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github.com/BioJulia/Automa.jl

A julia code generator for regular expressions
https://github.com/BioJulia/Automa.jl

Correct typos in documentation

93c2813db07a0a556f97392381daeefe65e8ba0d authored 12 months ago by Jakob Nybo Nissen <[email protected]>
Bugfix: Escape reference to Automa in error function

Without this bugfix, any code that throws the default error, but which haven't
imported the symb...

cfaa5294326b342428a051399a360b99322ce4cc authored 12 months ago by Jakob Nybo Nissen <[email protected]>
docs: Misc formatting and text fixes, add some internal links

docs(Theory): Fix NFA state number errors, spelling, and add alt-texts to images

docs(Regex): f...

2d30fac3d69ce9a98190f6318deff15ecdbb1a01 authored about 1 year ago by SundaraRaman R <[email protected]>
docs: add Actions badges to README, correct existing badge and link

01f608e5ff8c2476d45e53f46637c5dc06834047 authored about 1 year ago by SundaraRaman R <[email protected]>
Update issue and PR template to match BioJulia guidelines

In BioJulia discussion 11, and BioJulia/Contributing, we've decided to make the
template less ve...

82a27f043690fc3a489ad65ea241405f1576e25f authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump TranscodingStreams to 0.10

456eeef78f2955ec8e7e669cfbc3fada31d3f3b4 authored about 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump Documenter to 1.0

5ed0767355c2aa18f35b6b830f0c7f51c64db04c authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update README.md

cb54990e53eb1272054a81870f2ef3961535ae68 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Tweak Tokenizer docs

504497ad3644e5c3ec68fee4f003624e55e8b24f authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Bugfixes and doc improvements to Tokenizer

Issue 125 revealed several issues with the existing tokenizer implementation,
several of which a...

96115dca49d7d29880b12fe3db73b413d8c4a7ee authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update README.md

Correct automa image link.

733b8cf6777070c8da83dc2f843e931bb8a82b19 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Do not assert mark has set with special macros

Special macros like `@abspos` previously inserted an assert that the buffer's
mark had been set....

f676a6b02ea3f40c4eb87ad246111f677b8638fe authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Saner default for p_eof and p_end

49004a6368d8f3806dc79067cbc461b12d1b5e8d authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Disable SIMD capability

I've come to the conclusion that Julia does not make it possible to robustly
check what CPU inst...

887ebb5cb4bf38b52a6df6103bbb029ccc392e8a authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add more tests

78831496ec739316efda42ddf034b8871e62262a authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add validator convenience function

64abea8d6aa6f0a476bfe56908007c1d79fbdf55 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add documentation to pseudomacros

Add macros with the same name as pseudomacros.
These return a string explaining that the pseudom...

cbb3cddeeaf9e0f565e6b78d9ed165081aa9b36f authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove report_col kwarg

Instead of buffering an entire line, simply keep track of the number of columns
cleared from the...

09a124b6557a438a38a422a8144d63182ecd9d25 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update README.md

efd3344d22e8ed9d571a6b7e6dd61cf2080dd257 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove last Stream non-pseudomacros

The existence of these as real macros does not actually work with arbitrary
`CodeGenContext`s.
T...

eb2b2610ac5ee50084587034d2c871275b25417b authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Simplify Machine struct layout

Previously, `Machine`s contained the fields `start_state::Int` and
`states::UnitRange{Int}`. How...

5b79fe10292065561171dd2fde99f9a364dc8996 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove Stream module

This module doesn't make any sense in v1 for two reasons:
First, we can not longer consider the ...

83796edc14ed46a0067d2f28c85a19dc66ed2dcf authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Make more use of magical macros

ac02cdc58c9e659ef224ae85bec136ac82f532fe authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add generate_io_validator

b7ef8ce13b76ebd5e1d5f49f3c8e58530c833658 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Export machine2dot

9d2222e2d478361218d3e97a9ae34fae844b33d8 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add default error in generated reader function

074d6af4de925fa19caea5fe96c3c521447f55db authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Fix Project

d032b16538e19e420295aea1dfeb20d8d8544dc5 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Comment generate_reader better

fce5489e3d2584ac78fb00a71b3f180f448444fe authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Rewrite documentation

4966b66f0b7481665f6edac87d464410296f0afe authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Fix warnings when running tests

666c8b4f8afd11ad9b0f16a6db30ec38ad7922e6 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Do not make TranscodingStreams an extension

Since Automa doesn't just extend an existing function but adds a new function
based on Transcodi...

cbd1568d2736e595e7f321cae53475bc983b38b6 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Fix preconditions

Allow preconditions to be set to `:enter` only, and have directly conflicting
preconditions reso...

f971db32b992e992762581975b7ceefd9b1494f8 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools

cc9fb668f79ee13f14d53a2892790a5c26f45ed2 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add input error code to generate_code function

The user probably wants to use the input error code in most use cases, except
when running a mac...

