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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

Changed -f option to -x. Added backend options that are now in the frontend to

the man page.

github.com/BioJulia/ragel - d4c50bf113f2cb7dbc47a3f3d36221317dcaf64f authored almost 17 years ago by Adrian Thurston <[email protected]>
Changed -f option to -x.

github.com/BioJulia/ragel - 2911a2019dd1a095ce1f1fe99666008ce5f8fb2a authored almost 17 years ago by Adrian Thurston <[email protected]>
Tab expansion.

github.com/BioJulia/ragel - 46b3ebf56186b787070cdb3530d1519c5f832e48 authored almost 17 years ago by Adrian Thurston <[email protected]>
Editing pass of chapter 6.

github.com/BioJulia/ragel - 8f6fd5785a7af4b8441ffcd063614ff17fe3a2a7 authored almost 17 years ago by Adrian Thurston <[email protected]>
More fixes to chapter 5.

github.com/BioJulia/ragel - c56e08d1736ef1141660468fbdc902ea44ff7a8c authored almost 17 years ago by Adrian Thurston <[email protected]>
Edits to chapter 5.

github.com/BioJulia/ragel - 6569f5f3a6b82878bb249c4555ea559f7eb93a87 authored almost 17 years ago by Adrian Thurston <[email protected]>
Edits to chapter four.

github.com/BioJulia/ragel - e801ba5d99171cb7dd78c746a0e3b1bc5b01c035 authored almost 17 years ago by Adrian Thurston <[email protected]>
Use the phrase "leaving" instead of "pending out".

github.com/BioJulia/ragel - 844716fba1e8667471ae1303b8409504cfd8d5d4 authored almost 17 years ago by Adrian Thurston <[email protected]>
Editing of chapter three. Removed the main label and reduced the state size in

the two diagrams that need to the updated for 6.0.

github.com/BioJulia/ragel - c6d652a2ed858766551f9c79fb498854383c598e authored almost 17 years ago by Adrian Thurston <[email protected]>
Updates to the second half of chapter two.

github.com/BioJulia/ragel - 8b41bd82481ed217d5b9c9975cd300f49e251e1a authored almost 17 years ago by Adrian Thurston <[email protected]>
Improvments to chapter 2.

github.com/BioJulia/ragel - 8e4fff0ae44b0293215af5201074c775b37d5bf9 authored almost 17 years ago by Adrian Thurston <[email protected]>
Patch from Kenny MacDermid, runs ranlib on archives.

github.com/BioJulia/ragel - 82ca96df5c65b5db8a4fb069248a973dc8a183fa authored almost 17 years ago by Adrian Thurston <[email protected]>
More fixes for ruby 1.9.

github.com/BioJulia/ragel - 44eae7b90e8926049e89290203ff4d4fe5623fd7 authored almost 17 years ago by Adrian Thurston <[email protected]>
Fixes for ruby 1.9.

github.com/BioJulia/ragel - 3e5b611e2167be35d6b0485d40fab5a437a79ba5 authored almost 17 years ago by Adrian Thurston <[email protected]>
Added note.

github.com/BioJulia/ragel - 47af31bf2124b528fadfc9ed08c3e2df7d248f9f authored almost 17 years ago by Adrian Thurston <[email protected]>
Fixes for gcc 4.3.

github.com/BioJulia/ragel - a46133def8877ad9e9857a3ae98bfa411e33667f authored almost 17 years ago by Adrian Thurston <[email protected]>
Fixes for compiling with gcc 4.3.

github.com/BioJulia/ragel - 0608d06e91634eb98ed959c66522de8a57cd9044 authored almost 17 years ago by Adrian Thurston <[email protected]>
Remainder of warnings fixed.

github.com/BioJulia/ragel - a44375d6c97c57cdc1ce153ad3d4039611cb50f3 authored almost 17 years ago by Adrian Thurston <[email protected]>
More warning elimination concerning constness.

github.com/BioJulia/ragel - c39d4e956ddd6c562463ee5422f99835f4b8dace authored almost 17 years ago by Adrian Thurston <[email protected]>
Made paramSpec in ParamCheck a const char*.

github.com/BioJulia/ragel - c02be1288e0aba59937fd34c5159aa8ebdc0e839 authored almost 17 years ago by Adrian Thurston <[email protected]>
More warning elimination.

github.com/BioJulia/ragel - 35ebce8160cd9bda1ea697ebea3d2e5c442f3931 authored almost 17 years ago by Adrian Thurston <[email protected]>
Eliminated warnings from gcc 4.3 about conversion from string constants to

char* and about && within ||.

