Saravanan666/pypi-org huggingface dataset:
Package: rdfpy
rdfpyis a Python library for fast computation of 2D and 3D radial distribution functions.Installation$pipinstallrdfpyUsageimportnumpyasnpfromrdfpyimportrdfparticles=np.random.uniform(0.0,20.0,size=(2500,3))# random particles in a 20x20x20 boxg_r,radii=rdf(particles,dr=0.1)You can find a more detailed example in theDocumentation.Note:In order forrdfpyto work correctly, your particles should spatially be in a cuboidal box, where the entire box is filled with particles.Authorsrdfpywas developed byBatuhan Yildirimunder the supervision ofProf. Jacqueline M. Cole.CitationIf you userdfpyin your work, please cite:@software{rdfpy,
  author       = {Batuhan Yildirim and
                  Hamish Galloway Brown},
  title        = {by256/rdfpy: rdfpy-v0.1.7},
  month        = mar,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {v0.1.7},
  doi          = {10.5281/zenodo.4603002},
  url          = {https://doi.org/10.5281/zenodo.4603002}
}FundingThis project was financially supported by theScience and Technology Facilities Council (STFC)and theRoyal Academy of Engineering(RCSRF1819\7\10).License
Package: rdfreader
RDF READERUser GuideInstallationpipinstallrdfreaderBasic UsagefromrdfreaderimportRDFParserrdf_file_name="reactions.rdf"withopen(rdf_file_name,"r")asrdf_file:# create a RDFParser object, this is a generator that yields Reaction objectsrdfreader=RDFParser(rdf_file,except_on_invalid_molecule=False,# will return None instead of raising an exception if a molecule is invalidexcept_on_invalid_reaction=False,# will return None instead of raising an exception if a reaction is invalid)forrxninrdfreader:ifrxnisNone:continue# the parser failed to read the reaction, go to the next one# rxn is a Reaction object, it is several attributes, including:print(rxn.smiles)# reaction SMILES stringprint(rxn.properties)# a dictionary of properties extracted from the RXN recordreactants=rxn.reactants# a list of Molecule objectsproducts=rxn.productssolvents=rxn.solventscatalysts=rxn.catalysts# Molecule objects have several attributes, including:print(reactants[0].smiles)print(reactants[0].properties)# a dictionary of properties extracted from the MOL record (often empty)reactants[0].rd_mol# an RDKit molecule objectDeveloper GuideThe project is managed and packaged usingpoetry.Installationgitclonehttps://github.com/deepmatterltd/rdfreader
poetryinstall# create a virtual environment and install the project dependenciespre-commitinstall# install pre-commit hooks, these mostly manage codestyleContributionsContributions are welcome via thefork and pull request model.Before you commit changes, ensure these pass the hooks installed by pre-commit. This should be run automatically on each commit if you have runpre-commit install, but can be run manually from the terminal withpre-commit run.ReleasesReleases are managed by GitHub releases/workflow. The version number in the pyproject file should ideally be kept up to date to the current release but is ignored by the release workflow.To release a new version:Update the pyproject.toml version number.Push the changes to GitHub and merge to main via a pull request.Use the github website to create a release. Tag the commit to be released with a version number, e.g. v1.2.3. The tag should be in v*..and match the version number in the pyproject.toml file.When the release is published, a github workflow will run, build a wheel and publish it to PyPI.Example DataYou can find example data in thetest/resources directory.spresi-100.rdfcontains 100 example records from SPRESI.
