Add aqua, remove pirated methods

[ReubenJ]

These methods were picked up by Aqua as being pirated. They should be defined in HerbCore. See Herb-AI/HerbCore.jl#31. Removing these methods from this package means this is also a breaking change.

Aqua tests are now included in CI so that this won't happen by accident in the future.

The reason for changing the RuleNode(..., grammar) and UniformHole(..., grammar) constructors to functions was also for type-piracy reasons--defining a new constructor in this package (HerbGrammar) for a type defined in another package (HerbCore). They could have been moved to HerbCore as constructors, but then testing the constructors becomes difficult because they need a ContextSensitiveGrammar to test them, and that is defined in this package. So, in the end, it was just easier to change them to functions.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 56.45%. Comparing base (96f8fb3) to head (6bcebbc).
Report is 12 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #96      +/-   ##
==========================================
+ Coverage   53.32%   56.45%   +3.13%     
==========================================
  Files           7        7              
  Lines         557      542      -15     
==========================================
+ Hits          297      306       +9     
+ Misses        260      236      -24     

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[pwochner]

Looks good. I like the examples that you added in the docstrings.

[ReubenJ]

Will address tomorrow

[ReubenJ]

Just noticed we can also drop TreeView and DataStructures as dependencies.

This brings the using HerbGrammar time down a bit:

Before

julia> @time_imports using HerbGrammar
      5.8 ms  MacroTools
      0.6 ms  SimpleTraits
      5.2 ms  Preferences
      0.4 ms  PrecompileTools
      0.6 ms  StaticArraysCore
    101.5 ms  StaticArrays
      1.1 ms  ArnoldiMethod
      0.7 ms  Statistics
      0.3 ms  StaticArrays → StaticArraysStatisticsExt
      0.5 ms  Compat
      0.5 ms  Inflate
      2.0 ms  OrderedCollections
     12.8 ms  DataStructures
      0.4 ms  Compat → CompatLinearAlgebraExt
               ┌ 9.7 ms SuiteSparse_jll.__init__()
     11.7 ms  SuiteSparse_jll
      0.9 ms  Serialization
               ┌ 6.6 ms SparseArrays.CHOLMOD.__init__() 57.96% compilation time
    116.0 ms  SparseArrays 3.27% compilation time
      0.5 ms  Statistics → SparseArraysExt
               ┌ 0.0 ms Distributed.__init__()
     16.6 ms  Distributed 53.83% compilation time
      0.7 ms  Mmap
      2.0 ms  SharedArrays
      8.2 ms  Graphs
      0.6 ms  LaTeXStrings
      0.6 ms  JLLWrappers
               ┌ 2.8 ms Bzip2_jll.__init__() 54.90% compilation time
      3.4 ms  Bzip2_jll 44.12% compilation time
               ┌ 1.3 ms Zlib_jll.__init__()
      3.4 ms  Zlib_jll
               ┌ 1.5 ms FreeType2_jll.__init__()
      2.1 ms  FreeType2_jll
      0.4 ms  Libuuid_jll
               ┌ 0.9 ms Expat_jll.__init__()
      1.5 ms  Expat_jll
               ┌ 7.9 ms Fontconfig_jll.__init__() 80.06% compilation time
      8.6 ms  Fontconfig_jll 72.95% compilation time
               ┌ 1.1 ms Graphite2_jll.__init__()
      1.8 ms  Graphite2_jll
               ┌ 2.0 ms Libiconv_jll.__init__()
      2.6 ms  Libiconv_jll
               ┌ 1.1 ms Libffi_jll.__init__()
      1.7 ms  Libffi_jll
               ┌ 11.6 ms CompilerSupportLibraries_jll.__init__()
     14.4 ms  CompilerSupportLibraries_jll
               ┌ 1.6 ms XML2_jll.__init__()
      2.3 ms  XML2_jll
               ┌ 2.4 ms Gettext_jll.__init__()
      3.1 ms  Gettext_jll
               ┌ 1.3 ms PCRE2_jll.__init__()
      3.1 ms  PCRE2_jll
               ┌ 10.3 ms Glib_jll.__init__()
     11.0 ms  Glib_jll
               ┌ 2.0 ms LLVMOpenMP_jll.__init__()
      2.7 ms  LLVMOpenMP_jll
               ┌ 2.0 ms Pixman_jll.__init__()
      2.6 ms  Pixman_jll
               ┌ 1.1 ms libpng_jll.__init__()
      1.7 ms  libpng_jll
               ┌ 3.4 ms Cairo_jll.__init__()
      4.1 ms  Cairo_jll
               ┌ 3.6 ms HarfBuzz_jll.__init__()
      4.3 ms  HarfBuzz_jll
               ┌ 6.2 ms ICU_jll.__init__()
      7.0 ms  ICU_jll
               ┌ 1.1 ms HarfBuzz_ICU_jll.__init__()
      1.9 ms  HarfBuzz_ICU_jll
               ┌ 4.4 ms OpenSSL_jll.__init__()
      5.2 ms  OpenSSL_jll
               ┌ 0.0 ms tectonic_jll.__init__()
      0.8 ms  tectonic_jll
               ┌ 0.0 ms Requires.__init__()
      0.7 ms  Requires
               ┌ 2.7 ms JpegTurbo_jll.__init__()
      3.5 ms  JpegTurbo_jll
               ┌ 1.2 ms LERC_jll.__init__()
      2.0 ms  LERC_jll
               ┌ 1.3 ms Zstd_jll.__init__()
      2.1 ms  Zstd_jll
               ┌ 1.5 ms Libtiff_jll.__init__()
      2.2 ms  Libtiff_jll
               ┌ 1.5 ms LittleCMS_jll.__init__()
      2.3 ms  LittleCMS_jll
               ┌ 1.5 ms OpenJpeg_jll.__init__()
      2.4 ms  OpenJpeg_jll
               ┌ 6.3 ms Poppler_jll.__init__()
      7.3 ms  Poppler_jll
               ┌ 63.2 ms TikzPictures.__init__() 42.66% compilation time
     67.6 ms  TikzPictures 39.89% compilation time
      1.0 ms  TikzGraphs
      0.8 ms  CommonSubexpressions
      0.8 ms  TreeView
      5.4 ms  AbstractTrees
      1.1 ms  HerbCore
    928.5 ms  HerbGrammar

After

julia> @time_imports using HerbGrammar
      2.9 ms  Serialization
      2.1 ms  HerbCore
    924.6 ms  HerbGrammar

and brings the number of transitive dependencies down by a lot:

Before

julia> length(Pkg.dependencies())
104

After

julia> length(Pkg.dependencies())
3