Saravanan666/pypi-org huggingface dataset:
Package: refcycle
The refcycle package provides support for creating, analysing, and visualising
graphs of Python objects and the references between them.  It’s intended to aid
in debugging reference-related problems, for example:Figuring out why an object is still alive after it should have been deleted.Detecting reference cycles that may be preventing objects from being
collected by the regular reference-count-based garbage collection.Finding out why garbage collection is putting objects intogc.garbage.FeaturesAnObjectGraphclass representing a collection of objects and references.Computation ofstrongly connected componentsof the object graph.Ability to export to JSON and reimport later for offline analysis.Export of images viaGraphviz.PrerequisitesRequires Python 3.7 or later.Theexport_imagemethod for exporting a graph in image form requiresGraphvizto be installed.Refcycle is CPython only.DocumentationUp-to-date documentation can be found on “Read the Docs”, athttp://refcycle.readthedocs.org/en/latest/index.html.Installing refcycleThe latest release of refcycle is available from the Python Package Index, athttps://pypi.python.org/pypi/refcycle.  On most systems, it can be installed in
the usual way usingpip:python -m pip install refcycleThe currently-in-development version can be obtained from the project’s GitHub
homepage:https://github.com/mdickinson/refcycle.LicenseThe refcycle package is copyright (c) 2013-2023 Mark Dickinson.Licensed under the Apache License, Version 2.0 (the “License”); you may not use
this file except in compliance with the License.  You may obtain a copy of the
License athttp://www.apache.org/licenses/LICENSE-2.0Unless required by applicable law or agreed to in writing, software distributed
under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, either express or implied.  See the License for the
specific language governing permissions and limitations under the License.
Package: refdata
AboutTheReference Data Repositoryprovides access to reference data sets (e.g., controlled vocabularies, gazetteers, etc.) that are accessible on the Web and that are useful for data cleaning and data profiling tools likeopencleanandAuctus.Data HostingIndividual datasets are hosted by data maintainers on different platforms. The only requirement is that the datasets (or individual dataset versions) are accessible via HTTP GET requests. Information about dataset is maintained in a central index (as a Json file) that is hosted on the Web (see for example theopenclean reference data collection).Datasets and Data FormatsEach dataset has a unique identifier. Different file formats are supported for the datasets, e.g., csv files, Json, SQLIte database files, etc.. Format information for each dataset is stored as part of its entry in the global index.Datasets are considered tabular (or sets of columns). Users may access only a single column from a dataset (e.g., country_name), multiple columns (e.b., country_name, captial_city) or the full dataset.Below is an example dataset descriptor.{"id":"encyclopaedia_britannica:us_cities","name":"Cities in the U.S.","description":"Names of cities in the U.S. from the Encyclopaedia Britannica.","url":"https://raw.githubusercontent.com/VIDA-NYU/openclean-reference-data/master/data/us_cities.tsv","checksum":"d361873f13b867805628d7db63987392835114f13da9ead0e11ccff2946631d2","webpage":"https://www.britannica.com/topic/list-of-cities-and-towns-in-the-United-States-2023068","schema":[{"id":"city","name":"City","description":"City Name","dtype":"text"},{"id":"state","name":"State","description":"U.S. State Name","dtype":"text"}],"format":{"type":"csv","parameters":{"delim":"\t"}}}The full schema for the data repository index content is defined inschema.yaml.Local Data RepositoryUsers maintain copies of the datasets for local access. By default, datasets are stored in a subfolder in the user’s cache directory.Getting StartedInstall the package usingpipfrom the GitHub repository:pipinstallgit+git://github.com:VIDA-NYU/reference-data-repository.gitThis repository contains anexample notebookthat demonstrates the basic features of the package.The package also includes a simple command line interfacerefdatathat can be used to list contents of the repository index and to interact with the local data store.Usage: refdata [OPTIONS] COMMAND [ARGS]...

  Command line interface for the Reference Data Repository.

Options:
  --help  Show this message and exit.

