reorganize directories and clean up build infrastructure

CamlPaml/Makefile

@@ -1,33 +0,0 @@
-PKGS = gsl
-
-lib:
-	ocamlbuild -cflags -for-pack,CamlPaml CamlPaml.cma CamlPaml.cmxa \
-		-ocamlc "ocamlfind ocamlc -package ${PKGS}" \
-		-ocamlopt "ocamlfind ocamlopt -package ${PKGS}" \
-		-ocamldep "ocamlfind ocamldep -package ${PKGS}"
-
-TESTPKGS = ${PKGS},oUnit
-test:
-	ocamlbuild test.native \
-		-ocamlc "ocamlfind ocamlc -package ${TESTPKGS} -linkpkg" \
-		-ocamlopt "ocamlfind ocamlopt -package ${TESTPKGS} -linkpkg" \
-		-ocamldep "ocamlfind ocamldep -package ${TESTPKGS}"
-	_build/test.native -verbose
-
-
-install: lib
-	ocamlfind install CamlPaml META _build/CamlPaml.cmi _build/CamlPaml.cma _build/CamlPaml.cmxa _build/CamlPaml.a
-
-uninstall:
-	ocamlfind remove CamlPaml
-
-reinstall:
-	make uninstall
-	make install
-
-clean:
-	rm -f *~
-	ocamlbuild -clean
-
-doc:
-	ocamlbuild CamlPaml.docdir/index.html

CamlPaml/_tags

@@ -1,4 +0,0 @@
-<**/*.ml> or <**/*.mli>: ocaml, pp(ocaml+twt), debug
-<**/NewickLexer.*>: ocaml, debug, -pp(ocaml+twt)
-<**/NewickParser.*>: ocaml, debug, -pp(ocaml+twt)
-<CamlPaml.cmxa>: ocaml, native, library, debug

Makefile

@@ -6,13 +6,13 @@ ARCH := `uname`.`uname -p`
 export ARCH
 
 PhyloCSF: CamlPaml
-	cd PhyloCSF; $(MAKE) clean; $(MAKE) $(MFLAGS)
-	cp PhyloCSF/_build/PhyloCSF.native PhyloCSF.$(ARCH)
+	cd src; $(MAKE) clean; $(MAKE) $(MFLAGS)
+	cp src/_build/PhyloCSF.native PhyloCSF.$(ARCH)
 
 CamlPaml: 
-	cd CamlPaml; $(MAKE) $(MFLAGS) reinstall
+	cd lib/CamlPaml; $(MAKE) $(MFLAGS) reinstall
 
 clean:
-	cd CamlPaml; $(MAKE) clean
-	cd PhyloCSF; $(MAKE) clean
+	cd lib/CamlPaml; $(MAKE) clean
+	cd src; $(MAKE) clean
 	rm -f PhyloCSF.*

PhyloCSF/Makefile

@@ -1,11 +0,0 @@
-PKGS = batteries,CamlPaml
-
-all:
-	ocamlbuild all.otarget \
-		-ocamlc "ocamlfind ocamlc -package ${PKGS} -linkpkg" \
-		-ocamlopt "ocamlfind ocamlopt -package ${PKGS} -linkpkg" \
-		-ocamldep "ocamlfind ocamldep -package ${PKGS}"
-
-clean:
-	rm -f *~
-	ocamlbuild -clean

PhyloCSF/_tags

@@ -1,4 +0,0 @@
-<**/*.ml> or <**/*.mli>: ocaml, pp(ocaml+twt)
-<all.otarget>: ocaml, native
-true: debug
-

lib/CamlPaml/Makefile

@@ -0,0 +1,26 @@
+LIBNAME = CamlPaml
+
+lib:
+	ocamlbuild ${LIBNAME}.cma ${LIBNAME}.cmxa
+
+test:
+	ocamlbuild test.native
+	_build/test.native -verbose
+
+
+install: lib
+	ocamlfind install ${LIBNAME} META _build/${LIBNAME}.cmi _build/${LIBNAME}.cma _build/${LIBNAME}.cmxa _build/${LIBNAME}.a
+
+uninstall:
+	ocamlfind remove ${LIBNAME}
+
+reinstall:
+	make uninstall
+	make install
+
+clean:
+	rm -f *~
+	ocamlbuild -clean
+
+doc:
+	ocamlbuild ${LIBNAME}.docdir/index.html

lib/CamlPaml/_tags

@@ -0,0 +1,5 @@
+<**/*.ml> or <**/*.mli>: ocaml, debug, pkg_gsl, for-pack(CamlPaml), pp(ocaml+twt)
+<**/NewickLexer.*>: -pp(ocaml+twt)
+<**/NewickParser.*>: -pp(ocaml+twt)
+<test.ml>: pkg_oUnit
+<test.native>: pkg_gsl, pkg_oUnit

