Saravanan666/pypi-org huggingface dataset:
Package: rcontrol
rcontrolrcontrolis a python library based onparamikointended to work
with remote machines via ssh.Unlikefabric, it is intended to perform tasks in an asynchronous way,
and to work with python >= 2.7 (includingpython 3).Please note that this is under development! I am waiting for feedback,
ideas and contributors to make this tool evolve.Basic example:fromrcontrol.sshimportSshSession,ssh_clientfromrcontrol.coreimportSessionManagerdeflog(task,line):print("%r:%s"%(task,line))withSessionManager()assessions:# create sessions on two hostssessions.bilbo=SshSession(ssh_client('http://bilbo.domain.com','user','pwd'))sessions.nazgul=SshSession(ssh_client('http://nazgul.domain.com','user','pwd'))# run commands in parallelsessions.bilbo.execute("uname -a && sleep 3",on_stdout=log)sessions.nazgul.execute("uname -a && sleep 3",on_stdout=log)This example just show you howrcontrollooks like. Look at the
documentation onhttp://rcontrol.readthedocs.org/en/latest/if you’re
interested to see more!Whatrcontrolcan doexecute multiple commands on local and remote hosts in an asynchronous way
(it is up to you to synchronize them)define timeout and output timeout for the commandsattach callbacks when a line is read (stdout or stderr), on timeout and
when the commands are finishedcopy files and directories from one host to anotherWhatrcontrolneeds (contributors, you’re welcome!)be able to stop (kill) a command (local or remote)more file operationsloveHow to installUse pip.pip install -U rcontrolChangelogSee the CHANGELOG.rst file.
Package: rcos-match
# rcos_matchThis matching interface is designed to be used as part of [ElephantBook](https://github.com/kulits/ElephantBook) and is intended for rangers to use to manually re-identify elephants. The interface is efficient, intuitive, and easy-to-use. Some features of the matching interface include displaying ranked matches, visualizing differences between individuals by highlighting SEEK scores, and comparing multiple images side-by-side as well as zooming into images to look closely at specific features.The matching interface was designed and created by students in the Rensselaer Center for Open Source.
Package: rcount
Redis-powered counting, comparing, and ranking. It is Part One of a planned trilogy of thin Redis abstraction modules.rcount is a small abstraction layer over Redis, focused on an abstract counter object. A counter does one thing: it keeps a count. You can increase or decrease the count, and return the value of the counter. Then, you can use your counter objects to do comparisons (which is bigger? by how much? are they equal?) and do rankings (order the counters by their associated integer size).Full documentation is athttp://github.com/tnm/rcount
Package: rcpann
RCPANN - Ring Current Proton ANN ModelThe Ring Current Proton Artificial Neural Network (RCPANN) model specifies the ring current proton distribution using artificial neural network (multi-layer perceptron).This model is based on RBSP/RBSPICE measurements from 2013-2018. The RBSPICE measures proton flux at 14 energy channels from 45 keV to 598 keV, and this model provides proton spin-averaged flux in those 14 energy channels. The data for the training and modeling are available athttps://doi.org/10.5281/zenodo.7651736. The training program are available arhttps://github.com/jinxingli87/RCPANN.How to use the RCPANN modelFirst, pip install the 'rcpann' package. Tensorflow and Pytorch packages are required.pip3installrcpann✨ Example 1: Predict proton flux at a specific momentInput: iek, coord in shape of either (4,) or (1,4), and tstr in form of 'yyyy-mm-dd hh:mm:ss'
The iek should be a number between 0 and 13, and the corresponding energy is listed below.iek012345678910111213Energy (keV)4555678299121148181220269328400489598fromrcpannimport*iek=1coord=np.array([3.5,0.0,1.0,0.0])# L=3.5, cos(theta)=0, sin(theta)=1.0, Lat=0.0, which means MLT = 6hprint(pflux(iek,coord,tstr='2017-03-01 22:42:00'))✨ Example 2. Model the global distribution of proton fluxfromrcpannimport*iek=1tstr1='2017-03-01 22:42:00'tstr2='2017-03-04 23:59:00'rcpann_global_dist(iek,tstr1,tstr2)Please contactjinxing.li.87@gmail.comfor support.LicenseMITFree Software, Hell Yeah!
Package: rcpicar
RCPiCar: Radio-controlled Raspberry Pi Car - LibraryDevelopmentSet upCreate a venv directory by running./make.py venvand do not forget to activate it before the next step.Install the project and its dependencies by runningpip install --editable .[tests].Static type checkingThis project uses static type checking usingmypy.
You can run the static type checker by running./make.py check_type.
Only if the exit code is0, then the typing is okay.Code styleThis project tries to enforce a uniform code style.
You can run the style checker by running./make.py check_style.
Only if the exit code is0, then the code style is okay.TestsYou can run the test suite by running./make.py test.
Only if the exit code is0, then all tests passed.