Commands:
  checksum  Print file checksum.
  index     Data Repository Index.
      list      List repository index content.
      show      Show dataset descriptor from repository index.
      validate  Validate repository index file.
  store     Local Data Store.
      download  List local store content.
      list      List local store content.
      remove    Remove dataset from local store.
      show      Show descriptor for downloaded dataset.
Package: refdatatypes
refdatatypesPyton basic datatypes as a references. Solve problems with static class immutable datatypes.Installationpip3installrefdatatypesProblemclassA:static=1classB(A):passprint(f"int{A.static}")# get 1 correctlyprint(f"int{B.static}")# get 1 correctlyA.static=5print(f"int{A.static}")# get 5 correctlyprint(f"int{B.static}")# get 5 correctlyB.static=6print(f"int{A.static}")# expected 6, but get 5 incorrectlyprint(f"int{B.static}")# get 6 correctlyA.static=7print(f"int{A.static}")# get 7 correctlyprint(f"int{B.static}")# expected 7, but get unchanged 6, incorrectlySolutionfromrefdatatypes.refintimportRefIntclassAAA:static=RefInt(1)classBBB(AAA):passprint(f"refint{AAA.static.value}")# get 1 correctlyprint(f"refint{BBB.static.value}")# get 1 correctlyAAA.static.value=5print(f"refint{AAA.static.value}")# get 5 correctlyprint(f"refint{BBB.static.value}")# get 5 correctlyBBB.static.value=6print(f"refint{AAA.static.value}")# get 6 correctlyprint(f"refint{BBB.static.value}")# get 6 correctlyAAA.static.value=7print(f"refint{AAA.static.value}")# get 7 correctlyprint(f"refint{BBB.static.value}")# get 7 correctlyMore details you can find in included examplesstatic_class_attribute_problem.pyandstatic_class_attribute_solution.py.Safe datatypessafedatatypesis simple set of function and classes which enables
you to work safely with base python datatypes without error falls during
convert or item access.examplefromrefdatatypes.safedatatypesimportsafe_intmy_int=safe_int("None")# no errorprint(my_int)# prints: `0`example 2fromrefdatatypes.safedatatypesimportSafeDictmy_dict=SafeDict()my_dict["a"]=1print(my_dict["a"])# prints: `1`print(my_dict["b"])# prints: `None` with no errorprint(my_dict)# prints: `{'a': 1}`my_dict=SafeDict({"a":1},default_value=-1,autoset=True)print(my_dict["a"])# prints: `1`print(my_dict["b"])# prints: `-1` with no errorprint(my_dict)# prints: `{'a': 1, 'b': -1}`
Package: refdict
refdictUsageUsing string as chain keys to realize chain access(includingdict/list/tuple/str).String can perform as a reference of another item.Installpip install refdictFeaturesUsingrefdictjust like usingdict/list/tuple/str.Methods of built-in types:refdict({}).keys()orrefdict([]).append(123).Iteration and containment check:for x in refdict([1, 2, 3]).Slice and slice assignment:refdict([1, 2, 3])[:] => [1, 2, 3]....Chain accessing members using a string.refdict({'1':{'1':{'1':{'1':'1'}}}})['1.1.1.1'] => 1.Using reference string to reference another item.DescriptionUsereference prefixto turn a string into a reference of another item. The default reference prefix is@. Reference prefix can be changed by the parameterrefPrefixof the constructor of refdict.The[]operator can be used for chain access and reference access. The separator of keys is.by default, and it can be changed by the parameterseparatorof the constructor.Here is an example:data={'player':{'name':'DiscreteTom','items':['@potion.red'],'weapon':'@sword','attack':'@player.weapon.attack','me':'@player'},'potion':{'red':'restore your health by 20%',},'sword':{'attack':123},}rd=refdict(data)print(rd['player.items.0'])# => restore your health by 20%print(rd['player.attack'])# => 123print(rd['player.items.:'])# => ['@potion.red']print(rd.text('player.attack'))# => @player.weapon.attackprint('player.weapon'inrd)# => TrueWarningsRecursive referenceslikeitem: @itemwill causeinfinite loop, including indirect reference.data={'item':'@item',# => infinite loop!'wrapper':{'item':'@wrapper.item'# => infinite loop!},'a':'@b'# => infinite loop!'b':'@a'# => infinite loop!}FAQQ - Why I can't access the first item oflist/tuple/strusing[1]?A - Of course you should use[0]to access the first item, just like usinglist/tuple/str. It's a little bit counter-intuitive but reasonable.Q - Why I gotKeyErrorwhen usingrd['key1.key2']['key3.key4']?The first[]operator will return a non-refdict object, so you can't use chain keys in the following[]. To get a sub-refdict, you should use()operator, which means you should userd('key1.key2')['key3.key4'].