github.com/BioJulia/ragel - f356f9f3181d5e93c6617d5c66d744631ca81fcc authored almost 17 years ago by Adrian Thurston <[email protected]>
Updates to chapter one.

github.com/BioJulia/ragel - 4e8594ac656c9485ee3c1d28737f35ff5fa4fece authored almost 17 years ago by Adrian Thurston <[email protected]>
Started on ChangeLog for 6.0. Improved documentation of name finding.

github.com/BioJulia/ragel - 1b647197f07af5be8cb0a4a04b012b4deadf3795 authored almost 17 years ago by Adrian Thurston <[email protected]>
Added David Waite.

github.com/BioJulia/ragel - 1702e233de19b0408e13a8df4120b242b26d6fe0 authored almost 17 years ago by Adrian Thurston <[email protected]>
Merged in docs from 5.25 release

github.com/BioJulia/ragel - 434742cfff05118b1cd1e54cc8539c29c7ac2e26 authored almost 17 years ago by Adrian Thurston <[email protected]>
Patch from David Waite:

Large arrays are now created by copying in the data from smaller arrays using
System.arraycopy()...

github.com/BioJulia/ragel - 8941250197139cf243a4d4bf7940a7742a5395c6 authored almost 17 years ago by Adrian Thurston <[email protected]>
Improvements to the action ordering and duplicates section. Explicitly stated

that ragel does not compare action text. This tripped up a user.

github.com/BioJulia/ragel - 27970607e0880415da29b89b4cb387c3117c6e0c authored almost 17 years ago by Adrian Thurston <[email protected]>
Added missing initialization for dataExpr. Crash reported by Ryan Phelps.

github.com/BioJulia/ragel - 6fe99bdf61bcee7f52d9d90535b788b838f4b791 authored almost 17 years ago by Adrian Thurston <[email protected]>
One of the ST_* macros collides with a macro in windows.h.

github.com/BioJulia/ragel - d589296b1c3d577eb4376379160264dae0f94e38 authored almost 17 years ago by Adrian Thurston <[email protected]>
Dot file generation can now be invoked using the -V option to the parent. We

now require an input file. If standard in is used then we don't have a file
name on which to base...

github.com/BioJulia/ragel - ea882168614116a7bf4c3dba45cad0f95c47b19b authored almost 17 years ago by Adrian Thurston <[email protected]>
Added comment.

github.com/BioJulia/ragel - 80bbce810a1421659651afc1211b24b3b5174e15 authored almost 17 years ago by Adrian Thurston <[email protected]>
Now spawning child processes on windows.

github.com/BioJulia/ragel - e6302d14994c10735463b410e8be63b26d75226b authored almost 17 years ago by Adrian Thurston <[email protected]>
Path checks for windows.

github.com/BioJulia/ragel - 3ab6b2bb5e07a62f5acd8cbf5bfc2a3cf696c015 authored almost 17 years ago by Adrian Thurston <[email protected]>
Factored out the the fork+exec.

github.com/BioJulia/ragel - 3b1e24006d147a6a2a2e14f89fb6b9091d10ece2 authored almost 17 years ago by Adrian Thurston <[email protected]>
Able to build native windows executables using Cygwin+MinGW. Still need to port

the executable location searching and fork+exec code.

github.com/BioJulia/ragel - cee2765b598813066052c368a0f8ce543ad881ee authored almost 17 years ago by Adrian Thurston <[email protected]>
Rather than have the frontend process call the backend, the ragel program now

calls the frontend (itself with the -f option) and the backend.

github.com/BioJulia/ragel - e61ae8bfbd135f2fb6c7cd7667edc0ada69f5a57 authored almost 17 years ago by Adrian Thurston <[email protected]>
The backend is now called by the ragel program; updated the test harness and

the examples makefile.

github.com/BioJulia/ragel - 098a160efe43104f3b2d146d03c195a0b3916daa authored almost 17 years ago by Adrian Thurston <[email protected]>
Check the status of the backend.

github.com/BioJulia/ragel - 1c22fd04707dd3c39f49b171ce9776eaffb54059 authored almost 17 years ago by Adrian Thurston <[email protected]>
Changed the -l option in rlgen-cd to -L because it is covered in the frontend.

