path: root/support/biblio/readme.1st.ps

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%%Copyright: (c) 1988, 89, 90, 91, 92, 93 Miguel Santana
%%Copyright: (c) 1995, 96, 97, 98 Akim Demaille, Miguel Santana
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%%Copyright: (c) 1988, 89, 90, 91, 92, 93 Miguel Santana
%%Copyright: (c) 1995, 96, 97, 98 Akim Demaille, Miguel Santana
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() p n
(                                    BIBLIO) N
(                          bibliographic preprocessor) N
() N
() N
(                                09 April 2001) N
(                                27 June  2001) N
(                                07 Sept  2001 \(ver 1.1\)) N
(                                17 Sep   2001 \(ver 1.11\)) N
(                                04 Oct   2001 \(ver 1.2\)) N
(                                12 March 2002 \(ver 1.21\)) N
() N
(CONTENT) N
() N
(Abstract) N
() N
(0.  Copyright) N
(1.  Statement of Purpose) N
(2.  General Ideas) N
(3.  Structure of the Biblio-Database) N
(4.  Structure of the Format File \(Format Strings\)) N
(5.  Running Biblio) N
(6.  Examples) N
(7.  Additional Scripts) N
(8.  Installation Guide and Short Instruction) N
(9.  Perl To C) N
(10. To Do) N
(11. Known Bugs) N
() N
(===============================================================================) N
(     ) N
(                                     Abstract) N
() N
(Biblio is a programm for preprocessing your bibliographic references. It is) N
(written in Perl and does not use the LaTeX internal language. After ) N
(preprocessing the input TeX file it creates output TeX file with references) N
(included according to the formats prescribed either in a separate file ) N
(\(called "template" or "format file" further on\)) N
(or in the header of the input TeX file. Output TeX is ready for LaTeX.) N
(If you do not need details, move to the section 8 \(and 9\) of this text.) N
() N
() N
(-------------------------------------) N
() N
(0. COPYRIGHT) N
() N
(This  is  free software. But NO use in commercial purposes is allowed.) N
(There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR ) N
(PURPOSE.) N
() N
(-------------------------------------) N
() N
(1. STATEMENT OF PURPOSE) N
() N
(Don't reinvent a wheel - this should be your first reaction. Might be you are ) N
(right: many people use BibTeX or some other \(I don't know which but pretty sure ) N
(they do exist\) programs to pre-process their bibliographic references lists. ) N
(But what I did before was just including all citations directly into my ) N
(TeX-file. Before... Before this story has happened. ) N
() N
(I was writing an article and from the very beginning we \(I and my bosses\) ) N
(decided to send it to the Journal A. Of course, I wrote everything including ) N
(readme.1st) (Page 1/15) (Mar 12, 02 12:27) title
border
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(citations in the style of this journal. But when the work was almost finished ) p n
(we \(you know whom I mean\) decided to send the paper to another journal, say ) N
(Journal B. And of course it has different rules and standards. ) N
(No problem - one should say,- Use BibTeX. Yes, that's OK - is my reply. ) N
(But what I basicly needed was to change the order of names \(last, first, etc\) ) N
(in the authors list. Like instead of "J.J.Smith" now I needed "Smith, J.J.".) N
(Might be information I used was quite outdated, but I could not find the way to ) N
(handle this kind of things with the BibTeX. ) N
() N
(Another reason to start this project was handle somehow ordering of the ) N
(citation list. Normally articles in the "References and Notes" section should ) N
(appear in the same order as they are in the body-text. But sometimes it's quite ) N
(useful to have the list ordered according to the first author name or something ) N
(different.) N
() N
(And finally, some journals  prefer to have "as raw text as possible". They do ) N
(accept TeX-files but...  without cross references and citations which means, ) N
(that everything have to be done by hands and ONLY ONE file has to be submitted. ) N
(I don't like this idea! But I DO want to be published there! So, may be a ) N
(partial solution is \(for citations at least\) is to pre-process the TeX-file to ) N
(another TeX-file where all \\cite and \\bibitem commands are substituted by ) N
(normal text. Of course, according to some pattern. This solves one more ) N
(problem - I'm not very good in TeX programming and find it quite difficult to ) N
(make TeX command \\cite produce some nice output in the form $^{1,2,6}$ instead ) N
(of [1,2,6].) N
( ) N
(So, let's move to the GENERAL IDEAS) N
() N
(-----------------------------------------------------) N
() N
(2.GENERAL IDEAS) N
() N
(  A. This program pre-processes TeX-file making another TeX-file.) N
