filltex 1.7.0__py3-none-any.whl

fillbib.py

@@ -0,0 +1,465 @@
+#!/usr/bin/env python
+
+'''
+Query the ADS and INSPIRE databases to collect the citations used in a LaTeX file into a BibTeX file
+
+Idea and main implementation is taken by Michele Vallisneri, see http://www.vallis.org/salon/summary-2.html
+I changed the script to avoid the requests module, and added the INSPIRE database part.
+
+Usage:
+python fillbib.py <tex_file> <bib_file>. If <bib_file> is absent, it will try to guess it from the aux file"
+
+'''
+from __future__ import absolute_import, print_function
+import argparse
+import sys, os, re, html
+import json
+
+if sys.version_info.major>=3:
+    import urllib.request as urllib
+else:
+    import urllib
+
+
+def ads_citation(c): # download single ADS citation
+    #f= urllib.urlopen("http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode="+c+"&data_type=BIBTEX&db_key=AST&nocookieset=1")
+    #print("http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode="+c+"&data_type=BIBTEX&db_key=AST&nocookieset=1")
+    f= urllib.urlopen("https://ui.adsabs.harvard.edu/abs/"+c+"/exportcitation")
+
+    bib = f.read()
+    f.close()
+    if sys.version_info.major>=3:
+        bib=bib.decode()
+    bib = "@"+list(filter(lambda x:'adsnote' in x, bib.split("@")))[0].split("</textarea>")[0]
+    bib=html.unescape(bib)
+
+    return bib
+
+def inspire_citation(key,
+        generate=False,
+        max_num_authors=None,
+        num_authors_short=None,
+        journal_arXiv_fallback=False):
+    """
+    Generate a custom BiBTeX entry
+
+    * generate
+        if True we generate the BibTeX rather than using the default from iNSPIRE
+    * max_num_authors
+        maximum number of authors to include (all of them if None)
+    * num_authors_short
+        number of authors to include if the number of authors is longer than max_num_authors
+        if not specified, this defaults to max_num_authors
+    * journal_arXiv_fallback
+        use arXiv:eprint as the journal field if no journal is found
+    """
+    request = 'https://inspirehep.net/api/literature?q=' + key
+    data = json.loads(urllib.urlopen(request).read())
+    if data['hits']['total'] != 1:
+        return None
+    if not generate:
+        bib = urllib.urlopen(data['hits']['hits'][0]['links']['bibtex']).read()
+        inspire_key = data['hits']['hits'][0]['metadata']['texkeys'][0]
+        if sys.version_info.major >= 3:
+            return bib.decode().replace(inspire_key, key)
+        else:
+            return bib.replace(inspire_key, key)
+    metadata = data['hits']['hits'][0]['metadata']
+
+    doctype = metadata["document_type"][0]
+
+    # BibTeX entry as a dictionary
+    bibtex = {}
+
+    # Find all authors
+    if "authors" in metadata:
+        num_authors = len(metadata["authors"])
+        if max_num_authors is not None and num_authors > max_num_authors:
+            short_author_list = True
+            if num_authors_short is None:
+                num_authors_short = max_num_authors
+        else:
+            short_author_list = False
+        author_list = []
+        for idx, author in enumerate(metadata['authors']):
+            if short_author_list and idx >= num_authors_short:
+                author_list.append("others")
+                break
+            author_list.append(author['full_name'])
+        bibtex['author'] = " and ".join(author_list)
+
+    # Find all collaborations
+    if "collaborations" in metadata:
+        collab_list = []
+        for collab in metadata["collaborations"]:
+            collab_list.append(collab["value"])
+        bibtex["collaboration"] = ", ".join(collab_list)
+
+    try:
+        bibtex["title"] = "{" + metadata["titles"][0]["title"] + "}"
+    except KeyError:
+        pass
+
+    try:
+        bibtex["eprint"] = metadata["arxiv_eprints"][0]["value"]
+        bibtex["archivePrefix"] = "arXiv"
+        bibtex["primaryClass"] = metadata["arxiv_eprints"][0]["categories"][0]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["doi"] = metadata["dois"][0]["value"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["journal"] = metadata["publication_info"][0]["journal_title"]
+    except KeyError:
+        if journal_arXiv_fallback:
+            bibtex["journal"] = "arXiv:" + bibtex["eprint"]
+        pass
+
+    try:
+        bibtex["volume"] = metadata["publication_info"][0]["journal_volume"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["number"] = metadata["publication_info"][0]["journal_issue"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["pages"] = metadata["publication_info"][0]["page_start"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["year"] = metadata["publication_info"][0]["year"]
+    except KeyError:
+        try:
+            bibtex["year"] = metadata["preprint_date"][0:4]
+            bibtex["month"] = str(int(metadata["preprint_date"][5:7]))
+        except KeyError:
+            pass
+
+    # Format BibTeX entry
+    s = "@{}{{{}".format(doctype, key)
+    for field, value in bibtex.items():
+        s += ",\n    {} = \"{}\"".format(field, value)
+    s += "\n}"
+
+    return s
+
+def test_ads(): # test single ADS web scraping (both published articles and preprints)
+    test_key = ["2016PhRvL.116f1102A","2016arXiv160203837T"]
+    known_output= '@ARTICLE{2016PhRvL.116f1102A,\n   author = {{Abbott}, B.~P. and {Abbott}, R. and {Abbott}, T.~D. and {Abernathy}, M.~R. and \n\t{Acernese}, F. and {Ackley}, K. and {Adams}, C. and {Adams}, T. and \n\t{Addesso}, P. and {Adhikari}, R.~X. and et al.},\n    title = "{Observation of Gravitational Waves from a Binary Black Hole Merger}",\n  journal = {Physical Review Letters},\narchivePrefix = "arXiv",\n   eprint = {1602.03837},\n primaryClass = "gr-qc",\n     year = 2016,\n    month = feb,\n   volume = 116,\n   number = 6,\n      eid = {061102},\n    pages = {061102},\n      doi = {10.1103/PhysRevLett.116.061102},\n   adsurl = {http://adsabs.harvard.edu/abs/2016PhRvL.116f1102A},\n  adsnote = {Provided by the SAO/NASA Astrophysics Data System}\n}\n\n'
+    assert [ads_citation(tk) == known_output for tk in test_key]
+
+def test_inspire(): # test single INSPIRE web scraping
+    test_key = "Abbott:2016blz"
+    known_output = '@article{Abbott:2016blz,\n    author = "Abbott, B.P. and Abbott, R. and Abbott, T.D. and Abernathy, M.R. and Acernese, F. and others",\n    collaboration = "LIGO Scientific, Virgo",\n    title = "{Observation of Gravitational Waves from a Binary Black Hole Merger}",\n    eprint = "1602.03837",\n    archivePrefix = "arXiv",\n    primaryClass = "gr-qc",\n    doi = "10.1103/PhysRevLett.116.061102",\n    journal = "Phys.Rev.Lett.",\n    volume = "116",\n    number = "6",\n    year = "2016"\n}'
+    assert inspire_citation(test_key, generate=True, max_num_authors=5) == known_output
+
+def fillbib_tex(args):
+
+    if args.bibtex is None:     # Get the name of the bibfile from the aux file
+        basename = args.texfile[0].split('.tex')[0]
+        auxfile = basename + '.aux'
+        for line in open(auxfile,'r'):
+            m = re.search(r'\\bibdata\{(.*)\}',line)   # match \citation{...}, collect the ... note that we escape \, {, and }
+            if m:
+                bibfile = list(filter(lambda x:x!=basename+'Notes', m.group(1).split(',')))[0]  # Remove that annyoing feature of revtex which creates a *Notes.bib bibfile. Note this is not solid if you want to handle multiple bib files.
