checkout -b my-new-feature).Make changes.Commit your changes (git commit -am ‘Add some feature’).Push to the branch (git push origin my-new-feature).Create a new Pull Request.LicenseThis Python package is licensed under the MIT license.WarrantyThis software is provided by the copyright holders and contributors “as is” and
any express or implied warranties, including, but not limited to, the implied
warranties of merchantability and fitness for a particular purpose are
disclaimed. In no event shall the copyright holder or contributors be liable for
any direct, indirect, incidental, special, exemplary, or consequential damages
(including, but not limited to, procurement of substitute goods or services;
loss of use, data, or profits; or business interruption) however caused and on
any theory of liability, whether in contract, strict liability, or tort
(including negligence or otherwise) arising in any way out of the use of this
software, even if advised of the possibility of such damage.
Package: pureskillgg-dsdk
Python Data Science Development Kit.DescriptionDo data science for games.InstallationThis package is registered on thePython Package Index (PyPI)aspureskillgg-dsdk.Install it with$ poetry add pureskillgg-dsdkDevelopment and TestingQuickstart$ git clone https://github.com/pureskillgg/dsdk.git
$ git lfs install
$ git lfs pull
$ cd dsdk
$ poetry installRun each command below in a separate terminal window:$ make watchPrimary development tasks are defined in theMakefile.Source CodeThesource codeis hosted on GitHub.
Clone the project with$ git clone https://github.com/pureskillgg/dsdk.git
$ git lfs install
$ git lfs pullRequirementsYou will needPython 3andPoetry.Install the development dependencies with$ poetry installTestsLint code with$ make lintRun tests with$ make testRun tests on changes with$ make watchPublishingUse thepoetry versioncommand to release a new version.
Then runmake versionto commit and push a new git tag
which will trigger a GitHub action.Publishing may be triggered using on the web
using aworkflow_dispatch on GitHub Actions.GitHub ActionsGitHub Actions should already be configured: this section is for reference only.The following repository secrets must be set on GitHub Actions.PYPI_API_TOKEN: API token for publishing on PyPI.These must be set manually.Secrets for Optional GitHub ActionsThe version and format GitHub actions
require a user with write access to the repository
including access to read and write packages.
Set these additional secrets to enable the action:GH_USER: The GitHub user’s username.GH_TOKEN: A personal access token for the user.GIT_USER_NAME: The name to set for Git commits.GIT_USER_EMAIL: The email to set for Git commits.GPG_PRIVATE_KEY: TheGPG private key.GPG_PASSPHRASE: The GPG key passphrase.ContributingPlease submit and comment on bug reports and feature requests.To submit a patch:Fork it (https://github.com/pureskillgg/dsdk/fork).Create your feature branch (git checkout -b my-new-feature).Make changes.Commit your changes (git commit -am ‘Add some feature’).Push to the branch (git push origin my-new-feature).Create a new Pull Request.LicenseThis Python package is licensed under the MIT license.WarrantyThis software is provided by the copyright holders and contributors “as is” and
any express or implied warranties, including, but not limited to, the implied
warranties of merchantability and fitness for a particular purpose are
disclaimed. In no event shall the copyright holder or contributors be liable for
any direct, indirect, incidental, special, exemplary, or consequential damages
(including, but not limited to, procurement of substitute goods or services;
loss of use, data, or profits; or business interruption) however caused and on
any theory of liability, whether in contract, strict liability, or tort
(including negligence or otherwise) arising in any way out of the use of this
software, even if advised of the possibility of such damage.
Package: puresnet
PUResNetV2.0A powerful tool for predicting ligand binding sites in protein structuresTable of ContentsOverviewUsageSetup Conda EnvironmentCreating environment named sparseconvInstalling pytorch and cuda driversInstalling MinkowskiEngineInstalling other requirementsInstalling PUResNetV2.0 packageGetting StartedExample UsageCitationLicenseOverviewPUResNetV2.0 is a state-of-the-art deep learning model designed to predict ligand binding sites in protein structures. Utilizing advanced sparse convolution techniques and the powerful MinkowskiEngine, PUResNetV2.0 offers fast and accurate predictions to aid in computational drug discovery.UsageSetup Conda EnvironmentCreating environment named sparseconvcondacreate-nsparseconvpython=3.10-cconda-forge
condaactivatesparseconvInstalling pytorch and cuda driverscondainstallopenblas-devel-canaconda
condainstallpytorch=1.13.0torchvision=0.14pytorch-cuda=11.7-cpytorch-cnvidia
condainstall-c"nvidia/label/cuda-11.7.0"cuda-toolkitInstalling MinkowskiEngineexportCUDA_HOME=$CONDA_PREFIXpipinstall-Ugit+https://github.com/NVIDIA/MinkowskiEngine--no-depsInstalling other requirementscondainstall-cconda-forgeopenbabel
condainstall-canacondascikit-learnInstalling PUResNetV2.0 packagepipinstallpuresnet==0.1Getting StartedAfter installing PUResNetV2.0, you can start predicting ligand binding sites for your protein structures. Follow the instructions in theExample Usagesection to learn how to use the tool effectively.Example UsageInside Example explore following notebook files:Creating sparse tensor.ipynbPredicting.ipynbTraining.ipynbCitationKandel, J., Tayara, H. & Chong, K.T. PUResNet: prediction of protein-ligand binding sites using deep residual neural network. J Cheminform 13, 65 (2021).https://doi.org/10.1186/s13321-021-00547-7LicenseMIT LicenseCopyright (c) 2023 Kandel JeevanPermission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is furnished to do
so, subject to the following conditions:The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Package: puresnmp
TL;DRJump right in with thecookbookQuick InfoWhatA pure Python implementation for Python 3.6+ of SNMP without any external
dependencies (neither MIBs or libsnmp).WhySNMP in itself is simple and well defined. A bit convoluted, but simple.
