Compile newick_parser

[ArtPoon]

Currently we're carrying around these files:

• newick_parser.c
• newick_parser.h
• newick_lexer.c

These were generated from the source files newick_lexer.l and newick_parser.y ages ago and we've had a difficult time reproducing this process since. Unfortunately this is a problem for making a portable distribution.

I have been able to compile the above source files in Ubuntu 18.04 as follows:

bison -d newick_parser.y
flex newick_lexer.l
gcc newick_parser.tab.c lex.yy.c -lfl -lm -ligraph

which yields the default binary a.out.

How do we generate the .c and .h files mentioned at the top of this post?

[ArtPoon]

Ok, newick_praser.tab.h and newick_parser.h are nearly identical:

art@orolo:~/git/clmp/src$ diff newick_parser.tab.h newick_parser.h
33,34c33,34
< #ifndef YY_YY_NEWICK_PARSER_TAB_H_INCLUDED
< # define YY_YY_NEWICK_PARSER_TAB_H_INCLUDED
---
> #ifndef YY_YY_NEWICK_PARSER_H_INCLUDED
> # define YY_YY_NEWICK_PARSER_H_INCLUDED
56a57,64
> /* Tokens.  */
> #define COLON 258
> #define SEMICOLON 259
> #define LPAREN 260
> #define RPAREN 261
> #define COMMA 262
> #define STRING 263
> #define NUMBER 264
63c71
< #line 25 "newick_parser.y" /* yacc.c:1909  */
---
> #line 26 "newick_parser.y" /* yacc.c:1909  */
68c76
< #line 69 "newick_parser.tab.h" /* yacc.c:1909  */
---
> #line 77 "newick_parser.h" /* yacc.c:1909  */
81c89
< #endif /* !YY_YY_NEWICK_PARSER_TAB_H_INCLUDED  */
---
> #endif /* !YY_YY_NEWICK_PARSER_H_INCLUDED  */

so there should be some option for removing the tab annotation.

[ArtPoon]

lex.yy.c is similar to newick_lexer.c but my version of flex is different (2.6.4 versus 2.5.35)

[ArtPoon]

Give up if we can get packages working on macOS and Windows - this is only an issue if we need to change parser.