Regenerate Julia interface to ViennaRNA header files

- update to Clang.jl v0.18.1

- include header files for constraints, this needs a patch to the
  ViennaRNA header files to be able to be parsed by Clang.jl

- the gen/patches-for-headers directory contains the patches to be
  applied to the ViennaRNA header files, with the patches only applied
  to a temporary copy of the header files that are used to generate
  the Julia interface

gen/Project.toml

@@ -2,5 +2,5 @@
 Clang = "40e3b903-d033-50b4-a0cc-940c62c95e31"
 
 [compat]
-Clang = "0.17.1"
+Clang = "0.18.1"
 julia = "1.7"

gen/README.md

@@ -1,4 +1,6 @@
-# How to generate the wrappers
+# ViennaRNA libRNA wrapper generator
+
+## How to generate the wrappers
 
 1. `cd` to this directory
 2. run `julia --project generator.jl`
@@ -7,3 +9,13 @@
 
 1. `cd` to this directory
 2. run `julia --project` and then in the Julia REPL, run `pkg> up`
+
+## Notes on patches to headers
+
+Some headers of ViennaRNA have to be patched to be able to be parsed
+by Clang.jl.  These patches can be found are under the directory
+`patches-for-headers/`.  The patches are applied to a temporary copy
+of the header files that is deleted after parsing by the
+`generator.jl` script that generates the `../lib/LibRNA.jl` file.
+This only needs to be done once on a developer's machine when the
+header files change.

gen/generator.jl

@@ -5,6 +5,18 @@ import Pkg
 cd(@__DIR__)
 Pkg.activate(".")
 
+function find_files_matching_regex(root_dir::AbstractString, regex::Regex)
+    matching_files = String[]
+    for (root, dirs, files) in walkdir(root_dir)
+        for file in files
+            if occursin(regex, file)
+                push!(matching_files, joinpath(root, file))
+            end
+        end
+    end
+    return matching_files
+end
+
 # Stack environment from parent dir on top of env from this dir.  This
 # is so we can import ViennaRNA_jll and always have the same version
 # as the parent dir.
@@ -37,8 +49,19 @@ open("./prologue.jl", "w") do io
     println(io, "#### end prologue.jl")
 end
 
-include_dir = normpath(ViennaRNA_jll.artifact_dir, "include")
+#include_dir = normpath(ViennaRNA_jll.artifact_dir, "include")
+#viennarna_dir = joinpath(include_dir, "ViennaRNA")
+tmpdir = mktempdir()
+run(`cp -r $(normpath(ViennaRNA_jll.artifact_dir, "include")) $tmpdir/`)
+include_dir = joinpath(tmpdir, "include")
 viennarna_dir = joinpath(include_dir, "ViennaRNA")
+patches_dir = abspath(joinpath("patches-for-headers"))
+patch_files = filter(f -> endswith(f, ".patch"), readdir(patches_dir; join=true))
+cd(include_dir) do
+    for patch in patch_files
+        run(pipeline(`patch -p2`, stdin=patch)) #joinpath(patches_dir, "soft_special_missing_includes.patch")))
+    end
+end
 
 options = load_options(joinpath(@__DIR__, "generator.toml"))
 print("options =\n  ")
@@ -48,6 +71,8 @@ args = get_default_args()
 append!(args, [
     "-I$include_dir",
     "-DVRNA_DISABLE_C11_FEATURES",
+#    "-DVRNA_DISABLE_BACKWARD_COMPATIBILITY",
+#    "-DMAXALPHA=20",
 ])
 
 accept_headers = [
@@ -68,10 +93,17 @@ accept_headers = [
     "subopt_zuker.h",
     "treedist.h",
     "utils/basic.h",
+    "constraints/basic.h",
+    "constraints/hard.h",
+    "constraints/ligand.h",
+    "constraints/SHAPE.h",
+    "constraints/soft.h",
+    "constraints/soft_special.h",
 ]
 headers = [joinpath(viennarna_dir, header) for header in accept_headers]
 # there is also an experimental `detect_headers` function for auto-detecting top-level headers in the directory
-# headers = detect_headers(clang_dir, args)
+#headers = detect_headers(viennarna_dir, args)
+#headers = find_files_matching_regex(viennarna_dir, r".*\.h")
 
 # create context
 ctx = create_context(headers, args, options)

gen/patches-for-headers/soft_special_missing_includes.patch

@@ -0,0 +1,14 @@
+diff --git a/src/ViennaRNA/constraints/soft_special.h b/src/ViennaRNA/constraints/soft_special.h
+index 1902c930..654bc85e 100644
+--- a/src/ViennaRNA/constraints/soft_special.h
++++ b/src/ViennaRNA/constraints/soft_special.h
+@@ -1,6 +1,9 @@
+ #ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_SPECIAL_H
+ #define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_SPECIAL_H
+
++#include "ViennaRNA/fold_compound.h"
++#include "ViennaRNA/model.h"
++
+ /**
+  *  @file     constraints/soft_special.h
+  *  @ingroup  soft_constraints, modified_bases