5af00fec323c36f52376faf1432c68bc7a566712 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Enforce action dict symbols are same as machines

Before this PR, a user could forget or mis-spell a symbol in the action Dict
passed to generate_...

959e8c97bc6109584327cd7362d5f7deef849c9e authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove dead eps nodes

The `re2nfa` function will create NFAs which include useless eps nodes.
Here, I define a useless...

1852afc1a061c9ab2fbf481f713afc165cdebe6a authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Error with shortest known ambiguity

NFAs with ambiguities often contain multiple ambiguities. Displaying the
simplest ambiguity when...

dc963e6dfd93e1627f30dd5e3fae35ca981eb3e3 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Check preconditions before declaring NFA ambiguous

If two edges in equivalent paths have distinct preconditions, these could be
used to distinguish...

c2b23fe7842d3a9e160b0954bcbd9abd0bbd1a5d authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Also trigger default error when cs > 0

e8e43eea62dd2890f5f370aa39d9260109f728da authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Always remove dead nodes

Currently, the functions `re2nfa` and `nfa2dfa` can produce dead (unreachable)
nodes, which is p...

e2210bc9c0ff777b46f9ad4debbfdf32a80e43a8 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove SIMD and inline generator

Honestly, four generators and a tokenizer was excessive.
Inline generator was probably not reall...

563c7dfd5650775d4fe4d864d584cb293deef610 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Rename generate_validator_function

88ec2946b3096785df5e8fc986221edd60ced67a authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Make TranscodingStreams an optional dependency

Many potential users of Automa are not interested in parsing from IOs, but only
buffers. For tho...

64bde544546cf024a396a33ee10c3abb86b0a20d authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Also check ambiguities for final and all actions

An oversight in the ambiguity check meant that actions placed on non-epsilon
edges were accident...

6a4da4876640fe17f70d262d6f8084ec69f86ed4 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Enable ambiguity check

c1b2641e03a7c494d06753564f7c1e045da88690 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove loop unrolling

6f1f6f9c29cc901758a21e831222cd26e00fcf39 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Export user-facing names

One of the issues with using Automa is that its lack of exports makes it unclear
what is interna...

e1bfb7566a25f721c25130086fdb52e0d5f26eef authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add generate_code convenience function

78f95a2793baa2b48edda7d354d4ab6e2bfb7f0b authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Make clean work

9098fafa76d760dfe2c0a664c257a2ff7e2d341f authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Allow CodeGenContext to be elided

e66a282646495166c9931945773abc5f2145dc4a authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add todo to gitignore

d759de2d91141476b89328c010e9c6cb50858027 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Make generate_buffer_validator goto into kwarg

36fcaa50d340a531c347a4a587d300cc6f22b00e authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Fix bug in execute_debug

7d2cf2d4896ee2d9db424484d3acbeae0ab29be4 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add tests for regex set operations

cb5054eaeb4479a2df8914b7e94b070d24318c2b authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Make Variables easier to construct

e631e50566bc051d382afef46c7a3ef9cba27eb2 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump CI version to Julia 1.6

8a088ed03c4d9af302633cc82935e41cfe6769d7 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Small tweaks

43f5f86f1d46f38d1925ca2914ca95540fb046b6 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add SnoopPrecompile

1e427d88ab9d4617227d22d535d633b9c072f9f8 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update benchmarks

465272f0dfa0dc7c6f4ab5b9a29d652cbc175753 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Rename p_eof to is_eof

p_eof only have two valid values: -1 and p_end. By instead using is_eof::Bool
to distinguish the...

29760dca93944a1581fa3419f4e52b9eb187d717 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Minor polish

ff7a726270f6af6e2c3dc5e8cabd49572ad190a8 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Improve string/char and RE operations

a369784789fbc81d7987efa5db84c8b8357412e5 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Disallow final actions in looping regex

Currently, Automa allows you to add a :final action to a regex like "a*", where
it is not possib...

358936ce9e75ed11db5f756cef921ae4a12fae15 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Disallow direct modification of actions field

Instead of doing `re.actions[:exit] = [:foo]`, do `onexit(re, :foo)`. It's
cleaner, and avoids m...

fd95f2d92f3cb08cf6fdc891011396935c210a26 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add check for invalid RE.action keys

nfa2dfa now errors if any RE object has a .actions field with an unsupported
key. This prevents ...

74ef3d9b83ac8e0c001ca4c4caa1741978f32b8e authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Rewrite tokenizer

The tokenizer has a completely new design and API.
* It's now much easier to use
* It's now lazy...

d3a5e0e177033ac3853d911cea2d2ae70f947d1f authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add documentation preview

0fc38481b9785d25d13b24d3dfa5b18561582d5d authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove checkbounds option

With the :goto generator, checking bounds is not permitted anyway.
And the table generator is so...

