Re-enable tests

Makefile

@@ -4,9 +4,8 @@ LITE_BUILD_DIR=_lite_build
 PACKAGES=lacaml lbfgs ocephes
 PACKAGES_TEST=$(PACKAGES) kaputt dsfo
 PACKAGES_COVERED:=$(PACKAGES_TEST) bisect_ppx
-PACKAGES_INSTALL=cppo $(PACKAGES)
-PACKAGES_INSTALL_TEST=cppo $(PACKAGES_COVERED)
-CPPO_TAG:=-plugin-tag 'package(cppo_ocamlbuild)'
+PACKAGES_INSTALL=$(PACKAGES)
+PACKAGES_INSTALL_TEST=$(PACKAGES_COVERED)
 
 SOURCE_DIRS=util unc stats cls rgr uns
 INSTALL_EXTS=a o cma cmi cmo cmt cmx cmxa cmxs
@@ -17,7 +16,7 @@ default: FORCE
 	@echo "available targets:"
 	@echo "  build      	compiles Oml"
 	@echo "  lite       	compiles only Oml_lite"
-	@echo "  tests      	runs unit tests"
+	@echo "  test       	runs unit tests"
 	@echo "  doc        	generates ocamldoc documentations"
 	@echo "  clean      	deletes all produced files"
 	@echo "  setup      	opam install Oml dependencies"
@@ -58,16 +57,14 @@ clean:
 
 omltest.native:
 	ocamlbuild -build-dir $(TEST_BUILD_DIR) \
-		$(CPPO_TAG) \
 		-use-ocamlfind $(foreach package, $(PACKAGES_TEST),-package $(package)) \
-		-I src/lib $(foreach sd, $(SOURCE_DIRS), -I src/lib$(sd)) -I src/test omltest.native
+		$(foreach sd, $(SOURCE_DIRS), -I src/lib$(sd)) -I src/lib -I src/test omltest.native
 
 test: omltest.native
 	time ./omltest.native ${TEST}
 
 covered_test.native:
 	ocamlbuild -build-dir $(TEST_BUILD_DIR) \
-		$(CPPO_TAG) \
 		-use-ocamlfind $(foreach package, $(PACKAGES_COVERED),-package $(package)) \
 		-I src/lib $(foreach sd, $(SOURCE_DIRS), -I src/lib$(sd)) -I src/test omltest.native
 