Package: refellips
refellipsSpectroscopic ellipsometry data analysis in Python. Documentation athttps://refellips.readthedocs.io.
There is now an article published describingrefellips. Please consider citing it if you use the package."Robertson, H., Gresham, I.J., Prescott, S.W., Webber, G.B., Wanless, E.J., Nelson, A., 2022.SoftwareX20, 101225.https://doi.org/10.1016/j.softx.2022.101225"
Package: reference-data-manager
Bioinformatics Reference Data Manager (BRDM)DescriptionBRDM is an application used to automatically update, backup and restore the reference data that required for bioinformatic analysis.RequirementsminicondaDeployment ProceduresDownload rdm_env_setting.yaml from githubwget https://raw.githubusercontent.com/AAFC-BICoE/reference-data-manager/master/rdm_env_setting.yamlCreate the conda environment for the programconda env create -n rdm_env --file rdm_env_setting.yamlRun the programSet up the config fileThe location of the sample configuration file config.yaml.sample/path/to/conda/envs/lib/python3.6/site-package/brdmDefault option to set up the config file: Copy the sample configuration to config.yaml and modify config.yamlcd /path/to/conda/envs/lib/python3.6/site-package/brdm
  cp config.yaml.sample config.yaml
  nano config.yamlIf the location or the name of your configuration file is different with that of default option, the path of your config file has to be provided by argument --config-fileview the options of the programsource activate rdm_env
  brdm -hRun the programsource activate rdm_env
  brdm [option]
  (an example: brdm --update-ncbi-blast)Some suggestions for executing the programAll the NCBI database should be updated outside of business hours. Abuse of the Entrez or NCBI services can lead to temporary
loss of access.Construct the precise queries for NCBI subsetsThe purpose of the NCBI subsets is to construct database for specific markers in a group of taxa;
it is suggested to provide information such as names of the markers, taxa and range of the sequence length in a query.Confirm and refine your queries by testing them on NCBI website.Due to the approach of constructing the subset database, sequences (e.g. wgs) that not exist in NCBI nt database cannot be included in subset database. The condition such as "and not wgs" is suggested to be added in your queries, in order to get the appropriate accession IDs and sequences.The approach of constructing the subset database: Only accession IDs for each subsets are downloaded directly from NCBI; Sequences are retrieved from NCBI nt blast database;Ncbi nt blast database consists of GenBank+EMBL+DDBJ+PDB+RefSeq sequences, but excludes EST, STS, GSS, WGS, TSA, patent sequences as well as phase 0, 1, and 2 HTGS sequences.
Package: referencefinder
this is basic tools for finding reference in papersUsage>>> from ReferenceFinder import ReferenceUtils
>>> docx_file_path = 'paper.docx'
>>> result_file_path = 'final_reference_result.txt'
>>> ref_finder = ReferenceUtils()
>>> ref_finder.find_references(docx_file_path, result_file_path)
>>> print('find references complete  !!!!!!')