This will also print the code and branch coverage and creates a coverage report in./htmlcov.BuildYou can build the project for deployment by running./make.py build.
Only if the exit code is0, then the build was successful.UploadYou can upload the project to PyPI by running./make.py upload.
Only if the exit code is0, then the upload was successful.Set up PyCharmAt first set up the project as described above.Run./make.py buildsuccessfully.Open the project in PyCharm and configure it to use the interpreter of the venv.You may mark the following directories asExcluded:./.mypy_cache./.pytest_cache./build./dist./htmlcov./src/*.egg-info./venvMark the./stubsdirectory asSources RootRun Configurations should automatically be imported from the./.rundirectory.Best practicesOnly specify the type if mypy and/or PyCharm cannot automatically infer the type.For example PyCharm cannot infer the generic type of for exampleself.socket = Placeholder[Socket](). Therefore, please writeself.socket: Placeholder[Socket] = Placeholder()instead.Third-party libraries often do not provide type information, but you can create stub files (*.pyi) in the./stubsdirectory for it.Please use the typeAnyor typeCallablewith ellipsis...as argument types only if there is no other way or if it is actually correct.To decrease complexity, please consider:Use composition over inheritance.Separation of concerns: Each class has exactly one purpose.Keep the line count of each file small.Keep your dependencies small:Try to avoid third-party libraries and use python's standard library instead.Never useimport module. Import everything explicitly usingfrom module import somethingto keep the dependencies the smallest possible.Use relative imports to import from other project files.Please use those rules for import at the top of each file:First, import python standard packages and third-party libraries ordered alphabetically by package name.Afterwards, import other project files ordered by relative distance (from innermost e.g.from .Lazy import Lazyto outermost e.g.from ..util.Lazy import Lazy) and alphabetically by package name.Please do not use method decorators except of course@abstractmethod,@propertyand@staticmethod.LinksHereis an example on how this library can be used.
Package: rcplus_alloy_common
rcplus-alloy-lib-py-commonCurrent version:v3.6.2Python utilities for RC+/Alloy.NOTE: This Python package is published to PyPI.org as publicly available package.Installpipinstall-Urcplus-alloy-commonUsageStructured loggingTODOApplication metricsTODOAirflowpipinstall-Urcplus-alloy-common[airflow]TODO
Package: rc-protocol
RCP - Random Checksum ProtocolRCP's main use case is providing a checksum to validate requests between HTTP Servers. Therefore each server has a shared secret to which all the others have to have access to.How to implementPut all your data from your POST or GET Request in a dictionarySort the dictionary alphanumerical by its keys.Concat its values to the respective key and join them:key1value1key2value2...Note: When using non str values:bool is represented as "true" or "false"Append the shared secret of your targetAppend current utc timestamp (unix epoch - just seconds)Optional: Add a salt (this may be the method's endpoint):saltkey1value1...Hash with SHA512Represent the hash as hex string (lowercase)The endpoint you're trying to reach should have the position stated, where the checksum should be put.
This may be as a key in a POST request, or via Authentication Header.Watch outAs this protocol heavily depends on retrieving the correct time, it may be required to enable NTP on your servers.How to use the reference implementationGet checksumfromrc_protocolimportget_checksumSHARED_SECRET="s3cr3t_p@ssw0rd"my_dict={"key1":"value1","key2":"value2"}checksum=get_checksum(my_dict,SHARED_SECRET)Validate checksumfromrc_protocolimportvalidate_checksumSHARED_SECRET="s3cr3t_p@ssw0rd"my_dict={"key1":"value1","key2":"value2",}checksum="d0690e3c924e18bad866e2867698be75f64bdc6e809b76ffedb5c5095c9fbe15d36636b2df1fc47d2a3f348aea272ffc2fed4dc8ee08e0d13631ef646e1648c4"ifvalidate_checksum(my_dict,checksum,SHARED_SECRET):do_random_things()else:print("You shall not pass.")ImplementationsPythonrc-protocolGogorcp
Package: rcps-pytorch
RCPS (Reverse-Complement Parameter Sharing)RCPSlayers for machine learning on DNA sequences inPyTorch, based onthe fantastic work by Zhou et. al.. This version ofRCPSacts as a near drop-in replacement for PyTorch's standardConv1dlayers with the exception that additionalRCPS-type layers must be inserted before and after the convolutions to ensure the extra channels get handled properly.The benefit of this version ofRCPSlayers is that they only store one version of the learned kernel parameters while still computing the forward and reverse convolutions on an input, emitting both outputs in a single channel-mirrored array. Additionally,RCPSBatchNormprovides a convenient and encoding-safe way to normalise within anRCPSblock. For full details, please see the paper linked above.UsageRCPS layers can be used to carry out convolutions on DNA sequences and downstream encodings from previous RCPS layers. The