myocamlbuild.ml

@@ -34,6 +34,47 @@ let add_ml_and_mlt_and_depends () =
           ]
     end
 
+(* For unknown reasons this rule is not firing?
+   Or maybe it is insufficient to trigger the generation of a
+   full module needed for test. Using this would prevent
+   the need for stub code such as functions.ml.
+let add_lite_ml_and_mlt_and_depends () =
+  let dmlt  = "%.mlt" in
+  let doml  = "oml_%.ml" in
+  let domll = "oml_lite_%.ml" in
+  let pmld  = "%.ml.depends" in
+  let pmlj  = "%.mlj" in
+  let pmljd = "%.mlj.depends" in
+  rule "concat oml_ and oml_lite_ prefixed ml and mlt files, and build dependencies"
+    ~insert:`top
+    ~deps:[ dmlt; doml; domll ]
+    ~prods:[ pmld; pmlj; pmljd ]
+    begin fun env _build ->
+      let mlt  = env dmlt in
+      let oml  = env doml in
+      let omll = env domll in
+      let mlj  = env pmlj in
+      let ml_depends  = env pmld in
+      let mlj_depends = env pmljd in
+      let ocamldep_tags =
+        (Tags.union (tags_of_pathname oml) (tags_of_pathname omll))
+        ++ "ocaml" ++ "ocamldep"
+      in
+      Seq [ Cmd ( S [ A "cat";  P omll;                       Sh ">";  P mlj])
+          ; Cmd ( S [ A "cat";  P oml;                        Sh ">>"; P mlj])
+          ; Cmd ( S [ A "echo"; A (sprintf "# 0 %S" mlt);     Sh ">>"; P mlj])
+          ; Cmd ( S [ A "echo"; A "(*BISECT-IGNORE-BEGIN*)";  Sh ">>"; P mlj])
+          ; Cmd ( S [ A "cat";  P mlt;                        Sh ">>"; P mlj])
+          ; Cmd ( S [ A "echo"; A "(*BISECT-IGNORE-END*)";    Sh ">>"; P mlj])
+          (* Now build the dependencies for the mlj file. *)
+          ; Cmd ( S [ A "ocamlfind"; A "ocamldep"; T ocamldep_tags ; A "-ml-synonym"
+                    ; Sh "'.mlj'"; A "-modules"; P mlj;       Sh ">";  P mlj_depends])
+          (* Fake the ml.depends to be the same as mlj.depends. *)
+          ; Cmd ( S [ A "sed"; A "-E"; A "s/mlj/ml/g"; P mlj_depends;
+                                                              Sh ">" ; P ml_depends])
+          ]
+    end *)
+
 let report_dependencies pth =
   let () = printf "here are the %s dependencies\n" pth in
   List.iter (function | `just_try, s  -> printf "just_try: %s\n" s
@@ -105,18 +146,22 @@ let () =
       | Before_rules    -> ()
       | After_rules     ->
           begin
-            Pathname.define_context "src/lib/"      ["src/lib/util"];
-            Pathname.define_context "src/lib/unc"   ["src/lib/util"; "src/lib/unc"];
-            Pathname.define_context "src/lib/stats" ["src/lib/util"; "src/lib/unc"; "src/lib/stats"];
-            Pathname.define_context "src/lib/cls"   ["src/lib/util"; "src/lib/unc"; "src/lib/stats"; "src/lib/cls"];
-            Pathname.define_context "src/lib/rgr"   ["src/lib/util"; "src/lib/unc"; "src/lib/stats"; "src/lib/rgr"];
-            Pathname.define_context "src/lib/uns"   ["src/lib/util"; "src/lib/unc"; "src/lib/uns"];
 
             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 ();
               Options.make_links := true;
+              Pathname.define_context "src/test"
+                [ "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"       ["src/lib/util"; "src/lib/stats"];
+              Pathname.define_context "src/lib/unc"   ["src/lib/util"; "src/lib/stats"];
+              Pathname.define_context "src/lib/stats" ["src/lib/util"; ];
+              Pathname.define_context "src/lib/cls"   ["src/lib/util"; "src/lib/stats"];
+              Pathname.define_context "src/lib/rgr"   ["src/lib/util"; "src/lib/unc"; "src/lib/stats"];
+              Pathname.define_context "src/lib/uns"   ["src/lib/util"; "src/lib/unc" ];
             end;
 
             (* To build without interfaces

src/lib/cls/naive_bayes.ml

@@ -0,0 +1,22 @@
+(*
+   Copyright 2016
+     Leonid Rozenberg <leonidr@gmail.com>
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+*)
+
+(** See message above add_lite_ml_and_mlt_and_depends for explanation. *)
+if Filename.basename Sys.argv.(0) <> "omltest.native" then
+  failwith ("Linked the Functions tests stub file into: " ^ Sys.argv.(0))
+
+include Oml_naive_bayes

src/lib/cls/naive_bayes.mlt

@@ -17,6 +17,7 @@
 
 open Test_utils
 module P = Probabilities
+module List = ListLabels
 
 let () =
   let add_simple_test = Test.add_simple_test_group "Naive Bayes" in

src/lib/online.mlt

@@ -17,13 +17,12 @@
 
 open Test_utils
 open Util
-module D = Statistics.Descriptive
+module D = Descriptive
 
