Merge pull request #74837 from bcdarwin/biocaml

ocamlPackages_latest.phylogenetics: init at unstable-2019-11-15

pkgs/development/ocaml-modules/biocaml/default.nix

@@ -0,0 +1,30 @@
+{ stdenv, buildDunePackage, fetchFromGitHub
+, ounit, async, base64, camlzip, cfstream
+, core, ppx_jane, ppx_sexp_conv, rresult, uri, xmlm }:
+
+buildDunePackage rec {
+  pname = "biocaml";
+  version = "0.10.0";
+
+  owner = "biocaml";
+
+  minimumOCamlVersion = "4.07";
+
+  src = fetchFromGitHub {
+    inherit owner;
+    repo   = pname;
+    rev    = "v${version}";
+    sha256 = "0dghqx6jbzihmga8jjwwavs0wqksgcns4z1nmwj0ds9ik3mcra30";
+  };
+
+  buildInputs = [ ppx_jane ppx_sexp_conv ];
+  checkInputs = [ ounit ];
+  propagatedBuildInputs = [ async base64 camlzip cfstream core rresult uri xmlm ];
+
+  meta = with stdenv.lib; {
+    description = "Bioinformatics library for Ocaml";
+    homepage = "http://${owner}.github.io/${pname}";
+    maintainers = [ maintainers.bcdarwin ];
+    license = licenses.gpl2;
+  };
+}

pkgs/development/ocaml-modules/cfstream/default.nix

@@ -0,0 +1,30 @@
+{ stdenv, buildDunePackage, fetchFromGitHub, m4, core_kernel, ounit }:
+
+buildDunePackage rec {
+  pname = "cfstream";
+  version = "1.3.0";
+
+  minimumOCamlVersion = "4.04.1";
+
+  src = fetchFromGitHub {
+    owner = "biocaml";
+    repo   = pname;
+    rev    = version;
+    sha256 = "1bpzpci0cx6r3sdk183mm603wgzvvj46nlx0lpx44108anxcxbak";
+  };
+
+  patches = [ ./git_commit.patch ];
+
+  buildInputs = [ m4 ];
+  checkInputs = [ ounit ];
+  propagatedBuildInputs = [ core_kernel ];
+
+  doCheck = true;
+
+  meta = with stdenv.lib; {
+    inherit (src.meta) homepage;
+    description = "Simple Core-inspired wrapper for standard library Stream module";
+    maintainers = [ maintainers.bcdarwin ];
+    license = licenses.lgpl21;
+  };
+}

pkgs/development/ocaml-modules/cfstream/git_commit.patch

@@ -0,0 +1,13 @@
+diff --git a/lib/jbuild b/lib/jbuild
+index fcc5a39..d72d50c 100644
+--- a/lib/jbuild
++++ b/lib/jbuild
+@@ -10,7 +10,7 @@
+ (rule (
+   (targets (GIT_COMMIT))
+   (deps (../bin/git_commit.sh))
+-  (action (with-stdout-to ${@} (run ${<})))
++  (action (with-stdout-to ${@} (run echo "None")))
+ ))
+ 
+ (rule (

pkgs/development/ocaml-modules/gnuplot/default.nix

@@ -0,0 +1,22 @@
+{ stdenv, buildDunePackage, fetchFromBitbucket, gnuplot, core }:
+
+buildDunePackage rec {
+  pname = "gnuplot";
+  version = "0.5.3";
+
+  src = fetchFromBitbucket {
+    owner  = "ogu";
+    repo   = "${pname}-ocaml";
+    rev    = "release-${version}";
+    sha256 = "00sn9g46pj8pfh7faiyxg3pfhq7w9knafyabjr464bh6qz5kiin3";
+  };
+
+  propagatedBuildInputs = [ core gnuplot ];
+
+  meta = with stdenv.lib; {
+    inherit (src.meta) homepage;
+    description = "Ocaml bindings to Gnuplot";
+    maintainers = [ maintainers.bcdarwin ];
+    license = licenses.lgpl21;
+  };
+}

pkgs/development/ocaml-modules/owl-base/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildDunePackage, fetchFromGitHub, integers, stdlib-shims }:
+{ stdenv, buildDunePackage, fetchFromGitHub, stdlib-shims }:
 
 buildDunePackage rec {
   pname = "owl-base";

pkgs/development/ocaml-modules/owl/default.nix

@@ -7,9 +7,8 @@ buildDunePackage rec {
 
   inherit (owl-base) version src meta;
 