Added a passthrough in the frontend for the backend options.

github.com/BioJulia/ragel - ec6d12f83e8a1b50ace2e954aae74e1fe616f310 authored almost 17 years ago by Adrian Thurston <[email protected]>
Added cfilebuf, which wrappes a FILE struct.

github.com/BioJulia/ragel - e5d757e9185dfc8408038376a93b9cf920f6df04 authored almost 17 years ago by Adrian Thurston <[email protected]>
Now executing the backend.

github.com/BioJulia/ragel - 7f71f99c9f36c345497c6385b67f289836549500 authored almost 17 years ago by Adrian Thurston <[email protected]>
Added name finding for backend executable. If any forward slash is found in

argv0 then it is assumed that the path is explicit and the path to the backend
executable should ...

github.com/BioJulia/ragel - e6cc384738ef970fe09f92a2d5202c12e7e261b1 authored almost 17 years ago by Adrian Thurston <[email protected]>
The 'write eof' statement no longer exists.

github.com/BioJulia/ragel - aea0c84ecbc686fa376cd6b1a02b4f8d847ff064 authored almost 17 years ago by Adrian Thurston <[email protected]>
Added description of eof variable. Updated description of error actions.

github.com/BioJulia/ragel - f8676dfbdfa3c55e580be3b5b851a291cef93b7e authored almost 17 years ago by Adrian Thurston <[email protected]>
Updated the description of error actions to reflect the EOF embedding when the

state is not final when compilation is complete.

github.com/BioJulia/ragel - 3cfb34085fe249ade4c6f9b10c907ac4ab2eb0f2 authored almost 17 years ago by Adrian Thurston <[email protected]>
Updated documentation for pending out actions: noted the EOF action embedding

into a final state that remains final when compilation is complete. Regenerated
the exaction exam...

github.com/BioJulia/ragel - e7a3db977345af4aa5b5237ca466e36177cf4c2c authored almost 17 years ago by Adrian Thurston <[email protected]>
Updated description of the entering action operator. The fixbackbox.awk script

is no longer needed for genfigs.sh. The genfigs.sh script now uses ragel and
rlgen-dot from the c...

github.com/BioJulia/ragel - c141a5db882435eca82617c2dcb4b1c7dc24719f authored almost 17 years ago by Adrian Thurston <[email protected]>
Improvements to intro and layout in state embedding sections.

github.com/BioJulia/ragel - 88aa0824b5a445f24faddd7f33ba6c7dc5e94bbc authored almost 17 years ago by Adrian Thurston <[email protected]>
These examples need the eof pointer now that >, % and error actions also embed

into the EOF event.

github.com/BioJulia/ragel - 3032242a1dcbae646d9802f7957201b53513ab72 authored about 17 years ago by Adrian Thurston <[email protected]>
Go back to 3.X semantics for >, % and error actions. The > operator also embeds

a leaving action/priority into the start state if it is final. If EOF happens
in a state with a l...

github.com/BioJulia/ragel - aec7759ee8c3901799481393e1f49ad9e63a55a9 authored about 17 years ago by Adrian Thurston <[email protected]>
Added an item.

github.com/BioJulia/ragel - 88b2123344c8b6b944b1bf08eb7a16f70f081cba authored about 17 years ago by Adrian Thurston <[email protected]>
Formatting fix.

github.com/BioJulia/ragel - 28eb9bbba72cab8c9d77aa6d76106e1ce9f0ca9d authored about 17 years ago by Adrian Thurston <[email protected]>
Did gotos faked with if statements and execution of EOF transitions for the

flat table code generators.

github.com/BioJulia/ragel - dd29d4ba0f4cc7de3786726ad2ad232bc01ed9b6 authored about 17 years ago by Adrian Thurston <[email protected]>
Gotos faked with if statements and execution of EOF transitions for

RubyFTabCodeGen.

github.com/BioJulia/ragel - b0ea1c71f7de3ba9bbbd102d12a40229771c370a authored about 17 years ago by Adrian Thurston <[email protected]>
Emulating gotos using a series of if tests. Eof transitions now working.

github.com/BioJulia/ragel - 82e8f189f8b06811bf6f52b251beea134bba9faf authored about 17 years ago by Adrian Thurston <[email protected]>
Need to record when the out label is used.

github.com/BioJulia/ragel - 672ab5add059d57c9181d050290ca244c3240319 authored about 17 years ago by Adrian Thurston <[email protected]>
Updated examples for the first of the 6.0 changes: removed write eof and added

eof pointer.

github.com/BioJulia/ragel - fa7aae7416f8bd4f8765c2fb7390b75cceb1040a authored about 17 years ago by Adrian Thurston <[email protected]>
Scanner EOF transitions are now taken in Java code. Restructured the Java

driver; a switch statement with fallthrough cases are now used to emulate
gotos.

github.com/BioJulia/ragel - daaafb3af537c09463f400483ec8f9abbce4c5bf authored about 17 years ago by Adrian Thurston <[email protected]>
Scanner EOF transitions are now taken (C/D code only).