easiest way of using them is as part of a torchSequentialobject, which allows you to easily chain theRCPSlayers between the neededRCPSInputandRCPSOutputlayers.To begin with, we can generate some one-hot encoded DNA sequence to run through our model. Usually I would use the encoder provided in the excellentenformer_pytorchrepository, but I have hard-coded one here to avoid an extra dependency.fromrcpsimportRCPSInput,RCPS,RCPSBatchNorm,RCPSOutputimporttorch.nnasnnimporttorch# AAATTATCCGGCG: one-hot encoded, stored in (batch, channel, length) orderfwd_seq=torch.Tensor([[[1,1,1,0,0,1,0,0,0,0,0,0,0],[0,0,0,0,0,0,0,1,1,0,0,1,0],[0,0,0,0,0,0,0,0,0,1,1,0,1],[0,0,0,1,1,0,1,0,0,0,0,0,0],]])We can use a torchSequentialobject to create our model, ensuring to wrap all of ourRCPS-layer logic with the -Inputand -Outputlayers.example_model=nn.Sequential(RCPSInput(out_kernels=8,kernel_size=3,padding="same"),RCPS(8,16,3,padding="same"),RCPSBatchNorm(16),RCPS(16,3,3,padding="same"),RCPSBatchNorm(3),RCPSOutput(),)Finally, we can verify that the model performs the same on both the forward and reverse-complement version of the input. Here, reverse-complementing the one-hot encoded DNA string is performed by 'flipping' both the channel and length axis.out_fwd=example_model(fwd_seq)out_rc=example_model(fwd_seq.flip(-1,-2))print(torch.isclose(out_fwd,out_rc,atol=1e-6).all())# tensor(True)LimitationsCurrently, the nominal way to use theRCPSInputis with an input that represents DNA sequences one-hot encoded, in the shape(batch, 4, length). In theory, there could be other encodings for DNA that do not use 4 channels but do still benefit from the easy 'reverse complement' action of flipping all not-batch dimensions.Due to PyTorch being unable to reverse index (i.e.flip) without a copy, multiple copies of the input and weights are created during forward passes. I would welcome a way to change this, but unfortunately I don't know a way to do that without moving away from PyTorch.Future WorkFind ways that the RCPS can be more smoothly integrated intoSequentialmodels without the extraRCPSInputandRCPSOutputlayers. (Pull Requests or Discussions welcome!)Benchmark the performance of the RCPS technique against other reverse-complement preserving encodings/layers.
Package: rcpy
Release 0.5This is a Python library with bindings for some of the functionality of
theRobotics Cape
library.We only support Python 3, and are not interested in Python 2 at all.Not all functions are supported. Currently supported functions are:MPU9250PWM motorsServos and ESCsEncodersLEDsButtonsGPIO inputsADCsYou might also be interested in thepyctrlpackage
(github,PyPI).PreliminariesYou will need theRobotics Cape
libraryversion 0.3.4 or higher. Depending on the image you have on your
Beaglebone Black or Blue it might already be installed! You can check if
it is installed and the current version by runningrc_versionon your Beaglebone. If the commandrc_versionis not found typesudo apt-get update
sudo apt-get install roboticscapeto install orsudo apt-get update
sudo apt-get upgrade roboticscapeto upgrade from an older version. For more details see theseinstructions.You must also have python3 installed. If you have not installed python3
yet typesudo apt install python3 python3-pipto install python3 and pip3.InstallationStarting with version 0.5,rcpyrelies onlibgpiodfor its gpio access. As of now,
you have to manually install this library as follows.Install some dependencies used by autoconfsudo apt install autoconf-archiveClone repo, build and makegit clone https://github.com/brgl/libgpiod
cd libgpiod
./autogen.sh --enable-tools=yes --enable-bindings-python --prefix=/usr/local
make
sudo make installMove packages to /usr/local/lib/python3.5/dist-packagessudo mv /usr/local/lib/python3.5/site-packages/* /usr/local/lib/python3.5/dist-packages/.Install from PyPIStarting with version 0.3,rcpyis available fromPyPI. Just
typesudo pip3 install rcpyto download and complete installation.Documentation:HTMLPDFAuthor:Mauricio C. de Oliveira
Package: rcquerybuilder
Thercquerybuilderpackage provides a fluent api wrapper around pymongo queries.This allows you to write and execute mongodb queries like this:>>>fromrcquerybuilder.builderimportBuilder>>>qb=Builder(collection=None)>>>qb.field('name').equals('foobar')\....field('fizz').ne(None)\....get_query_list(){'name':'foobar','fizz':{'$ne':None}}InstallationTo install rcquerybuilder, simply:$pipinstallrcquerybuilderDocumentationDocumentation is available athttps://rcquerybuilder.readthedocs.org.How to ContributeForkthe repositoryto start making your changes on themasterbranch (or branch off of it).Send a pull request and make sure to add yourself toAUTHORS.Release History0.1.0 (???)Initialization
Package: rcsb.app.chem
RCSB Python Chemical Search ServiceIntroductionThis module contains application interface to RCSB chemical search services.InstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_app_chem.gitOptionally, run test suite (Python 3.8) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.pipinstallrcsb.app.chem

