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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

The "data" variable can now be overridden using the variable statement. This is

applicable in Ruby and Java code only.

github.com/BioJulia/ragel - 0791b5fe251377005113e87cf28d34910bd157df authored over 17 years ago by Adrian Thurston <[email protected]>
Added an item.

github.com/BioJulia/ragel - ae8c1cf5108f3f31a69f07e26b0479df0c455f04 authored over 17 years ago by Adrian Thurston <[email protected]>
Adjusted whitespace in xml output.

github.com/BioJulia/ragel - 35a49213842e4793032f4c0e63392e9f15acbf37 authored over 17 years ago by Adrian Thurston <[email protected]>
Documentation updates.

github.com/BioJulia/ragel - edba9d1d539c9224aa70810cf2928d6204d2d2ea authored over 17 years ago by Adrian Thurston <[email protected]>
Can cleanup the xml code generation and remove the holdte and execte tags

following the previous commit.

github.com/BioJulia/ragel - f40a647192521e729f692eb1a5e7cd261d35b0ec authored over 17 years ago by Adrian Thurston <[email protected]>
The p varialbe is now set up at the beginning of a scanner action, rather than

at the end. This leaves scanner actions free to manipulate p and removes the
need for the special...

github.com/BioJulia/ragel - ec84302b555eefabb91927532f31b274af41a5df authored over 17 years ago by Adrian Thurston <[email protected]>
Changed the names of the generated scanner actions to match the types of

generated scanner actions.

github.com/BioJulia/ragel - 2ef05308a93d53df9f25a54280bf0b2c5b002bbc authored over 17 years ago by Adrian Thurston <[email protected]>
Use the variable feature for pullscan.

github.com/BioJulia/ragel - 0e7b3e25bccd42d1385abea5b6011189bf733a40 authored over 17 years ago by Adrian Thurston <[email protected]>
Include the offset of p in the test.

github.com/BioJulia/ragel - c2aea7910c8934bb91d14f01c0385cc8170781a8 authored over 17 years ago by Adrian Thurston <[email protected]>
Put the scanner action generators together.

github.com/BioJulia/ragel - c7c63a899e841ee4c3e12506b885a968669a1553 authored over 17 years ago by Adrian Thurston <[email protected]>
Updated documentation for -S and -M.

github.com/BioJulia/ragel - 0205b71aab5317bea8c83872ec7f8d55bc7adbc6 authored over 17 years ago by Adrian Thurston <[email protected]>
Bug fix: when -S or -M was given the ragel version number was not emitted,

causing the backend to reject the intermediate format. From Tim Potter.

github.com/BioJulia/ragel - 7508b821588f887c6ba9e1eb34ddcb367a4cb81f authored over 17 years ago by Adrian Thurston <[email protected]>
Need to isolate the start state of a scanner before setting the to-state and

from-state actions which clear and set tokstart.

github.com/BioJulia/ragel - 7555fdc4ce176c4a9e724881b9a5a8f976aefe56 authored over 17 years ago by Adrian Thurston <[email protected]>
Version 5.21.

github.com/BioJulia/ragel - a5a4f8c9a0ee69fe14837f493ce8ff3491b214c8 authored over 17 years ago by Adrian Thurston <[email protected]>
Typo fixes from Barry Arthur.

github.com/BioJulia/ragel - 4a29f359e78c409ee9d7cfc2255122f345419952 authored over 17 years ago by Adrian Thurston <[email protected]>
Updated copyright date and added Java and Ruby to the list of supported host

languages.

github.com/BioJulia/ragel - ba17e1605d6df322185eaaf0760fa792b5a54c02 authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed an inconsistency in the value of p following an error. In the C directly

executable code (rlgen-cd -G2) p was left at the character where the error
occurred, which is cor...

github.com/BioJulia/ragel - bb93f1b2fb3fb0525bac738039e2e8d59a852f63 authored over 17 years ago by Adrian Thurston <[email protected]>
Added an item.