Package: referencer
referencer-pyGenerate a markdown reference from your public API docstrings and add it to your readme.FeaturesUsespydoc-markdownunder the hoodGetting StartedThe package uses semantic versioning. It means that major versions  could include breaking changes.$pipinstallreferencerDocumentationreferencerpackageREADME.md--in-placeAPI Referenceclicli(package,document,**options)Command-line interfaceUsage: referencer [OPTIONS] PACKAGE DOCUMENT

Options:
  --in-place               [default: False]
  --package-pattern TEXT   [default: from \.(\w+) import (\w+)]
  --document-section TEXT  [default: ## Reference]
  --version                Show the version and exit.
  --help                   Show this message and exit.generate_documentgenerate_document(package,document,package_pattern='from\\.(\\w+) import (\\w+)',document_section='## API Reference')Generate documentgenerate_referencegenerate_reference(package,package_pattern='from\\.(\\w+) import (\\w+)')Generate referenceContributingvirtualenv.python-ppython3.7source.python/bin/activate
makeinstall
maketestChangelogv0.xInitial version
Package: references-parser
Installpipinstallreferences-parserUsageUse help to see CLI parameters➜python-mreferences_parserparse--helpUsage:python-mreferences_parserparse[OPTIONS]PATH

Options:-s,--saveTEXTPathtofilewheretosavetheresultofparsing.-p,--parserTEXTParsertouse.Availableparsers:ieee,ssau.Default:ssau.-v,--verboseWhethertoprintoutputtostdoutornot-b,--beautifyINTEGERNumberoflinewrapsbetweenreferences.Default:1--helpShowthismessageandexit.Usual way of using the scriptpython-mreferences_parserparsein.txtWebsite referencesIt's hard to fully parse a website automatically, so some manual interactions are required.How to add a website reference:Add the links directly to the input file.Invoke theprepare-urlscommand like this:python-mreferences_parserprepare-urlsin.txtThen, the URL in the file will be replaced with a BibTeX-annotated URL:@online{Google,
    title={Google},
    date={18.05.2023},
    year={2023},
    origin={TODO: Author or place or corp here},
    base={TODO: Base resource title here},
    url={<https://google.com>}
}Here, you can fill in the fieldsorigin(mandatory)andbasewith the required information.Then, you can use parsers as usual, but pay attention that the result contains[Б.м.], which you may want to delete.ExamplesFollowexamplesfolder to see input and outputs file examplesContributionIf you want to improve the program - just fork it and make a pool request
Package: referer-parser
# referer-parser Python libraryThis is the Python implementation of [referer-parser] [referer-parser], the library for extracting search marketing data from referer _(sic)_ URLs.The implementation uses the shared 'database' of known referers found in [`referers.yml`] [referers-yml].The Python version of referer-parser is maintained by [Don Spaulding] [donspaulding].## Installation$ pip install referer_parser## UsageCreate a new instance of a Referer object by passing in the url you want to parse:```pythonfrom referer_parser import Refererreferer_url = 'http://www.google.com/search?q=gateway+oracle+cards+denise+linn&hl=en&client=safari'r = Referer(referer_url)```The `r` variable now holds a Referer instance.  The important attributes are:```pythonprint(r.known)              # Trueprint(r.referer)            # 'Google'print(r.medium)             # 'search'print(r.search_parameter)   # 'q'print(r.search_term)        # 'gateway oracle cards denise linn'print(r.uri)                # ParseResult(scheme='http', netloc='www.google.com', path='/search', params='', query='q=gateway+oracle+cards+denise+linn&hl=en&client=safari', fragment='')```Optionally, pass in the current URL as well, to handle internal referers```pythonfrom referer_parser import Refererreferer_url = 'http://www.snowplowanalytics.com/about/team'curr_url = 'http://www.snowplowanalytics.com/account/profile'r = Referer(referer_url, curr_url)```The attributes would be```pythonprint(r.known)              # Trueprint(r.referer)            # Noneprint(r.medium)             # 'internal'print(r.search_parameter)   # Noneprint(r.search_term)        # Noneprint(r.uri)                # ParseResult(scheme='http', netloc='www.snowplowanalytics.com', path='/about/team', params='', query='', fragment='')```The `uri` attribute is an instance of ParseResult from the standard library's `urlparse` module.## Contributing1. Fork it2. Create your feature branch (`git checkout -b my-new-feature`)3. Commit your changes (`git commit -am 'Add some feature'`)4. Push to the branch (`git push origin my-new-feature`)5. Create new Pull Request## DistributionThe distribution process for Python looks like this:$ ./sync_data.py$ # Make changes to codebase.