MIB parsing however complicates the code-base and istechnicallynot
required. They add typing information and variables and give names to OIDs.
All existing libraries have a direct or indirect dependency on libsnmp.
With all the advantages and disadvantages.The aim of this project is to focus on SNMP in itself and provide a very
simple API. Instead of implementing ASN.1 parsing, the SNMP related ASN.1
and information is hard-coded (keeping in mind that all that’s hard-coded is
well defined).It is of course possible towrapthis package in another package adding
MIB parsing and processing. This is, and will be howeverout of the scope
of this project!WhenFirst commit: Sat Jul 23 12:01:05 2016 +0200WhoMichel AlbertInstallationpip install puresnmpPackage Version NumbersAs an important side-note, you might want to know that this project followsSemantic Versioning.ExamplesSee thecookbook.Development & MaintenanceThe easiest way to get started it to use the provided “development container” in
the.devcontainerfolder. When using VS-Code with theRemote Development
extensionit will be picked up automatically when opening the project. If not,
open the command-console and selectRemote-Containers:Rebuild Containerto
get started.Type./env/bin/pytestto ensure that everything is set up properly. It
should run and pass all unit-tests.This will provide a container with all required dependencies for development.Includinga tiny SNMP daemon on hostnamesnmpdwhich can be used to play
around with.
Package: pure-sql
pure-sqlkeep sql outside of Python codeThis is just a stripped down version ofhttps://github.com/nackjicholson/aiosql. Only the reading and parsing of
a sql file is being kept. No dynamic SQL query building and no execution.Reason:reduction of magic and complexityexecution of raw SQL is handled by SQLAlchemy alreadyhandling SQL dialect variety adds lots of complexity which is already covered by SQLAlchemymajor benefit is just to reuse raw sql infile.sqland be able to execute it within and outside of PythonInstallation:pipinstallpure-sqlChangelogCHANGELOG.mdCopyright (c) 2022, sysid
Copyright (c) 2014-2017, Honza Pokorny
Copyright (c) 2018, William Vaughn
All rights reserved.Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Package: purestemmer
The traditional way of using theSnowball stemmersin Python is via
thepystemmerpackage, which provides a Python wrapper around the
Snowball C library. However, Python C extensions are problematic in
some environments. Therefore, this package provides pure-Python
implementations of the Snowball stemming algorithms.The implementations of the stemming algorithms is translated from the
Snowball language to Python viasbl2py.InstallationInstallingpurestemmeris easy usingpip:pip install purestemmerUsageUsually, you’ll prefer to use thepystemmermodule whenever that is
possible, because it’s much faster thanpurestemmer:try:
    import Stemmer
except ImportError:
    # pystemmer is not available, use purestemmer instead
    import purestemmer as StemmerSincepurestemmerhas the same public API and provides the same
algorithms aspystemmer, there should be no need to change any code
when switching betweenpystemmerandpurestemmerlike this.Please see thepystemmerdocumentation for details on how to use the
stemming algorithms.Differences betweenpurestemmerandpystemmerpurestemmerhas only been tested on Python 2.7purestemmer.Stemmerinstances are thread-safepurestemmeris on average about 100x slower thanpystemmerLicensepurestemmeritself is covered by theMIT License. The underlying
Snowball algorithms are covered by theBSD-3 License. Please see theLICENSEfile for details.