+        bibfile = bibfile + '.bib'
+
+    else:    # Bibfile specified from argv
+        basename = args.texfile[0].split('.tex')[0]
+        auxfile = basename + '.aux'
+        bibfile = args.bibtex.split('.bib')[0] + '.bib'
+
+    if args.updatepublished:
+        with open(basename+".tex", 'r') as texfile:
+            texdata = texfile.read()
+
+    # Get all citations from aux file. Citations will look like \citation{2004PhRvD..69j4017P,2004PhRvD..69j4017P}
+    cites = set() # use a set (no repetitions)
+    for line in open(auxfile,'r'):
+        m = re.search(r'\\citation\{(.*)\}',line)   # find \citation{...}
+        if m:
+            cites.update(m.group(1).split(','))     # split by commas
+
+    cites= cites.difference([
+        'REVTEX41Control','apsrev41Control',
+        'REVTEX42Control','apsrev42Control']) # Remove annoying entries of revtex
+
+    print("Seek:", cites)
+
+    # Check what you already have in the bib file
+    haves = []
+    if os.path.isfile(bibfile):
+        for line in open(bibfile,'r'):
+            m = re.search(r'@.*?\{(.*),',line)  # .*\{ means "any # of any char followed by {"; .*?\{ means "the shortest string matching any # of any char followed by {"
+            if m:
+                haves.append(m.group(1))
+    print("Have:", haves)
+
+
+    # Query ADS and INSPIRE
+    bibtex = open(bibfile,'a')      # open for appending
+
+    for c in cites:
+        if c and c not in haves: # c is something and you don't have it already
+
+            if not c[0].isalpha(): # The first charachter is a number: could be on ADS
+
+                try:
+                    bib = ads_citation(c)
+
+                    cfound = bib.split("{")[1].split(',')[0]
+                    
+                    if  cfound == c: # Check you got what you where looking for
+                        pass
+                    elif 'arXiv' in c: # Take care of preprint on ADS
+
+                        if args.updatepublished and '.tmp.' not in cfound:
+                            print("ADS replace", c, "-->", cfound)
+                            # This substitute the new ID into the tex file. Use at your own risk. The .tmp. condition fixes those stupid MNRAS temp entries.
+                            texdata = texdata.replace(c, cfound)
+
+                        else: 
+                            # This subsitute the arxiv id back in to the bib file
+                            bib = bib.split("{")[0]+"{"+c+","+",".join(bib.split(",")[1:])
+
+                    bibtex.write(bib)
+                    print("ADS Found:", c)
+                except:
+                    print("ADS Not found:", c)
+
+            else: # The first charachter is not a number: could be on INSPIRE
+
+                try:
+                    bib = inspire_citation(c,
+                        generate=args.generate,
+                        max_num_authors=args.max_num_authors,
+                        num_authors_short=args.num_authors_short,
+                        journal_arXiv_fallback=args.journal_arXiv_fallback)
+                    bibtex.write(bib)
+                    print("INSPIRE Found:", c)
+                except:
+                    print("INSPIRE Not found:", c)
+
+
+
+    bibtex.close()
+
+    if args.updatepublished:
+        with open(basename+".tex", 'w') as texfile:
+            texfile.write(texdata)
+
+    # Clean up journal names
+    if args.journals:
+        journals(bibfile)
+
+    
+def fillbib_list(args):
+    for c in args.keys:
+        if not c[0].isalpha():
+            bib = ads_citation(c)
+            if bib is None:
+                sys.stderr.write("ADS Not Found: {}\n".format(c))
+            else:
+                print(bib)
+        else:
+            bib = inspire_citation(c,
+                    generate=args.generate,
+                    max_num_authors=args.max_num_authors,
+                    num_authors_short=args.num_authors_short,
+                    journal_arXiv_fallback=args.journal_arXiv_fallback)
+            if bib is None:
+                sys.stderr.write("INSPIRE Not Found: {}\n".format(c))
+            else:
+                print(bib)
+
+
+def curly(x):
+   '''Just a curly bracket sandwich.'''
+   return "{"+x+"}"
+
+def journals(bibfile):
+    '''
+    Clean up the names of some journals using their ISO4 standards.
+    Journal abbreviations are taken from https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html
+    If your favourite journal is missing, please add it and send a pull request. Thanks!
+    '''
+
+    # The format is: [ADS name, INSPIRE name, ISO4 abbreviation]
+    journals = [
+            ####
+            # These are the journals from the ADS macros: https://ui.adsabs.harvard.edu/help/actions/journal-macros
+            # I could not find them all on INSPIRE, some are missing.