github.com/BioJulia/ragel - 58679392108ecbd86169082fa02fdd5b7a9f323a authored over 17 years ago by Adrian Thurston <[email protected]>
Renamed errintrans.rl -> erract6.rl.

github.com/BioJulia/ragel - 145b30b90fdcfb0c5f8de1c4dd231a2a406fea06 authored over 17 years ago by Adrian Thurston <[email protected]>
Added new sections (import/export/variable) and expanded on running the

executables.

github.com/BioJulia/ragel - 15f3fc02455d1644c1401aeb5730cfee1c8497ef authored over 17 years ago by Adrian Thurston <[email protected]>
Notes for version 5.21.

github.com/BioJulia/ragel - d541cba3e604b9a1190a00814ab526a90bd72d38 authored over 17 years ago by Adrian Thurston <[email protected]>
The alphabet type is now communicated from the frontend to the backend using a

one-word internal name instead of an array offset.

The Ruby host language types were just copied...

github.com/BioJulia/ragel - 015024b626946d0a7e601a9b4f391889c232bf86 authored over 17 years ago by Adrian Thurston <[email protected]>
Casting from an array to a pointer is not legal d code.

github.com/BioJulia/ragel - f07f48a8beb3c3f9615cccccfc9184c175f44e00 authored over 17 years ago by Adrian Thurston <[email protected]>
Added Victor Hugo Borja.

github.com/BioJulia/ragel - 9d4fa0f8a37ef279267f4de2e4b150c7688eb222 authored over 17 years ago by Adrian Thurston <[email protected]>
The version number is now included in the intermediate file. A error is emitted

if there is a mismatch.

Added an item and removed an item from the TODO.

github.com/BioJulia/ragel - cb1f23a2294f98185ce9efaa65324b8afd02497c authored over 17 years ago by Adrian Thurston <[email protected]>
Parse errors in the intermediate XML file now cause the backend to exit

immediately. The recovery infrastructure isn't there and segfaults are likely.

When no input is ...

github.com/BioJulia/ragel - 2ababce876d0eea1de989e53ebfa9fae602d196f authored over 17 years ago by Adrian Thurston <[email protected]>
The "curstate" argument to the variable statement has been changed to "cs".

Updated the tests.

github.com/BioJulia/ragel - 22966e3c50763511b15ae8bb17253b3c3dbb6bbc authored over 17 years ago by Adrian Thurston <[email protected]>
In the variable statement changed the name "curstate" to "cs" (the default

name used for the current state) and implemented the other names as their
defaults. Now all varia...

github.com/BioJulia/ragel - 40a0ec58dec7120aceed67a487c53b8c28b2741e authored over 17 years ago by Adrian Thurston <[email protected]>
Added a language-independent test case for the negative sense of conditions and

the necessary transformation support.

github.com/BioJulia/ragel - fa4d8daacbf13234e82298bd3ff3762b88f740ea authored over 17 years ago by Adrian Thurston <[email protected]>
Can now embed the negative sense of a condition.

Added new condition embedding syntax:
expr inwhen cond - The transitions into the machin...

github.com/BioJulia/ragel - 2ad5e8b2762d90e74ae815760697f45b50545180 authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed bugs in the binary searching for condition keys in both the Ruby and Java

code generation.

github.com/BioJulia/ragel - c1f4f16963afc8dd71300c096718b35ebad1148c authored over 17 years ago by Adrian Thurston <[email protected]>
Work on the state action embedding operator section.

github.com/BioJulia/ragel - d45f13aae7bb723562fd176c37932c8db8d01ca0 authored over 17 years ago by Adrian Thurston <[email protected]>
A better solution to resolving the - ambiguity: force a shortest match of term.

github.com/BioJulia/ragel - 6682667b71c89be8df021b7697011f7d61da0d16 authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed typos from from Josh Purinton. Made a few other improvements.

github.com/BioJulia/ragel - b70f7e3564e021881ba57f2c4448c3960fdf651f authored over 17 years ago by Adrian Thurston <[email protected]>
Bug fix: when fhold was used in scanner pattern actions which get executed on

the last character of the pattern (pattern matches which do not require any
lookahead), fhold was...

