Saravanan666/pypi-org huggingface dataset:
Package: bibcites
bibcitesCommand-line utility which reads a BibTeX file, finds entries with a DOI, looks up the corresponding number of citations usingOpenCitations, saves this number to theaddendumfield of each entry, and writes results to a new BibTex file.Installationpython -m pip install bibcitesshould do the trickUsageUsage: bibcites [OPTIONS] BIBFILE

  Reads a BibTeX file (BIBFILE), finds entries with a DOI, looks up the
  corresponding number of citations using OpenCitations
  (https://opencitations.net), saves this number to the 'addendum' field of
  each entry, and writes results to a new BibTex file.

  Optionally, using option -s, print out a list of entries with DOI sorted by
  number of citations.

Options:
  -o TEXT     output BibTex file
  -f TEXT     format of text to save to 'addendum' field
  -s          print list sorted by cites
  -v          enable verbose output
  -t TEXT     only process entries of this type (may be used several times to
              process several types)
  -n INTEGER  size limit for OpenCitations queries
  --help      Show this message and exit.bibcites myfile.bibwill read the contents ofmyfile.bib, look up all entries with aDOIfield inOpenCitations, append “[X citations]” to theaddendumfield of each entry, and save the result tomyfile_withcites.bibTo get verbose output, use-voption.To set a custom file name for the output BibTeX file, use the-o <customfilename>option.To set a custom format to theaddendumfield, use the-foption, e.g.,-f 'Cited {:s} times'. Use the{:s}specifier because the citation count is a string.To print out a list of processed entries, sorted by decreasing number of citations, use the-soption.To process only entries of certain types, use the-toption one or more times, e.g.,-t article -t book.To limit the size of OpenCitations queries, use-noption (default is-n 50).ContactAll questions and suggestions are welcome and should be directed atMathieu Daëron.
Package: bib-cleaner
Bib CleanerBib Cleaner removes unnecessary entries from your bib files. Documentation @https://bib-cleaner.readthedocs.io.Use caseYou have been writing a TeX document for a while, and adding citation entries to your.bibfile (say it’s calledmaster.bib).In the course of writing, some entries in yourmaster.bibhave become obsolete. You don’t use them in your TeX document anymore.Of course, LaTeX compiles quite happily with these extra entries.You take a step back, sip some coffee, go for a walk, all the while pondering “Man, I wish I could justremovethose extra bib entries”. You yearn for a world where all.bibfiles everywhere carry only what they have to, and no more.I gotchu. Enterbib_cleaner.InstallationThis should work:$ pip install bib_cleanerVerify if it installed by typing the following in the command-line:$ bib_cleaner -hYou should see the help:usage: bib_cleaner [-h] [-t TEXFILES [TEXFILES ...]] [-o OUTPUTBIB] masterfile

Produce a minimal bib file with only the entries found in your .tex file(s)

positional arguments:
masterfile            master bib file with used and unused citations (.bib)

optional arguments:
-h, --help            show this help message and exit
-t TEXFILES [TEXFILES ...], --texfiles TEXFILES [TEXFILES ...]
                        content files to select entries from (.tex)
-o OUTPUTBIB, --outputbib OUTPUTBIB
                        output file name with extensionExamplesAfter installation, navigate to your TeX directory try:$ bib_cleaner master.bibOf course, replacemaster.bibwith the name of your bib file with obsolete bib entries.bib_cleanerwill automatically detect all the TeX files (.tex) in that directory and use them to determine which bib entries are obsolete.Specify TeX filesIf you only want to use some TeX files, specify them with:$ bib_cleaner master.bib --texfiles chapter1.tex chapter2.texor:$ bib_cleaner master.bib -t chapter1.tex chapter2.texSpecify output file nameIf you want to change the output bib file name from the defaultnew.bib, do:$ bib_cleaner master.bib -t chapter1.tex --outputbib chapter1.bibor:$ bib_cleaner master.bib -t chapter1.tex -o chapter1.bibTODORemove typically unused lines from.bibfiles (likefile ={...}orabstract ={...})Detect and remove bib entries with identical tags / raise conflictAdd tests for the command-line interfaceCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.3.0 (2019-12-20)AddedOption to store output innew.bibIntro and examples toREADME.rst0.2.1 (2019-12-20)Addedget_minimal_bibsfunction.tests fortex_to_tagsandget_minimal_bibs.FixedDocumentation builds.Deploy from Travis.RemovedSupport forPython 3.5(no f-string support)0.1.0 (2019-12-16)First release on PyPI.
