Merge pull request #306202 from vbgl/ocaml-phylogenetics-0.2.0
ocamlPackages.phylogenetics: unstable-2022-05-06 → 0.2.0
This commit is contained in:
commit
e35cb7bf9c
23
pkgs/development/ocaml-modules/binning/default.nix
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23
pkgs/development/ocaml-modules/binning/default.nix
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@ -0,0 +1,23 @@
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{ lib
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, buildDunePackage
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, fetchurl
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}:
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buildDunePackage rec {
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pname = "binning";
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version = "0.0.0";
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minimalOCamlVersion = "4.08";
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src = fetchurl {
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url = "https://github.com/pveber/binning/releases/download/v${version}/binning-v${version}.tbz";
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hash = "sha256-eG+xctsbc7lQ5pFOUtJ8rjNW/06gygwLADq7yc8Yf/c=";
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};
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meta = {
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description = "A datastructure to accumulate values in bins";
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license = lib.licenses.cecill-b;
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homepage = "https://github.com/pveber/binning/";
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maintainers = [ lib.maintainers.vbgl ];
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};
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}
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56
pkgs/development/ocaml-modules/biotk/default.nix
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56
pkgs/development/ocaml-modules/biotk/default.nix
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@ -0,0 +1,56 @@
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{ lib
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, buildDunePackage
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, fetchurl
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, angstrom-unix
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, binning
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, ocaml-crunch
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, camlzip
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, core_kernel
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, core_unix
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, csvfields
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, fmt
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, gsl
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, ppx_csv_conv
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, ppx_deriving
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, rresult
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, tyxml
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, uri
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, vg
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}:
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buildDunePackage rec {
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pname = "biotk";
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version = "0.2.0";
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minimalOCamlVersion = "4.13";
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src = fetchurl {
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url = "https://github.com/pveber/biotk/releases/download/v${version}/biotk-${version}.tbz";
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hash = "sha256-FQvbVj5MmraSN6AmOckKgJ/LB14E/pCsPvPvNppcv7A=";
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};
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nativeBuildInputs = [ ocaml-crunch ];
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buildInputs = [ ppx_csv_conv ];
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propagatedBuildInputs = [
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angstrom-unix
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binning
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camlzip
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core_kernel
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core_unix
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csvfields
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fmt
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gsl
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ppx_deriving
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rresult
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tyxml
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uri
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vg
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];
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meta = {
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description = "Toolkit for bioinformatics in OCaml";
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license = lib.licenses.cecill-c;
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};
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}
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@ -582,6 +582,13 @@ with self;
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propagatedBuildInputs = [ ppxlib base ];
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propagatedBuildInputs = [ ppxlib base ];
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};
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};
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ppx_conv_func = janePackage {
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pname = "ppx_conv_func";
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hash = "sha256-61jX8yHZYOnMx1Jlqaq9zSOz25HLOa0Wv/iG6Hu82zI=";
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meta.description = "Part of the Jane Street's PPX rewriters collection";
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propagatedBuildInputs = [ ppxlib base ];
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};
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ppx_custom_printf = janePackage {
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ppx_custom_printf = janePackage {
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pname = "ppx_custom_printf";
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pname = "ppx_custom_printf";
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hash = "1k8nmq6kwqz2wpkm9ymq749dz1vd8lxrjc711knp1wyz5935hnsv";
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hash = "1k8nmq6kwqz2wpkm9ymq749dz1vd8lxrjc711knp1wyz5935hnsv";
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@ -597,6 +604,13 @@ with self;
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propagatedBuildInputs = [ core_kernel ppxlib js_of_ocaml js_of_ocaml-ppx sedlex ];
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propagatedBuildInputs = [ core_kernel ppxlib js_of_ocaml js_of_ocaml-ppx sedlex ];
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};
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};
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ppx_csv_conv = janePackage {
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pname = "ppx_csv_conv";
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hash = "sha256-ctwgUs1buBZiNqac4760LhWd2/PMZRuxx8SE5T7yZ+g=";
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meta.description = "Generate functions to read/write records in csv format";
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propagatedBuildInputs = [ csvfields ppx_conv_func ];