github.com/BioJulia/ragel - f6d9bebb8cba84b1a5a5be55e9c4a5e86280d879 authored over 17 years ago by Adrian Thurston <[email protected]>
Improved the message for 5.16.

github.com/BioJulia/ragel - d37e2dc86f9f2689a2713c2a046ac56e96619bdb authored over 17 years ago by Adrian Thurston <[email protected]>
Removed unused variable.

github.com/BioJulia/ragel - 6f8c273cdaee435b5757b4fa0cd382861dfdd6d3 authored over 17 years ago by Adrian Thurston <[email protected]>
Implemented sortByStateId which is called for table-based code generators. The

frontend will normally sort, however it may be possible that the intermediate
file gets edited, i...

github.com/BioJulia/ragel - b0bf96a6636c619b5f9669b287ff65ef6d96237a authored over 17 years ago by Adrian Thurston <[email protected]>
Added an item.

github.com/BioJulia/ragel - 01d0b082c946074ceeaac04efbf3b280d5395288 authored over 17 years ago by Adrian Thurston <[email protected]>
Slight reorganization for 5.20 notes.

github.com/BioJulia/ragel - a240ac156f1ab52b0dbf9b6c4ee17cf79bdfef6c authored over 17 years ago by Adrian Thurston <[email protected]>
Documentation for 5.20.

github.com/BioJulia/ragel - 791d61721a201d20b895c07c8dda10b1451a85f6 authored over 17 years ago by Adrian Thurston <[email protected]>
Added a language-independent test based on cppscan3.rl. Added the necessary

transformations as well.

github.com/BioJulia/ragel - 4aa8d919a54dbd6fa0749628f70a86a050f44f8d authored over 17 years ago by Adrian Thurston <[email protected]>
Some cleanup and fixes to the runtests script. The -P option will be changing.

Its use from runtests is currently disabled.

github.com/BioJulia/ragel - f8172875fa56489a6ffc89a3acdef75dd2ed71bb authored over 17 years ago by Adrian Thurston <[email protected]>
Added clang4, a new language independent test case derived from clang1. Also

added the transformations necessary to support it.

github.com/BioJulia/ragel - d0cc9ce8f781cc852363ef4ce64cea2519a1a891 authored over 17 years ago by Adrian Thurston <[email protected]>
Organized ideas for 6.0.

github.com/BioJulia/ragel - 1624eee0dd4b1d11ab4d5264bdb6a466db651648 authored over 17 years ago by Adrian Thurston <[email protected]>
A test for the ruby frontend scanner.

github.com/BioJulia/ragel - fbedb1510f93c71228aa2ed432aa1b0fb07867b0 authored over 17 years ago by Adrian Thurston <[email protected]>
Added an item.

github.com/BioJulia/ragel - ba7ff26c0bd53f9f3a6a2d578db19ee965781b3e authored over 17 years ago by Adrian Thurston <[email protected]>
Should use the most recent version of Ragel and Kelbt for building the parsers.

github.com/BioJulia/ragel - e57802ceb4cbb93ef0f99ee9d6f2341981d183f7 authored over 17 years ago by Adrian Thurston <[email protected]>
Delete the temporary file.

github.com/BioJulia/ragel - ae0b8e5d9c57bc177ad5a1f75c4f0fde9eeb5f34 authored over 17 years ago by Adrian Thurston <[email protected]>
Added support for Ruby comments and regular expression literals.

github.com/BioJulia/ragel - 0cd2233ecac77db4c4a31746defd0f858d32c1be authored over 17 years ago by Adrian Thurston <[email protected]>
The runtests script was improved so that the Java and Ruby test cases don't

need ALLOW_GENFLAGS set.

github.com/BioJulia/ragel - 33979d1c69a31198eeb05e5a73553feccb8b4ecb authored over 17 years ago by Adrian Thurston <[email protected]>
Various fixes which get the existing ruby test cases (via the language

independent test cases) working. Fixes to control flow, scanners, action
execution and others.