Package: bibcli
bib – command-line bibliography managerWhat?bib is acommand-line bibliography manager. That means itmanages
bibliograpies. From thecommand-line.What does that mean? Basically, bib stores all of your references in aBibTeXfile, along with notes and PDFs
that might be associated with them. To make that useful, it provides a
command-line interface foradding new items,importing PDFs, creatingnotes,exporting sub-bibliographies,listing the items according to a
query,etc.Why?I've used Zotero for some time. It's nice, it does everything that I need it to.
The problem is… it does to much. It is, in the language of the cool-hackerboys,
“bloated”. Aside from that, I believe (as it has been said elsewhere), thatplaintext is the only truly portable format. Finally, I like to pretend I'm
smarter than I am, so I use the command line.To my surprise, there wasn't any command line bibliography manager. So I build
one.I'm not saying it's good (although I'd like it to be), nor that you'll like it
(I hope you do try it). But I like it, and would love contributions. Anyway,
enough pointless talking.Installationbib is available at the Python Package Index. That means, if you have Python andpipinstalled, it should be enough to$pipinstallbibIf you want to install from source, clone the repository and use thesetup.pyas you would with any other Python package.Licensebib is free software. The details can be found in theLICENSE.txtfile, or
otherwise reading about the GNU Public License v3+.ContributingThis is currently a small, one-person project. Also, I don't have much
experience in writing distributed code, so if you have any suggestions, they are
highly appreciated. Otherwise, I can't really direct contributions because I
haven't worked in many-people code bases. Any input onthatwould also be
helpful.
Package: bibcodex
bibcodexLibrary to access, analyze, and display bibliographic information.Installationpip install bibcodexExamplesImport thepandasandbibcodextogether and load a dataframe:importbibcodeximportpandasaspd# You should always cast your search variables (pmid, doi) to str.df=pd.read_csv("data/sample_data.csv",dtype={'pmid':str})Valid download methods are:icite,doi2pmid,semanticScholar, orpubmed:# Set the index to search querydf=df.set_index("doi")# Download the information, and combine it with the original dataframe:info=df.bibcodex.download('semanticScholar')print(df.combine_first(info[["title"]]))"""doi                      title10.1001/jama.2017.18444  Progressive Massive Fibrosis in Coal Miners Fr...10.1001/jama.2018.0126   Birth Defects Potentially Related to Zika Viru...10.1001/jama.2018.0708   Association Between Estimated Cumulative Vacci...10.1001/jama.2018.10488  Electronic Cigarette Sales in the United State..."""All search queries are cached locally in./cache. To clear the cache use:df.codex.clear()APIReturned fieldspubmedtitle, issue, pages, abstract, journal, authors, pubdate, mesh_terms, publication_types, chemical_list, keywords, doi, references, delete, languages, vernacular_title, affiliations, pmc, other_id, medline_ta, nlm_unique_id, issn_linking, countrysemanticScholarabstract, arxivId, authors, citationVelocity, citations, corpusId, fieldsOfStudy, influentialCitationCount, isOpenAccess, isPublisherLicensed, is_open_access, is_publisher_licensed, numCitedBy, numCiting, paperId, references, s2FieldsOfStudy, title, topics, url, venue, yeariciteyear, title, authors, journal, is_research_article, relative_citation_ratio, nih_percentile, human, animal, molecular_cellular, apt, is_clinical, citation_count, citations_per_year, expected_citations_per_year, field_citation_rate, provisional, x_coord, y_coord, cited_by_clin, cited_by, references, doidoi2pmidlive, status, errmsg, pmcid, pmid, versionsRoadmapAPI