() N
(  B. Citations are inserted from the DataBase\(s\) which has form of a separate ) N
(file. Fields of the records in this file are absolutely ARBITRARY, except for ) N
(LABEL and TYPE. Field AUTHOR has also some special meaning which will be ) N
(clarified further on.) N
(This DataBase has form of) N
(======================================================) N
(LABEL   = Landau) N
(TYPE    = book) N
(AUTHORL = Landau|Lifshits) N
(AUTHORF = L     |E.) N
(AUTHORM = D.    |M.) N
(TITLE   = Statistical Physics) N
(PUBL    = Pergamon) N
(PLACE   = Oxford) N
(YEAR    = 1980) N
(----------) N
(LABEL   = Vasilevskaya) N
(TYPE    = article0) N
(AUTHORL = Vasilevskaya|Klochkov|Khalatur|Khokhlov|Brinke) N
(AUTHORF = V.          |A.      |P.      |A.      |G.) N
(AUTHORM = V.          |A.      |G.      |R.      |) N
(TITLE   = Microphase separation within comb-like copolymer with attractive  side) N
(-chains: computer simulations.) N
(JOURNAL = Macromol. Theory and Simul.) N
(STATE   = accepted) N
(----------) N
(LABEL   = Helfand1) N
(TYPE    = article) N
(readme.1st) (Page 2/15) (Mar 12, 02 12:27) title
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(AUTHORL = Helfand|Wasserman) p n
(AUTHORF = E.     |Z.) N
(AUTHORM =        |R.) N
(JOURNAL = Macromolecules) N
(VOL     = 9) N
(PAGE    = 879) N
(YEAR    = 1976) N
(----------) N
(LABEL   = 3dFlex) N
(TYPE    = article) N
(AUTHORP =         |        |      |ten) N
(AUTHORL = Subbotin|Saariaho|Ikkala|Brinke) N
(AUTHORF = A.      |M.      |O.    |G.) N
(TITLE   = Elasticity of comb copolymer cylindrical brushes) N
(JOURNAL = Macromolecules) N
(PAGE    = 3447) N
(YEAR    = 2000) N
(VOL     = 33) N
(----------) N
(LABEL   = Dobrynin1) N
(TYPE    = article) N
(AUTHORL = Dobrynin|Erukhimovich) N
(AUTHORF = A.|I.) N
(AUTHORM = V.|Y.) N
(TITLE   = Computer-aided comparative investigation of architecture influence of ) N
(block copolymer phase diagrams) N
(JOURNAL = Macromolecules) N
(PAGE    = 276) N
(EPAGE   = 281) N
(YEAR    = 1993) N
(VOL     = 26) N
(COMMENT = Read it before you have graduated!!! ) N
(----------) N
(====================================================================) N
() N
(Please, note that the last entry has EPAGE \(which means "end page"\) and title ) N
(also included whereas record "Helfand1" contains much less information. ) N
(This will not cause any problem. The only person to whom you have to agree is ) N
(yourself: if you call the first \(starting\) page of the paper \(book, etc\) "PAGE",) N
(do it for all entries. If you prefer to call it "EGAP" - it's your choice! ) N
() N
(One can use abbreviation in the form of TeX commands, like) N
("\\mml" can mean "Macromol." if we include line "\\def\\mml{Macromol.}") N
(somewhere in the tex-source. To do so see "-a" option: to point to the ) N
(abbreviations file "-a abbr.tex" should be used. Note: Biblio will not check) N
(consistency of your abbreviations!!!) N
() N
(LABEL and TYPE are predefined! Also AUTHOR is predefined. "AUTHOR" without "L", ) N
("R" or anything else at the end. It is predefined in the sense, that entries in ) N
(the database, which start with "AUTHOR" \("AUTHORL", "AUTHORF"\) are considered to) N
(be arrays with separator "|". There are two equivalent ways to represent them ) N
(in the DataBase:) N
(* one is shown above \(with "|" as separator\)) N
(* the "Dobrynin1" entry can be also written in the form) N
(==============) N
(AUTHORL = Dobrynin) N
(AUTHORF = A.  ) N
(AUTHORM = V.) N
(AUTHORL = Erukhimovich) N
(AUTHORF = I.  ) N
(AUTHORM = Y.) N
(===============) N
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(The only important issue is the order of this entries: the first AUTHORF belongs) p n
(to the first AUTHORL. In principle you can include anything between them, like:) N
(===============) N
(AUTHORL = Dobrynin) N
(YEAR    = 1993) N
(AUTHORF = A.  ) N
(AUTHORM = V.) N
(PAGE    = 276) N
(AUTHORL = Erukhimovich) N
(AUTHORF = I.  ) N
(AUTHORM = Y.) N
(==============) N
(It will produce the same result. ) N
() N
(If there are several entries for the same key \(like YEAR\) which is NOT supposed) N
(to be array \(i.e. does not start with AUTHOR\), then only the last one will ) N
(influence the final result.) N
() N
(The fact that all arrays should start with AUTHOR does not mean that you can ) N
(apply it to the authors' list only. It will become more transparent further.) N
() N
( C. Of course you want some nice output. Your LaTeX document should look like:) N
() N
(====) N
(\\documentstyle[12pt,a4]{article}) N
(\\title{Blah-blah}) N
(\\begin{document}\\maketitle) N
() N
(Text text \\cite{Dobrynin1}.) N
(Text Text text \\cite {Dobrynin1,3dFlex}) N
() N
(\\begin{thebibliography}) N
() N
(\\end{thebibliography}) N
() N
(Something more you need \(list of figures or whatever\)) N
