Restore documentation generation and full tests

.ocamlinit

@@ -1,10 +1,5 @@
 (* Need to list all of the sub directories so that Utop
   knows where to look. *)
-(*
-#directory "_lite_build/src/lib" ;;
-#load_rec "oml_lite.cma" ;;
-print_endline "Loaded Oml_lite" ;;
-*)
 
 #directory "_build/src";;
 #load_rec "oml.cma";;

Makefile

@@ -1,11 +1,13 @@
 TEST_BUILD_DIR="_test_build"
 COVERED_TEST_BUILD_DIR="_covered_test_build"
+DOC_BUILD_DIR="_doc_build"
 
-.PHONY: all clean test build setup doc
+.PHONY: all clean test build full setup doc
 
 default: FORCE
 	@echo "available targets:"
-	@echo "  build      	compiles Oml_lite and Oml if possible"
+	@echo "  build      	compiles Oml"
+	@echo "  full      	  compiles Omlf"
 	@echo "  test       	runs unit tests"
 	@echo "  doc        	generates ocamldoc documentations"
 	@echo "  clean      	deletes all produced files"
@@ -25,10 +27,15 @@ setup-test:
 #### Building
 
 build:
+	ocaml pkg/pkg.ml build --with-lacaml false --with-lbfgs false --with-ocephes false
+
+full:
 	ocaml pkg/pkg.ml build
 
 clean:
-	ocaml pkg/pkg.ml clean
+	ocaml pkg/pkg.ml clean --build-dir $(TEST_BUILD_DIR)
+	ocaml pkg/pkg.ml clean --build-dir $(COVERED_TEST_BUILD_DIR)
+	ocaml pkg/pkg.ml clean --build-dir $(DOC_BUILD_DIR)
 
 #### Testing
 
@@ -58,14 +65,18 @@ clean_reports:
 
 #### Documentation
 
-oml.odocl:
-	cp src/lib/oml.mlpack oml.odocl
+#oml.odocl:
+#	cp src/lib/oml.mlpack oml.odocl
 
 # including the cmi as build targets triggers all of the including logic
 # to get saner documentation.
 doc:
-	$(OCAMLBUILD) -build-dir $(DOC_BUILD_DIR) \
-		$(foreach package, $(PACKAGES),-package $(package)) \
-		$(foreach sd, $(SOURCE_DIRS), -I src/lib$(sd)) -I src/lib oml.cmi doc.docdir/index.html
+	ocamlbuild -classic-display -use-ocamlfind -plugin-tag 'package(str)' -no-links -build-dir $(DOC_BUILD_DIR) -docflags '-colorize-code,-charset,utf-8' doc/api.docdir/index.html
+
+# topkg doc --build-dir $(DOC_BUILD_DIR)
+#
+#	$(OCAMLBUILD) -build-dir $(DOC_BUILD_DIR) \
+#		$(foreach package, $(PACKAGES),-package $(package)) \
+#		$(foreach sd, $(SOURCE_DIRS), -I src/lib$(sd)) -I src/lib oml.cmi doc.docdir/index.html
 
 FORCE:

_tags

@@ -15,9 +15,9 @@ true: safe_string, annot, bin_annot, principal, warn(A-42-44-48-50)
 <src-full/**> : package(lacaml), package(ocephes), package(lbfgs)
 <src/**/*.mlj> : package(kaputt)
 <src-full/**/*.mlj> : package(kaputt)
-<src-full/cls/*.mlj> : package(dsfo)
-<test/**> : package(kaputt)
+<test/**> : package(kaputt), package(lacaml), package(ocephes), package(lbfgs)
 