access: Pubmed (Parsed MEDLINE data)API access: Semantic Scholar (PMID)API access: iCiteAPI access: Semantic Scholar (DOI)API access: DOI to PMID NLMwww.ncbi.nlm.nih.gov/pmc/tools/idconv/API access: Pubmed (XML)API access: arXivAPI access: CoLILAPI access, validation of inputAPI access, multi item requestsAPI access, chunkingAPI access, include status_code in download resultsAPI access, better error handlingAPI caching, clearingCodex, validate PMIDCodex, validate DOICodex, build dataframe from itemsTesting harnessFull testing coverageCode lintingpypi libraryREADME with examplesStatus bar for long downloadsEmbedding functions (SPECTER)ClusteringVisualization (streamlit)DevelopmentBuilt with ❤ ️by@metasemantic. Package is linted byblackand conforms to standards byflake8. Pull requests accepted, but please provide tests with full coverage for new code.
Package: bibcopy
#-- bibtexTidying 0.1.0 --Author: Jian Ding and ShiBo Xu and Kun Chen
Email:qbei113043@163.comMentor: X. Fu and TingYu Luo##[Purpose]
This software is trying to help users to tidy up their bibtex files.##[Prerequisite]Python3MySQL##[Requires Projects]bibtexparsermysqlclient##[Github]https://gitee.com/chen-kun19/summer-program##[Manual]How to install it?use command following.For WindowspipinstallbibtexTidyingFor Linuxsudoapt-getupdatesudoapt-getinstalllibmysqlclient-devsudopipinstallmysqlclientpipinstallbibtexTidyingHow to use it?Type following code in your python files:from bibtexTidying import bibcopyThen you can use all the function in module bibcopy!##[Function]
1.Formating your bibtex files.##[Known Issues]:
1.##[Bug Report]:
Any bug or documentation error you found , please submit an issue on github parge:https://gitee.com/chen-kun19/summer-program
Package: bibcure
Description(Beta version)Bibcure helps in boring tasks by keeping your bibfile up to
date and normalized.RequirementsBibcure uses the wonderfulBibtex
parser. In this
moment we waiting for new release of bibtexparser to solve some bugs.Install$ sudo pip install bibcurescihub2pdf(beta)If you want download articles via a DOI number, article title
or a bibtex file, using the database of libgen or sci-hub, seebibcure/scihub2pdfFeatures and how to usebibcureGiven a bib file…$ bibcure -i input.bib -o output.bibcheck sure the Arxiv items have been published, then update
them(requires internet connection)complete all fields(url, journal, etc) of all bib items using DOI
number(requires internet connection)find and create DOI number associated with each bib item which has
not DOI field(requires internet connection)abbreviate jorunals namesdoi2bibGiven a DOI number…$ doi2bib 10.1038/s41524-017-0032-0get bib item given a doi(requires internet connection)You can easily append a bib into a bibfile, just do$ doi2bib 10.1038/s41524-017-0032-0 >> file.bibYou also can generate a bibtex from a txt file containing a list of DOIs$ doi2bib --input file_with_dois.txt --output refs.bibtitle2bibGiven a title…$ title2bib An useful papersearch papers related and return a bib for the selected
paper(requires internet connection)You can easily append a bib into a bibfile, just do$ title2bib An useful paper --first >> file.bibYou also can generate a bibtex from a txt file containing a list of
“titles”$ title2bib --input file_with_titles.txt --output refs.bib --firstarxivcheckGiven a arxiv id…$ arxivcheck 1601.02785check if has been published, and then returns the updated bib
(requires internet connection)Given a title…$ arxivcheck --title An useful paper published on arxivsearch papers related and return a bib the first item. You can easily