$ # Bump version number in setup.py$ pushd python$ python setup.py sdist bdist_wheel --universal$ twine upload dist/referer-parser-X.Y.Z.tar.gz$ popd## Copyright and licenseThe referer-parser Python library is copyright 2012-2016 Don Spaulding.Licensed under the [Apache License, Version 2.0] [license] (the "License");you may not use this software except in compliance with the License.Unless required by applicable law or agreed to in writing, softwaredistributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.See the License for the specific language governing permissions andlimitations under the License.[referer-parser]: https://github.com/snowplow/referer-parser[referers-yml]: https://github.com/snowplow/referer-parser/blob/master/referers.yml[donspaulding]: https://github.com/donspaulding[license]: http://www.apache.org/licenses/LICENSE-2.0
Package: referredby
referredbyA Python module for parsing referrer URLs, in particular for common search engines.It’s main entry point is thereferredby.whomethod:>>> import referredby
>>> referredby.who('http://id.search.yahoo.com/search?fr=mkg030&p=friendly%20cat')
SearchEngine(name='Yahoo! Indonesia', domain='id.search.yahoo.com', keywords=['friendly', 'cat'])The list of search engines that it matches is borrowed from Spiros Denaxas’sURI::ParseSearchStringproject.Release notes0.1.4Add a bunch of new Google country domainsSupport Python 30.1.3Addgoogleadservices.comdomain0.1.2Improve matching of Yahoo mailAdd mail engine matching to thewho()method0.1.1Add more flexible matching of Yahoo search domains
Package: refery
ReferyRefery is a functional test tool written in Python.Installpipinstall-UreferyUsageusage: refery [-h] -f <path> [--verbosity <verbose|silent|normal>] [--junit-file <path>]

options:
  -h, --help            show this help message and exit
  -f <path>, --test-file <path>
                        Path to the YAML test file.
  --verbosity <verbose|silent|normal>
                        Output's verbosity, defaults to 'normal'.
  --junit-file <path>   Optional path to a JUnit XML file in which to write the outputAs you can see,refery's only mandatory argument is a path to the YAML file
describing the collection of test suites to be run.Writing testsIndividual tests are represented by test cases and a test suite is a collection
of test cases.Test suitesTest suites are a given as aYAML sequencewhich is the
value associated to theYAML mappingkeytestsuites.Each test suite is a YAML mapping which accepts the following fields:FieldDescriptionOptionalnameName of the test suite.❌testsYAML sequence containing the test cases.✅setupCommand to execute before each test case.✅teardownCommand to execute after each test case.✅fatalIndicates if a failure in a test case means an abortion of the runner. Defaults tofalse.✅Test casesEach test case is a YAML mapping accepting the following fields:NameDescriptionOptionalnameName of the test case.❌binaryPath to the tested executable.❌argsYAML sequence containing the arguments passed to the executable.✅refPath to an executable with the desired behaviour.✅stdinString passed as standard input.✅stdoutExpected standard output.✅stderrExpected standard error.✅exit_codeExpected exit code.✅skippedBoolean indicating whether the test case shall be ignored.✅timeoutTimeout in seconds, after which the test case is stopped marked as failed.✅stdout_mode/stderr_modeThe testing mode of the two output streams.Can be of two kinds:strict: The actual value shall be the same as the expected value.exists: If the expected value is not empty, the actual value shall not be empty and reciprocally.Bothstdout_modeandstderr_modedefault tostrict.✅If therefis specified, it is used to test the standard output, standard
error and exit code. If any of these fields is specified, they take precedence
overref.For example, take the following test case:hello:ref:bin/hello.shexit_code:0Thestdoutandstderrare tested according tobin/hello.shbut the exit
code must be equal to0, no matter what is actually returned bybin/hello.sh.Default valueAn optional YAML mapping can be used to specify default values for all test
cases. It must be passed as a value to thedefaultkey and can contain all
fields accepted by test cases. For each test case, if a field is already
defined, the one defined in the test case takes precedence.Here is an example of a valid input file :default:binary:my_hello.shref:bin/hellostderr_mode:existstestsuites:-name:hellofatal:truetests:-name:simple_hello-name:hello_with_nametimeout:1args:-John Doe-name:goodbyetests:-name:byeref:bin/goodbyetimeout:1args:---bye-John DoeThis defines two test suites, the first containing two test cases and the second
only one.