() N
(\\end{document}) N
(====) N
() N
(Note, that NOTHING is between \\begin{thebibliography} and ) N
(\\end{thebibliography}. These two are just signs for Biblio to insert your) N
(references list in between.) N
() N
(What does Biblio do? It reads your TeX-file and finds all references \(which you ) N
(have in \\cite command\) in the database. Then it inserts them according to some ) N
(formats \(see further\) between \\begin{thebibliography} and \\end{thebibliography}.) N
(It can do it in two ways:) N
() N
(FIRST: insert them as "\\bibitem{LABEL} TEXT OF THE REF" and not touching ) N
(anything else \(text of the ref is according to the format, of course\);) N
() N
(SECOND: insert them in some special way, where you can define what \\cite will ) N
(produce and what kind of numbering you want in the references list. For example,) N
(if you like $^{1,5-7}$ more than standard [1,5-7], normally produced by \\cite, ) N
(and) N
(\(1\) ref1) N
(\(2\) ref2) N
(instead of) N
([1] ref1) N
([2] ref2) N
(produced by \\bibitem.) N
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() p n
(\(Hint: your choice between FIRST and SECOND you can do by using "--nobibitem" ) N
(parameter, and "cite_format" and "ref_format" fields in the format file\).) N
() N
(After it's done, you can process output file with normal LaTeX. ) N
() N
(\(Hint: You can find script "libtex" which will help you to handle it.\)) N
() N
( D. All formats are stored in the format file \(see -f command line option\)) N
(or just in your TeX document's header. About rules \(how to write this formats\)) N
(you can read below.) N
() N
() N
( E. So, your checklist is:) N
(    1. Input TeX file.) N
(    2. References database.) N
(    3. Format file) N
() N
(If you have all these you have to do) N
() N
(biblio  -o outdoc.tex -d refsdata.db refsdata1.db -f formats.db   indoc.tex) N
() N
(where ) N
(- outdoc.tex  - output filename ) N
(  \(if not given, them "biblio."-prefix is added to "indoc.tex") N
(  like "biblio.indoc.tex"\)) N
(- refsdata.db - references database \(may be more than one\)) N
(- formats.db  - format file \(only ONE\)) N
(- indoc.tex   - input file) N
() N
(The order of the parameters is not important.) N
() N
(-------------------------------------) N
() N
(3. STRUCTURE OF THE BIBLIO-DATABASE) N
() N
(It has form described in 2.B. It consists of records. After each record a ) N
(separator has to be placed. By default, it is "----------\\n". You can easily ) N
(change it by command line option "--separator". Only on separator can be used!) N
() N
(Each record has fields. One line per one field - is a rule! ) N
(You cannot change it \(without looking into the source, of course\)! ) N
() N
(Each field has a structure NAME = VALUE.   ) N
() N
(Fields' names LABEL and TYPE are predefined - each record has to have them. ) N
(Otherwise it will be ignored.) N
() N
(Field AUTHOR has a special structure. ) N
(Usage is quite obvious from an example) N
() N
(AUTHORP =         |        |      |ten) N
(AUTHORL = Subbotin|Saariaho|Ikkala|Brinke) N
(AUTHORF = A.      |M.      |O.    |G.) N
(AUTHORM = V.     ) N
() N
(There are 4 authors: Subbotin A.V.; Saariaho M.; Ikkala O. and ten Brinke G.) N
() N
(P, L, F and M are from "prefix", "last", "first", "middle".) N
() N
(Sign "|" separates authors. It is reserved and cannot be changed!) N
() N
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(You can use as many fields as you like. If you don't use them in the ) p n
(output - no problem, part of them will be ignored.) N
() N
(You can have several databases. Use inline option "-d" to say Biblio names) N
(of databases you want to use.) N
() N
(That's all!) N
() N
(-------------------------------------) N
() N
(4. STRUCTURE OF THE FORMAT FILE \(FORMAT STRING\)) N
() N
(Your output \(formated entries from database put into the TeX document\) has to ) N
(be formated according to the rules described in the so called format file \(or ) N
(templates\) or just in the beginning of your TeX document. ) N
(The first way is preferable - it gives taste of more structural ordering.) N
(Use option "-f" to point to a format file. Otherwise Biblio will try to find ) N
(formats in the TeX-file and, if not succeeded, will complain and halt.) N
() N
(What we want to format?) N
(1. References list \(what you normally have at the end of your paper\)) N
(2. Citations in the text \(what you do with \\cite\)) N
() N
(Before reading this, read 2.C from "General Ideas" section.) N
() N
(How to write formats? That's the hardest part!) N
() N
(Let's start from an) N
(EXAMPLE:) N
(-------------------) N
(% this is template for Macromolecules) N
(% no ordering of the references is needed. Otherwise add line) N
(% '%ordering= AUTHORL' - ordering with key field 'AUTHORL') N
() N
(%begin{biblio}) N
() N
(%cite_format={\(%s\)}) N