github.com/BioJulia/ragel - 481c68889c2ff3a4ceaf2b54beae710399605bb5 authored about 17 years ago by Adrian Thurston <[email protected]>
EOF actions and targets for processing tokens are now set in scanner final

states. EOF transitions (present when an EOF targets are present) are now
passed to the backend a...

github.com/BioJulia/ragel - 71d0bc06fbb42913987956b50f706cd7318cb154 authored about 17 years ago by Adrian Thurston <[email protected]>
Not yet supporting minimization of states with eof targets.

github.com/BioJulia/ragel - ffbaba66dffbf1e4a850cc30fd80d1aa8b25ae4c authored about 17 years ago by Adrian Thurston <[email protected]>
Added the eofTarget to StateAp. This will be used only to track the transition

back to the start state in scanners.

github.com/BioJulia/ragel - 51dc48d873416dadc9ded6ff214413ec93ccdf5e authored about 17 years ago by Adrian Thurston <[email protected]>
Removed the write eof command.

github.com/BioJulia/ragel - 9331691d783a5eb3fb8f6c0adc1741ea31e9d96f authored about 17 years ago by Adrian Thurston <[email protected]>
Added an override for the eof variable.

github.com/BioJulia/ragel - 48158586099d8acab15b923ccaddaf9743109846 authored about 17 years ago by Adrian Thurston <[email protected]>
Introcuded the "eof" variable for indicating the end of file. The p variable is

checked against eof when the processing loop is broken out of due to p == pe.
If p == eof at this...

github.com/BioJulia/ragel - 560bf98e060a99866cac602a22715616d7d865ec authored about 17 years ago by Adrian Thurston <[email protected]>
Added missing include.

github.com/BioJulia/ragel - b8d15ad40d6cf52da0cfded624889c38cfd949a5 authored about 17 years ago by Adrian Thurston <[email protected]>
Remove the 'noend' write option. This example is referenced a lot and as a

first example it shouldn't contain a special purpose write option like 'noend'.

github.com/BioJulia/ragel - 7370f58d087d426b7f8404339f2d005526ffa0cc authored about 17 years ago by Adrian Thurston <[email protected]>
Documentation for version 5.24.

github.com/BioJulia/ragel - 90f05a7573fc8befbfd40282a57a61e160f1fb3e authored about 17 years ago by Adrian Thurston <[email protected]>
Added documentation for prepush and postpop.

github.com/BioJulia/ragel - 3c0416a84ff26e68220449c9ff2c0c687bbcaddc authored about 17 years ago by Adrian Thurston <[email protected]>
Added two new statements: prepush and postpop. These are code blocks that are

written out during call and return statements immediately before pushing the
current state to the...

github.com/BioJulia/ragel - 920373c721cf8072ad8fb78029c7ec45a8d3ef21 authored about 17 years ago by Adrian Thurston <[email protected]>
Removed non-issue.

github.com/BioJulia/ragel - d240c0e58d2820cdba2db6463c7db274a717fcbf authored about 17 years ago by Adrian Thurston <[email protected]>
If the condition embedding code runs out of available characters in the

keyspace an error message is emitted. A paragraph about this was added to the
manual.

github.com/BioJulia/ragel - 8e8f4b63624b4d572e76a92d7343cbb25b330003 authored about 17 years ago by Adrian Thurston <[email protected]>
The first example that appears in the manual uses the special-purpose 'noend'

write option. This tends to trip people up. Added a basic example which appears
first.

github.com/BioJulia/ragel - 5962b37fde291dbda794a07ec0f2b55f765886ee authored about 17 years ago by Adrian Thurston <[email protected]>
Patch from Victor Hugo Borja <[email protected]>

This patch implements -T1 -F0 -F1 and -G0 in the ruby code generator.
Goto-driven code generatio...

github.com/BioJulia/ragel - 1ed1d2bba7c78690aa2fa473e6ee89170c37027e authored about 17 years ago by Adrian Thurston <[email protected]>
Added some notes on the fixed size stack issue.

github.com/BioJulia/ragel - b18c092f45ac8733c5bb1e7242be6ea85b942a77 authored about 17 years ago by Adrian Thurston <[email protected]>
Should be crediting Arbor.

github.com/BioJulia/ragel - 7a42a1522c5d95b7ffeea0680b3b4b767d5c2580 authored about 17 years ago by Adrian Thurston <[email protected]>
Added item.

github.com/BioJulia/ragel - 3f41e5dd3077b4a75b252f1161268ed623484151 authored about 17 years ago by Adrian Thurston <[email protected]>
Updates to TODO and error message.