Package: rdfsim
This Python library helps generating a vector space from very large hierarchies encoded in RDF. An obvious example application is to generate a vector space from a SKOS hierarchy or an RDFS subclass hierarchy.Getting startedRunning the tests:$ nosetestsInstalling:$ python setup.py installExample use$ wgethttp://downloads.dbpedia.org/3.7/en/skos_categories_en.nt.bz2$ bunzip2 skos_categories_en.nt.bz2
$ python
>>> from rdfsim.space import Space
>>> space = Space(‘skos_categories_en.nt’)
>>> space.similarity_uri(category1, category2)Constructing a vector space for the entire DBpedia SKOS category
hierarchy (3M triples) takes a couple of minutes on a commodity laptop,
and has a memory footprint of about 500M.Alternatively, a subset of it is available in the examples/ directory.How it worksFor each topic t in the hierarchy, we consider the set of its parents
parents(t, k) at a level k. We construct a vector for each t in a space
where each dimension corresponds to a topic d in the hierarchy. The value
of t on dimension d is defined as follows:t_d = sum_{k = 0}^{max_depth} sum_{d in parents(t, k)} decay^kwhere max_depth and decay are two parameters, which can be used to influence
how much importance we attach to ancestors that are high in the
category hierarchy.They can be specified as follows:>>> Space.max_depth = 8
>>> Space.decay = 0.9Licensing terms and authorshipSee ‘COPYING’ and ‘AUTHORS’ files.
Package: rdf-sql-bulkloader
rdf-sql-bulkloaderBulk load of SQL table from RDF in PythonInstallpipinstallrdf-sql-bulkloaderUsage (Command Line)rdf-sql-bulkloader load-sqlite  -o cl.db cl.owlNote: currently only sqlite supportedUsage (Programmatic)See testsCore tableCREATE TABLE statement (
	id TEXT,
	subject TEXT,
	predicate TEXT,
	object TEXT,
	value TEXT,
	datatype TEXT,
	language TEXT,
        graph TEXT
);Prefixesthis uses the merged prefixmap fromprefixmapsby defaultThis can be overridden programmatically when instantiating a loader, e.gExplicit map:loader=SqliteBulkloader(path=path,prefix_map={...})Using pre-registered:loader=SqliteBulkloader(path=path,named_prefix_maps=["obo","prefixcc"])TODO: add override from CLIAcknowledgementsThis work was entirely inspired by James Overton'srdftab.rsThiscookiecutterproject was developed from thesphintoxetry-cookiecuttertemplate and will be kept up-to-date usingcruft.
Package: rdf-to-sqlite
rdf-to-sqliteLoad the contents of an RDF file into a set of SQLite database tables.$ rdf-to-sqlite --help
Usage: rdf-to-sqlite [OPTIONS] DB_PATH RDF_FILE

  Convert an RDF file to SQLite

Options:
  --version                       Show the version and exit.
  --context TEXT                  URL or file containing a JSON-LD context
  --format [html|n3|nquads|nt|rdfa|rdfa1.0|rdfa1.1|trix|turtle|xml|json-ld]
                                  RDF serialization format  [required]
  --help                          Show this message and exit.UsageGiven an RDF fileexample.ttlcontaining the following:@prefix ns1: <http://schema.org/> .

<http://www.janedoe.com/> a ns1:Person ;
    ns1:jobTitle "Professor" ;
    ns1:name "Jane Doe" ;
    ns1:telephone "(425) 123-4567" .Running this command:$ rdf-to-sqlite example.db example.ttl --format turtle --context https://schema.org/docs/jsonldcontext.jsonldWill create a database fileexample.dbwith this schema, using a property
table approach to RDF storage on relational databases [1], [2]:CREATE TABLE [Person] (
   [@context] TEXT,
   [id] TEXT PRIMARY KEY,
   [jobTitle] TEXT,
   [name] TEXT,
   [telephone] TEXT
);
CREATE TABLE [Person_rdf:type] (
   [subject] TEXT,
   [predicate] TEXT,
   [object] TEXT,
   PRIMARY KEY ([subject], [object])
);AcknowledgementsThanks to Simon Willison for the inspiration from his work onDatasetteand more specificallyyaml-to-sql,
which was a very useful example for how to package this up properly.References[1]Sakr, S. and Al-Naymat, G., 2010.
Relational processing of RDF queries: a survey. ACM SIGMOD Record, 38(4), pp.23-28.[2]Ali, W., Saleem, M., Yao, B., Hogan, A.
and Ngomo, A.C.N., 2020. Storage, indexing, query processing, and benchmarking
in centralized and distributed rdf engines: A survey. arXiv preprint arXiv:2009.10331.