lib/CamlPaml/myocamlbuild.ml

@@ -0,0 +1,185 @@
+open Ocamlbuild_plugin
+open Command (* no longer needed for OCaml >= 3.10.2 *)
+
+(**
+   Overview of tags:
+   - [pkg_batteries] to use Batteries as a library, without syntax extensions
+   - [use_batteries] and [use_batteries_r] to use both Batteries and all the non-destructive syntax extensions
+   - [pkg_sexplib.syntax] with [syntax_camlp4o] or [syntax_camlp4r] for sexplib
+*)
+
+
+(**
+   {1 OCamlFind}
+*)
+
+let run_and_read      = Ocamlbuild_pack.My_unix.run_and_read
+
+let blank_sep_strings = Ocamlbuild_pack.Lexers.blank_sep_strings
+
+module OCamlFind =
+struct
+  (* this lists all supported packages *)
+  let find_packages () =
+    blank_sep_strings &
+      Lexing.from_string &
+      run_and_read "ocamlfind list | cut -d' ' -f1"
+
+  (* this is supposed to list available syntaxes, but I don't know how to do it. *)
+  let find_syntaxes () = ["camlp4o"; "camlp4r"]
+
+  (* ocamlfind command *)
+  let ocamlfind x = S[A"ocamlfind"; x]
+
+  let  before_options () =
+    (* by using Before_options one let command line options have an higher priority *)
+    (* on the contrary using After_options will guarantee to have the higher priority *)
+
+    (* override default commands by ocamlfind ones *)
+    Options.ocamlc     := ocamlfind & A"ocamlc";
+    Options.ocamlopt   := ocamlfind & A"ocamlopt";
+    Options.ocamldep   := ocamlfind & A"ocamldep";
+    Options.ocamldoc   := ocamlfind & A"ocamldoc";
+    Options.ocamlmktop := ocamlfind & A"ocamlmktop"
+
+  let get_ocamldoc_directory () =
+    let ocamldoc_directory = run_and_read "ocamlfind ocamldoc -customdir" in
+    let length             = String.length ocamldoc_directory             in
+      assert (length != 0);
+      let char = ocamldoc_directory.[length - 1] in
+	if (char = '\n') || (char = '\r') then String.sub ocamldoc_directory 0 (length - 1)
+	else ocamldoc_directory
+
+  let after_rules () =
+       (* When one link an OCaml library/binary/package, one should use -linkpkg *)
+       flag ["ocaml"; "byte";   "link"; "program"] & A"-linkpkg";
+       flag ["ocaml"; "native"; "link"; "program"] & A"-linkpkg";
+
+
+       (* For each ocamlfind package one inject the -package option when
+	* compiling, computing dependencies, generating documentation and
+	* linking. *)
+       List.iter begin fun pkg ->
+         flag ["ocaml"; "compile";  "pkg_"^pkg] & S[A"-package"; A pkg];
+         flag ["ocaml"; "ocamldep"; "pkg_"^pkg] & S[A"-package"; A pkg];
+         flag ["ocaml"; "doc";      "pkg_"^pkg] & S[A"-package"; A pkg];
+         flag ["ocaml"; "link";     "pkg_"^pkg] & S[A"-package"; A pkg];
+       end (find_packages ());
+
+       (* Like -package but for extensions syntax. Morover -syntax is useless
+	* when linking. *)
+       List.iter begin fun syntax ->
+         flag ["ocaml"; "compile";  "syntax_"^syntax] & S[A"-syntax"; A syntax];
+         flag ["ocaml"; "ocamldep"; "syntax_"^syntax] & S[A"-syntax"; A syntax];
+         flag ["ocaml"; "doc";      "syntax_"^syntax] & S[A"-syntax"; A syntax];
+       end (find_syntaxes ());
+
+       (* The default "thread" tag is not compatible with ocamlfind.
+          Indeed, the default rules add the "threads.cma" or "threads.cmxa"
+          options when using this tag. When using the "-linkpkg" option with
+          ocamlfind, this module will then be added twice on the command line.
+
+          To solve this, one approach is to add the "-thread" option when using
+          the "threads" package using the previous plugin.
+        *)
+       flag ["ocaml"; "pkg_threads"; "compile"]  (S[A "-thread"]);
+       flag ["ocaml"; "pkg_threads"; "link"]     (S[A "-thread"]);
+end
+
+(**
+   {1 OCaml Batteries Included}
+*)
+
+module Batteries =
+struct
+  let before_options () = ()
+
+  let after_rules () =
+    flag ["ocaml"; "link"; "byte";   "use_ocamldoc_info"] (S[A "-I"; A "+ocamldoc"; A "odoc_info.cma"]);
+    flag ["ocaml"; "link"; "native"; "use_ocamldoc_info"] (S[A "-I"; A "+ocamldoc"(*; A "odoc_info.cmxa"*)]);