append a bib into a bibfile, just do$ arxivcheck --title An useful paper published on arxiv >> file.bibYou also can interact with results, just pass –ask parameter$ arxivcheck --ask --title An useful paper published on arxivscihub2pdfGiven a bibtex file$ scihub2pdf -i input.bibGiven a DOI number…$ scihub2pdf 10.1038/s41524-017-0032-0Given a title…$ scihub2bib --title An useful paperLocation folder as argument$ scihub2pdf -i input.bib -l somefoler/Use libgen instead sci-hub$ scihub2pdf -i input.bib --uselibgenSci-Hub vs LibGenSci-hub:StableAnnoying CAPTCHAFastLibgenUnstalbeNo CAPTCHASlow
Package: bibdatamanagement
Bibliography managementThe goal is to provide an easy way to extract in python custom data set in theannotefield of a bib file.InstallationBibdataManagementlibrary is stored in IPESE pypi server located onhttps://ipese-internal.epfl.ch/registry/pypi. andhttps://pypi.org/project/bibdatamanagement/To include the library in your projects, do the following inrequirements.txt:Include the packagebibdatamanagement >= 0.6.0Otherwise, the package can be installed by using apipcommand.pip install bibdatamanagementData formatThe package is designed to extract data in a specific format. The initial development was made for technologies parameter
used to model it.+- ENTRY # row_key:set: general description of tech
param1 = min:value1:max [unit1] # short_name: a comment about the param and its value
param2 = value2 [unit2]
+- /ENTRYWhere the fields described as follows:FieldsDescriptionMandatoryENTRYThe name of the tech to which the parameters belongTruerow_keyAn identifierFalsesetUse to retrieve all values from a user (e.g. all values forscenario_oil)Falsegeneral_descriptionA comment on the tech or on the paperFalseparamName of the parameter characterisedFalsevalueValue of the parameterTrueminMinimal value that the parameter can haveFalsemaxMaximal value that the parameter can haveFalseunitUnit of the parameterTrueThe minimal information to provide is the+- ENTRY       +- /ENTRY. The fields after the#are optional, as well as
the min and max values.Nb: spaces in the key/value line are for readability but are not requiredUsageThe minimal workflow to access the data in the.bibis the following.frombibdata_management.bibdata_managementimportBibDataManagementbib_file='your_path/your_file.bib'bibdata=BibDataManagement(bib_file)df_bib=bibdata.get_data(tech_name='YOUR_ENTRY',set_name='YOUR_SET')One can also add a.csvfile that contains the default value for parameters description (short name, long name, description).bibdata = BibDataManagement(bib_file, 'your_default_file.csv')DocumentationMore information on the fields and the methods is available in thedocumentation websiteSuggestions and contributionsAll suggestions or implementation must be tracked with dedicated issues and reported at theproject GitHubIf you want to make the format evolve or implement a new python function, create an issue before anything else.AuthorJoseph Loustau, IPESE
Package: bibdec
The goal of this project is to provide an easy-to-use tool that autogenerates a bibliography.
Specifically, the code provides a decorator that allows you to add citations to your functions.
Then, if one of the decorated functions is called, their relevant citation keys are added to
a dictionary together with the function signature that generated those citation keys. Once the
program is finished running, you can request a list of used citation keys to see which cites
you used where. Also, you can export the bibliography as a bibtex file containing only the
references that are used at least once.InstallationThe library is available on PyPI, so you can install it with pip:pip install bibdecSimple exampleBelow is a minimal example demonstrating with only one key. However, you can also decorate a
function with multiple keys, or even have conditional citations based on the function signature.