 "_build": -traverse
 "_test_build": -traverse
 "_covered_test_build": -traverse
+"_doc_build": -traverse

doc/api.odocl

@@ -1 +1,2 @@
 Oml
+Oml_full

myocamlbuild.ml

@@ -8,12 +8,15 @@ let target_with_extension ext =
 let is_test_target () =
   List.exists (function
     | "oml_test.native"
-    | "oml_lite_test.native" -> true
+    | "omlf_test.native" -> true
     | s when (Filename.basename s = "oml_test.native"
-           || Filename.basename s = "oml_lite_test.native") -> true
+           || Filename.basename s = "omlf_test.native") -> true
     | _                      -> false)
     !Options.targets
 
+let is_doc_target () =
+  target_with_extension "html"
+
 let add_ml_and_mlt_and_depends () =
   rule "concat ml and mlt files, and build dependencies"
     ~insert:`top
@@ -107,8 +110,7 @@ let add_compile_mlj_to_byte_rule () =
       Ocaml_compiler.prepare_compile build mlj;
       Cmd ( S [ !Options.ocamlc; A"-c"; Ocaml_arch.forpack_flags_of_pathname mlj
               ; T tags
-              ; (*!Options.ocaml_ppflags tags
-              ; *) Ocaml_utils.ocaml_include_flags mlj
+              ; Ocaml_utils.ocaml_include_flags mlj
               ; A "-o"; Px cmo
               ; A "-impl"; P mlj])
     end
@@ -136,8 +138,7 @@ let add_compile_mlj_to_native_rule () =
       Ocaml_compiler.prepare_link cmx cmi ["cmx"; "cmi"] build;
       Cmd ( S [ !Options.ocamlopt; A"-c"; Ocaml_arch.forpack_flags_of_pathname mlj
               ; T tags
-              ; (*!Options.ocaml_ppflags tags
-              ; *) Ocaml_utils.ocaml_include_flags mlj
+              ; Ocaml_utils.ocaml_include_flags mlj
               ; A "-o"; Px cmx (* FIXME ocamlopt bug -o cannot be after the input file *)
               ; A "-impl"; P mlj])
     end
@@ -165,7 +166,6 @@ let to_mli_assoc =
   List.map (fun s ->
     String.capitalize_ascii (Filename.chop_extension (Filename.basename s)), s)
 
-  (*
 let imto_regex =
   Str.regexp "include module type of \\([A-Z][a-zA-Z_]+\\)"
 
@@ -181,6 +181,7 @@ let rec include_includes modassoc mli =
       let ap = Str.match_end () in
       try
         let file = List.assoc md modassoc in
+        Printf.printf "inserting %s for %s ----\n" file md;
         let bef  = String.sub ff pos (np - pos) in
         let ic   =
           if not (Sys.file_exists file) then begin
@@ -194,6 +195,7 @@ let rec include_includes modassoc mli =
         close_in ic;
         loop ap (incf :: bef :: acc)
       with Not_found -> (* Missing module in modassoc *)
+        Printf.printf "didn't find %s \n" md;
         let bef  = String.sub ff pos (ap - pos - 1) in
         loop (ap - 1) (bef :: acc)
     with Not_found ->
@@ -205,7 +207,6 @@ let rec include_includes modassoc mli =
       let oc = open_out mli in
       List.iter (output_string oc) (List.rev lst);
       close_out oc
-      *)
 