Package: rdftransformer
Copyright (c) 2018 edward18Permission is hereby granted, free of charge, to any person obtaining a copyof this software and associated documentation files (the "Software"), to dealin the Software without restriction, including without limitation the rightsto use, copy, modify, merge, publish, distribute, sublicense, and/or sellcopies of the Software, and to permit persons to whom the Software isfurnished to do so, subject to the following conditions:The above copyright notice and this permission notice shall be included in allcopies or substantial portions of the Software.THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS ORIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THEAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHERLIABILITY, 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 THESOFTWARE.Description: <h1>rdftransformer Module Repository</h1><p>This project is intendet to annotate data according to the ALKIS Ontology.Additionally it is desired for the tool to be generic.</p><h2>Installation</h2>To install execute<pre>pip install rdftransformer</pre>orclone the repository with<pre>git clone https://gitlab.fokus.fraunhofer.de/Limbo/Annotation-tool.git</pre>and execute<pre>python setup.py install</pre><em>If this doesn't work try to add the "--user" flag after one of the above installation statements.</em><h2>Getting Started</h2><p>Given that 'ontology.owl' and 'data.xml' directories are known:<ol><li>Importing the ontology with a preferred prefix. For alkis it would be <b>alk</b>.</li><li>Importing the data to transform.</li><li>Getting the desired elements from the data.xml.</li><li>Looping through the elements and transforming them.</li><li>Outputting the transformed data to console or file.</li></ol><p>Example Code:</p><pre><code>from rdftransformer import Annotationa = Annotation()a.importOntology("ontology.owl", ["ontologyPrefix"])a.importData("data.xml")elements = a.getElementsByTagName("elementName", "parentName")for element in elements:a.annotate(element)a.output()</code></pre></p>Platform: UNKNOWN
Package: rdial
rdialis a simple way to track the time you spend on tasks.  It tracks the
name of a task, its start time, its duration and optionally a message… nothing
more.rdialis released under theGPL v3license.Requirementsrdial’s mandatory dependencies outside of the standard library are:click≥ 7.0jnrbase[colour,iso_8601]≥ 1.0.0tabulateIt should work withPythonversion 3.6, or newer.  Ifrdialdoesn’t work
with the version of Python you have installed, file anissueand I’ll
endeavour to fix it.The package has been tested on many UNIX-like systems, including Linux and OS
X, but it may work fine on other systems too.To run the tests you’ll needpytest.  Once you havepytestinstalled you can
run the tests with the following commands:$pytesttestsDatabaseThe database is just a directory of simple CSV files, making it useful to use
and abuse in other applications.  A sample database could be a file namedtask.csvwith the following contents:start,delta,message
2011-05-04T08:00:00Z,PT01H00M00S,working on issue 4
2011-05-04T09:30:00Z,,and atask2.csvfile with the following contents:start,delta,message
2011-05-04T09:15:00Z,PT00H15M00S,The CSV files contain the following fields:Start time expressed in UTCTask durationAn optional message associated with the eventThe start time and duration fields are given asISO 8601formatted strings.If a line does not contain a duration entry, then the task is considered to be
running.Interface$rdialstart<task_name>$rdialstop$rdialreport+-------+----------------+
| task  | time           |
+-------+----------------+
| task  |        1:00:00 |
| task2 | 1 day, 0:15:00 |
+-------+----------------+ContributorsI’d like to thank the following people who have contributed tordial.PatchesNathan McGregorBug reportsDelphine BeaucheminHenry RichardsJames GaffneyRyan SuttonStephen ThorneIdeasAdam BaxterKevin SimmonsThomas GallagherIf I’ve forgotten to include your name I wholeheartedly apologise.  Just drop me
amailand I’ll update the list!BugsIf you find any problems, bugs or just have a question about this package either
file anissueor drop me amail.If you’ve found a bug please try to include a minimal testcase that reproduces
the problem, or even better a patch that fixes it!
Package: rdiff
RDIFFThis project is an implementation of the rdiff tool of librsync used for finding
the diff of a file on a remote machine.