+            ####
+            ['\\aj', 'Astron. J.', 'Astron. J.'],
+            ['\\actaa', 'Acta Astron.', 'Acta Astronom.'],
+            ['\\araa', 'Ann. Rev. Astron. Astrophys.', 'Annu. Rev. Astron. Astrophys.'],
+            ['\\apj', 'Astrophys. J.', 'Astrophys. J.'],
+            ['\\apjl', 'Astrophys. J. Lett.', 'Astrophys. J. Lett.'],
+            ['\\apjs', 'Astrophys. J. Suppl.', 'Astrophys. J. Supp. S.'],
+            ['\\ao', 'Appl. Opt.', 'Appl. Optics'],
+            ['\\apss', 'Astrophys. Space Sci.', 'Astrophys. Space Sci.'],
+            ['\\aap', 'Astron. Astrophys.', 'Astron. Astrophys.'],
+            ['\\aapr', 'Astron. Astrophys. Rev.', 'Astron. Astrophys. Rev.'],
+            ['\\aaps', 'Astron. Astrophys. Suppl. Ser.', 'Astron. Astrophys. Sup.'],
+            ['\\azh', '', 'Astron. Zh.'], #Not sure. Various names on inspire
+            ['\\baas', 'Bull. Am. Astron. Soc.', 'Bull. Am. Astron. Soc.'],
+            ['\\bac', 'Bull. Astron. Inst. Czech.', 'B. Astron. I. Czech.'],
+            ['\\caa', 'Chin. Astron. Astrophys.', 'Chinese Astron. Astr.'],
+            ['\\cjaa', 'Chin. J. Astron. Astrophys.', 'Chinese J. Astron. Ast.'],
+            ['\\icarus', 'Icarus', 'Icarus'],
+            ['\\jcap', 'JCAP', 'J. Cosmology Astropart. Phys.'],
+            ['\\jrasc', 'J. Roy. Astron. Soc. Canada', 'J. Roy Astron. Soc. Can.'],
+            ['\\memras', 'Mem. Roy. Astron. Soc.', 'Mem. R. Astron. Soc.'],
+            ['\\mnras', 'Mon. Not. Roy. Astron. Soc.', 'Mon. Not. R. Astron. Soc.'],
+            ['\\na', 'New Astron.', 'New Astron.'],
+            ['\\nar', 'New Astron. Rev.', 'New Astron. Rev.'],
+            ['\\pra', 'Phys. Rev. A', 'Phys. Rev. A'],
+            ['\\prb', 'Phys. Rev. B', 'Phys. Rev. B'],
+            ['\\prc', 'Phys. Rev. C', 'Phys. Rev. C'],
+            ['\\prd', 'Phys. Rev. D', 'Phys. Rev. D'],
+            ['\\pre', 'Phys. Rev. E', 'Phys. Rev. E'],
+            ['\\prl', 'Phys. Rev. Lett.', 'Phys. Rev. Lett.'],
+            ['\\pasa', 'Publ. Astron. Soc. Austral.', 'Publ. Astron. Soc. Aust.'],
+            ['\\pasp', 'Publ. Astron. Soc. Pac.', 'Publ. Astron. Soc. Pac.'],
+            ['\\pasj', 'Publ. Astron. Soc. Jap.', 'Publ. Astron. Soc. Jpn.'],
+            ['\\rmxaa', 'Rev. Mex. Astron. Astrofis.', 'Rev. Mex. Astron. Astr.'],
+            ['\\qjras', 'Q. J. Roy. Astron. Soc.', 'Q. J. Roy. Astron. Soc.'],
+            ['\\skytel', 'Sky Telesc.', 'Sky Telescope'],
+            ['\\solphys', 'Solar Phys.', 'Sol. Phys.'],
+            ['\\sovast', 'Sov. Astron.', 'Sov. Astron.'],
+            ['\\ssr', 'Space Sci. Rev.', 'Space Sci. Rev.'],
+            ['\\zap', 'Z. Astrophys.', 'Z. Astrophys.'],
+            ['\\nat', 'Nature', 'Nature'],
+            ['\\iaucirc', 'IAU Circ.', 'IAU Circ.'],
+            ['\\aplett', 'Astrophys. Lett.', 'Astrophys. Lett.'],
+            ['\\apspr', '', 'Astrophys.~Space~Phys.~Res.'], #Could not find it on INSPIRE
+            ['\\bain', 'Bull. Astron. Inst. Netherlands', 'B. Astron. I. Neth.'],
+            ['\\fcp', 'Fund. Cosmic Phys.', 'Fund. Cosmic Phys.'],
+            ['\\gca', 'Geochim. Cosmochim. Acta', 'Geochim. Cosmochim. Ac.'],
+            ['\\grl', 'Geophys. Res. Lett.', 'Geophys. Res. Lett.'],
+            ['\\jcp', 'J. Chem. Phys.', 'J. Chem. Phys.'],
+            ['\\jgr', 'J. Geophys. Res.', 'J. Geophys. Res.'],
+            ['\\jqsrt', 'J. Quant. Spectrosc. Radiat. Trans.', 'J. Quant. Sprectrosc. Ra.'],
+            ['\\memsai', 'Mem. Soc. Ast. It.', 'Mem. Soc. Astron. Ital.'],
+            ['\\nphysa', 'Nucl. Phys. A', 'Nucl. Phys. A'],
+            ['\\physrep', 'Phys. Rept.', 'Phys. Rep.'],
+            ['\\physscr', 'Phys. Scripta', 'Phys. Scripta'],
+            ['\\planss', 'Planet. Space Sci.', 'Planet. Space Sci.'],
+            ['\\procspie', 'Proc. SPIE Int. Soc. Opt. Eng.', 'P. Soc. Photo.-Opt. Ins.'],
+            ####
+            # [Davide Gerosa] These are journals that I personally encountered. 
+            # Will keep on adding to this list.
+            ####
+            ['Advances in Space Research','Adv. Space Res.','Adv. Space Res.'], #ISI list not correct
+            ['American Institute of Physics Conference Series','AIP Conf. Proc.','AIP Conf. Proc.'],
+            ['Annals of Data Science','Ann. Data Sci.','Ann. Data Sci.'],
+            ['Astronomy and Computing','Astron. Comput.','Astron. Comput.'],
+            ['Astroparticle Physics','Astropart. Phys.','Astropart. Phys.'],
+            ['Astrophysics and Space Science Library','Astrophys. Space Sci. Libr.','Astrophys. Space Sc. L.'],
+            ['Astrophysics and Space Science Library','Astrophys. Space Sci. Libr.','Astrophys. Space Sc. L.'],
+            ['Bulletin of the American Astronomical Society','Bull. Am. Astron. Soc.','Bull. Am. Astron. Soc.'],
+            ['Classical and Quantum Gravity','Class. Quant. Grav.','Class. Quantum Grav.'], #ISI list not correct
+            ['Communications in Mathematical Physics', 'Commun. Math. Phys.', 'Commun. Math. Phys.'],
+            ['Frontiers in Astronomy and Space Sciences','Front. Astron. Space Sci.','Front. Astron. Space Sci.'],
+            ['General Relativity and Gravitation', 'Gen. Rel. Grav.', 'Gen. Relat. Gravit.'],
+            ['International Journal of Modern Physics D', 'Int. J. Mod. Phys. D', 'Int. J. Mod. Phys. D'], 
+            ['iScience', 'iScience', 'iScience'], 
+            ['Journal of High Energy Physics','JHEP','J. High Energy Phys.'],
+            ['Journal of Machine Learning Research','J. Machine Learning Res.','J. Mach. Learn. Res.'],
+            ['Journal of Mathematical Analysis and Applications','J. Math. Anal. Appl.','J. Math. Anal. Appl'],
+            ['Journal of Physics Conference Series','J. Phys. Conf. Ser.','J. Phys. Conf. Ser.'],
+            ['Journal of Statistical Physics','J. Statist. Phys.','J. Stat. Phys.'],
+            ['Journal of the Royal Statistical Society B','J. Roy. Statist. Soc. B','J. Roy. Statist. Soc. B'],
+            ['Living Reviews in Relativity', 'Living Rev. Rel.', 'Living Rev. Relativ.'],
+            ['Machine Learning: Science and Technology','Mach. Learn. Sci. Tech.','Mach. Learn. Sci. Tech.'], #ISI list not correct
+            ['Machine Learning','Machine Learning','Mach. Learn.'],
+            ['Nature Astronomy', 'Nature Astron.', 'Nat. Astron.'],
+            ['Nature Methods', 'Nature Meth.', 'Nat. Methods'],
+            ['Nature Reviews Physics','Nature Rev. Phys.','Nat. Rev. Phys.'],
+            ['Physica A Statistical Mechanics and its Applications','Physica A','Physica A'],
+            ['Physica D Nonlinear Phenomena', 'Physica D', 'Physica D'],
+            ['Physical Review', 'Phys. Rev.', 'Phys. Rev.'],
+            ['Physical Review Research', 'Phys. Rev. Res.', 'Phys. Rev. Res.'],