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};
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ppx_disable_unused_warnings = janePackage {
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ppx_disable_unused_warnings = janePackage {
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pname = "ppx_disable_unused_warnings";
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pname = "ppx_disable_unused_warnings";
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hash = "0sb5i4v7p9df2bxk66rjs30k9fqdrwsq1jgykjv6wyrx2d9bv955";
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hash = "0sb5i4v7p9df2bxk66rjs30k9fqdrwsq1jgykjv6wyrx2d9bv955";
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@ -698,6 +698,13 @@ with self;
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propagatedBuildInputs = [ ppxlib base ];
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propagatedBuildInputs = [ ppxlib base ];
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};
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};
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ppx_conv_func = janePackage {
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pname = "ppx_conv_func";
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hash = "sha256-HPHSZHdR9ll+7EbWc36shTdRPFYB0lkApidk+XL3clI=";
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meta.description = "Part of the Jane Street's PPX rewriters collection";
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propagatedBuildInputs = [ ppxlib base ];
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};
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ppx_custom_printf = janePackage {
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ppx_custom_printf = janePackage {
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pname = "ppx_custom_printf";
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pname = "ppx_custom_printf";
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hash = "sha256-V30ijRgcma/rwysPxNAFnuJIb7XFrfi7mfjJxN+rSak=";
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hash = "sha256-V30ijRgcma/rwysPxNAFnuJIb7XFrfi7mfjJxN+rSak=";
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@ -712,6 +719,13 @@ with self;
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propagatedBuildInputs = [ async async_unix core_kernel core_unix ppxlib js_of_ocaml js_of_ocaml-ppx sedlex virtual_dom ];
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propagatedBuildInputs = [ async async_unix core_kernel core_unix ppxlib js_of_ocaml js_of_ocaml-ppx sedlex virtual_dom ];
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};
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};
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ppx_csv_conv = janePackage {
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pname = "ppx_csv_conv";
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hash = "sha256-RdPcDPLzoSf45Zeon3f4HcEvlwB6Q6sAINX3LHmjmj8=";
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meta.description = "Generate functions to read/write records in csv format";
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propagatedBuildInputs = [ csvfields ppx_conv_func ];
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};
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ppx_demo = janePackage {
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ppx_demo = janePackage {
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pname = "ppx_demo";
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pname = "ppx_demo";
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hash = "sha256-t/jz94YpwmorhWlcuflIZe0l85cESE62L9I7NMASVWM=";
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hash = "sha256-t/jz94YpwmorhWlcuflIZe0l85cESE62L9I7NMASVWM=";
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@ -1,32 +1,27 @@
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{ lib
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{ lib
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, ocaml
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, buildDunePackage
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, buildDunePackage
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, fetchFromGitHub
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, fetchurl
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, ppx_deriving
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, ppx_deriving
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, bppsuite
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, bppsuite
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, alcotest
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, alcotest
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, angstrom-unix
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, angstrom-unix
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, biocaml
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, biotk
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, core
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, core
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, gsl
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, gsl
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, lacaml
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, lacaml
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, menhir
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, menhir
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, menhirLib
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, menhirLib
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, printbox-text
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, printbox-text
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, yojson
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}:
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}:
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lib.throwIf (lib.versionAtLeast ocaml.version "5.0")
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"phylogenetics is not compatible with OCaml ${ocaml.version}"
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buildDunePackage rec {
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buildDunePackage rec {
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pname = "phylogenetics";
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pname = "phylogenetics";
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version = "unstable-2022-05-06";
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version = "0.2.0";
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src = fetchFromGitHub {
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src = fetchurl {
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owner = "biocaml";
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url = "https://github.com/biocaml/phylogenetics/releases/download/v${version}/phylogenetics-${version}.tbz";
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repo = pname;
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hash = "sha256-JFpYp3pyW7PrBjqCwwDZxkJPA84dp6Qs8rOPvHPY92o=";
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rev = "cd7c624d0f98e31b02933ca4511b9809b26d35b5";
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sha256 = "sha256:0w0xyah3hj05hxg1rsa40hhma3dm1cyq0zvnjrihhf22laxap7ga";
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};
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};
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minimalOCamlVersion = "4.08";
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minimalOCamlVersion = "4.08";
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@ -36,13 +31,14 @@ buildDunePackage rec {
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nativeBuildInputs = [ menhir ];
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nativeBuildInputs = [ menhir ];
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propagatedBuildInputs = [
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propagatedBuildInputs = [