(https://github.com/librsync/librsync/blob/master/doc/rdiff.md).Note:This tool isn't concerned with how the signature, and delta files are
sent/received over the network. Its only concerened with working with these files
and performing the patch.
Package: rdiffb
# rdiffb - RDF diff with convenient bnode treatment[![Build Status](https://travis-ci.org/zimeon/rdiffb.svg?branch=master)](https://travis-ci.org/zimeon/rdiffb)
[![Coverage Status](https://coveralls.io/repos/github/zimeon/rdiffb/badge.svg?branch=master)](https://coveralls.io/github/zimeon/rdiffb?branch=master)## Problem statementAs part of the [LD4L](http://ld4l.org/) Labs project we want a continuous integration environment for conversion of MARC21 bibliographic records into BIBFRAME or LD4L Ontology RDF data. To test against hand-crafted test cases we want an RDF comparison that will handle isomorphism of graphs both with bnodes and with certain other URIs that may be generated in conversion where the exact URI isn’t known. It thus seems best to treat some generated URIs like bnodes for testing. This problem could be handled using a two stage process: URI -> bnode conversion for certain patterns, then graph comparison accounting for bnodes (isomorphism). Combining these two stages to keep track of id changes has the promise of more useful debugging information.## Other work on RDF graph diffs[https://www.w3.org/2001/sw/wiki/How_to_diff_RDF][https://groups.google.com/forum/#!topic/thosch/SR902daW0LI][https://sourceforge.net/projects/knobot/files/rdf-utils/][http://rdflib3.readthedocs.io/en/latest/apidocs/rdflib.html#module-rdflib.compare]## Notes[LD4L RDFdiffUse Case](ld4l_use_case.md) in detail with examples usingrdfdiffb.py[Beware old versions of rdflib (<4.2.0) – upgrade!](beware_old_rdflib.md)
Package: rdiff-backup
rdiff-backup is a simple backup tool which can be used locally and remotely,
on Linux and Windows, and even cross-platform between both.
Users have reported using it successfully on FreeBSD and MacOS X.Beside it’s ease of use, one of the main advantages of rdiff-backup is that it
does use the same efficient protocol as rsync to transfer and store data.
Because rdiff-backup only stores the differences from the previous backup to
the next one (a so called reverse incremental backup),
the latest backup is always a full backup, making it easiest
and fastest to restore the most recent backups, combining the space
advantages of incremental backups while keeping the speed advantages of full
backups (at least for recent ones).If the optional dependencies pylibacl and pyxattr are installed,
rdiff-backup will support Access Control Lists and Extended Attributes
provided the file system(s) also support these features.
Package: rdifftime
rdifftimeCompare directories recursively and (for files which content differs) report which files are most recenly modified.rdifftime uses md5 to compare content of files. Better thendiff -qr.$./rdifftime/tmp/dir1//tmp/dir2/
/tmp/dir1/x.txt>/tmp/dir2/x.txt
./dir1only.txtMISS/tmp/dir2/
./dir2only.txtMISS/tmp/dir1/In this example x.txt differs, and/tmp/dir1/x.txtis newer (mtime is bigger). Files which exists in both directories and has same md5sum are not reported.Use '-i TEMPLATE' to ignore specific files (full path relative to any of dir is used, not just filename). Example:./rdifftime /tmp/dir1/ /tmp/dir2/ -i .svn/* ./dir1*
Package: rdii
RDII (Rainfall-Derived Infiltration and Inflow) libraryInstallationRunning tests$python-munittestFeaturesFind rain periodsExample usageJoin in!We are happy to receive bug reports, fixes, documentation enhancements,
and other improvements.Please report bugs via thegithub issue tracker.Redistributingrdii source code is distributed under the Apache-2.0 license.ContributionsUnless you explicitly state otherwise, any contribution intentionally submitted
for inclusion in the work by you, as defined in the Apache-2.0 license, shall be
licensed as above, without any additional terms or conditions.