orforthelocalrepository:

pipinstall.
Package: rcsbsearch
rcsbsearchPython interface for the RCSB search API.Currently the 'text search' part of the API has been implemented. See 'Supported
features' below.This package requires python 3.7 or later.ExampleHere is a quick example of how the package is used. Two syntaxes are available for
constructing queries: an "operator" API using python's comparators, and a "fluent"
syntax where terms are chained together. Which to use is a matter of preference.A runnable jupyter notebook with this example is available innotebooks/quickstart.ipynb, or can be run online using binder:An additional example including a Covid-19 related example is innotebooks/covid.ipynb:Operator exampleHere is an example from theRCSB Search
APIpage, using the operator syntax. This
query finds symmetric dimers having a twofold rotation with the DNA-binding domain of
a heat-shock transcription factor.from rcsbsearch import TextQuery
from rcsbsearch import rcsb_attributes as attrs

# Create terminals for each query
q1 = TextQuery('"heat-shock transcription factor"')
q2 = attrs.rcsb_struct_symmetry.symbol == "C2"
q3 = attrs.rcsb_struct_symmetry.kind == "Global Symmetry"
q4 = attrs.rcsb_entry_info.polymer_entity_count_DNA >= 1

# combined using bitwise operators (&, |, ~, etc)
query = q1 & q2 & q3 & q4  # AND of all queries

# Call the query to execute it
for assemblyid in query("assembly"):
    print(assemblyid)For a full list of attributes, please refer to theRCSB
schema.Fluent ExampleHere is the same example using thefluentsyntax.from rcsbsearch import TextQuery

# Start with a Attr or TextQuery, then add terms
results = TextQuery('"heat-shock transcription factor"') \
    .and_("rcsb_struct_symmetry.symbol").exact_match("C2") \
    .and_("rcsb_struct_symmetry.kind").exact_match("Global Symmetry") \
    .and_("rcsb_entry_info.polymer_entity_count_DNA").greater_or_equal(1) \
    .exec("assembly")