More complex examples are available in the example section of the documentation.frombibdecimportBibliographybibtex="""
@article{key1,
author = {Some Author},
title = {Some paper},
journal = {Some Journal},
year ={1999},
volume ={42},
number = {100 -- 150}
}
"""bibliography=Bibliography(bibtex)@bibliography.register_cites("key1")deff(a):returna+2print("Before calling the function:")print(bibliography.citations)print(bibliography.active_bibliography)f(0)print("After calling the function:")print(bibliography.citations)print(bibliography.active_bibliography)Output:Before calling the function:
{}

After calling the function:
{'__main__.f()': {'key1'}}
@article{key1,
author = {Some Author},
journal = {Some Journal},
number = {100 -- 150},
title = {Some paper},
volume = {42},
year = {1999}
}
Package: bib-dedupe
BibDedupeOverviewBibDedupe is an open-sourcePython library for deduplication of bibliographic records, tailored for literature reviews.
Unlike traditional deduplication methods, BibDedupe focuses on entity resolution, linking duplicate records instead of simply deleting them.FeaturesAutomated Duplicate Linking with Zero False Positives: BibDedupe automates the duplicate linking process with a focus on eliminating false positives.Preprocessing Approach: BibDedupe uses a preprocessing approach that reflects the unique error generation process in academic databases, such as author re-formatting, journal abbreviation or translations.Entity Resolution: BibDedupe does not simply delete duplicates, but it links duplicates to resolve the entitity and integrates the data. This allows for validation, and undo operations.Programmatic Access: BibDedupe is designed for seamless integration into existing research workflows, providing programmatic access for easy incorporation into scripts and applications.Transparent and Reproducible Rules: BibDedupe's blocking and matching rules are transparent and easily reproducible to promote reproducibility in deduplication processes.Continuous Benchmarking: Continuous integration tests running on GitHub Actions ensure ongoing benchmarking, maintaining the library's reliability and performance across datasets.Efficient and Parallel Computation: BibDedupe implements computations efficiently and in parallel, using appropriate data structures and functions for optimal performance.DocumentationExplore theofficial documentationfor comprehensive information on installation, usage, and customization of BibDedupe.CitationIf you use BibDedupe in your research, please cite it as follows:Wagner, G. (2024) BibDedupe - An open-source Python library for deduplication of bibliographic records. Available athttps://github.com/CoLRev-Environment/bib-dedupe.Contribution GuidelinesWe welcome contributions from the community to enhance and expand BibDedupe. If you would like to contribute, please follow ourcontribution guidelines.LicenseBibDedupe is released under theMIT License, allowing free and open use and modification.ContactFor any questions, issues, or feedback, please open anissueon our GitHub repository.Happy deduplicating with BibDedupe!
Package: bibdesk2zotero
bibdesk2zoteroThis is a little utility for rewriting a BibDesk BibTeX file so that it can be
read by Zotero with the file references intact. BibDesk and Zotero mostly get
along except for the way BibFile stores links to documents like PDFs. This
utility Base64 decodes all Bdesk-File paths, parses the serializedplist,
extracts the relative path to the file and adds it back to the bibliographic
entry as an absolute path.Installpip install bibdesk2zoteroUse$ bibdesk2zotero citations.bib /path/to/pdf/files/ > new-citations.bib
Package: bibelen
I'm trying to make the code:Scrape the Bible text off bible.com for any defined Bible translation.
      The URL for the Bible text is:https://www.bible.com/no/bible/"+TRANSLATION_NUMBER+"/"+BOOK+"."+CHAPTER+".nb"
      The translation number defines which translation is used.  E.g. the Norwegian 1988 translation is version number 102.
      The Bible book is a three-letter abbreviation for the book.  The abbreviations used on the site are defined in the array "booklist" (not to be confused with bbooklist, which are the abbreviations used on Logos)Separate out just the text - remove all HTML tags, and add Logos program tags.
