From 2058f3011866c8097cea58254c160fd9c0416012 Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Tue, 23 Apr 2024 08:49:55 +0200 Subject: [PATCH 1/5] ocamlPackages.streaming: init at 0.8.0 --- .../ocaml-modules/streaming/default.nix | 26 +++++++++++++++++++ pkgs/top-level/ocaml-packages.nix | 2 ++ 2 files changed, 28 insertions(+) create mode 100644 pkgs/development/ocaml-modules/streaming/default.nix diff --git a/pkgs/development/ocaml-modules/streaming/default.nix b/pkgs/development/ocaml-modules/streaming/default.nix new file mode 100644 index 000000000000..f2a8c883f724 --- /dev/null +++ b/pkgs/development/ocaml-modules/streaming/default.nix @@ -0,0 +1,26 @@ +{ lib +, buildDunePackage +, fetchurl +, stdlib-shims +}: + +buildDunePackage rec { + pname = "streaming"; + version = "0.8.0"; + + minimalOCamlVersion = "4.08"; + + src = fetchurl { + url = "https://github.com/odis-labs/streaming/releases/download/${version}/streaming-${version}.tbz"; + hash = "sha256-W+3GYZpsLj1SnQhuSmjXdi/85fMajWpz4b7x5W0bnJs="; + }; + + propagatedBuildInputs = [ stdlib-shims ]; + + meta = { + homepage = "https://odis-labs.github.io/streaming"; + license = lib.licenses.isc; + description = "Fast, safe and composable streaming abstractions"; + maintainers = [ lib.maintainers.vbgl ]; + }; +} diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix index f379917ca0da..49807d6368f5 100644 --- a/pkgs/top-level/ocaml-packages.nix +++ b/pkgs/top-level/ocaml-packages.nix @@ -1715,6 +1715,8 @@ let stog_asy = callPackage ../applications/misc/stog/asy.nix { }; stog_markdown = callPackage ../applications/misc/stog/markdown.nix { }; + streaming = callPackage ../development/ocaml-modules/streaming { }; + stringext = callPackage ../development/ocaml-modules/stringext { }; syslog = callPackage ../development/ocaml-modules/syslog { }; From 09e010c4d8a31fd00b16a7c790f89d02e21b6205 Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Tue, 23 Apr 2024 08:50:01 +0200 Subject: [PATCH 2/5] ocamlPackages.binning: init at 0.0.0 --- .../ocaml-modules/binning/default.nix | 23 +++++++++++++++++++ pkgs/top-level/ocaml-packages.nix | 2 ++ 2 files changed, 25 insertions(+) create mode 100644 pkgs/development/ocaml-modules/binning/default.nix diff --git a/pkgs/development/ocaml-modules/binning/default.nix b/pkgs/development/ocaml-modules/binning/default.nix new file mode 100644 index 000000000000..244b96220f7b --- /dev/null +++ b/pkgs/development/ocaml-modules/binning/default.nix @@ -0,0 +1,23 @@ +{ lib +, buildDunePackage +, fetchurl +}: + +buildDunePackage rec { + pname = "binning"; + version = "0.0.0"; + + minimalOCamlVersion = "4.08"; + + src = fetchurl { + url = "https://github.com/pveber/binning/releases/download/v${version}/binning-v${version}.tbz"; + hash = "sha256-eG+xctsbc7lQ5pFOUtJ8rjNW/06gygwLADq7yc8Yf/c="; + }; + + meta = { + description = "A datastructure to accumulate values in bins"; + license = lib.licenses.cecill-b; + homepage = "https://github.com/pveber/binning/"; + maintainers = [ lib.maintainers.vbgl ]; + }; +} diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix index 49807d6368f5..5a218122a3a6 100644 --- a/pkgs/top-level/ocaml-packages.nix +++ b/pkgs/top-level/ocaml-packages.nix @@ -88,6 +88,8 @@ let biniou = callPackage ../development/ocaml-modules/biniou { }; + binning = callPackage ../development/ocaml-modules/binning { }; + biocaml = janeStreet_0_15.biocaml; bisect_ppx = callPackage ../development/ocaml-modules/bisect_ppx { }; From fd728608d1e517e7cd54d9927b936fb46b52bb2c Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Tue, 23 Apr 2024 08:50:06 +0200 Subject: [PATCH 3/5] ocamlPackages.