+    flag ["ocaml"; "docfile";        "use_ocamldoc_info"] (S[A "-I"; A "+ocamldoc"]);
+    flag ["ocaml"; "docdir";         "use_ocamldoc_info"] (S[A "-I"; A "+ocamldoc"]);
+    flag ["ocaml"; "doc";            "use_ocamldoc_info"] (S[A "-I"; A "+ocamldoc"]);
+
+    (*The command-line for [use_batteries] and [use_batteries_r]*)
+
+    let cl_use_boilerplate = [A"-package"; A "batteries.pa_type_conv.syntax,batteries,sexplib.syntax"]
+    and cl_use_batteries   = [A"-package"; A "batteries.pa_openin.syntax,batteries.pa_where.syntax,batteries.pa_batteries.syntax"; A "-package"; A "batteries"]
+    and cl_use_batteries_o = []
+              (*[cl_use_batteries_o]: extensions which only make sense in original syntax*)
+    and cl_camlp4o         = [A"-syntax";  A "camlp4o"]
+    and cl_camlp4r         = [A"-syntax";  A "camlp4r"] in
+
+    let cl_boilerplate_original = cl_use_boilerplate @ cl_camlp4o
+    and cl_boilerplate_revised  = cl_use_boilerplate @ cl_camlp4r
+    and cl_batteries_original   = cl_use_batteries   @ cl_use_batteries_o @ cl_camlp4o
+    and cl_batteries_revised    = cl_use_batteries   @ cl_camlp4r in
+
+      (** Tag [use_boilerplate] provides boilerplate syntax extensions,
+	  in original syntax*)
+
+    flag ["ocaml"; "compile";  "use_boilerplate"] & S cl_boilerplate_original ;
+    flag ["ocaml"; "ocamldep"; "use_boilerplate"] & S cl_boilerplate_original ;
+    flag ["ocaml"; "doc";      "use_boilerplate"] & S cl_boilerplate_original ;
+    flag ["ocaml"; "link";     "use_boilerplate"] & S cl_boilerplate_original ;
+
+      (** Tag [use_boilerplate_r] provides boilerplate syntax extensions,
+	  in original syntax*)
+
+    flag ["ocaml"; "compile";  "use_boilerplate_r"] & S cl_boilerplate_revised ;
+    flag ["ocaml"; "ocamldep"; "use_boilerplate_r"] & S cl_boilerplate_revised ;
+    flag ["ocaml"; "doc";      "use_boilerplate_r"] & S cl_boilerplate_revised ;
+    flag ["ocaml"; "link";     "use_boilerplate_r"] & S cl_boilerplate_revised ;
+
+    (** Tag [use_batteries] provides both package [batteries]
+	and all syntax extensions, in original syntax. *)
+
+    flag ["ocaml"; "compile";  "use_batteries"] & S cl_batteries_original ;
+    flag ["ocaml"; "ocamldep"; "use_batteries"] & S cl_batteries_original ;
+    flag ["ocaml"; "doc";      "use_batteries"] & S cl_batteries_original ;
+    flag ["ocaml"; "link";     "use_batteries"] & S cl_batteries_original ;
+
+    (** Tag [use_batteries_r] provides both package [batteries]
+	and all syntax extensions, in revised syntax. *)
+
+    flag ["ocaml"; "compile";  "use_batteries_r"] & S cl_batteries_revised;
+    flag ["ocaml"; "ocamldep"; "use_batteries_r"] & S cl_batteries_revised;
+    flag ["ocaml"; "doc";      "use_batteries_r"] & S cl_batteries_revised;
+    flag ["ocaml"; "link";     "use_batteries_r"] & S cl_batteries_revised
+
+
+(*    flag ["ocaml"; "compile";  "use_batteries"] & S[A "-verbose";
+						    A"-package"; A "batteries.syntax.full";
+						    A"-syntax";  A "batteries.syntax.full"];
+    flag ["ocaml"; "ocamldep"; "use_batteries"] & S[A "-verbose";
+						    A"-package"; A "batteries.syntax.full";
+						    A"-syntax"; A "batteries.syntax.full"];
+    flag ["ocaml"; "doc";      "use_batteries"] & S[A "-verbose";
+						    A"-package"; A "batteries.syntax.full";
+						    A"-syntax"; A "batteries.syntax.full"];
+    flag ["ocaml"; "link";     "use_batteries"] & S[A "-verbose";
+						    A"-package"; A "batteries.syntax.full";
+						    A"-syntax"; A "batteries.syntax.full"];*)
+
+
+end
+
+let _ = dispatch begin function
+   | Before_options ->
+       OCamlFind.before_options ();
+       Batteries.before_options ()
+   | After_rules ->
+       OCamlFind.after_rules ();
+       Batteries.after_rules ()
+
+
+   | _ -> ()
+end
+
+
+
+(**
+   which ocamlrun  ->   header
+
+   print_backtrace -> ajouter "-b" après le header
+**)

src/Makefile

@@ -0,0 +1,6 @@
+all:
+	ocamlbuild all.otarget
+
+clean:
+	rm -f *~
+	ocamlbuild -clean

src/_tags

@@ -0,0 +1,3 @@
+<**/*.ml> or <**/*.mli>: pp(ocaml+twt)
+true: debug, pkg_batteries, pkg_CamlPaml
+