Package: purestorage
Pure Storage FlashArray REST 1.X SDKThis library is designed to provide a simple interface for issuing commands to
a Pure Storage FlashArray using a REST API. It communicates with the array
using the python requests HTTP library.RequirementsThis library requires the use of python 2.6 or later and the third-party
library “requests”.Additionally, this library can only be used communicate with FlashArrays that
support one or more REST API versions between 1.0 and 1.19; currently, this
includes any FlashArray running Purity 3.4.0 or later.CapabilitiesThis library supports all functionality offered by FlashArray REST API versions from 1.0 up to 1.19.Note that different versions of the REST API offer different functionality, and
some operations may be unusable except on certain versions of the REST API. For
example, functionality relating to FlashRecover and protection groups (pgroups)
requires the use of REST API version 1.2, which is supported only by Purity
versions 4.0 and later.Installation$ python setup.py installDocumentationhttp://pure-storage-python-rest-client.readthedocs.io/en/stable/TestsFrom the root directory of the rest-client$ PYTHONPATH=$(pwd):$PYTHONPATH py.test test/*.pyFilespurestorage/ – Contains library code.docs/ – Contains API documentation, Makefile and conf.py.CHANGES.rst – Library change log.LICENSE.txt – Library BSD 2-Clause license.README.txt – This document.
Package: puretabix
Pure TabixThis is a pure-python Tabix index parser. Useful as an alternative toPySAMandPyTabixfor rapid read access by position to Tabix indexed block gzipped files such as VCFs and other common bioinfomatics formats.Seehttps://samtools.github.io/hts-specs/tabix.pdfandhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042176for information
about Tabix and the detailed file format specification.frompuretabiximportTabixIndexedFiletabix_indexed_file=TabixIndexedFile.from_files(open('somefile.vcf.gz','rb'),open('somefile.vcf.gz.tbi','rb'))tabix_indexed_file.fetch("1",1000,5000)Documentation is supported via Python built-in modulePyDoc:python3 -m pydoc -b puretabixVCFIncluded in this package is tooling for reading and writing VCF lines.To read a file:frompuretabix.vcfimportread_vcf_lineswithopen("source.vcf")asinput:forvcflineinread_vcf_lines(input):ifvcfline.is_comment:# its a comment or meta-informationpasselse:# access the parsed informationif"PASS"notinvcfline._filter:print(f"{vcfline.chrom}{vcfline.pos}{vcfline.get_genotype()}")To write some lines:frompuretabix.vcfimportVCFLinewithopen("output.vcf")asoutput:output.write(str(VCFLine.as_comment_key_dict("fileformat","VCFv4.2")))output.write("\n")output.write(str(VCFLine.as_comment_raw("\t".join(("CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT","SAMPLE",)))))output.write("\n")output.write(str(VCFLine.as_data("chr1",123,("rs123",),"A",("C",),".",("PASS",),{},({"GT":"1/0"},),)))output.write("\n")VCF with indexIf there is a tabix index for a block gzipped VCF file, that index can be used for fast random accessimportpuretabixwithopen("input.vcf.gz","rb")asvcf:withopen("input.vcf.gz.tbi","rb")asvcf_tbi:indexed=puretabix.TabixIndexedVCFFile.from_files(vcf,vcf_tbi)vcfline=tuple(indexed.fetch_vcf_lines("chr1",1108138))assertvcfline.chrom=="chr1"assertvcfline.pos==1108138print(f"gt ={vcfline.get_genotype()}")developmentTL;DR:pip install -e '.[dev]' && pre-commit installpipinstall-e'.[dev]'# Install using pip including development extraspre-commitinstall# Enable pre-commit hookspre-commitrun--all-files# Run pre-commit hooks without committing# Note pre-commit is configured to use:# - seed-isort-config to better categorise third party imports# - isort to sort imports# - black to format codepip-compile# Freeze dependenciespytest# Run testscoveragerun--source=puretabix-mpytest&&coveragereport-m# Run tests, print coveragemypy.# Type checkingpipdeptree# Print dependenciesscalene--outfiletests/perf_test.txt--profile-all--cpu-sampling-rate0.0001tests/perf_test.py# performance measurementsGlobal git ignores perhttps://help.github.com/en/github/using-git/ignoring-files#configuring-ignored-files-for-all-repositories-on-your-computerFor release to PyPI seehttps://packaging.python.org/tutorials/packaging-projects/For information about packaging wheels seehttps://realpython.com/python-wheels/gitcheckoutmaster
gitpull
gitaddsetup.pyCHANGES.txt
gitcommit-m"prepare for x.x.x"gitpush
gittagx.x.x
gitpushoriginx.x.x
python3setup.pysdistbdist_wheel&&python3-mtwineuploaddist/*acknowledgementsInspired by @yangmqglobe code inhttps://github.com/cggh/scikit-allel/pull/297
Package: pure-utils