(%ref_format=${^{%s}}$) N
() N
(%% normal article:) N
(% ARTICLE [$AUTHOR0P~L,~F~M; $ {\\it $JOURNAL$}  {\\bf $YEAR$}, {\\it $VOL$}, $PAGE) N
($.]) N
() N
(%% article which is submitted or accepted) N
(% ARTICLE0[$AUTHOR0P~L,~F~M; $ {\\it $JOURNAL$}  $STATE$.]) N
() N
(%% normal book) N
(% BOOK    [$AUTHOR0P~L,~F~M; $ {\\it $TITLE$}; $PUBL$: $PLACE$, $YEAR$.]) N
() N
(%% article in a book AUTHORE, AUTHORG and AUTHORH - last, first ) N
(%% and middle names of the editor ) N
(% EDBOOK  [$AUTHOR0P~L,~F~M; $ in {\\it $BOOKTITLE$}, edited by $AUTHOR0I~E,~G~H;) N
($; $PUBL$: $PLACE$, $YEAR$.]) N
() N
(%% article in a book without editor) N
(% INBOOK  [$AUTHOR0P~L,~F~M; $ in {\\it $BOOKTITLE$}, p.$PAGE$ $PUBL$: $PLACE$, $) N
(YEAR$.]) N
() N
(% EPRINT [$AUTHOR0P~L,~F~M; $ in {\\it $BOOKTITLE$} $INFO$, $YEAR$.]) N
() N
(%end{biblio}) N
(-------------------) N
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(4.0. Syntax) p n
() N
(  A. Each line starts with %-sign. This is needed because in principle this can ) N
(     be included into your TeX-document, so it has to be considered as a comment) N
(     by LaTeX. Lines, starting with %% are "REAL"  comments \(i.e. they are ) N
(     comments for Biblio too\).) N
() N
(  B. All this information has to be stored either in a template file \(format ) N
(     file\) [use option -f filename] or just in the header of your TeX document.) N
(     In both cases it has to start with '%begin{biblio}' line and end with ) N
(     '%end{biblio}'.) N
(     Only one template file is allowed \(you cannot read from 2 for the) N
(     same document\).) N
() N
(  C. There are some OPTIONAL reserved keys. If omitted, default values are ) N
(     assumed and warning is printed.) N
(     Reserved keys are) N
(     C.1.  cite_format:  has a form %cite_format={\(%s\)}) N
(           %s just means "string". {\(%s\)} will produce output in your) N
(           references list like) N
(           ) N
(           \(1\) Simpson,....) N
(           \(2\) Tompson...) N
(           ...) N
() N
(           or %cite_format={%s.} will produce) N
() N
(           1. Simpson,....) N
(           2. Tompson...) N
(           ...) N
() N
() N
(     C.2.  ref_format: has a form  %ref_format=${^{%s}}$) N
(           This means how your \\cite command output will look like.) N
(           For example, we have \\cite{Aw1,Paper3,John} in the TeX document and ) N
(           %ref_format=${^{%s}}$ in your format file. Then you get) N
() N
(           ${^{2,4,5}}$    \(numbers depend on what is ordering, of) N
(                            course\)) N
(           or) N
(           ${^{2-4}}$   if they all are going one by one in your refslist.) N
() N
(           in the output TeX file instead of your \\cite command.) N
(           If you have  %ref_format={[%s]} then) N
() N
(           {[2,4,5]}) N
(           or) N
(           {[2-4]}) N
(          ) N
(     C.3.  ordering: has a form  %ordering= AUTHORL) N
(           This means that the field AUTHORL has to be considered as a key field) N
(           in ordering of your references. You can put whatever you want there, ) N
(           like YEAR, VOL,...) N
(           If this filed is not present in some entries, it considered to be ) N
(           empty. ) N
() N
(  D. Each TYPE \(TYPE is article, book or something like this\) has to have an ) N
(     entry in the format file. This entry \(format string\) has a form) N
(     ) N
(     % TYPE [format string] ) N
() N
(     \(it MUST be in ONE line!!!\)) N
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(     where the "format string" says to Biblio how to output information about ) p n
(     your reference of the type TYPE.) N
(     "[" and "]" MUST be there! They say where you start your format line and ) N
(     where it ends \(if you need to use inside the format line, don't worry: ) N
(     the first [ is the start and the last ] is the end  of the string; ) N
(     all the rest are just characters\). ) N
(     Everything between $-signs is a filed name. $VOL$ will be substituted by ) N
(     54 if you have an entry ) N
(     VOL = 54 ) N
(     for this given article in your database. ) N
(     It's a bit more tricky for AUTHOR \(see below\). ) N
(     All the other words are just normal text or LaTeX commands. ) N
(     Example:) N
() N
(     Let say, you have the following item in your database file) N
() N
(     LABEL   = LifshitzGrosbergKhokhlov1) N
(     TYPE    = article) N
(     AUTHORL = Lifshitz|Grosberg|Khokhlov) N
(     AUTHORF = I.      |A.      |A.) N
(     AUTHORM = M.      |Yu.     |R.) N
(     JOURNAL = Rev. Mod. Phys.) N
(     VOL     = 50) N
(     PAGE    = 683) N
(     EPAGE   = 713) N
(     YEAR    = 1978) N
(     TITLE   = Some problems of the statistical physics of...) N
() N
(     and an entry ) N
(     ) N
