Merge e5c646f into 34c8b10

.gitignore

@@ -1,9 +1,11 @@
 _build
 _test_build
-_lite_build
+_covered_test_build
+_doc_build
 report_dir/
 *.native
 *.byte
+*.install
 bisect*.out
 oml.docdir
 oml.odocl

.merlin

@@ -1,5 +1,8 @@
 PKG kaputt
-S ./src/lib/**
+PKG lacaml lbfgs ocephes
+S src/**
+S src-full/**
+S test
+S scripts
 B _build/**
 B _driver/**
-PKG lacaml lbfgs ocephes

.ocamlinit

@@ -1,2 +1,14 @@
-#directory "_lite_build/src/lib" ;;
-#load_rec "oml_lite.cma";;
+(* Need to list all of the sub directories so that Utop
+  knows where to look. *)
+
+#directory "_build/src";;
+#load_rec "oml.cma";;
+print_endline "Loaded Oml" ;;
+
+#require "ocephes";;
+#require "lacaml";;
+#require "lbfgs";;
+
+#directory "_build/src-full";;
+#load_rec "oml_full.cma";;
+print_endline "Loaded Oml Full" ;;

Makefile

@@ -1,98 +1,65 @@
+TEST_BUILD_DIR="_test_build"
+COVERED_TEST_BUILD_DIR="_covered_test_build"
+DOC_BUILD_DIR="_doc_build"
+PACKAGES_INSTALL=ocephes lacaml lbfgs
+PACKAGES_INSTALL_TEST=kaputt bisect_ppx dsfo
 
-TEST_BUILD_DIR=_test_build
-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)'
-
-SOURCE_DIRS=/util /unc /stats /cls /rgr /uns
-INSTALL_EXTS=a o cma cmi cmo cmt cmx cmxa cmxs
-
-.PHONY: all clean test build install uninstall setup default doc omltest.native oml.cmxa oml_lite.cmxa lite
+.PHONY: all clean test build full setup doc
 
 default: FORCE
 	@echo "available targets:"
-	@echo "  build      	compiles Oml"
-	@echo "  lite       	compiles Oml_lite"
-	@echo "  tests      	runs unit tests"
-	@echo "  doc        	generates ocamldoc documentations"
-	@echo "  clean      	deletes all produced files"
-	@echo "  setup      	opam install Oml dependencies"
-	@echo "  setup-test 	opam install Oml and testing dependencies"
-	@echo "  install    	copies executable and library files"
-	@echo "  install-lite	copies executable and library files"
-	@echo "  covered_test	runs unit tests with coverage"
-	@echo "  report     	generate Bisect_ppx coverage report"
-
+	@echo "	build			compiles"
+	@echo "	build_lite		compiles without C dependencies."
+	@echo "	test			runs unit tests"
+	@echo "	test_lite		test without C dependencies"
+	@echo "	covered_test		runs unit tests with coverage"
+	@echo "	covered_test_lite	runs unit tests without C dependencies with coverage"
+	@echo "	setup			opam install packages necessary for full build"
+	@echo "	setup_test		opam install packages necessary for testing"
+	@echo "	doc			generates ocamldoc documentations"
+	@echo "	clean			deletes all produced files"
+	@echo "	report			generate Bisect_ppx coverage report"
 
 # This should be called something else.
 setup:
 	opam install $(PACKAGES_INSTALL)
 
-setup-test:
+setup_test:
 	opam pin add dsfo git://github.com/rleonid/dsfo
 	opam install $(PACKAGES_INSTALL_TEST)
 
 #### Building
 
-oml.cmxa:
-	ocamlbuild $(CPPO_TAG) -use-ocamlfind $(foreach package, $(PACKAGES),-package $(package)) -I src/lib oml.cma oml.cmxa oml.cmxs
+build:
+	ocaml pkg/pkg.ml build
 