github.com/BioJulia/ragel - 4ba899107aab08e917b8ef4069c399d92409e77e authored over 17 years ago by Adrian Thurston <[email protected]>
Declaration of stacks now works.

github.com/BioJulia/ragel - 1f3435ef4904be4e7a4ff3f4a0557ca45eb4dee1 authored over 17 years ago by Adrian Thurston <[email protected]>
First cut of a test-suite transformation for Ruby. Some of the tests work.

github.com/BioJulia/ragel - 357812388806c579809923f7169e166243b0a725 authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed break and hold.

github.com/BioJulia/ragel - 24e699bf1b13e83457f098134ba1b4208572c528 authored over 17 years ago by Adrian Thurston <[email protected]>
Use the new import feature of Ragel for bringing in defines from the parser

header as machine definitions instead of repeating them in scanner.

github.com/BioJulia/ragel - acd3f21a3f5f9ba4a729b36cb3069a6e012df752 authored over 17 years ago by Adrian Thurston <[email protected]>
When building on kubuntu 6.10 the -n option to echo is on by default causing

the \ character to be interpreted as an escape. Filtering through tr is one way
around this.

github.com/BioJulia/ragel - cff741f1cacc932e38d2c4e84464ddb7e7a24c6e authored over 17 years ago by Adrian Thurston <[email protected]>
Removed malloc.h includes. This is not a standard header and does not exist on

OSX. Use stdlib.h instead.

github.com/BioJulia/ragel - bd06e4b9f09986bbb097da9975371a054e3fcd24 authored over 17 years ago by Adrian Thurston <[email protected]>
Removed claim that generated code runs nearly as fast as hand-coded parsers, as

this claim is not substantiated.

github.com/BioJulia/ragel - c1102466a41456794b82260b54f1052dd746e063 authored over 17 years ago by Adrian Thurston <[email protected]>
The cs variable is now always initialized, unless the "nocs" option is given to

the write init command. If there is no main machine, cs is initialized to the
entry point of the ...

github.com/BioJulia/ragel - c80367122a7f7fe58fcb1a1c07dcf36211f5edf7 authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed parallel make dependency bug. Patch from Jeremy Hinegardner.

github.com/BioJulia/ragel - 55da3df7d968c19730d39c8edcf6187d81a4d157 authored over 17 years ago by Adrian Thurston <[email protected]>
In the SEE ALSO section changed rlcodegen to rlgen-cd, rlgen-dot and

rlgen-java.

github.com/BioJulia/ragel - 2c7eb15c76a4ea1e9016f29615c242cb8d53f144 authored over 17 years ago by Adrian Thurston <[email protected]>
Some fixes which silence warnings emitted by the microsoft compiler. Adapted

from patch by Josef Goettgens.

github.com/BioJulia/ragel - 054bd8a0cab31d6f41dc5b26581e148a7c876a02 authored over 17 years ago by Adrian Thurston <[email protected]>
The IDENT_* functions don't need to be virtual.

github.com/BioJulia/ragel - 0743475ab26641f413c1a8ddef0b72be56b3b4a2 authored over 17 years ago by Adrian Thurston <[email protected]>
Documented version 5.19.

github.com/BioJulia/ragel - df06ec5bebc086554badc5db315f895a68b91641 authored over 17 years ago by Adrian Thurston <[email protected]>
Updated the manual section on instantiation to reflect the 5.19 features.