(     % ARTICLE [$AUTHOR0P~L,~F~M; $ {\\it $JOURNAL$}  {\\bf $YEAR$}, {\\it $VOL$}, ) N
($PAGE$.]) N
(     ) N
(     in your format file \(I assume also '%cite_format={\(%s\)}'\).) N
(     Then output will be) N
() N
(     \(1\) ~Lifshitz,~I.~M.; ~Grosberg,~A.~Yu.; ~Khokhlov,~A.~R. ) N
(         {\\it {Rev. Mod. Phys.}}  {\\bf {1978}}, {\\it {50}}, {683}.) N
(           ) N
() N
(4.1. AUTHOR-word:) N
() N
(  A. Word AUTHOR is reserved and assumed to be an array. ) N
(     This means, that AUTHORLFM is in fact) N
(     hash index with keys AUTHORL, AUTHORF, AUTHORM, ) N
(     or, if you like) N
(     AUTHOR[L]='Smith') N
(     AUTHOR[F]='J.') N
(     AUTHOR[M]='A.') N
() N
(  B. After the word AUTHOR follows the max number of authors to show ) N
(     \(let us call it max_A\). ) N
(     If actual number of authors n_A > max_A, ) N
(     then "$reservedET_AL" will be written after the ) N
(     author number max_A and  names of all the others will be omitted. ) N
(     "max_A==0" \(zero\) means "max_A==infty") N
(  C. $AUTHOR0L, F; $ means that fields should be written as follows:) N
(         1\) "AUTHORL") N
(         2\) ", ") N
(         3\) "AUTHORF") N
(         4\) "; "  \(let us  denote it as "last_sep"\)) N
(         5\) go to "1\)" for the next author) N
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() p n
() N
(     For example, for the Lifshitz' article above:) N
() N
(     $AUTHOR0L, F, M; $ produces) N
(     Lifshitz, I. M.; Grosberg, A. Yu.;  Khokhlov, A. R.) N
() N
(     or) N
() N
(     $AUTHOR1L, F; $ produces) N
(     Lifshitz, I. et al) N
( ) N
(     Note, there is no the middle name in the 2nd example, because there is ) N
(     no "M" in the format line.) N
() N
(  D. There is a special sign "|" which means that AUTHOR format line is ended ) N
(     in fact and everything after it is so called "and_word". ) N
(     This "and_word" \(normally, it contains only "and"\) is something  what is ) N
(     written before the last author if the number of authors in larger than 1. ) N
() N
(     Example:) N
(     $AUTHOR0L, F, M; |and$ produces) N
(     Lifshitz, I. M.; Grosberg, A. Yu.; and  Khokhlov, A. R.) N
(     ) N
() N
(     Note, that) N
(         1\) if "et al" have to be printed, "and_word" will not be there!) N
() N
(            $AUTHOR2L, F; |and$ produces) N
(            Lifshitz, I.; Grosberg, A. Yu. et al) N
() N
(         2\) if number of authors is larger than 2 but less or equal to max_A: ) N
(            before the "end_word" the "last_sep" has to be written) N
(            otherwise - if only 2 authors: print "and_word", but no "last_sep") N
() N
(            Example:  Q.W. Rom and R.T. Lai) N
(                 but  Q.W. Rom, T.G. Doi, and R.T. Lai  ) N
(               here:  last_sep="," ; and_word="and"\)) N
() N
(                      This example corresponds to     ) N
(                      $AUTHOR0FM L, |and$) N
() N
() N
(4.2. Fields LABEL, TYPE and AUTHOR are predefined. All the others can be named ) N
(   by you. The only condition is: your fields in the database and in the formats) N
(   have to coincide. If some field is present in the format string but there ) N
(   is no value of it in the database, sign $reservedEMPTY_FIELD_SIGN will be ) N
(   printed out instead \(see command line parameter --empty_field_sign\);) N
(   by default $reservedEMPTY_FIELD_SIGN == '???'.) N
(   My suggestion is: use YEAR, VOL, PAGE, etc. for the year, volume and page and) N
(   don't name page as RTY45 - this is mush less readable.) N
() N
(-------------------------------------) N
() N
(5. RUNNING BIBLIO) N
() N
(So, now you have references database and format file. It is time to talk about) N
(command line parameters. Here they are:) N
() N
( ESSENTIAL PARAMETERS) N
() N
(+ -o output.file  => $OUT_TEX ; ) N
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(                     if no given, assuming $OUT_TEX = "biblio.$TEX_NAME") p n
(+ -f format.file  => $FORMAT_NAME  ) N
(                     \(can introduce templates for Macromolecules, ) N
(                     etc. If given, "in-tex" parameters will be) N
(                     ignored!!!\)) N
() N
(+ -d dbase.file   => @REFS_FILES \(where all info about refs is!\)) N
(  accepts many arguments) N
() N
(+ -a abbrev.file  => file of abbreviations \(tex file\)) N
(                     if given, will be inserted just BEFORE) N
(                     "\\begin{references}" in the output.file.) N
(                     Consists of anything you want, but the idea is) N
(                     to use it like "\\def\\mml{Macromol.}") N
(                     and  have entry) N
(                        JOURNAL = \\mml) N
(                     instead of) N
(                        JOURNAL = Macromol.) N
(                     in the dbase.file.) N
() N
(+ -v <number>     => verbosity level \(0-5\) $verbosity_level) N