 (* In order for these tests to work well, we have to span the range of
    acceptable floats as well. If we're uniformly sampling from [0, largest_float]
    we'll have different characteristics if largest_float is tiny or huge:
-   this will influence the significand in the algorithms.
-*)
+   this will influence the significand in the algorithms.  *)
 
 let () =
   let add_random_test

src/lib/rgr/multivariate.mlt

@@ -20,8 +20,8 @@ open Test_utils
 
 open Util
 
-module Descriptive = Statistics.Descriptive
-module Vectors = Uncategorized.Vectors
+module Descriptive = Descriptive
+module Vectors = Vectors
 
 let looe_manually lambda pred resp =
   let predi = Array.to_list pred |> List.mapi (fun i p -> (i, p)) in

src/lib/rgr/tikhonov.mlt

@@ -18,7 +18,7 @@
 open Test_utils
 open Util
 
-module Matrices = Uncategorized.Matrices
+module Matrices = Matrices
 
 let () =
   let add_random_test

src/lib/rgr/univariate.ml

@@ -0,0 +1,22 @@
+(*
+   Copyright 2016
+     Leonid Rozenberg <leonidr@gmail.com>
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+*)
+
+(** See message above add_lite_ml_and_mlt_and_depends for explanation. *)
+if Filename.basename Sys.argv.(0) <> "omltest.native" then
+  failwith ("Linked the Functions tests stub file into: " ^ Sys.argv.(0))
+
+include Oml_univariate

src/lib/stats/functions.ml

@@ -0,0 +1,22 @@
+(*
+   Copyright 2016
+     Leonid Rozenberg <leonidr@gmail.com>
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+*)
+
+(** See message above add_lite_ml_and_mlt_and_depends for explanation. *)
+if Filename.basename Sys.argv.(0) <> "omltest.native" then
+  failwith ("Linked the Functions tests stub file into: " ^ Sys.argv.(0))
+
+include Oml_functions

src/lib/unc/estimations.mlt

@@ -16,7 +16,7 @@
 *)
 open Test_utils
 open Util
-module D = Statistics.Descriptive
+module D = Descriptive
 
 let () =
   let add_random_test

src/lib/uns/pca.ml

@@ -16,8 +16,7 @@
 *)
 
 open Lacaml.D
-
-open Uncategorized.Lacaml_util
+open Lacaml_util
 
 type t = { variances   : vec
          ; components  : mat

src/lib/uns/pca.mlt

@@ -18,7 +18,6 @@
 open Test_utils
 open Util
 open Lacaml.D
-module Matrices = Uncategorized.Matrices
 
 let () =
   let matrix_size = 100 in

src/test/omltest.ml

@@ -21,29 +21,29 @@ open Test_utils
 module Rank = Rank
 module Util = Util
 
-module Estimations = Uncategorized.Estimations
-module Solvers = Uncategorized.Solvers
-module Svd = Uncategorized.Svd
-
-module Matrices = Uncategorized.Matrices
-module Vectors = Uncategorized.Vectors
-
-module Functions = Statistics.Functions
-module Descriptive = Statistics.Descriptive
-module Distributions = Statistics.Distributions
-module Hypothesis_test = Statistics.Hypothesis_test
-module Measures = Statistics.Measures
-module Sampling = Statistics.Sampling
-
+module Estimations = Estimations
+module Solvers = Solvers
+module Svd = Svd
+
+module Matrices = Matrices
+module Vectors = Vectors
+
+module Functions = Functions
+module Descriptive = Descriptive
+module Distributions = Distributions
+module Hypothesis_test = Hypothesis_test
+module Measures = Measures
+module Sampling = Sampling
 module Online = Online
 
-module Naive_bayes = Classification.Naive_bayes
-module Logistic_regression = Classification.Logistic_regression
 
-module Univariate = Regression.Univariate
-module Multivariate = Regression.Multivariate
-module Tikhonov = Regression.Tikhonov
-module Interpolate = Regression.Interpolate
+module Naive_bayes = Naive_bayes
+module Logistic_regression = Logistic_regression
+
+module Univariate = Univariate
+module Multivariate = Multivariate
+module Tikhonov = Tikhonov
+module Interpolate = Interpolate
 
 module Pca = Pca