Exports in D cannot use defines like C. Static const ints are used instead.
Removed a left-over d...

github.com/BioJulia/ragel - 8ff9e3adb79402be8c5b3669b8bf5f41174a7b9f authored over 17 years ago by Adrian Thurston <[email protected]>
Added a C test for importing and a D test for exporting.

github.com/BioJulia/ragel - a40e1200465104568eccd187c636cd3073fbbdf3 authored over 17 years ago by Adrian Thurston <[email protected]>
Handle the unset startState case in dot generation.

github.com/BioJulia/ragel - f3efff6031f2e10f992b9fe5b1b6762cd9ff0b47 authored over 17 years ago by Adrian Thurston <[email protected]>
Importing moved into the primary scanner. Import statements now open up a new

Scanner object which looks for outside code tokens that can be interpreted as
machine definitions...

github.com/BioJulia/ragel - bfbe24e249fe187a170591353c3cec06f099c0e7 authored over 17 years ago by Adrian Thurston <[email protected]>
Started on a scanner for importing definitions.

github.com/BioJulia/ragel - d1f9c18f099743b090a70ab1618a4caef885a004 authored over 17 years ago by Adrian Thurston <[email protected]>
Moved scanner class into a new header rlscan.h.

github.com/BioJulia/ragel - beb36e1365c6bf1d424a9fb7c66fe87348ed264e authored over 17 years ago by Adrian Thurston <[email protected]>
Silence warnings about definite and/or possible use before initialization.

github.com/BioJulia/ragel - aeb84ec29bd4ae6617604db17eb6aecad775fd60 authored over 17 years ago by Adrian Thurston <[email protected]>
If the main machine is not present then do not emit an error. Generate the

machine without a start state and do not initialize cs in the write init code.

github.com/BioJulia/ragel - 975c2d985d3c4f0b90af89964dc68fac9f0effb3 authored over 17 years ago by Adrian Thurston <[email protected]>
Added tests for exports and entry points. For machine exports, added "ex_" in

between the machine name and the export name.

github.com/BioJulia/ragel - 0e9748592dd7f9233c34996e9caf843551cfe98e authored over 17 years ago by Adrian Thurston <[email protected]>
Added exports and entry points to Java and Ruby code generation.

github.com/BioJulia/ragel - f070afdbb38224aa16ff92689b958ee38cf1b8d8 authored over 17 years ago by Adrian Thurston <[email protected]>
The startstate, first final and error state writing can be moved to FsmCodeGen.

At this time entry points are written as well.

github.com/BioJulia/ragel - 903140b5af721bb6fc0319bab20bec41c118b91c authored over 17 years ago by Adrian Thurston <[email protected]>
All machine instantiations are now implicitly referenced and always generated,

even if they are not referenced. In the backend, entry points will be written
out alongside start...

github.com/BioJulia/ragel - 5891ba126f162ae38ce9c6297bffb169e7ea8bca authored over 17 years ago by Adrian Thurston <[email protected]>
In the port from flex to ragel, the Name separator :: in Ragel code was lost.

Added it back.

github.com/BioJulia/ragel - 478bb4d6cc95e9d0ecc0791e28f564b26c1da5be authored over 17 years ago by Adrian Thurston <[email protected]>
Implemented an export feature, for exporting single-character machine

definitions in #define format.

Changed function names: writeOut*() => write*().

github.com/BioJulia/ragel - 45708f34570ee21801a42415ff3a517ce1b2ac26 authored over 17 years ago by Adrian Thurston <[email protected]>
Switched from rlcodegen to rlgen-cd. Silenced a warning in statechart.rl.

github.com/BioJulia/ragel - 772cfeae2e912c8341e33f3b4eb8ca8907333cb7 authored over 17 years ago by Adrian Thurston <[email protected]>
Clean target missed new man pages, fixed.

github.com/BioJulia/ragel - e198d5b994667dd87b75d802ba3441a6c38436d0 authored over 17 years ago by Adrian Thurston <[email protected]>
Removed completed item. Added new item.

github.com/BioJulia/ragel - 7fd7979618620d7fb1034ff8437557844206b13d authored over 17 years ago by Adrian Thurston <[email protected]>
When multiple conditions are executed on a single character they need to have a

forced order. Previously, ordering relied on pointer-based sets, which caused
results to vary by ...

github.com/BioJulia/ragel - 4821a45415f38bc697ea4eef95da049ffade6dfc authored over 17 years ago by Adrian Thurston <[email protected]>
Removed item just completed.