+            ['Physical Review X', 'Phys. Rev. X', 'Phys. Rev. X'],
+            ['Physics Letters A', 'Phys. Lett. A', 'Phys. Lett. A'],
+            ['Proceedings of the Royal Society of London Series A', 'Proc. Roy. Soc. Lond. A', 'P. R. Soc. Lond. A'],
+            ['Rendiconti Lincei. Scienze Fisiche e Naturali', 'Rend. Lincei Sci. Fis. Nat.', 'Rend. Lincei-Sci. Fis.'],
+            ['Reports on Progress in Physics', 'Rept. Prog. Phys.', 'Rep. Prog. Phys.'],
+            ['Research Notes of the American Astronomical Society', 'Res. Notes AAS','Res. Notes AAS'],
+            ['Reviews of Modern Physics', 'Rev. Mod. Phys.', 'Rev. Mod. Phys.'],
+            ['Science Advances','Sci. Adv.','Sci. Adv.'],
+            ['SIAM Journal on Scientific Computing','SIAM J. Sci. Comput.','SIAM J. Sci. Comput.'],
+            ['The Journal of Open Source Software','J. Open Source Softw.','J. Open Source Softw.'],
+            ]
+
+    with open(bibfile, 'r') as bibtex :
+        filedata = bibtex.read()
+
+    for j in journals:
+        print(j)
+        if j[0]:
+            filedata = filedata.replace(curly(j[0]), curly(j[2]))
+        if j[1]:
+            filedata = filedata.replace(curly(j[1]), curly(j[2]))
+            filedata = filedata.replace('journal = "'+j[1], 'journal = "'+j[2])
+
+    ### Clean up arxiv repeated information in ADS records:
+    filedata = filedata.replace('arXiv e-prints', '{}')
+    filedata = re.sub('pages = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('Pages = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('eid = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('Eid = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('doi = {[0-9]+.[0-9]+/arXiv.[0-9]+.[0-9]+},','',filedata)
+
+    with open(bibfile, 'w') as bibtex :
+        bibtex.write(filedata)
+
+
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--generate", action="store_true",
+            help="Generate the BibTeX entries from the metadata "
+                "(this is useful to customize the generated BiBTeX file)")
+    parser.add_argument("--journal_arXiv_fallback", dest="journal_arXiv_fallback", action="store_true",
+            help="Set the journal entry to be arXiv for unpublished preprints "
+                "(iNSPIRE entries only, requres --generate)")
+    parser.add_argument("--max-num-authors", dest="max_num_authors", type=int,
+            help="Include at most this many authors for each bibtex entry"
+                "(iNSPIRE entries only, requres --generate)")
+    parser.add_argument("--num-authors-short", type=int,
+            help="Number of authors to list if the number of authors is larger than max_num_authors"
+                "(iNSPIRE entries only, defaults to max-num-authors, requres --generate)")
+    subparsers = parser.add_subparsers(help="Subcommands")
+
+    parser_tex = subparsers.add_parser("tex", help="Create a bibliography for a tex document")
+    parser_tex.add_argument("--bibtex", help="The BiBTeX file to use (if not specified we try to find out)")
+    parser_tex.add_argument("texfile", nargs=1, help="The (La)TeX file to process")
+    parser_tex.add_argument('--journals', dest='journals', help="Replace known journal abbreviations", default=True, action='store_true')
+    parser_tex.add_argument('--updatepublished', dest='updatepublished', help="Replace ADS arxiv entries in .tex file if published", default=True, action='store_true')
+    parser_tex.set_defaults(func=fillbib_tex)
+
+    parser_list = subparsers.add_parser("list", help="Create a bibliography given a list of ADS/iNSPIRE keys")
+    parser_list.add_argument("keys", nargs="+", help="ADS/iNSPIRE keys to fetch")
+    parser_list.set_defaults(func=fillbib_list)
+
+
+    args = parser.parse_args()
+    args.func(args)
+    #try:
+    #    args.func(args)
+    #except:
+    #    parser.print_usage()
+
+
+

filltex-1.7.0.data/scripts/fillbib

@@ -0,0 +1,465 @@
+#!python
+
+'''
+Query the ADS and INSPIRE databases to collect the citations used in a LaTeX file into a BibTeX file
+
+Idea and main implementation is taken by Michele Vallisneri, see http://www.vallis.org/salon/summary-2.html
+I changed the script to avoid the requests module, and added the INSPIRE database part.
+
+Usage:
+python fillbib.py <tex_file> <bib_file>. If <bib_file> is absent, it will try to guess it from the aux file"
+
+'''
+from __future__ import absolute_import, print_function
+import argparse
+import sys, os, re, html
+import json
+
+if sys.version_info.major>=3:
+    import urllib.request as urllib
+else:
+    import urllib
+
+
+def ads_citation(c): # download single ADS citation
+    #f= urllib.urlopen("http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode="+c+"&data_type=BIBTEX&db_key=AST&nocookieset=1")
+    #print("http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode="+c+"&data_type=BIBTEX&db_key=AST&nocookieset=1")
+    f= urllib.urlopen("https://ui.adsabs.harvard.edu/abs/"+c+"/exportcitation")
+
+    bib = f.read()
+    f.close()
+    if sys.version_info.major>=3:
+        bib=bib.decode()
+    bib = "@"+list(filter(lambda x:'adsnote' in x, bib.split("@")))[0].split("</textarea>")[0]
+    bib=html.unescape(bib)
+
+    return bib
+
+def inspire_citation(key,
+        generate=False,
+        max_num_authors=None,
+        num_authors_short=None,
+        journal_arXiv_fallback=False):
+    """
+    Generate a custom BiBTeX entry
+
+    * generate
+        if True we generate the BibTeX rather than using the default from iNSPIRE
+    * max_num_authors
+        maximum number of authors to include (all of them if None)
+    * num_authors_short
+        number of authors to include if the number of authors is longer than max_num_authors
+        if not specified, this defaults to max_num_authors
+    * journal_arXiv_fallback
+        use arXiv:eprint as the journal field if no journal is found
+    """
+    request = 'https://inspirehep.net/api/literature?q=' + key
+    data = json.loads(urllib.urlopen(request).read())
+    if data['hits']['total'] != 1:
+        return None
+    if not generate:
+        bib = urllib.urlopen(data['hits']['hits'][0]['links']['bibtex']).read()
+        inspire_key = data['hits']['hits'][0]['metadata']['texkeys'][0]
+        if sys.version_info.major >= 3:
+            return bib.decode().replace(inspire_key, key)
+        else:
+            return bib.replace(inspire_key, key)
+    metadata = data['hits']['hits'][0]['metadata']
+
+    doctype = metadata["document_type"][0]
+
+    # BibTeX entry as a dictionary
+    bibtex = {}
+
+    # Find all authors
+    if "authors" in metadata:
+        num_authors = len(metadata["authors"])
+        if max_num_authors is not None and num_authors > max_num_authors:
+            short_author_list = True
+            if num_authors_short is None:
+                num_authors_short = max_num_authors
+        else:
+            short_author_list = False
+        author_list = []
+        for idx, author in enumerate(metadata['authors']):
+            if short_author_list and idx >= num_authors_short:
+                author_list.append("others")
+                break
+            author_list.append(author['full_name'])
+        bibtex['author'] = " and ".join(author_list)
+
+    # Find all collaborations
+    if "collaborations" in metadata:
+        collab_list = []
+        for collab in metadata["collaborations"]:
+            collab_list.append(collab["value"])
+        bibtex["collaboration"] = ", ".join(collab_list)
+
+    try:
+        bibtex["title"] = "{" + metadata["titles"][0]["title"] + "}"
+    except KeyError:
+        pass
+
+    try:
+        bibtex["eprint"] = metadata["arxiv_eprints"][0]["value"]
+        bibtex["archivePrefix"] = "arXiv"
+        bibtex["primaryClass"] = metadata["arxiv_eprints"][0]["categories"][0]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["doi"] = metadata["dois"][0]["value"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["journal"] = metadata["publication_info"][0]["journal_title"]
+    except KeyError:
+        if journal_arXiv_fallback:
+            bibtex["journal"] = "arXiv:" + bibtex["eprint"]
+        pass
+
+    try:
+        bibtex["volume"] = metadata["publication_info"][0]["journal_volume"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["number"] = metadata["publication_info"][0]["journal_issue"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["pages"] = metadata["publication_info"][0]["page_start"]
+    except KeyError:
+        pass
+
+    try:
+        bibtex["year"] = metadata["publication_info"][0]["year"]
+    except KeyError:
+        try:
+            bibtex["year"] = metadata["preprint_date"][0:4]
+            bibtex["month"] = str(int(metadata["preprint_date"][5:7]))
+        except KeyError:
+            pass
+
+    # Format BibTeX entry
+    s = "@{}{{{}".format(doctype, key)
+    for field, value in bibtex.items():
+        s += ",\n    {} = \"{}\"".format(field, value)
+    s += "\n}"
+
+    return s
+
+def test_ads(): # test single ADS web scraping (both published articles and preprints)
+    test_key = ["2016PhRvL.116f1102A","2016arXiv160203837T"]
+    known_output= '@ARTICLE{2016PhRvL.116f1102A,\n   author = {{Abbott}, B.~P. and {Abbott}, R. and {Abbott}, T.~D. and {Abernathy}, M.~R. and \n\t{Acernese}, F. and {Ackley}, K. and {Adams}, C. and {Adams}, T. and \n\t{Addesso}, P. and {Adhikari}, R.~X. and et al.},\n    title = "{Observation of Gravitational Waves from a Binary Black Hole Merger}",\n  journal = {Physical Review Letters},\narchivePrefix = "arXiv",\n   eprint = {1602.03837},\n primaryClass = "gr-qc",\n     year = 2016,\n    month = feb,\n   volume = 116,\n   number = 6,\n      eid = {061102},\n    pages = {061102},\n      doi = {10.1103/PhysRevLett.116.061102},\n   adsurl = {http://adsabs.harvard.edu/abs/2016PhRvL.116f1102A},\n  adsnote = {Provided by the SAO/NASA Astrophysics Data System}\n}\n\n'
+    assert [ads_citation(tk) == known_output for tk in test_key]
+
+def test_inspire(): # test single INSPIRE web scraping
+    test_key = "Abbott:2016blz"
+    known_output = '@article{Abbott:2016blz,\n    author = "Abbott, B.P. and Abbott, R. and Abbott, T.D. and Abernathy, M.R. and Acernese, F. and others",\n    collaboration = "LIGO Scientific, Virgo",\n    title = "{Observation of Gravitational Waves from a Binary Black Hole Merger}",\n    eprint = "1602.03837",\n    archivePrefix = "arXiv",\n    primaryClass = "gr-qc",\n    doi = "10.1103/PhysRevLett.116.061102",\n    journal = "Phys.Rev.Lett.",\n    volume = "116",\n    number = "6",\n    year = "2016"\n}'
+    assert inspire_citation(test_key, generate=True, max_num_authors=5) == known_output
+
+def fillbib_tex(args):
+
+    if args.bibtex is None:     # Get the name of the bibfile from the aux file
+        basename = args.texfile[0].split('.tex')[0]
+        auxfile = basename + '.aux'
+        for line in open(auxfile,'r'):
+            m = re.search(r'\\bibdata\{(.*)\}',line)   # match \citation{...}, collect the ... note that we escape \, {, and }
+            if m:
+                bibfile = list(filter(lambda x:x!=basename+'Notes', m.group(1).split(',')))[0]  # Remove that annyoing feature of revtex which creates a *Notes.bib bibfile. Note this is not solid if you want to handle multiple bib files.
+        bibfile = bibfile + '.bib'
+
+    else:    # Bibfile specified from argv
+        basename = args.texfile[0].split('.tex')[0]
+        auxfile = basename + '.aux'
+        bibfile = args.bibtex.split('.bib')[0] + '.bib'
+
+    if args.updatepublished:
+        with open(basename+".tex", 'r') as texfile:
+            texdata = texfile.read()
+
+    # Get all citations from aux file. Citations will look like \citation{2004PhRvD..69j4017P,2004PhRvD..69j4017P}
+    cites = set() # use a set (no repetitions)
+    for line in open(auxfile,'r'):
+        m = re.search(r'\\citation\{(.*)\}',line)   # find \citation{...}
+        if m:
+            cites.update(m.group(1).split(','))     # split by commas
+
+    cites= cites.difference([
+        'REVTEX41Control','apsrev41Control',
+        'REVTEX42Control','apsrev42Control']) # Remove annoying entries of revtex
+
+    print("Seek:", cites)
+
+    # Check what you already have in the bib file
+    haves = []
+    if os.path.isfile(bibfile):
+        for line in open(bibfile,'r'):
+            m = re.search(r'@.*?\{(.*),',line)  # .*\{ means "any # of any char followed by {"; .*?\{ means "the shortest string matching any # of any char followed by {"
+            if m:
+                haves.append(m.group(1))
+    print("Have:", haves)
+
+
+    # Query ADS and INSPIRE
+    bibtex = open(bibfile,'a')      # open for appending
+
+    for c in cites:
+        if c and c not in haves: # c is something and you don't have it already
+
+            if not c[0].isalpha(): # The first charachter is a number: could be on ADS
+
+                try:
+                    bib = ads_citation(c)
+
+                    cfound = bib.split("{")[1].split(',')[0]
+                    
+                    if  cfound == c: # Check you got what you where looking for
+                        pass
+                    elif 'arXiv' in c: # Take care of preprint on ADS
+
+                        if args.updatepublished and '.tmp.' not in cfound:
+                            print("ADS replace", c, "-->", cfound)
+                            # This substitute the new ID into the tex file. Use at your own risk. The .tmp. condition fixes those stupid MNRAS temp entries.
