Ensure patched node.h is included instead of original Prodigal code

meson.build

@@ -17,6 +17,8 @@ py_mod = import('python')
 python = py_mod.find_installation(pure: false)
 py_dep = python.dependency()
 
+# setup include dir with patched `node.h`
+inc = include_directories('pyrodigal/prodigal')
 
 # --- SIMD detection -----------------------------------------------------------
 
@@ -124,7 +126,6 @@ if not neon_supported
   endif
 endif
 
-
 # --- Prodigal -----------------------------------------------------------------
 
 training_splits = ['training_header.c']
@@ -167,20 +168,15 @@ foreach p : prodigal_sources
   )
 endforeach
 
-prodigal_inc = include_directories(
-  'pyrodigal/prodigal',
-  'vendor/Prodigal',
-)
-
 prodigal = static_library('prodigal',
     prodigal_files,
     dependencies: m_dep,
-    include_directories : prodigal_inc,
+    include_directories : inc,
 )
 
 prodigal_training = static_library('training',
     training,
-    include_directories : prodigal_inc
+    include_directories : inc
 )
 
 # --- Pyrodigal ----------------------------------------------------------------

pyrodigal/impl/meson.build

@@ -3,15 +3,15 @@ impl = []
 impl += static_library(
     'impl_generic',
     'generic.c',
-    include_directories : prodigal_inc,
+    include_directories : inc,
     extra_files : ['generic.h', 'generic.pxd'],
 )
 
 if mmx_supported
     impl += static_library(
         'impl_mmx', 
         'mmx.c', 
-        include_directories : prodigal_inc, 
+        include_directories : inc, 
         c_args : mmx_flags,
         extra_files : ['mmx.h', 'mmx.pxd'],
     )
@@ -21,7 +21,7 @@ if sse2_supported
     impl += static_library(
         'impl_sse2', 
         'sse.c', 
-        include_directories : prodigal_inc, 
+        include_directories : inc, 
         c_args : sse2_flags,
         extra_files : ['sse.h', 'sse.pxd'],
     )
@@ -31,7 +31,7 @@ if avx2_supported
     impl += static_library(
         'impl_avx', 
         'avx.c', 
-        include_directories : prodigal_inc, 
+        include_directories : inc, 
         c_args : avx2_flags,
         extra_files : ['avx.h', 'avx.pxd'],
     )
@@ -41,7 +41,7 @@ if avx512_supported
     impl += static_library(
         'impl_avx512', 
         'avx512.c', 
-        include_directories : prodigal_inc, 
+        include_directories : inc, 
         c_args : avx512_flags,
         extra_files : ['avx512.h', 'avx512.pxd'],
     )
@@ -51,7 +51,7 @@ if neon_supported
     impl += static_library(
         'impl_neon', 
         'neon.c', 
-        include_directories : prodigal_inc, 
+        include_directories : inc, 
         c_args : neon_flags,
         extra_files : ['neon.h', 'neon.pxd'],
     )

pyrodigal/meson.build

@@ -75,7 +75,7 @@ endif
 
 python.extension_module('lib',
     ['lib.pyx'],
-    include_directories: prodigal_inc,
+    include_directories: inc,
     dependencies : py_dep,
     link_with : [prodigal, prodigal_training, impl],
     install: true,

pyrodigal/prodigal/bitmap.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/bitmap.h

pyrodigal/prodigal/dprog.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/dprog.h

pyrodigal/prodigal/fptr.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/fptr.h

pyrodigal/prodigal/gene.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/gene.h

pyrodigal/prodigal/meson.build

@@ -0,0 +1,16 @@
+prodigal_sources = [
+    'node.h',
+    '__init__.pxd',
+    'bitmap.pxd',
+    'dprog.pxd',
+    'gene.pxd',
+    'metagenomic.pxd',
+    'node.pxd',
+    'sequence.pxd',
+    'training.pxd',
+]
+
+python.install_sources(
+    prodigal_sources, 
+    subdir : 'pyrodigal' / 'prodigal'
+)

pyrodigal/prodigal/metagenomic.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/metagenomic.h

pyrodigal/prodigal/sequence.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/sequence.h

pyrodigal/prodigal/training.h

@@ -0,0 +1 @@
+../../vendor/Prodigal/training.h