Package: refextract
AboutA small library for extracting references used in scholarly communication.Install$pipinstallrefextractUsageTo get structured information from a publication reference:>>>fromrefextractimportextract_journal_reference>>>reference=extract_journal_reference('J.Phys.,A39,13445')>>>print(reference){'extra_ibids':[],'is_ibid':False,'misc_txt':u'','page':u'13445','title':u'J. Phys.','type':'JOURNAL','volume':u'A39','year':'',}To extract references from a PDF:>>>fromrefextractimportextract_references_from_file>>>references=extract_references_from_file('1503.07589.pdf')>>>print(references[0]){'author':[u'F. Englert and R. Brout'],'doi':[u'doi:10.1103/PhysRevLett.13.321'],'journal_page':[u'321'],'journal_reference':[u'Phys. Rev. Lett. 13 (1964) 321'],'journal_title':[u'Phys. Rev. Lett.'],'journal_volume':[u'13'],'journal_year':[u'1964'],'linemarker':[u'1'],'raw_ref':[u'[1] F. Englert and R. Brout,\u201cBroken symmetry and the mass of gauge vector mesons\u201d, Phys. Rev. Lett. 13 (1964) 321, doi:10.1103/PhysRevLett.13.321.'],'texkey':[u'Englert:1964et'],'year':[u'1964'],}To extract directly from a URL:>>>fromrefextractimportextract_references_from_url>>>references=extract_references_from_url('https://arxiv.org/pdf/1503.07589.pdf')>>>print(references[0]){'author':[u'F. Englert and R. Brout'],'doi':[u'doi:10.1103/PhysRevLett.13.321'],'journal_page':[u'321'],'journal_reference':[u'Phys. Rev. Lett. 13 (1964) 321'],'journal_title':[u'Phys. Rev. Lett.'],'journal_volume':[u'13'],'journal_year':[u'1964'],'linemarker':[u'1'],'raw_ref':[u'[1] F. Englert and R. Brout,\u201cBroken symmetry and the mass of gauge vector mesons\u201d, Phys. Rev. Lett. 13 (1964) 321, doi:10.1103/PhysRevLett.13.321.'],'texkey':[u'Englert:1964et'],'year':[u'1964'],}Notesrefextractdepends onpdftotext.Acknowledgmentsrefextractis based on code and ideas from the following people, who
contributed to thedocextractmodule in Invenio:Alessio DeianaFederico PoliGerrit RindermannGraham R. ArmstrongGrzegorz SzpuraJan Aage LavikJavier Martin MontullMicha MoskovicSamuele KaplunThorsten SchwanderTibor SimkoLicenseGPLv2
Package: refextract-cli
refexThe refexence Extractor is a command-line interface (CLI) application that usesrefextractto extract references from a PDF file. The PDF file can be open on Okular or provided as a file path or URL.Instalationpip install refextract-cliUsageWhen provided no source, it looks for an Okular instance and process the current PDF.refexFor generating Google Scholar search links and sort the results, use:refex-g--sortyearIf rofi is available, you can use:refex--rofi