-  buildInputs = [ eigen ];
   checkInputs = [ alcotest ];
-  propagatedBuildInputs = [ stdio stdlib-shims openblasCompat owl-base ];
+  propagatedBuildInputs = [ eigen stdio stdlib-shims openblasCompat owl-base ];
 
   # tests not enabled for now due to owlbarn/owl/issues/460
 }

pkgs/development/ocaml-modules/phylogenetics/default.nix

@@ -0,0 +1,28 @@
+{ stdenv, buildDunePackage, fetchFromGitHub, ppx_deriving
+, alcotest, biocaml, gnuplot, lacaml, menhir, owl }:
+
+buildDunePackage rec {
+  pname = "phylogenetics";
+  version = "unstable-2019-11-15";
+
+  src = fetchFromGitHub {
+    owner  = "biocaml";
+    repo   = pname;
+    rev    = "91c03834db065cf4a86f33affbb9cfd216defc9f";
+    sha256 = "0i9m0633a6a724as35ix8z3p1gj267cl0hmqrpw4qfq39zxmgnxb";
+  };
+
+  minimumOCamlVersion = "4.08";  # e.g., uses Float.min
+
+  checkInputs = [ alcotest ];
+  propagatedBuildInputs = [ biocaml gnuplot lacaml menhir owl ppx_deriving ];
+
+  doCheck = false;  # many tests require bppsuite
+
+  meta = with stdenv.lib; {
+    inherit (std.meta) homepage;
+    description = "Bioinformatics library for Ocaml";
+    maintainers = [ maintainers.bcdarwin ];
+    license = licenses.cecill-b;
+  };
+}

pkgs/top-level/ocaml-packages.nix

@@ -73,6 +73,8 @@ let
 
     bigstringaf = callPackage ../development/ocaml-modules/bigstringaf { };
 
+    biocaml = callPackage ../development/ocaml-modules/biocaml { };
+
     bistro = callPackage ../development/ocaml-modules/bistro { };
 
     bitstring = callPackage ../development/ocaml-modules/bitstring { };
@@ -138,6 +140,8 @@ let
 
     cairo2 = callPackage ../development/ocaml-modules/cairo2 { };
 
+    cfstream = callPackage ../development/ocaml-modules/cfstream { };
+
     charInfo_width = callPackage ../development/ocaml-modules/charInfo_width { };
 
     checkseum = callPackage ../development/ocaml-modules/checkseum { };
@@ -293,6 +297,10 @@ let
 
     gmap = callPackage ../development/ocaml-modules/gmap { };
 
+    gnuplot = callPackage ../development/ocaml-modules/gnuplot {
+      inherit (pkgs) gnuplot;
+    };
+
     herelib = callPackage ../development/ocaml-modules/herelib { };
 
     higlo = callPackage ../development/ocaml-modules/higlo { };
@@ -470,7 +478,9 @@ let
 
     metrics-lwt = callPackage ../development/ocaml-modules/metrics/lwt.nix { };
 
-    metrics-unix = callPackage ../development/ocaml-modules/metrics/unix.nix { };
+    metrics-unix = callPackage ../development/ocaml-modules/metrics/unix.nix {
+      inherit (pkgs) gnuplot;
+    };
 
     mezzo = callPackage ../development/compilers/mezzo { };
 
@@ -621,6 +631,8 @@ let
 
     pgsolver = callPackage ../development/ocaml-modules/pgsolver { };
 
+    phylogenetics = callPackage ../development/ocaml-modules/phylogenetics { };
+
     piqi = callPackage ../development/ocaml-modules/piqi {
       base64 = base64_2;
     };