+                            texdata = texdata.replace(c, cfound)
+
+                        else: 
+                            # This subsitute the arxiv id back in to the bib file
+                            bib = bib.split("{")[0]+"{"+c+","+",".join(bib.split(",")[1:])
+
+                    bibtex.write(bib)
+                    print("ADS Found:", c)
+                except:
+                    print("ADS Not found:", c)
+
+            else: # The first charachter is not a number: could be on INSPIRE
+
+                try:
+                    bib = inspire_citation(c,
+                        generate=args.generate,
+                        max_num_authors=args.max_num_authors,
+                        num_authors_short=args.num_authors_short,
+                        journal_arXiv_fallback=args.journal_arXiv_fallback)
+                    bibtex.write(bib)
+                    print("INSPIRE Found:", c)
+                except:
+                    print("INSPIRE Not found:", c)
+
+
+
+    bibtex.close()
+
+    if args.updatepublished:
+        with open(basename+".tex", 'w') as texfile:
+            texfile.write(texdata)
+
+    # Clean up journal names
+    if args.journals:
+        journals(bibfile)
+
+    
+def fillbib_list(args):
+    for c in args.keys:
+        if not c[0].isalpha():
+            bib = ads_citation(c)
+            if bib is None:
+                sys.stderr.write("ADS Not Found: {}\n".format(c))
+            else:
+                print(bib)
+        else:
+            bib = inspire_citation(c,
+                    generate=args.generate,
+                    max_num_authors=args.max_num_authors,
+                    num_authors_short=args.num_authors_short,
+                    journal_arXiv_fallback=args.journal_arXiv_fallback)
+            if bib is None:
+                sys.stderr.write("INSPIRE Not Found: {}\n".format(c))
+            else:
+                print(bib)
+
+
+def curly(x):
+   '''Just a curly bracket sandwich.'''
+   return "{"+x+"}"
+
+def journals(bibfile):
+    '''
+    Clean up the names of some journals using their ISO4 standards.
+    Journal abbreviations are taken from https://images.webofknowledge.com/images/help/WOS/A_abrvjt.html
+    If your favourite journal is missing, please add it and send a pull request. Thanks!
+    '''
+
+    # The format is: [ADS name, INSPIRE name, ISO4 abbreviation]
+    journals = [
+            ####
+            # These are the journals from the ADS macros: https://ui.adsabs.harvard.edu/help/actions/journal-macros
+            # I could not find them all on INSPIRE, some are missing.
+            ####
+            ['\\aj', 'Astron. J.', 'Astron. J.'],
+            ['\\actaa', 'Acta Astron.', 'Acta Astronom.'],
+            ['\\araa', 'Ann. Rev. Astron. Astrophys.', 'Annu. Rev. Astron. Astrophys.'],
+            ['\\apj', 'Astrophys. J.', 'Astrophys. J.'],
+            ['\\apjl', 'Astrophys. J. Lett.', 'Astrophys. J. Lett.'],
+            ['\\apjs', 'Astrophys. J. Suppl.', 'Astrophys. J. Supp. S.'],
+            ['\\ao', 'Appl. Opt.', 'Appl. Optics'],
+            ['\\apss', 'Astrophys. Space Sci.', 'Astrophys. Space Sci.'],
+            ['\\aap', 'Astron. Astrophys.', 'Astron. Astrophys.'],
+            ['\\aapr', 'Astron. Astrophys. Rev.', 'Astron. Astrophys. Rev.'],
+            ['\\aaps', 'Astron. Astrophys. Suppl. Ser.', 'Astron. Astrophys. Sup.'],
+            ['\\azh', '', 'Astron. Zh.'], #Not sure. Various names on inspire
+            ['\\baas', 'Bull. Am. Astron. Soc.', 'Bull. Am. Astron. Soc.'],
+            ['\\bac', 'Bull. Astron. Inst. Czech.', 'B. Astron. I. Czech.'],
+            ['\\caa', 'Chin. Astron. Astrophys.', 'Chinese Astron. Astr.'],
+            ['\\cjaa', 'Chin. J. Astron. Astrophys.', 'Chinese J. Astron. Ast.'],
+            ['\\icarus', 'Icarus', 'Icarus'],
+            ['\\jcap', 'JCAP', 'J. Cosmology Astropart. Phys.'],
+            ['\\jrasc', 'J. Roy. Astron. Soc. Canada', 'J. Roy Astron. Soc. Can.'],
+            ['\\memras', 'Mem. Roy. Astron. Soc.', 'Mem. R. Astron. Soc.'],
+            ['\\mnras', 'Mon. Not. Roy. Astron. Soc.', 'Mon. Not. R. Astron. Soc.'],
+            ['\\na', 'New Astron.', 'New Astron.'],
+            ['\\nar', 'New Astron. Rev.', 'New Astron. Rev.'],
+            ['\\pra', 'Phys. Rev. A', 'Phys. Rev. A'],
+            ['\\prb', 'Phys. Rev. B', 'Phys. Rev. B'],
+            ['\\prc', 'Phys. Rev. C', 'Phys. Rev. C'],
+            ['\\prd', 'Phys. Rev. D', 'Phys. Rev. D'],
+            ['\\pre', 'Phys. Rev. E', 'Phys. Rev. E'],
+            ['\\prl', 'Phys. Rev. Lett.', 'Phys. Rev. Lett.'],
+            ['\\pasa', 'Publ. Astron. Soc. Austral.', 'Publ. Astron. Soc. Aust.'],
+            ['\\pasp', 'Publ. Astron. Soc. Pac.', 'Publ. Astron. Soc. Pac.'],
+            ['\\pasj', 'Publ. Astron. Soc. Jap.', 'Publ. Astron. Soc. Jpn.'],
+            ['\\rmxaa', 'Rev. Mex. Astron. Astrofis.', 'Rev. Mex. Astron. Astr.'],
+            ['\\qjras', 'Q. J. Roy. Astron. Soc.', 'Q. J. Roy. Astron. Soc.'],
+            ['\\skytel', 'Sky Telesc.', 'Sky Telescope'],
+            ['\\solphys', 'Solar Phys.', 'Sol. Phys.'],
+            ['\\sovast', 'Sov. Astron.', 'Sov. Astron.'],
+            ['\\ssr', 'Space Sci. Rev.', 'Space Sci. Rev.'],
+            ['\\zap', 'Z. Astrophys.', 'Z. Astrophys.'],
+            ['\\nat', 'Nature', 'Nature'],
+            ['\\iaucirc', 'IAU Circ.', 'IAU Circ.'],
+            ['\\aplett', 'Astrophys. Lett.', 'Astrophys. Lett.'],
+            ['\\apspr', '', 'Astrophys.~Space~Phys.~Res.'], #Could not find it on INSPIRE
+            ['\\bain', 'Bull. Astron. Inst. Netherlands', 'B. Astron. I. Neth.'],
+            ['\\fcp', 'Fund. Cosmic Phys.', 'Fund. Cosmic Phys.'],
+            ['\\gca', 'Geochim. Cosmochim. Acta', 'Geochim. Cosmochim. Ac.'],
+            ['\\grl', 'Geophys. Res. Lett.', 'Geophys. Res. Lett.'],
+            ['\\jcp', 'J. Chem. Phys.', 'J. Chem. Phys.'],
+            ['\\jgr', 'J. Geophys. Res.', 'J. Geophys. Res.'],
+            ['\\jqsrt', 'J. Quant. Spectrosc. Radiat. Trans.', 'J. Quant. Sprectrosc. Ra.'],
+            ['\\memsai', 'Mem. Soc. Ast. It.', 'Mem. Soc. Astron. Ital.'],
+            ['\\nphysa', 'Nucl. Phys. A', 'Nucl. Phys. A'],
+            ['\\physrep', 'Phys. Rept.', 'Phys. Rep.'],
+            ['\\physscr', 'Phys. Scripta', 'Phys. Scripta'],
+            ['\\planss', 'Planet. Space Sci.', 'Planet. Space Sci.'],
+            ['\\procspie', 'Proc. SPIE Int. Soc. Opt. Eng.', 'P. Soc. Photo.-Opt. Ins.'],
+            ####
+            # [Davide Gerosa] These are journals that I personally encountered. 