-lite:
-	mv src/lib/_tags src/lib/_tags_orig && \
-	cp src/lib/_lite_tags src/lib/_tags && \
-	ocamlbuild -build-dir $(LITE_BUILD_DIR) $(CPPO_TAG) -tag 'cppo_D(OML_LITE)' -use-ocamlfind -I src/lib oml_lite.cma oml_lite.cmxa oml_lite.cmxs && \
-	mv src/lib/_tags_orig src/lib/_tags || \
-	mv src/lib/_tags_orig src/lib/_tags
+build_lite:
+	ocaml pkg/pkg.ml build --with-lacaml false --with-lbfgs false --with-ocephes false
 
-build: oml.cmxa
 
 clean:
-	ocamlbuild -clean
-	ocamlbuild -build-dir $(TEST_BUILD_DIR) -clean
-	ocamlbuild -build-dir $(LITE_BUILD_DIR) -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
 
-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
-
-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
-
-covered_test: covered_test.native
-	time ./omltest.native ${TEST}
+test:
+	ocaml pkg/pkg.ml build --build-dir $(TEST_BUILD_DIR) -n omltest && \
+		time ocaml pkg/pkg.ml test --build-dir $(TEST_BUILD_DIR)
 
-test_environment:
-	ocamlbuild -build-dir $(TEST_BUILD_DIR) \
-		-use-ocamlfind $(foreach package, $(PACKAGES_COVERED),-package $(package)) \
-		-I src/lib -I src/test oml.cma omltest.native
+test_lite:
+	ocaml pkg/pkg.ml build --build-dir $(TEST_BUILD_DIR) --with-lacaml false --with-lbfgs false --with-ocephes false -n omltest && \
+		time ocaml pkg/pkg.ml test --build-dir $(TEST_BUILD_DIR)
 
-#### Installing
+covered_test:
+	ocaml pkg/pkg.ml build --build-dir $(COVERED_TEST_BUILD_DIR) --with-coverage true -n omltest && \
+		time ocaml pkg/pkg.ml test --build-dir $(COVERED_TEST_BUILD_DIR)
 
-install:
-	cd pkg/full && ocamlfind install oml META $(foreach ext, $(INSTALL_EXTS), ../../_build/src/lib/oml.$(ext))
-
-uninstall:
-	ocamlfind remove oml
-
-install-lite:
-	cd pkg/lite && ocamlfind install oml-lite META $(foreach ext, $(INSTALL_EXTS), ../../${LITE_BUILD_DIR}/src/lib/oml_lite.$(ext))
-
-uninstall-lite:
-	ocamlfind remove oml-lite
+covered_test_lite:
+	ocaml pkg/pkg.ml build --build-dir $(COVERED_TEST_BUILD_DIR) --with-lacaml false --with-lbfgs false --with-ocephes false --with-coverage true -n omltest && \
+		time ocaml pkg/pkg.ml test --build-dir $(COVERED_TEST_BUILD_DIR)
 
 #### Test Coverage
 
@@ -103,20 +70,17 @@ report_dir:
 # (ie. the *.ml has the *.mlt inside of it with our label), we get proper
 # alignment of the html!
 report: report_dir
-	cd $(TEST_BUILD_DIR) && \
+	cd $(COVERED_TEST_BUILD_DIR) && \
 	bisect-ppx-report -html ../report_dir ../$(shell ls -t bisect*.out | head -1) && \
 	cd -
 
 clean_reports:
 	rm -rf report_dir bisect*.out
 
-
 #### Documentation
 
-oml.odocl:
-	cp src/lib/oml.mlpack oml.odocl
-
-doc: oml.odocl
-	ocamlbuild -use-ocamlfind $(foreach package, $(PACKAGES),-package $(package)) -I src/lib  oml.docdir/index.html
+doc:
+	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)
 FORCE:

README.md

@@ -12,7 +12,8 @@ The API is available [online](http://hammerlab.github.io/oml/index.html).
 ### Goals
 