() N
(+ -h or --help    => short help information ) N
() N
(+ --nobibitem     => $optionsKEEP_BIBITEM_AND_CITE=0. Default is 1!!!) N
(                     \(read 2.C too\)) N
(                     If not given, Biblio will insert all references ) N
(\(formated, of course\) into the out-TeX document, and that's it! You will ) N
(have  \\cite-commands as you had them before.  List of references will be ) N
(produced by LaTeX itself \(with \\bibitem\). ) N
(If given \(but NO --uselist\), it will print your references as a simple text,) N
(flushed left. ) N
() N
() N
(+ --uselist       => $optionsREFS_AS_TEX_LIST=1 Default is 0!!!             ) N
(                     Will output the references list as a TeX list) N
(with counter. Looks much better than \\flushleft \(try it!\)) N
() N
(     ) N
(\(if no --nobibitem nor --uselist is given it is assumed to use \\bibitem) N
( if --nobibitem is given, it will use \\flushleft) N
( if --nobibitem AND --uselist are given it will use \\list) N
(\)) N
() N
() N
( ADDITIONAL PARAMETERS) N
() N
(     key                             variable in the source,default value) N
(                                                  and some info) N
() N
(+ --etal "{\\it{et al}}"           => form of "et al"-string in $reservedET_AL) N
(                                     \(see 4.1.C\)) N
(+ --separator "----------\\n"      => separator in the database-file) N
() N
(+ --not_insert_empty_field_sign   => $optionsINSERT_EMPTY_FIELDS_SIGN=0) N
(                                     If some field is present in the format ) N
(string for the given TYPE, but is not in the database, Biblio will ) N
(insert some sign instead \(see --empty_field_sign\). ) N
() N
(+ --empty_field_sign xxx          => $reservedEMTY_FIELD_SIGN = '???') N
(                                     \(see --not_insert_empty_field_sign\)) N
() N
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(+ --start_refs                    => @STARTREFS=  ) p n
(  accepts many arguments      \('begin{references}','begin{thebibliography}'\);) N
(                                  Tells where Biblio has to start inserting ) N
(                                  the references list.) N
() N
(+ --end_refs                      => my @ENDREFS=  ....) N
(   accepts many arguments) N
() N
(? --bibitem_string                => my $BIBITEM = '%'."\\n".'\\bibitem{';   ) N
(  ) N
(+ --version                       => version info) N
() N
(+ --movepoint                     => added in ver1.1) N
(                                     make "word.\\cite{} Another sent") N
(                                     from "word \\cite{}. Another sent") N
(      Everything in the variable $what_we_call_point='.,;:' is considered ) N
(      to be a "point".) N
(      This way of making citations is required by some journals ) N
(      \(for instance, Macromolecules\)  which have citation in the form) N
(                           "in recent works$^1-5$") N
(      There point \(or comma,...\) has to be placed BEFORE citation, like) N
(                  'works.$^{1-5}$' but NOT 'works$^{1-5}$.') N
(      NOTE: this will work only for point IN THE SAME LINE, like) N
(      'was show recently \\cite{q2,lab4,yt6}. Therefore') N
(      but NOT for) N
(      'was show recently \\cite{q2,lab4,yt6}) N
(      . Therefore'                     ) N
(    ) N
(\(not everything is accomplished. So, ?-sign means, that in your version ) N
(this parameter might be still not working\)) N
() N
(-------------------------------------) N
() N
(6. EXAMPLES) N
() N
(   A. I have a couple of format files \(in the directory called "formats"\) ) N
(and a database. First, about the structure, I decided to follow. \(It does ) N
(NOT mean you have to do it in the same way!\)) N
() N
(Types I use are) N
() N
(ARTICLE   just regular article) N
(ARTICLE0  submitted or accepted article) N
() N
(BOOK      regular book) N
(EDBOOK    article in a book \(with an editor!\)) N
(INBOOK    article in a book without editor) N
() N
(EPRINT    electronic preprint) N
() N
(Some examples of format files you can find in the "formats" directory.) N
() N
(Example of a database is called "refers.db".) N
() N
(  ) N
(  B. Document "EXAMPLES/2sorts/2sorts.tex" is an introduction ) N
(to one of my articles.  You can use it as an example. ) N
(It needs templates which are in the "formats" dir. ) N
(Just type "./libtex" and that's it!) N
() N
(  C. Document "EXAMPLES/2sorts/2sorts_formats.tex" is ) N
(the same as in B., but all formats are included into the header ) N
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(of the document. Read this header to find out how to compile it.) p n
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(  D. Document "EXAMPLES/hairy/hairy.tex" shows how to use abbreviations.) N