+            # Will keep on adding to this list.
+            ####
+            ['Advances in Space Research','Adv. Space Res.','Adv. Space Res.'], #ISI list not correct
+            ['American Institute of Physics Conference Series','AIP Conf. Proc.','AIP Conf. Proc.'],
+            ['Annals of Data Science','Ann. Data Sci.','Ann. Data Sci.'],
+            ['Astronomy and Computing','Astron. Comput.','Astron. Comput.'],
+            ['Astroparticle Physics','Astropart. Phys.','Astropart. Phys.'],
+            ['Astrophysics and Space Science Library','Astrophys. Space Sci. Libr.','Astrophys. Space Sc. L.'],
+            ['Astrophysics and Space Science Library','Astrophys. Space Sci. Libr.','Astrophys. Space Sc. L.'],
+            ['Bulletin of the American Astronomical Society','Bull. Am. Astron. Soc.','Bull. Am. Astron. Soc.'],
+            ['Classical and Quantum Gravity','Class. Quant. Grav.','Class. Quantum Grav.'], #ISI list not correct
+            ['Communications in Mathematical Physics', 'Commun. Math. Phys.', 'Commun. Math. Phys.'],
+            ['Frontiers in Astronomy and Space Sciences','Front. Astron. Space Sci.','Front. Astron. Space Sci.'],
+            ['General Relativity and Gravitation', 'Gen. Rel. Grav.', 'Gen. Relat. Gravit.'],
+            ['International Journal of Modern Physics D', 'Int. J. Mod. Phys. D', 'Int. J. Mod. Phys. D'], 
+            ['iScience', 'iScience', 'iScience'], 
+            ['Journal of High Energy Physics','JHEP','J. High Energy Phys.'],
+            ['Journal of Machine Learning Research','J. Machine Learning Res.','J. Mach. Learn. Res.'],
+            ['Journal of Mathematical Analysis and Applications','J. Math. Anal. Appl.','J. Math. Anal. Appl'],
+            ['Journal of Physics Conference Series','J. Phys. Conf. Ser.','J. Phys. Conf. Ser.'],
+            ['Journal of Statistical Physics','J. Statist. Phys.','J. Stat. Phys.'],
+            ['Journal of the Royal Statistical Society B','J. Roy. Statist. Soc. B','J. Roy. Statist. Soc. B'],
+            ['Living Reviews in Relativity', 'Living Rev. Rel.', 'Living Rev. Relativ.'],
+            ['Machine Learning: Science and Technology','Mach. Learn. Sci. Tech.','Mach. Learn. Sci. Tech.'], #ISI list not correct
+            ['Machine Learning','Machine Learning','Mach. Learn.'],
+            ['Nature Astronomy', 'Nature Astron.', 'Nat. Astron.'],
+            ['Nature Methods', 'Nature Meth.', 'Nat. Methods'],
+            ['Nature Reviews Physics','Nature Rev. Phys.','Nat. Rev. Phys.'],
+            ['Physica A Statistical Mechanics and its Applications','Physica A','Physica A'],
+            ['Physica D Nonlinear Phenomena', 'Physica D', 'Physica D'],
+            ['Physical Review', 'Phys. Rev.', 'Phys. Rev.'],
+            ['Physical Review Research', 'Phys. Rev. Res.', 'Phys. Rev. Res.'],
+            ['Physical Review X', 'Phys. Rev. X', 'Phys. Rev. X'],
+            ['Physics Letters A', 'Phys. Lett. A', 'Phys. Lett. A'],
+            ['Proceedings of the Royal Society of London Series A', 'Proc. Roy. Soc. Lond. A', 'P. R. Soc. Lond. A'],
+            ['Rendiconti Lincei. Scienze Fisiche e Naturali', 'Rend. Lincei Sci. Fis. Nat.', 'Rend. Lincei-Sci. Fis.'],
+            ['Reports on Progress in Physics', 'Rept. Prog. Phys.', 'Rep. Prog. Phys.'],
+            ['Research Notes of the American Astronomical Society', 'Res. Notes AAS','Res. Notes AAS'],
+            ['Reviews of Modern Physics', 'Rev. Mod. Phys.', 'Rev. Mod. Phys.'],
+            ['Science Advances','Sci. Adv.','Sci. Adv.'],
+            ['SIAM Journal on Scientific Computing','SIAM J. Sci. Comput.','SIAM J. Sci. Comput.'],
+            ['The Journal of Open Source Software','J. Open Source Softw.','J. Open Source Softw.'],
+            ]
+
+    with open(bibfile, 'r') as bibtex :
+        filedata = bibtex.read()
+
+    for j in journals:
+        print(j)
+        if j[0]:
+            filedata = filedata.replace(curly(j[0]), curly(j[2]))
+        if j[1]:
+            filedata = filedata.replace(curly(j[1]), curly(j[2]))
+            filedata = filedata.replace('journal = "'+j[1], 'journal = "'+j[2])
+
+    ### Clean up arxiv repeated information in ADS records:
+    filedata = filedata.replace('arXiv e-prints', '{}')
+    filedata = re.sub('pages = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('Pages = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('eid = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('Eid = {arXiv:[0-9]+.[0-9]+},','',filedata)
+    filedata = re.sub('doi = {[0-9]+.[0-9]+/arXiv.[0-9]+.[0-9]+},','',filedata)
+
+    with open(bibfile, 'w') as bibtex :
+        bibtex.write(filedata)
+
+
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--generate", action="store_true",
+            help="Generate the BibTeX entries from the metadata "
+                "(this is useful to customize the generated BiBTeX file)")
+    parser.add_argument("--journal_arXiv_fallback", dest="journal_arXiv_fallback", action="store_true",
+            help="Set the journal entry to be arXiv for unpublished preprints "
+                "(iNSPIRE entries only, requres --generate)")