   1. Perform simple and sophisticated mathematical and statistical analysis
-      inside of (mostly) OCaml. Please see [Oml_lite](#oml_lite) for details.
+      inside of (mostly) OCaml. Please see [Oml_full](#oml_full) section
+      for details.
   2. Have a descriptive, simple, and typed approach to those algorithms.
       - _descriptive_: what a function does should be easy to understand from
         the type and name.
@@ -27,37 +28,38 @@ The API is available [online](http://hammerlab.github.io/oml/index.html).
 ### Building
 
   - `make setup` will `opam install` the necessary packages for Oml.
-    [Oml_lite](#oml_lite) has no dependencies.
-  - `make` will compile source.
-  - `make test
+    [Oml_full](#oml_full) has no dependencies.
+  - `make build` will compile source.
   - `make test` for tests.
         - We use [Kaputt](http://kaputt.x9c.fr/) as the testing framework. Tests
         are found in `*.mlt` files and are joined with their respective source
-        files only when we build a test target.
+        files only when building a test target.
         - `make TEST={ModuleName} test` will run the test in `ModuleName`,
            ex `make TEST=Descriptive test`
-        - `make setup-test` will install packages necessary for testing.
+        - `make setup_test` will install packages necessary for testing.
   - `make covered_test` for [Bisect_ppx](https://github.com/rleonid/bisect_ppx)
       instrumented test coverage.
 
-### <a name="oml_lite">Oml_lite</a>
+### <a name="oml_full">Oml_full</a>
 
-  Oml_lite is a subset of Oml that excludes any code with a `C` or `Fortran`
-  dependency.
+  Oml_full is a superset of Oml that includes `C` and/or `Fortran` dependencies.
+  It is generally more useful and incorporates `Oml` in a typed equivalent way.
+  The goal is to provide a flexible end-user target for those who don't need
+  `C` dependent functionality.
 
 ### Dependencies
 
-  `make setup` will `opam install` these:
+  For the "full" Oml package `make setup` will `opam install` these:
 
   - [Lacaml](https://github.com/mmottl/lacaml) for BLAS/LAPACK bindings.
   - [LBFGS](https://github.com/Chris00/L-BFGS-ocaml) for bindings to LBFGS
       optimization routines.
   - [ocephes](https://github.com/rleonid/ocephes) for special functions.
+
+  And for testing:
+
   - [Kaputt](http://kaputt.x9c.fr/) for testing.
   - [Bisect_ppx](https://github.com/rleonid/bisect_ppx) for code coverage.
-      - See [Bisect](http://bisect.x9c.fr/) for initial implementation
-      - and [Ocveralls](https://github.com/sagotch/ocveralls/) for pushing to
-          [Coveralls](https://coveralls.io/).
 
 ### Contributing
 

_tags

@@ -4,7 +4,20 @@
 # 48 : implicit elimination of optional arguments (ex. ?n, ?c, ?ofsx, ?incx)
 # 50 : ambiguous documentation comment.
 # I'd like to get rid of 42,44 and 50
-true: annot, bin_annot, principal, warn(A-42-44-48-50), warn_error(A-42-44-48-50)
+true: safe_string, annot, bin_annot, principal, warn(A-42-44-48-50)
+
+# warn_error(A-42-44-48-50)
+
+<src> : include
+<src/*> : include
+<src-full> : include
+<src-full/*> : include
+<src-full/**> : package(lacaml), package(ocephes), package(lbfgs)
+<src/**/*.mlj> : package(kaputt)
+<src-full/**/*.mlj> : package(kaputt)
+<test/**> : package(kaputt)
+
 "_build": -traverse
 "_test_build": -traverse
-"_lite_build": -traverse
+"_covered_test_build": -traverse
+"_doc_build": -traverse

doc/api.odocl

@@ -0,0 +1,2 @@
+Oml
+Oml_full