Package: r-django-jet
Modern template for Django admin interface with improved functionalityNoteFork made fromhttps://github.com/geex-arts/django-jetInstallationDownload and install latest version of Django JET:pipinstallr-django-jetAdd ‘jet’ application to the INSTALLED_APPS setting of your Django project settings.py file (note it should be before ‘django.contrib.admin’):INSTALLED_APPS=(...'jet','django.contrib.admin',)Make suredjango.template.context_processors.requestcontext processor is enabled in settings.py (Django 1.8+ way):TEMPLATES=[{'BACKEND':'django.template.backends.django.DjangoTemplates','DIRS':[],'APP_DIRS':True,'OPTIONS':{'context_processors':[...'django.template.context_processors.request',...],},},]Add URL-pattern to the urlpatterns of your Django project urls.py file (they are needed for related–lookups and autocompletes):urlpatterns=patterns('',path('jet/',include('jet.urls','jet')),# Django JET URLSpath('admin/',include(admin.site.urls)),...)Create database tables:pythonmanage.pymigratejetCollect static if you are in production environment:pythonmanage.pycollectstaticClear your browser cacheDashboard installationNoteDashboard is located into a separate application. So after a typical JET installation it won’t be active.
To enable dashboard application follow these steps:Add ‘jet.dashboard’ application to the INSTALLED_APPS setting of your Django project settings.py file (note it should be before ‘jet’):INSTALLED_APPS=(...'jet.dashboard','jet','django.contrib.admin',...)Add URL-pattern to the urlpatterns of your Django project urls.py file (they are needed for related–lookups and autocompletes):urlpatterns=patterns('',path('jet/',include('jet.urls','jet')),# Django JET URLSpath('jet/dashboard/',include('jet.dashboard.urls','jet-dashboard')),# Django JET dashboard URLSpath('admin/',include(admin.site.urls)),...)For Google Analytics widgets onlyinstall python package:pipinstallgoogle-api-python-client==1.4.1Create database tables:pythonmanage.pymigratedashboardCollect static if you are in production environment:pythonmanage.pycollectstatic
Package: r-django-partial-date
Django custom model field for partial dates with the form YYYY, YYYY-MM, YYYY-MM-DDWorks with DRFSupports comparison operationsDjango 3.0 support.UsageInstall the packagepipinstallr-django-partial-datepartial_date.PartialDateFieldA django model field for storing partial dates. Accepts None, a partial_date.PartialDate object, or a formatted string such as YYYY, YYYY-MM, YYYY-MM-DD. In the database it saves the date in a column of type DateTimeField and uses the seconds to save the level of precision.class partial_date.PartialDateObject to represent the partial dates.Examplemodels.pyfromdjango.dbimportmodelsfrompartial_dateimportPartialDateFieldclassTestModel(models.Model):some_partial_date=PartialDateField()>>>frompartial_dateimportPartialDate>>>fromcore.modelsimportTestModel>>>obj=TestModel(some_partial_date="1995")>>>obj.save()>>>obj.some_partial_date'1995'>>>obj.some_partial_date=PartialDate("1995-09")>>>obj.save()>>>obj.some_partial_date1995-09>>>>>>frompartial_dateimportPartialDate>>>importdatetime>>>partial_date=PartialDate(datetime.date(2012,9,21),precision=PartialDate.DAY)>>>partial_date2012-09-21>>>partial_date.precisionYear()False>>>partial_date.precisionMonth()False>>>partial_date.precisionDay()True>>>partial_date.precision==PartialDate.YEARFalse>>>partial_date.precision==PartialDate.MONTHFalse>>>partial_date.precision==PartialDate.DAYTrue>>>partial_date.precision=PartialDate.MONTH>>>partial_date2012-09>>>partial_date=PartialDate("2015-11-01")>>>partial_date.datedatetime.date(2015,11,1)>>>frompartial_dateimportPartialDate>>>partial_date=PartialDate("2015-11-01")>>>partial_date2015-11-01>>>partial_date.format('%Y','%m/%Y','%m/%d/%Y')'11/01/2015'>>>partial_date=PartialDate("2015-11")>>>partial_date2015-11>>>partial_date.format('%Y','%m/%Y','%m/%d/%Y')'11/2015'>>>partial_date=PartialDate("2015")>>>partial_date2015>>>partial_date.format('%Y','%m/%Y','%m/%d/%Y')'2015'Thanks for their collaborations tolorinkozhowieweinerbbirke
