Merge branch 'jbuilder'

with this commit series, bistro is not compatible anymore with core pre-0.9
pveber · Jun 21, 2017 · b8714b4 · b8714b4
2 parents 241fc77 + 020702a
commit b8714b4
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Showing 42 changed files with 92 additions and 658 deletions.
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,5 @@ _build
 _bistro
 *.byte
 *.native
+.merlin
+bistro.install
diff --git a/Makefile b/Makefile
diff --git a/_oasis b/_oasis
diff --git a/_tags b/_tags
diff --git a/app/bistro_demo.ml b/app/bistro_demo.ml
@@ -1,10 +1,11 @@
 (** {:{http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29506}GEO Series GSE29506} *)
 
-open Core.Std
+open Core
 open Bistro.Std
 open Bistro.EDSL
 open Bistro_bioinfo.Std
 open Bistro_engine
+open Bistro_utils
 
 let common_spec =
   let open Command.Spec in

diff --git a/app/bistro_main.ml b/app/bistro_main.ml
diff --git a/app/bistro_test.ml → app/bistro_test_app.ml b/app/bistro_test.ml → app/bistro_test_app.ml
@@ -1,4 +1,5 @@
-open Core.Std
+open Core
+open Bistro_test
 
 let () =
   Command.group ~summary:"Bistro test app" [

diff --git a/app/jbuild b/app/jbuild
@@ -0,0 +1,13 @@
+(jbuild_version 1)
+
+(executable
+ ((name bistro_demo)
+  (modules (bistro_demo))
+  (libraries (bistro.bioinfo bistro.utils))
+))
+
+(executable
+ ((name bistro_test_app)
+  (modules (bistro_test_app))
+  (libraries (bistro.bioinfo bistro_test bistro.utils))
+))
diff --git a/opam → bistro.opam b/opam → bistro.opam
@@ -7,23 +7,12 @@ homepage: "https://github.com/pveber/bistro/"
 dev-repo: "https://github.com/pveber/bistro.git"
 bug-reports: "https://github.com/pveber/bistro/issues"
 license: "GPL"
-build: [
-  ["./configure" "--prefix=%{prefix}%"]
-  [make]
-]
-install: [make "install"]
-remove: [
-  ["ocamlfind" "remove" "bistro"]
-  ["ocamlfind" "remove" "ppx_bistro"]
-]
+build: ["jbuilder" "build" "-p" name "-j" jobs]
 depends: [
-  "oasis" {build & >= "0.4"}
-  "ocamlfind" {build}
-  "core" {<"v0.9.0"}
+  "jbuilder" {build & >= "1.0+beta8"}
+  "core" {>= "0.9.0"}
   "lwt"
   "ocamlgraph" {>= "1.8.7"}
-  "ppx_tools"
-  "pvem"
   "rresult"
   "sexplib" {>= "113.24.00"}
   "tyxml" {>= "4.0"}

diff --git a/configure b/configure
diff --git a/lib/bioinfo/deseq2.ml b/lib/bioinfo/deseq2.ml
@@ -174,7 +174,7 @@ let unique xs =
   let rec aux seen = function
     | [] -> []
     | h :: t ->
-      if List.mem seen h then
+      if List.mem ~equal:( = ) seen h then
         aux seen t
       else
         h :: aux (h :: seen) t

diff --git a/lib/bioinfo/jbuild b/lib/bioinfo/jbuild
@@ -0,0 +1,7 @@
+(jbuild_version 1)
+
+(library
+ ((name bistro_bioinfo)
+  (public_name bistro.bioinfo)
+  (libraries (bistro core))
+))