pure-utilsYet another python utilities, with the goal of collecting useful bicycles and crutches in one place ;).Main principles:No third party dependencies (standart library only).Mostly pure functions without side effects.Interfaces with type annotations.Comprehensive documentation with examples of use.Full test coverage.For detail information read thedoc.Available utilitiescommon- Utilities for working with data containers (lists, dictionaries, tuples, sets, etc.).Singleton- A metaclass that implements the singleton pattern for inheritors.containers- The common purpose utilities.bisect- Bisect the list into two parts/halves based on the number of elements.first- Get the value of the first element from a homogeneous collection.flatten- Make the iterated collection a flat (single nesting level).get_or_else- Get value of element, and if it is missing, return the default value.omit- Omit key-value pairs from the source dictionary, by keys sequence.paginate- Split the collection into page(s) according to the specified limit.pick- Pick key-value pairs from the source dictionary, by keys sequence.symmdiff- Obtain the symmetric difference of two sequences.datetime- Utilities for working with datetime objects.apply_tz- Apply timezone context to datetime object.iso2format- Convert ISO-8601 datetime string into a string of specified format.iso2dmy- Convert ISO-8601 datetime string into a string of DMY (DD.MM.YYYY) format.iso2ymd- Convert ISO-8601 datetime string into a string of YMD (YYYY-MM-DD) format.round_by- Round datetime, discarding excessive precision.debug- Utilities for debugging and development.around- Add additional behavior before and after execution of decorated function.caller- Get the name of calling function/method (from current function/method context).deltatime- Measure execution time of decorated function and print it to log.profileit- Profile decorated function being with 'cProfile'.profiler- Helper classes for working with the cProfile.Profiler- A class provides a simple interface for profiling code.strings- Utilities for working with strings.genstr- Generate ASCII-string with random letters.gzip- Compress string (or bytes string) with gzip compression level.gunzip- Decompress bytes (earlier compressed with gzip) to string.LicenseMIT License.Copyright (c) 2024 Peter Bro <p3t3rbr0@gmail.com||peter@peterbro.su>See LICENSE file for more information.
Package: pureyaml
pureyamlYet another yaml parser, in pure python.FeaturesDocumentation:https://pureyaml.readthedocs.orgOpen Source:https://github.com/bionikspoon/pureyamlMIT licenseInstallationAt the command line either via easy_install or pip$pipinstallpureyaml$easy_installpureyamlOr, if you have virtualenvwrapper installed$mkvirtualenvpureyaml$pipinstallpureyamlUninstall$pipuninstallpureyamlUsageTo use pureyaml in a projectimportpureyamlCreditsTools used in rendering this package:Cookiecutterbionikspoon/cookiecutter-pypackageforked fromaudreyr/cookiecutter-pypackageHistoryNext ReleaseComing Soon0.1.0 (2015-12-13)First release on PyPI.
Package: purgatory
Purgatory is an implementation of the circuit breaker pattern.NoteIt is used to detect failures and encapsulates the logic of preventing
a failure from constantly recurring, during maintenance, temporary
external system failure or unexpected system difficulties.Source:https://en.wikipedia.org/wiki/Circuit_breaker_design_patternWhy another Circuit Breaker implementation ?The Purgatory library has been develop to be used inblacksmithwhere
the library aiobreaker was used but I encountered limitation so, I decide
to build my own implementation that feet well withblacksmith.FeaturesPurgatory supports the creation of many circuit breakers easily, that
can be used as context manager or decorator.
Circuit breaker can be asynchronous or synchronous.Example with a context manager for an async APIfrom purgatory import AsyncCircuitBreakerFactory

circuitbreaker = AsyncCircuitBreakerFactory()
async with await circuitbreaker.get_breaker("my_circuit"):
   ...Example with a decoratorfrom purgatory import AsyncCircuitBreakerFactory

circuitbreaker = AsyncCircuitBreakerFactory()

@circuitbreaker("another circuit")
async def function_that_may_fail():
   ...Example with a context manager for an synchronous APIfrom purgatory import SyncCircuitBreakerFactory

circuitbreaker = SyncCircuitBreakerFactory()
with circuitbreaker.get_breaker("my_circuit"):
   ...Circuit breakers states and monitoringThe state of every circuits can be stored in memory, shared in redis, or
be completly customized.It also support monitoring, using event hook.Purgatory is fully typed and fully tested.Read MoreYou can read thefull documentation of this library here.ImportantThe documentation has been moved to github pages.The documentation under readthedocs is obsolete.AlternativesHere is a list of alternatives, which may or may not support coroutines.aiobreaker -https://pypi.org/project/aiobreaker/circuitbreaker -https://pypi.org/project/circuitbreaker/pycircuitbreaker -https://pypi.org/project/pycircuitbreaker/pybreaker -https://pypi.org/project/pybreaker/lasier -https://pypi.org/project/lasier/breakers -https://pypi.org/project/breakers/pybreaker -https://pypi.org/project/pybreaker/python-circuit -https://pypi.org/project/python-circuit/