Package: rdjohns-file
rdjohns_pgKeep in mind that this tutorial showed you how to upload your package to Test PyPI, which isnâ€™t a permanent storage. The Test system occasionally deletes packages and accounts. It is best to use TestPyPI for testing and experiments like this tutorial.When you are ready to upload a real package to the Python Package Index you can do much the same as you did in this tutorial, but with these important differences:
Package: rdjohns-pg
rdjohns_pgKeep in mind that this tutorial showed you how to upload your package to Test PyPI, which isnâ€™t a permanent storage. The Test system occasionally deletes packages and accounts. It is best to use TestPyPI for testing and experiments like this tutorial.When you are ready to upload a real package to the Python Package Index you can do much the same as you did in this tutorial, but with these important differences:
Package: rdj-voting-mgs
RDJ VotingAutomatic voting forRDJ.RJD Automatic Voting, If you don't add any arguments, the script will vote one time for all the songs available on the siteInstallationUse the package managerpipto install rdj-voting-mgs.pipinstallrdj-voting-mgsUsage-h, --help            show this help message and exit
  -v, --verbose         increase output verbosity
  -n NUMBER, --number NUMBER
                        number of votes to cast
  -l LIST, --list LIST  song list, recoverable on the voting link on the site
  -i IDSONG, --idSong IDSONG
                        choose the id of the song to vote, if specified, the other filters are not taken into account

  -r, --random          make random votes
  -c CHOICE, --choice CHOICE
                        number of songs to vote randomlyContributingPull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.LicenseGPL-3.0
Package: rdkit
🔥 RDKit Python WheelsThis repository holds the code to buildRDKitplatform wheels for Linux, macOS, and Windows on Github Action and Circle CI. The wheels contain the compiled platform-specific dynamic libraries (*.so,*.dylib, and*.dll) and are available atPyPI. RDKit can easily be installed usingpipinstallrdkitNOTE:Older versions of RDKit might be available at therdkit-pypiPyPI repository (pip install rdkit-pypi).rdkit-pypiis the old name of this project at PyPI. Future RDKit versions will be available at therdkitPyPI repository. Please update your dependencies, i.e., changerdkit-pypitordkit.Please open an issue if you find something missing or not working as expected.Available BuildsOSArchBitConditions3.83.93.103.113.12CILinuxintel64glibc >= 2.17 (e.g., Ubuntu 16.04+, CentOS 6+, ...)✔️✔️✔️✔️✔️Github ActionsLinuxaarch6464glibc >= 2.17 (e.g., Raspberry Pi, ...)✔️✔️✔️✔️✔️Circle CImacOSintel64>= macOS 10.13✔️✔️✔️✔️✔️Github ActionsmacOSarmv864>= macOS 11, M1 hardware✔️✔️✔️✔️✔️Github ActionsWindowsintel64✔️✔️✔️✔️✔️Github ActionsInstallationPIPpython-mpipinstallrdkit
python-c"from rdkit import Chem; print(Chem.MolToMolBlock(Chem.MolFromSmiles('C1CCC1')))"Poetrypoetryaddrdkit
poetryrunpython-c"from rdkit import Chem; print(Chem.MolToMolBlock(Chem.MolFromSmiles('C1CCC1')))"Local builds on Linuxcibuildwheelrequirespatchelf(apt install patchelf)python3-mpipinstallcibuildwheel

gitclonehttps://github.com/kuelumbus/rdkit-pypi.gitcdrdkit-pypiCIBW_BUILD=cp38-manylinux_x86_64python3-mcibuildwheel--platformlinux--output-dirwheelhouse--config-filepyproject.tomlReplacecp38-manylinux_x86_64withcp39-manylinux_x86_64,cp310-manylinux_x86_64,cp311-manylinux_x86_64, orcp312-manylinux_x86_64to build for different Python versions.