github.com/BioJulia/ragel - 947b51210397908ceaa44eddd1e228e5eaea08f3 authored over 17 years ago by Adrian Thurston <[email protected]>
Added an option -l to rlgen-cd which inhibits the the writing of #line

directives.

github.com/BioJulia/ragel - 3894c9486f153ffa0ac4dd97000ce13ed2aacd93 authored over 17 years ago by Adrian Thurston <[email protected]>
These now live in rlgen-dot.

github.com/BioJulia/ragel - 3f6ccd131c51f193839c065d0e4be9a52b097055 authored over 17 years ago by Adrian Thurston <[email protected]>
Added a new syntax for verbose embeddings. This adds parentheses:

$from(action_name);

Verbose embeddings without parentheses can make code difficult to read
...

github.com/BioJulia/ragel - 4da8c7693e8df9da6aae936b46e0419246083d1d authored over 17 years ago by Adrian Thurston <[email protected]>
Added two entries.

github.com/BioJulia/ragel - 86fd9ecf13bc2df2c6af93170851ff3e521907cb authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed the distclean target, it was calling clean in the subdirs. Added a define

for strcasecmp which is not available on windows.

github.com/BioJulia/ragel - bdca4ae9eb15cdd3a4f50cf842891ad35dfbb5f3 authored over 17 years ago by Adrian Thurston <[email protected]>
Make use of @datadir@ and @mandir@ in doc/Makefile.in for specifying where

documentation should be installed. Patch from Marcus Rueckert. The prefix
variable should be lowe...

github.com/BioJulia/ragel - 93669bc82056fd996d675676226e486fb999c801 authored over 17 years ago by Adrian Thurston <[email protected]>
Added Josef Goettgens.

github.com/BioJulia/ragel - 4fa3472fca6ed9d815011423845a6595fc0e44eb authored over 17 years ago by Adrian Thurston <[email protected]>
Removed extra ;, spelling fix in comment.

github.com/BioJulia/ragel - 3981ae601c53972ff37e2b6ad0ce3f052e404301 authored over 17 years ago by Adrian Thurston <[email protected]>
The Action::numRefs() and RedAction::numRefs() functions should return int.

Since the numbers these functions return are usually very low and the result is
only checked with...

github.com/BioJulia/ragel - 35ef289dbfe0233d466739b6c302d7bec765e66f authored over 17 years ago by Adrian Thurston <[email protected]>
Added malloc.h includes. From Josef Goettgens.

github.com/BioJulia/ragel - 035446fb052e6ab889f5a4034cc44ed9e17f9a00 authored over 17 years ago by Adrian Thurston <[email protected]>
Fixed some references to Java left over from the split. Also, the line

directive function does not need to guard against java code.

github.com/BioJulia/ragel - ac20faa1a7973f533f69560d7dca752a8f4932c0 authored over 17 years ago by Adrian Thurston <[email protected]>
Added item.

github.com/BioJulia/ragel - 56472582e712351583999535d289a8ad458fbd26 authored over 17 years ago by Adrian Thurston <[email protected]>
Some additional fixes before release.

github.com/BioJulia/ragel - 380ad54740612610868de52b3b123b170440781c authored over 17 years ago by Adrian Thurston <[email protected]>
Enlarged the graphics. Improved the priority section and the lookahead section.

github.com/BioJulia/ragel - 211fb2341a1edfb0ceb7beed397df04484b3d984 authored over 17 years ago by Adrian Thurston <[email protected]>
Discontinuing ragel.spec. It is more appropriate for this to be written by

package maintenance developers.

github.com/BioJulia/ragel - 9c53659727166a7c9b8eeee19ed4816e34ba02d3 authored over 17 years ago by Adrian Thurston <[email protected]>
Updated the ChangeLog for 5.18.

github.com/BioJulia/ragel - 3c94b3ed03c3adaca0f44d0384321264d7a05b8a authored over 17 years ago by Adrian Thurston <[email protected]>