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(-------------------------------------) N
() N
(7. ADDITIONAL SCRIPTS) N
() N
(You can find some more scripts in the top directory.) N
() N
(   A. libtex ) N
(      is a useful script for processing TeX documents on the ) N
(      stage of their development. It can be easily adjusted ) N
(      \(open it in any text editor and change parameters\). The idea is ) N
(      to keep its copy at the same directory where your document \(tex file\)) N
(      is situated.) N
(      Then instead of running LaTeX itself you have to run "libtex" as) N
(      libtex filename) N
(      \("filename" WITHOUT tex extension!!! For 2sorts.tex it is "2sorts"\)) N
() N
(      JOURNAL - name of the template) N
(      PREFIX  - Biblio's home directory \(where in the "formats" directory all) N
(                formats are stored\)) N
() N
(   B. biblist_html  ) N
(      Makes an HTML formated list from your references database. I use \(as you ) N
(      could see in refers.db\) field URL for articles, which I have ) N
(      electronically. This script will run "biblist.pl" \(see below\) with --html ) N
(      key. This will produce nice html output with hyperlinks to your e-library) N
(      \(it will put prefix "--prefix" for all hyperlinks except starting already) N
(      with "http:" \)) N
(      Of course, you can use "--prefix /home/usrname/base/" if you want to make) N
(      all refs local.) N
() N
(   C. biblist) N
(      The same as the previous one but output in TeX format. Uses biblist.pl) N
(      without --html key.) N
() N
(   D. biblist.pl) N
(      Makes a list of references from the whole database file. Can output in ) N
(      TeX file or HTML. Has switches: almost all, which biblio has plus --html.) N
(      Does not have --uselist \(it is always on\), --start_refs, --end_refs.) N
(      And, of course, it does not need an input TeX file! Therefore you) N
(      always have to provide format file.) N
(      If --html is not given, produces TeX file.) N
(      HTML output needs special formats, of course. Example is in) N
(      EXAMPLES/formats/formats_html.biblist) N
(      ) N
(      Example of a format file for TeX output is in) N
(      EXAMPLES/formats/formats.biblist ) N
() N
(   E. bibcheck.pl  \(added 17 Sep 2001\)) N
(      Checks your database \(one ore more files containing references\).) N
(      Complains if it has:) N
(       - records with empty LABEL or TYPE) N
(       - several records with the same LABEL) N
(      Has specific parameter "--noexit" which means "do not exit if ) N
(      found a record without a label, just go on". By default it will) N
(      halt in this case.) N
(      Parameter -e \(or --errors\) says "after how many errors exit the program") N
(      \(default is 5\)) N
(      For instance:) N
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(        bibcheck.pl -e 10 -d myrefers.db onemorerefs.db) p n
(      or) N
(        bibcheck.pl --errors 10 -d myrefers.db onemorerefs.db ) N
(      will process files "myrefers.db" and "onemorerefs.db" but exit if at ) N
(      some point number of errors will exceed 10.) N
(      ) N
(   ) N
(That's all for the moment.) N
(    ) N
(-------------------------------------      ) N
() N
(8. INSTALLATION GUIDE and SHORT INSTRUCTIONS) N
() N
(I decided to put this section at the very end because now, I hope, you know what) N
(you are installing. ) N
() N
(After unpacking the archive you have:) N
() N
( * biblio.pl     - the main "executable") N
( * dir formats   - format files \(template\) and) N
(                   abbreviations file "abbr.tex". Ready for use.  ) N
( * biblist.pl; biblist.pl;  biblist_html; bibcheck.pl ) N
(                 - some additional scripts \(see section 7\).) N
( * dir EXAMPLES  - examples \(see section 6\).) N
( ) N
(and bash script "install" to help you to install.) N
() N
(1. Edit script "install" First two lines have to point to) N
(   * PREFIX to the directory, where you want to install biblio ) N
(     \(formats, examples, etc.\). It must NOT exist yet.) N
() N
(   * BINDIR to the binaries directory, where it will put links to biblio and ) N
(     biblist) N
() N
(   Edit biblio.pl and ADDSCRIPTS/biblist.pl: in the first line it should be) N
(   a full path to your Perl!!!) N
() N
(2. Run "./install". Then change dir to your PREFIX dir and check, that biblio.pl) N
(   and everything in the ADDSCRIPT directory is executable. If not, do) N
() N
(   chmod a+x name_of_the_file) N
() N
() N
(3. If installation script failed, you can do it yourself. ) N
(   Just create a directory for biblio.) N
(   Copy there everything you found in the current directory \(see above\).) N
(   Then) N
() N
(   ln -s biblio biblio.pl) N
() N
(   Chenge dir to your normal binaries dir and do) N
() N
(   ln -s biblio PREFIX/biblio) N