      The information on Logos formatting is found onhttps://wiki.logos.com/Personal_BooksWhat is needed here is basically the "field on/off:bible" and Bible verse link.  For instance, in John 1:1, you might get:{{field-off:bible}}
      KAPITTEL 1
[[@BibleNO2011:jn 1:1]]  1 {{field-on:bible}}I begynnelsen var Ordet, og Ordet var hos Gud, og Ordet var Gud. {{field-off:bible}}For the Bible verse link in Logos, the syntax is: [[@Bible "TRANSLATION" : "BOOK" "CHAPTER":"VERSE"]]
      The Bible book abbreviations in Logos are different than the ones used on bible.com, and are found in the list "bbooklist".I'm attaching my awesome code.Thanks - this will make studying the Bible much easier both for me, and for many other pastors and Bible students in Norway.Versions specific problems102Stars, stars everywhere 1 chr 29 : 22, 1 chr 22 : 9, 1 chr 21 : 12216Not split on the digits, be a bit smarter, all the numbers in Ezekiel disappearhttps://www.bible.com/bible/2216/EZK.29.BGO29The quotes are in a different container div.class=qt e.g.https://www.bible.com/bible/29/ACT.8.N11BMJohn 8 The passage about the adulterous woman, basically fix the numberinghttps://www.bible.com/bible/29/JHN.8.N11BM115Numbering issueshttps://www.bible.com/bible/115/REV.21.ELBverse 18, quotation issues 1 peter 2 : 6https://www.bible.com/bible/115/1PE.2.ELB30Numbering issues, John 8, Micha 1 : 2+ quotations...
Package: bibetal
bib et al. - The "One author et al." toolbibetal is a pure Python script that rewrites bib files to only contain one author / editor per entry. Other authors / editors are automatically replaced byand others, which in turn is parsed aset al.in most bibliographies.Installationbibetal can be installed usingpip:pip install bibetalUsageCurrently, bibetal only processes one file at a time and edits it in-place:bibetal <FILE>ContributingFeel free to contribute or propose ideas using theIssuesandPull requeststabs.
Package: bibexcel
BibExcel PackageA python executable to get JSON and Excel data from a bibexcel text fileGetting StartedThese instructions will get you a copy of the project up and running on your local machine for development and testing purposes.PrerequisitesThis script is intended to be run on Python 3Install withpip install bibexcelInstallpandasandjsonpackagesUsageConverting a bibexcel text file to JSON/Excel# Convert to a JSONpython3bibexcel-i'bibexcel.doc'-t'scopus'-f'bibexceltojson'-o'bibexcel.json'# Convert to a Excelpython3bibexcel-i'bibexcel.doc'-t'scopus'-f'jsontoexcel'-o'bibexcel.xlsx'AuthorsJose Eduardo Storopoli-Creator and Developer-storopoliLicenseThis project is licensed under the MIT License - see theLICENSE.mdfile for details
Package: bibgen
Bibgen is a Python script that allows styled
citations and bibliography generation using external bibliographic
databases. It supports databases such as BibTeX, JSON or Mendeley,
and generates styled citations and bibliography sections for several
document types including DocBook and reStructuredText. Textual
citations and entries in the generated bibliographies are styled using
rules found in CSL stylesheets. Thousands of those stylesheets are
readily available, for instance through the Zotero style repository.
Package: bibimbap
bibimbapbibimbap is a Python library for selenium based visual automation testing.InstallationUse the package managerpipto install bibimbap.pipinstallbibimbapUsagefrombibimbapimportganjang,gochujangprint('spam')g1=ganjang.Ganjang('https://example.com/page_to_test','https://example.com/page_to_test2',example.com')s=gochujang.Gochujang()s.add_ganjang(g1)s.set_webdriver("c:/geckodriver.exe")s.set_window_size(380,5000)s.set_xpath_to_element_to_capture("/html/body")s.set_path_to_save("c:/bibimbap_test/")s.capture_screens()