3b7a7aab9362e815b031a6002211cf1984611d11 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Some JET fixes

da2d7fe139de85a600f3c839fdb6336bf9256672 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Use `using` over `import`

There is no reason to use `import` over `using`. On the contrary, it muddles
the difference betw...

4849f74ee1d4a6f15601cfcd42e3b0f1a4700518 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Tweak: Allow | and & ops b/w chars/str and RE

4a1ee2deb76717f1f3d3dbbc7bce208bd411405f authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Add more comments

b4d26f4ce2691bf6d2c667eb35581616488971cf authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Export regex struct instead of module

Users should not have access to the module directly. Instead, export the RE
struct, and also all...

7a903fabb5aaf4dc3b5104ebbcc5eb0c751c56f0 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Do not store gensym symbols in default CodeGenContext

The gensym'd symbols in Automa's constant expressions are computed on
precompilation of Automa.
...

b40f3f2a91c61d96c4f25f2b0703670ad91d0f14 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Fix EOF check in machine error code

14109b6bf6b5dad7ae25f23fe0460f4f43163ce1 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Update FASTA example

ddcf22f58d16492b84fdd996934eb9f65f2199f6 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Bump ScanByte to 0.4.0

3b5c91363e55830f80336e03fcb51da45c45d958 authored over 1 year ago by Jakob Nybo Nissen <[email protected]>
Remove dependency on Printf

This dependency was used for something completely trivial.

7c6a696082ed71667519ae156a50373684dbc898 authored almost 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove unused files

8dd2672fd838430f673294b2c0c9c011ab9f469e authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Better error on compiling null regex

It is possible for users to construct a regex that matches the null set, i.e.
no strings, not ev...

82238fbd723b1f6608e332ceb9fcf01912cdf47c authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove StableSet and StableDict

These two data types were originally added to prevent nondeterminism when
compiling regex.
Inste...

3a06e84b400646707a95eba48c9e463bdd58aa30 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Fix variables in generate_reader

The code in generate_reader did not respect the Vars or CodeGenContext.

69d16f5cad2edadef5b9715a32afcebaa480ad09 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add generate_input_error_code to improve error messages

A current limitation of Automa is that it can be difficult to understand why
a certain string do...

7647e9f95b6cf600990a420d776b69d279452969 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Improve error message on ambiguous NFA

Now prints the minimal possible input to trigger the ambiguity.

d4bd3eca1ad8d9181f09a1d8831ba133926c7228 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add debug_execute

241c16ea9303c876886f57463cec59b8ce26fc47 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Improve debugging

8537d8aa1b0e3304f4f5fca18ae880659cf03d62 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Disable unambiguity check again (#98)

I want to release one more non-breaking release before v1, which requires us
to remove the break...

1e645f4f2f0771456da72c5712a0acd5c0a9fbf5 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Use smaller integer width for table generator (#97)

Most generators have < 128 states, basically all have < 32,000. This suggests
we should be able...

39b4c3c352e64de3d1a26a18ca642941b1c16ed5 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove ByteSet (#96)

Automa's dependency ScanByte implements a ByteSet. Use it instead.

3f4e69070f37eb5e5a1af9c71d9e53770e6dd64f authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Fixup parse_class (#94)

* Disallow unicode in parse_class
* Allow byte ranges in class

c7f06e35b16041b0572c6a5b0889e6d954e88624 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add workflow for downstream tests (#86)

6e75725e9923a69717b64f82bf79fee618e74355 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Small cleanup of Automa codegen (#92)

* Fix typo geybyte to getbyte
* Use optimized final state check for Tokenizer
* Make Tokenizer...

c7799997905d2add840dd7acfd9fbd5ba12e94a4 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Small tweaks to Tokenizer internals (#90)

* Remove unused argument generate_table_code
* Do not needlessly specialize on args in Tokenize...

7b54b665abd428e87114fb5fd311fda2b35a7b05 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #89 from jakobnissen/tokenize

# Closes #88

6abbdb4c82f39187c8883551063a3bbec75db145 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Have Tokenizer check if in accept state when EOF

In the code generated by generate_table_code for Tokenizer, if the loop exits
due to reaching EO...

38dc46ba616a6b7c476da77b1c30ef46d0eafaea authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #85 from jakobnissen/finallookup

Optimize away dict lookup when possible

46d6d336b576fd2dbc25b84e587d797478436631 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Optimize away dict lookup when possible

3964b0d1d25ecf31e0fd1bf2be8ab78e297dd03c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #79 from jakobnissen/fixexecute

Fix execute (issue 78)

9f06021b77bfe3c9f4b7ada88ea754afa26f2e91 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Fix execute (issue 78)

f8bae2beac226113b2813ad7aeeaa72ddd64d303 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Bump minor version

8eb8a89148a7fef057c9051ca42817a0bf616b48 authored almost 4 years ago by Kevin Bonham <[email protected]>