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angstrom-unix
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angstrom-unix
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biocaml
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biotk
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core
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core
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gsl
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gsl
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lacaml
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lacaml
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menhirLib
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menhirLib
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ppx_deriving
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ppx_deriving
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printbox-text
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printbox-text
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yojson
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];
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];
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checkPhase = ''
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checkPhase = ''
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26
pkgs/development/ocaml-modules/streaming/default.nix
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26
pkgs/development/ocaml-modules/streaming/default.nix
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@ -0,0 +1,26 @@
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{ lib
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, buildDunePackage
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, fetchurl
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, stdlib-shims
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}:
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buildDunePackage rec {
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pname = "streaming";
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version = "0.8.0";
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minimalOCamlVersion = "4.08";
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src = fetchurl {
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url = "https://github.com/odis-labs/streaming/releases/download/${version}/streaming-${version}.tbz";
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hash = "sha256-W+3GYZpsLj1SnQhuSmjXdi/85fMajWpz4b7x5W0bnJs=";
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};
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propagatedBuildInputs = [ stdlib-shims ];
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meta = {
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homepage = "https://odis-labs.github.io/streaming";
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license = lib.licenses.isc;
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description = "Fast, safe and composable streaming abstractions";
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maintainers = [ lib.maintainers.vbgl ];
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};
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}
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@ -88,8 +88,12 @@ let
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biniou = callPackage ../development/ocaml-modules/biniou { };
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biniou = callPackage ../development/ocaml-modules/biniou { };
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binning = callPackage ../development/ocaml-modules/binning { };
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biocaml = janeStreet_0_15.biocaml;
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biocaml = janeStreet_0_15.biocaml;
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biotk = janeStreet_0_15.biotk;
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bisect_ppx = callPackage ../development/ocaml-modules/bisect_ppx { };
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bisect_ppx = callPackage ../development/ocaml-modules/bisect_ppx { };
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bistro = callPackage ../development/ocaml-modules/bistro { };
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bistro = callPackage ../development/ocaml-modules/bistro { };
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@ -819,10 +823,18 @@ let
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cfstream = self.cfstream.override { inherit core_kernel; };
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cfstream = self.cfstream.override { inherit core_kernel; };
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};
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};
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biotk = let
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angstrom = self.angstrom.override { inherit ppx_let; };
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in callPackage ../development/ocaml-modules/biotk {
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angstrom-unix = self.angstrom-unix.override { inherit angstrom; };
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ppx_deriving = self.ppx_deriving.override { inherit (jsDeps) ppxlib; };
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uri = self.uri.override { inherit angstrom; };
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vg = self.vg.override { htmlcBackend = false; };
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};
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phylogenetics = let
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phylogenetics = let
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angstrom = self.angstrom.override { inherit ppx_let; };
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angstrom = self.angstrom.override { inherit ppx_let; };
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in callPackage ../development/ocaml-modules/phylogenetics {
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in callPackage ../development/ocaml-modules/phylogenetics {
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inherit biocaml;
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ppx_deriving = self.ppx_deriving.override { inherit (jsDeps) ppxlib; };
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ppx_deriving = self.ppx_deriving.override { inherit (jsDeps) ppxlib; };
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angstrom-unix = self.angstrom-unix.override { inherit angstrom; };
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angstrom-unix = self.angstrom-unix.override { inherit angstrom; };
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};
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};
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@ -1715,6 +1727,8 @@ let
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stog_asy = callPackage ../applications/misc/stog/asy.nix { };
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stog_asy = callPackage ../applications/misc/stog/asy.nix { };
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stog_markdown = callPackage ../applications/misc/stog/markdown.nix { };
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stog_markdown = callPackage ../applications/misc/stog/markdown.nix { };
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streaming = callPackage ../development/ocaml-modules/streaming { };
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stringext = callPackage ../development/ocaml-modules/stringext { };
|
stringext = callPackage ../development/ocaml-modules/stringext { };
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syslog = callPackage ../development/ocaml-modules/syslog { };
|
syslog = callPackage ../development/ocaml-modules/syslog { };
|
||||||
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Block a user