+    parser.add_argument("--max-num-authors", dest="max_num_authors", type=int,
+            help="Include at most this many authors for each bibtex entry"
+                "(iNSPIRE entries only, requres --generate)")
+    parser.add_argument("--num-authors-short", type=int,
+            help="Number of authors to list if the number of authors is larger than max_num_authors"
+                "(iNSPIRE entries only, defaults to max-num-authors, requres --generate)")
+    subparsers = parser.add_subparsers(help="Subcommands")
+
+    parser_tex = subparsers.add_parser("tex", help="Create a bibliography for a tex document")
+    parser_tex.add_argument("--bibtex", help="The BiBTeX file to use (if not specified we try to find out)")
+    parser_tex.add_argument("texfile", nargs=1, help="The (La)TeX file to process")
+    parser_tex.add_argument('--journals', dest='journals', help="Replace known journal abbreviations", default=True, action='store_true')
+    parser_tex.add_argument('--updatepublished', dest='updatepublished', help="Replace ADS arxiv entries in .tex file if published", default=True, action='store_true')
+    parser_tex.set_defaults(func=fillbib_tex)
+
+    parser_list = subparsers.add_parser("list", help="Create a bibliography given a list of ADS/iNSPIRE keys")
+    parser_list.add_argument("keys", nargs="+", help="ADS/iNSPIRE keys to fetch")
+    parser_list.set_defaults(func=fillbib_list)
+
+
+    args = parser.parse_args()
+    args.func(args)
+    #try:
+    #    args.func(args)
+    #except:
+    #    parser.print_usage()
+
+
+

filltex-1.7.0.data/scripts/filltex

@@ -0,0 +1,73 @@
+#!/bin/bash
+# Full tex compiler: run pdflatex, bibtex, query ADS and INSPIRE for citations and count words
+# Davide Gerosa
+
+# Install texshop engine
+if [[ $1 = 'install-texshop' ]]; then
+  TEXSHOP="${HOME}/Library/TeXshop/Engines/filltex.engine"
+  echo "Installing texshop engine in $TEXSHOP"
+  echo  ''#!/bin/bash '' > $TEXSHOP
+  echo  ''export PATH=$(dirname $(which filltex)):\${PATH}'' >> $TEXSHOP
+  echo  ''echo \$1 '' >> $TEXSHOP
+  echo  ''FILENAME=\${1%%.*} '' >> $TEXSHOP
+  echo  ''echo \$FILENAME '' >> $TEXSHOP
+  echo  ''filltex \$FILENAME '' >> $TEXSHOP
+  chmod +x $TEXSHOP
+exit
+fi
+
+
+# Actual script
+#SCRIPT=`realpath $0`
+#SCRIPT_LOCATION=`dirname $SCRIPT`
+
+
+START=$PWD #Where you started
+
+if [ ! -f ${START}/${1%.*}.tex ]; then
+  echo "File not found!"
+  exit 1
+fi
+FILE=${1%.*}
+echo "filltex is compiling ${FILE}.tex"
+
+# Get the journal abbreviations from ADS
+if grep -q 'aas_macros' ${FILE}.tex; then # check if you need them
+  if [ ! -f 'aas_macros.sty' ]; then
+    curl -s 'https://adsabs.harvard.edu/abs_doc/aas_macros.sty' > 'aas_macros.sty'
+  fi
+fi
+
+# The pdflatex command returns 0 if everyting is ok, or 1 if he gets an error. If there's an error, I want the script to exit.
+pdflatex --synctex=1 -halt-on-error ${FILE}.tex
+[[ $? -eq 1 ]] && echo "pdflatex got an error" && exit
+
+# Fill the bib fil with the ADS and INSPIRE references.
+# Use python 2
+#python ${SCRIPT_LOCATION}/fillbib.py "${FILE}"
+# Use python 3
+#python3 ${SCRIPT_LOCATION}/fillbib.py "${FILE}"
+#python ../filltex/fillbib.py tex ${FILE}
+fillbib tex ${FILE}
+
+
+for i in {1..2}; do
+
+  # Fill the bbl file from the bib file
+  for file in *.aux ; do
+      bibtex $file
+  done
+
+  pdflatex --synctex=1 -halt-on-error ${FILE}.tex
+  [[ $? -eq 1 ]] && echo "pdflatex got an error" && exit
+
+  pdflatex --synctex=1 -halt-on-error ${FILE}.tex
+  [[ $? -eq 1 ]] && echo "pdflatex got an error" && exit
+done
+
+# Count the words
+#perl ${SCRIPT_LOCATION}/texcount.pl "${FILE}".tex
+texcount "${FILE}".tex
+
+# open the pdf file if you like
+#open "${FILE}".pdf

filltex-1.7.0.dist-info/METADATA

@@ -0,0 +1,18 @@
+Metadata-Version: 2.4
+Name: filltex
+Version: 1.7.0
+Summary: Automatic queries to ADS and InSPIRE databases to fill LATEX bibliography
+Home-page: https://github.com/dgerosa/filltex
+Author: Davide Gerosa and Michele Vallisneri
+Author-email: dgerosa@star.sr.bham.ac.uk
+License: MIT
+License-File: LICENSE
+Dynamic: author
+Dynamic: author-email
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: summary
+
+See: `github.com/dgerosa/filltex <https://github.com/dgerosa/filltex>`_.

filltex-1.7.0.dist-info/RECORD

@@ -0,0 +1,8 @@
+fillbib.py,sha256=ypKf452OmfHToVtEMDTG2cBRG8_OWDwdCHDaSgooGnU,22636
+filltex-1.7.0.data/scripts/fillbib,sha256=lj_39ocfku8_MfdL8XVkc9k11eWhzyyrrC9HcuQv0PM,22623
+filltex-1.7.0.data/scripts/filltex,sha256=cwUCJB2vxM_aUnH5ELC_DyDhuA-k4G3mYiKnQeWMnvk,2025
+filltex-1.7.0.dist-info/licenses/LICENSE,sha256=02z8PApk_0N4ZQ8_rKArOOzClS7B0i4wNurOuUlHG0w,1070
+filltex-1.7.0.dist-info/METADATA,sha256=TGugmQARK4iqVZDSbZ6hg2DearLVN0QADrBYxT5r_TI,509
+filltex-1.7.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+filltex-1.7.0.dist-info/top_level.txt,sha256=dsEFVd7-rpq7Y4b2xsbUT1rUMnS46mx4cN6EnytACpI,8
+filltex-1.7.0.dist-info/RECORD,,

filltex-1.7.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

filltex-1.7.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Davide Gerosa
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

filltex-1.7.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+fillbib