(   ln -s biblist.pl PREFIX/ADDSCRIPT/biblist.pl) N
() N
(   where PREFIX has to be a real path \(like /usr/local/biblio\)) N
() N
(   Be sure about file permissions \(everybody, or at least you, has to be) N
(   able to execute!\).) N
() N
(That's all. Now you have commands "biblio" and "biblist") N
() N
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(About usage of additional scripts. What I normally do is like this:) p n
() N
(1. Copy libtex from ADDSCRIPTS to the directory where my current TeX document) N
(is. ) N
() N
(2. Edit it ) N
(   ) N
(   * JOURNAL is the name of the template) N
(   * PREFIX  is the place where you keep biblio \(and all its stuff\)  ) N
(   * REFS is your references database) N
(   * FORMATS is a place where you keep format files \(templates\)) N
(   * PROJECT is a name of your TeX file WITHOUT extension. ) N
(     Normally you do for file myarticle.tex) N
(        libtex  myarticle) N
(     and myarticle goes to PROJECT variable.) N
(     But you can just put it like) N
(     PROJECT=myarticle) N
(     in the text of libtex and then type ) N
(        libtex) N
(     only to compile your TeX document.) N
( ) N
(3. After running libtex \(if everything goes right\) you will have) N
(   a file named "myarticle.dvi" and "myarticle.1.tex" and some more, which are) N
(   not important.) N
() N
(Working version of libtex \(it works even without any installation\) is in the ) N
(EXAMPLES dir. Try it.) N
(-----) N
() N
(About biblist - it produces a full references list from all the entries you have) N
(in your database. Copy it somewhere and edit:) N
(REFSTEX is the output file;) N
(FORMATS is the format file. You can edit it, if you like.) N
() N
(Run biblist and you get references.tex file, and references.dvi file.) N
(-----) N
() N
(About biblist_html - does the same what biblist does, but outputs in HTML.) N
(About --prefix option you can read in 7.B and 7.C. Formats, of course, are ) N
(different from what you use for TeX output. I provide formats_html.biblist file) N
(\(find it in the "formats" directory\) - you can easily edit it.) N
() N
(-------------------------------------      ) N
() N
(9. PERL TO C) N
() N
(If everything went OK and you are going to use biblio, I have an idea about ) N
(speeding it up. You can use "perlcc" to make a real binary from Perl's script.) N
(Sometimes it is a good idea, sometimes not. What I found: binary of biblio ) N
(is 50% \(yeah, yeah - 50!\) faster than Perl-script. So it is worthy of trying!) N
(Do:) N
() N
(   perlcc -o biblio.exe  biblio.pl) N
() N
(and you will get biblio.exe executable \(it will take some time - translation to ) N
(C and then compilation\).) N
() N
(If you succeeded, make a link called "biblio"  to biblio.exe \(at the same ) N
(directory, where you have biblio.pl; so, you have to erase an old link biblio ) N
(pointing to biblio.pl\).) N
() N
(All the rest is the same.) N
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() p n
(If you are interested in C sources, try ) N
() N
(   perlcc -sav -o biblio.exe  biblio.pl) N
() N
(It will save sources for you! Just great! Althoug I don't think, this C-source ) N
(is really readable! :\)) N
() N
(-------------------------------------  ) N
() N
(10. TO DO) N
() N
(A lot of things are very raw. Only a couple of people tried it and I cannot say) N
(it was sufficiently tested. So if you discover any bug or have any suggestion ) N
(write directly to me \(rstepanyan@yahoo.com\).) N
() N
(This script now supports only very primitive way of citation: each citation) N
(is numbered and this number is its identifier. So, citation in the form ) N
("Smith\(1990a\)" are impossible. That is, probably, the first thing to do) N
(\(This kind of citations is used in Rev. of Modern Physics, for instance\).) N
() N
(I do not have too much time right now, but I am constantly thinking about it. ) N
() N
(-------------------------------------  ) N
() N
(11. Known Bugs) N
() N
(11.A.  Lost Lines \(for ver.1.2 only\)) N
( ) N
(From ver.1.2 there is no points and commas at the beginning of the line.) N
(Like in the piece of text) N
() N
(    Was shown in work) N
(    \\cite{lab2}. Blah-Blah-Blah) N
() N
(if we use --movepoint option we get) N
() N
(    Was shown in work) N
(    .\\cite{lab2} Blah-Blah-Blah) N
(                 ) N
(\(and ver.1.1 really did it this way\).) N
(But it should be \(and from ver.1.2 it IS\)) N
() N
(    Was shown in work.\\cite{lab2} Blah-Blah-Blah) N
() N
(That is exactly what is fixed now. Although it adds a new bug: if you have) N
() N
(    Was shown in work) N
(    % Blah-Blah-Blah) N
(    \\cite{lab2}. Blah-Blah-Blah#) N
() N
(then one line is LOST!!!! \(Guess why!\)) N
() N
(-------------------------------------) N
(Oh, now it is really the EOF!) S
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