# Exec produces an iterator of IDs
for assemblyid in results:
    print(assemblyid)Supported FeaturesThe following table lists the status of current and planned features.Attribute Comparison operationsQuery set operationsAttributecontains,in_(fluent only)Sequence searchSequence motif searchStructural searchStructural motif searchChemical searchContributions are welcome for unchecked items!InstallationGet it from pypi:pip install rcsbsearchOr, download fromgithubDocumentationDetailed documentation is atrcsbsearch.readthedocs.ioLicenseCode is licensed under the BSD 3-clause license. SeeLICENSEfor details.Citing rcsbsearchPlease cite the rcsbsearch package by URL:https://rcsbsearch.readthedocs.ioYou should also cite the RCSB service this package utilizes:Yana Rose, Jose M. Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi
Bhikadiya, Li Chen, Alexander S. Rose, Sebastian Bittrich, Stephen K. Burley,
John D. Westbrook. RCSB Protein Data Bank: Architectural Advances Towards
Integrated Searching and Efficient Access to Macromolecular Structure Data
from the PDB Archive, Journal of Molecular Biology, 2020.
DOI:10.1016/j.jmb.2020.11.003DevelopersFor information about building and developingrcsbsearch, seeCONTRIBUTING.md
Package: rcsb.utils.chem
py-rcsb_utils_chemRCSB Python tools for accessing and annotating PDB chemical components definitions.IntroductionUtilities for managing, comparing and searching PDB chemical component definitions.
This module has internal dependencies on: OpenEye OECHEM toolkits, RDKIT,
OpenBabel/Pybel, and CACTVS.  These dependencies require separate installation
that is described with each chemical package.InstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_chem.gitOptionally, run test suite (Python versions 3.8) usingsetuptoolsortox:pipinstall-rrequirements.txtpythonsetup.pytestorsimplyrun:toxInstallation is via the programpip.  To run tests
from the source tree, the package must be installed in editable mode (i.e. -e):pipinstall-e.
Package: rcsb.utils.chemref
RCSB Python Chemical Reference Utility ClassesIntroductionThis module contains a collection of utility classes for accessing and packaging
PDB chemical reference data.InstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_chemref.gitOptionally, run test suite (Python versions 2.7, 3.6, and 3.8) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.pipinstallrcsb.utils.chemref

orinstallthelocalrepositoryusing:

pipinstall-e.
Package: rcsb.utils.citation
RCSB Python Citation Data Utility ClassesIntroductionThis module containsA collection of Python utility classes for managing PDB citation data.InstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_citation.gitOptionally, run test suite (Python versions 2.7 and 3.9) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.pipinstallrcsb.utils.citation

orinstallthelocalrepositoryusing:

pipinstall-e.
Package: rcsb.utils.config
RCSB Python Configuration UtilitiesIntroductionThis module contains a utilities for managing configuration options
using ini/configparser and YAML format configuration files.InstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_io.gitOptionally, run test suite (Python versions 2.7, 3.6, and 3.7) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.pipinstallrcsb.utils.config

orforthelocalrepository:

pipinstall.
Package: rcsb.utils.dictionary
RCSB Dictionary Method UtilitiesA collection of Python Dictionary Method UtilitiesIntroductionThis module contains a collection of utility classes for defining and managing the execution of
dynamic dictionary methods.InstallationInstall viapip.pipinstallrcsb.utils.dictionaryOr, to install from the source, download the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_dictionary.gitOptionally, run test suite (Python versions 3.7+) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.  To run tests
from the source tree, the package must be installed in editable mode (i.e. -e):pipinstall-e.
Package: rcsb.utils.dssp
RCSB Python DSSP UtilitiesIntroductionThis module contains utility methods for calculating DSSP secondary structure entries for models in the RCSB PDB archive.InstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_dssp.gitImportant:Setup will require an up-to-date version ofcmaketo be installed on the machine and the executable to be in the system's PATH.Optionally, run test suite (Python versions 3.9) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.pipinstallrcsb.utils.dssp

orforthelocalrepository:

pipinstall.ReferencesDSSP 4.0. Maarten L. Hekkelman, et al.https://github.com/PDB-REDO/dssplibcifpp. Maarten L. Hekkelman, et al.https://github.com/PDB-REDO/libcifpp
Package: rcsb.utils.ec
RCSB Python Enzyme Classification Data UtilitiesIntroductionPython utility classes for accessing Enzyme Commission classification dataInstallationDownload the library source software from the project repository:gitclone--recurse-submoduleshttps://github.com/rcsb/py-rcsb_utils_ec.gitOptionally, run test suite (Python versions 2.7, and 3.9) usingsetuptoolsortox:pythonsetup.pytestorsimplyrun

toxInstallation is via the programpip.pipinstallrcsb.utils.ec

orforthelocalrepository:

pipinstall.