 let () =
   let additional_rules =
@@ -217,30 +218,31 @@ let () =
       | Before_rules    -> ()
       | After_rules     ->
           begin
+            let regular_source_dirs =
+                  [ "src"         (* For the Online stuff that hasn't been packaged. *)
+                  ; "src/util"
+                  ; "src/unc"
+                  ; "src/stats"
+                  ; "src/cls"
+                  ; "src/rgr"
+                  ; "src/uns"
+                  ]
+            in
+            let full_source_dirs =
+                  [ "src-full"
+                  ; "src-full/unc"
+                  ; "src-full/stats"
+                  ; "src-full/cls"
+                  ; "src-full/rgr"
+                  ; "src-full/uns"
+                  ]
+            in
+
             if is_test_target () then begin
               add_ml_and_mlt_and_depends ();
               (*add_lite_ml_and_mlt_and_depends (); *)
               add_compile_mlj_to_native_rule ();
               add_compile_mlj_to_byte_rule ();
-              let regular_source_dirs =
-                    [ "src"         (* For the Online stuff that hasn't been packaged. *)
-                    ; "src/util"
-                    ; "src/unc"
-                    ; "src/stats"
-                    ; "src/cls"
-                    ; "src/rgr"
-                    ; "src/uns"
-                    ]
-              in
-              let full_source_dirs =
-                    [ "src-full/unc"
-                    ; "src-full/stats"
-                    ; "src-full/cls"
-                    ; "src-full/rgr"
-                    ; "src-full/uns"
-                    ]
-              in
-
               Pathname.define_context "test" regular_source_dirs;
               Pathname.define_context "test" full_source_dirs;
               List.iter (fun dir -> Pathname.define_context dir [ "test"])
@@ -258,22 +260,31 @@ let () =
               (Ocaml_compiler.byte_compile_ocaml_implem "%.ml" "%.cmo");
             *)
 
-            (* For documentation.
-            if target_with_extension "html" then begin
-              Options.make_links := true;
-              Pathname.define_context "src/lib"
-                [ "src/lib"; "src/lib/util"; "src/lib/unc"; "src/lib/stats"
-                ; "src/lib/cls"; "src/lib/rgr"; "src/lib/uns"];
-              Pathname.define_context "src/lib/cls"   ["src/lib/util"; ];
-              Pathname.define_context "src/lib/rgr"   ["src/lib/util"; "src/lib/stats"];
+            if is_doc_target () then begin
+              Pathname.define_context "src" regular_source_dirs;
+              Pathname.define_context "src-full" full_source_dirs;
 
               (* Since ocamldoc doesn't work very well with
                  "include module type of ___" directives, we'll preprocess the
-                 mli files to manually insert the relevant signature. *)
+                 mli files to manually insert the relevant signature.
+                 1. Get all the mli's.
+                 2. Before compiling them, scan for "include m... sig"
+                 3. If we find this pattern and we have a signature file.
+                    3a. Recurse!
+                 4. Manually insert it into the mli.
+              *)
+              let mla =
+                (all_mli_files "src"
+                @ all_mli_files "src-full")
+                |> to_mli_assoc
+                |> fun l ->
+                    ("Oml_cls_intf", "src/cls/oml_cls_intf.ml") ::
+                    ("Oml_intf", "src-full/rgr/omlf_intf.ml") ::
+                    l
+              in
+              Printf.printf "We have these files:\n%!";
+              List.iter (fun (m,f) -> Printf.printf "%s\t\t%s\n%!" m f) mla;
 
-              let mla = all_mli_files "src" |> to_mli_assoc in
-              (*Printf.printf "We have these files:\n%!";
-              List.iter (fun (m,f) -> Printf.printf "%s\t\t%s\n%!" m f) mla; *)
               rule "For documentation ocaml: mli -> cmi"
                 ~insert:`top
                 ~deps:[ "%.mli"; "%.mli.depends" ]
@@ -283,7 +294,7 @@ let () =
                   include_includes mla mli;
                   Ocaml_compiler.compile_ocaml_interf "%.mli" "%.cmi" env build
                 end;
-            end *)
+            end
           end
   in
   dispatch additional_rules

pkg/pkg.ml

@@ -3,20 +3,25 @@
 #require "topkg"
 open Topkg
 
-let lacaml = Conf.with_pkg ~default:false "lacaml"
-let lbfgs = Conf.with_pkg ~default:false "lbfgs"
-let ocephes = Conf.with_pkg ~default:false "ocephes"
+let lacaml = Conf.with_pkg "lacaml"
+let lbfgs = Conf.with_pkg "lbfgs"
+let ocephes = Conf.with_pkg "ocephes"
 let kaputt = Conf.with_pkg "kaputt"
 let bisect_ppx = Conf.with_pkg "bisect_ppx"
 let coverage = Conf.with_pkg ~default:false "coverage"
+let documentation = Conf.with_pkg ~default:false "documentation"
 