github.com/BioJulia/ragel - 29b9d07ac44f22181c8dbd63c11337d08012ab5b authored about 17 years ago by Adrian Thurston <[email protected]>
Documentation for 5.23.

github.com/BioJulia/ragel - c83166aae40a6c1fba63f1799c94eec899126ee7 authored about 17 years ago by Adrian Thurston <[email protected]>
removed done item

github.com/BioJulia/ragel - efff4f8e50f02ce84a3103c1916d50bea3d5f829 authored about 17 years ago by Adrian Thurston <[email protected]>
Grammar fixes: changing "which" to "that" where appropriate.

github.com/BioJulia/ragel - 2b83c2521c28eb926fbc1ca139c5e4df010aec9c authored about 17 years ago by Adrian Thurston <[email protected]>
Renaming "Entering Actions" to "Starting Actions."

github.com/BioJulia/ragel - ecf544842764e58e3aa14abc84d681ef5a0cb898 authored about 17 years ago by Adrian Thurston <[email protected]>
added an item.

github.com/BioJulia/ragel - 71dd2c69c11b67c6a36421afe8054aa54b4ddf91 authored about 17 years ago by Adrian Thurston <[email protected]>
Added an item.

github.com/BioJulia/ragel - 07b091799eee5d78ab4eee262660c4e3878afdef authored over 17 years ago by Adrian Thurston <[email protected]>
Added item to look into.

github.com/BioJulia/ragel - a7a045e4f0da92ee8701af25d814a0abc10b85a2 authored over 17 years ago by Adrian Thurston <[email protected]>
Remainder of formatting changes.

github.com/BioJulia/ragel - 368d60bd22d7ccc43dd33fb6029a668f4bad8334 authored over 17 years ago by Adrian Thurston <[email protected]>
Formatting updates.

github.com/BioJulia/ragel - b620ed6842dde4757cd0aec62676e8eaf76eea38 authored over 17 years ago by Adrian Thurston <[email protected]>
Improved the error message given when there is a write statement but no machine

instantiations and hence no state machine.

github.com/BioJulia/ragel - d04ed47698af479de10efeda3d0828d02f620933 authored over 17 years ago by Adrian Thurston <[email protected]>
Added a section on recursion.

github.com/BioJulia/ragel - 6faf79632a5ead0891af99a9eaaa154e17b97ec7 authored over 17 years ago by Adrian Thurston <[email protected]>
Moved cases around.

github.com/BioJulia/ragel - a88c7f3b4628b2467f5a3d769f8daa9ec344636b authored over 17 years ago by Adrian Thurston <[email protected]>
Updates to "machine instantiation", "write init" and "write exports" sectons.

Added the "variables used by ragel" section.

github.com/BioJulia/ragel - a054adc9a58ca20c30bd2cc0a228c0293eddbfe3 authored over 17 years ago by Adrian Thurston <[email protected]>
Removed references to rlcodegen.

github.com/BioJulia/ragel - 07162fd2775a3a1c8ceb9640f7ca5b0444eb6e18 authored over 17 years ago by Adrian Thurston <[email protected]>
More formatting changes.

github.com/BioJulia/ragel - c49d844f33a73245b8290f17c83b90eed2b6d26c authored over 17 years ago by Adrian Thurston <[email protected]>
Started reworking formatting.

github.com/BioJulia/ragel - 6bf0baaaafe3780e29584bf04a8cfdbe0226a4fd authored over 17 years ago by Adrian Thurston <[email protected]>
Eliminated the use callcc as an alternative to goto. Instead, the named breaks

implementation used in the java code generator is imitated using control flow
variables.

github.com/BioJulia/ragel - 452d7ae1a79fa4ecfad0d59f56548d861683ab18 authored over 17 years ago by Adrian Thurston <[email protected]>
5.22 date wrong in changelog, fixed.

github.com/BioJulia/ragel - 72e9db02806a95611f591f1eaeb032ae56c5c155 authored over 17 years ago by Adrian Thurston <[email protected]>
Updates for release 5.22.

github.com/BioJulia/ragel - 4cb18b00babafb4b6cd6de3f571e72d45dfb43c1 authored over 17 years ago by Adrian Thurston <[email protected]>
Added variable statement to man page.

github.com/BioJulia/ragel - ea7f4cf31786805aee12c470e514a5bc676b9b60 authored over 17 years ago by Adrian Thurston <[email protected]>
Note on the data variable for ruby and java code.

github.com/BioJulia/ragel - 2d438951a2c5f5f1ae9b67020fb5f358dc57e640 authored over 17 years ago by Adrian Thurston <[email protected]>