 let () =
   let build =
     let cmd c os fpaths =
       let scmd =
-        if Conf.value c coverage
-        then Cmd.((Pkg.build_cmd c os) % "-package" % "bisect_ppx" %% of_list fpaths)
-        else Cmd.(Pkg.build_cmd c os %% of_list fpaths)
+        Cmd.(Pkg.build_cmd c os
+          %% (of_list ["-plugin-tag"; "package(str)"])       (* Cause of Str in myocamlbuild.ml *)
+          %% on (Conf.value c coverage) (of_list ["-package"; "bisect_ppx"])
+          %% on (Conf.pkg_name c = "omltest") (of_list [ "-package"; "dsfo"
+                                                       ; "-package"; "kaputt"
+                                                       ])
+          %% of_list fpaths)
       in
       OS.Cmd.run scmd
     in
@@ -36,9 +41,6 @@ let () =
         let kaputt = Conf.value c kaputt in
         (* TODO: Add dsfo! *)
         let full = full && kaputt in
-        Ok  [ Pkg.mllib ~api:["Oml"] "src/oml.mllib"
-            ; Pkg.mllib ~cond:full ~api:["Oml_full"] "src-full/oml_full.mllib"
-            ; Pkg.test "test/oml_test"
-            ]
+        Ok  [ Pkg.test (if full then "test/omlf_test" else "test/oml_test") ]
     | other ->
       R.error_msgf "Unrecognized package name: %s" other

test/omlf_modules.ml

@@ -20,20 +20,20 @@
    driver: oml_test.ml. *)
 
 (* Uncategorized. *)
-module Svd = Svd
+module Omlf_svd = Omlf_svd
 
 (* Statistics. *)
-module Oml_functions = Oml_functions
-module Distributions = Distributions
-module Hypothesis_test = Hypothesis_test
+module Omlf_functions = Omlf_functions
+module Omlf_distributions = Omlf_distributions
+module Omlf_hypothesis_test = Omlf_hypothesis_test
 
 (* Classification. *)
-module Logistic_regression = Logistic_regression
-module Oml_naive_bayes = Oml_naive_bayes
+module Omlf_logistic_regression = Omlf_logistic_regression
+module Omlf_naive_bayes = Omlf_naive_bayes
 
 (* Regression. *)
-module Multivariate = Multivariate
-module Tikhonov = Tikhonov
+module Omlf_multivariate = Omlf_multivariate
+module Omlf_tikhonov = Omlf_tikhonov
 
 (* Unsupervised. *)
-module Pca = Pca
+module Omlf_pca = Omlf_pca

test/omlf_test.ml

@@ -17,8 +17,8 @@
 
 open Test_utils
 
-module Oml_lite_modules = Oml_lite_modules
 module Oml_modules = Oml_modules
+module Omlf_modules = Omlf_modules
 
 let () =
   if Array.length Sys.argv > 1 then

test/test_utils.ml

@@ -174,7 +174,7 @@ module Test = struct
   let launch_tests () =
     TestMap.bindings !test_holder
     |> List.sort ~cmp:compare
-    |> fun l -> Printf.printf "%d\n" (List.length l); l
+    |> fun l -> Printf.printf "Testing %d groups.\n" (List.length l); l
     |> List.iter ~f:(fun (group, tests) ->
         Printf.printf "--%s--\n%!" group;
         List.rev tests |> run_tests)

tools/travis_ci_test.sh

@@ -42,7 +42,7 @@ echo Installing C and Fortran deps
 opam install ocephes lacaml lbfgs
 
 echo Compiling with C/Fortran deps
-make build
+make full
 
 echo Install bisect ppx and ocveralls for coverage reporting
 opam install bisect_ppx ocveralls