{ppx_conv_func,ppx_csv_conv}: init at 0.15.0 & 0.16.0 --- pkgs/development/ocaml-modules/janestreet/0.15.nix | 14 ++++++++++++++ pkgs/development/ocaml-modules/janestreet/0.16.nix | 14 ++++++++++++++ 2 files changed, 28 insertions(+) diff --git a/pkgs/development/ocaml-modules/janestreet/0.15.nix b/pkgs/development/ocaml-modules/janestreet/0.15.nix index f64e228a2b81..10675364396f 100644 --- a/pkgs/development/ocaml-modules/janestreet/0.15.nix +++ b/pkgs/development/ocaml-modules/janestreet/0.15.nix @@ -582,6 +582,13 @@ with self; propagatedBuildInputs = [ ppxlib base ]; }; + ppx_conv_func = janePackage { + pname = "ppx_conv_func"; + hash = "sha256-61jX8yHZYOnMx1Jlqaq9zSOz25HLOa0Wv/iG6Hu82zI="; + meta.description = "Part of the Jane Street's PPX rewriters collection"; + propagatedBuildInputs = [ ppxlib base ]; + }; + ppx_custom_printf = janePackage { pname = "ppx_custom_printf"; hash = "1k8nmq6kwqz2wpkm9ymq749dz1vd8lxrjc711knp1wyz5935hnsv"; @@ -597,6 +604,13 @@ with self; propagatedBuildInputs = [ core_kernel ppxlib js_of_ocaml js_of_ocaml-ppx sedlex ]; }; + ppx_csv_conv = janePackage { + pname = "ppx_csv_conv"; + hash = "sha256-ctwgUs1buBZiNqac4760LhWd2/PMZRuxx8SE5T7yZ+g="; + meta.description = "Generate functions to read/write records in csv format"; + propagatedBuildInputs = [ csvfields ppx_conv_func ]; + }; + ppx_disable_unused_warnings = janePackage { pname = "ppx_disable_unused_warnings"; hash = "0sb5i4v7p9df2bxk66rjs30k9fqdrwsq1jgykjv6wyrx2d9bv955"; diff --git a/pkgs/development/ocaml-modules/janestreet/0.16.nix b/pkgs/development/ocaml-modules/janestreet/0.16.nix index 35d2895f679f..526ea44808cd 100644 --- a/pkgs/development/ocaml-modules/janestreet/0.16.nix +++ b/pkgs/development/ocaml-modules/janestreet/0.16.nix @@ -698,6 +698,13 @@ with self; propagatedBuildInputs = [ ppxlib base ]; }; + ppx_conv_func = janePackage { + pname = "ppx_conv_func"; + hash = "sha256-HPHSZHdR9ll+7EbWc36shTdRPFYB0lkApidk+XL3clI="; + meta.description = "Part of the Jane Street's PPX rewriters collection"; + propagatedBuildInputs = [ ppxlib base ]; + }; + ppx_custom_printf = janePackage { pname = "ppx_custom_printf"; hash = "sha256-V30ijRgcma/rwysPxNAFnuJIb7XFrfi7mfjJxN+rSak="; @@ -712,6 +719,13 @@ with self; propagatedBuildInputs = [ async async_unix core_kernel core_unix ppxlib js_of_ocaml js_of_ocaml-ppx sedlex virtual_dom ]; }; + ppx_csv_conv = janePackage { + pname = "ppx_csv_conv"; + hash = "sha256-RdPcDPLzoSf45Zeon3f4HcEvlwB6Q6sAINX3LHmjmj8="; + meta.description = "Generate functions to read/write records in csv format"; + propagatedBuildInputs = [ csvfields ppx_conv_func ]; + }; + ppx_demo = janePackage { pname = "ppx_demo"; hash = "sha256-t/jz94YpwmorhWlcuflIZe0l85cESE62L9I7NMASVWM="; From 15526d81c5cea9e95b7d032972002dccc74521f2 Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Tue, 23 Apr 2024 08:50:12 +0200 Subject: [PATCH 4/5] ocamlPackages.biotk: init at 0.2.0 --- .../ocaml-modules/biotk/default.nix | 56 +++++++++++++++++++ pkgs/top-level/ocaml-packages.nix | 11 ++++ 2 files changed, 67 insertions(+) create mode 100644 pkgs/development/ocaml-modules/biotk/default.nix diff --git a/pkgs/development/ocaml-modules/biotk/default.nix b/pkgs/development/ocaml-modules/biotk/default.nix new file mode 100644 index 000000000000..33a98f71cb67 --- /dev/null +++ b/pkgs/development/ocaml-modules/biotk/default.nix @@ -0,0 +1,56 @@ +{ lib +, buildDunePackage +, fetchurl +, angstrom-unix +, binning +, ocaml-crunch +, camlzip +, core_kernel +, core_unix +, csvfields +, fmt +, gsl +, ppx_csv_conv +, ppx_deriving +, rresult +, tyxml +, uri +, vg +}: + +buildDunePackage rec { + pname = "biotk"; + version = "0.2.0"; + + minimalOCamlVersion = "4.13"; + + src = fetchurl { + url = "https://github.com/pveber/biotk/releases/download/v${version}/biotk-${version}.tbz"; + hash = "sha256-FQvbVj5MmraSN6AmOckKgJ/LB14E/pCsPvPvNppcv7A="; + }; + + nativeBuildInputs = [ ocaml-crunch ]; + + buildInputs = [ ppx_csv_conv ]; + + propagatedBuildInputs = [ + angstrom-unix + binning + camlzip + core_kernel + core_unix + csvfields + fmt + gsl + ppx_deriving + rresult + tyxml + uri + vg + ]; + + meta = { + description = "Toolkit for bioinformatics in OCaml"; + license = lib.licenses.cecill-c; + }; +} diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix index 5a218122a3a6..de27e8d83d8b 100644 --- a/pkgs/top-level/ocaml-packages.nix +++ b/pkgs/top-level/ocaml-packages.nix @@ -92,6 +92,8 @@ let biocaml = janeStreet_0_15.biocaml; + biotk = janeStreet_0_15.biotk; + bisect_ppx = callPackage ../development/ocaml-modules/bisect_ppx { }; bistro = callPackage ../development/ocaml-modules/bistro { }; @@ -821,6 +823,15 @@ let cfstream = self.cfstream.override { inherit core_kernel; }; }; + biotk = let + angstrom = self.angstrom.override { inherit ppx_let; }; + in callPackage ../development/ocaml-modules/biotk { + angstrom-unix = self.angstrom-unix.override { inherit angstrom; }; + ppx_deriving = self.ppx_deriving.override { inherit (jsDeps) ppxlib; }; + uri = self.uri.override { inherit angstrom; }; + vg = self.vg.override { htmlcBackend = false; }; + }; + phylogenetics = let angstrom = self.angstrom.override { inherit ppx_let; }; in callPackage ../development/ocaml-modules/phylogenetics { From b377e019cacb877c7e1f34714a7dc98064e08d04 Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Tue, 23 Apr 2024 08:50:17 +0200 Subject: [PATCH 5/5] =?UTF-8?q?ocamlPackages.phylogenetics:=20unstable-202?= =?UTF-8?q?2-05-06=20=E2=86=92=200.2.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../ocaml-modules/phylogenetics/default.nix | 22 ++++++++----------- pkgs/top-level/ocaml-packages.nix | 1 - 2 files changed, 9 insertions(+), 14 deletions(-) diff --git a/pkgs/development/ocaml-modules/phylogenetics/default.nix b/pkgs/development/ocaml-modules/phylogenetics/default.nix index 7c4f90b6f976..76856024c09a 100644 --- a/pkgs/development/ocaml-modules/phylogenetics/default.nix +++ b/pkgs/development/ocaml-modules/phylogenetics/default.nix @@ -1,32 +1,27 @@ { lib -, ocaml , buildDunePackage -, fetchFromGitHub +, fetchurl , ppx_deriving , bppsuite , alcotest , angstrom-unix -, biocaml +, biotk , core , gsl , lacaml , menhir , menhirLib , printbox-text +, yojson }: -lib.throwIf (lib.versionAtLeast ocaml.version "5.0") - "phylogenetics is not compatible with OCaml ${ocaml.version}" - buildDunePackage rec { pname = "phylogenetics"; - version = "unstable-2022-05-06"; + version = "0.2.0"; - src = fetchFromGitHub { - owner = "biocaml"; - repo = pname; - rev = "cd7c624d0f98e31b02933ca4511b9809b26d35b5"; - sha256 = "sha256:0w0xyah3hj05hxg1rsa40hhma3dm1cyq0zvnjrihhf22laxap7ga"; + src = fetchurl { + url = "https://github.com/biocaml/phylogenetics/releases/download/v${version}/phylogenetics-${version}.tbz"; + hash = "sha256-JFpYp3pyW7PrBjqCwwDZxkJPA84dp6Qs8rOPvHPY92o="; }; minimalOCamlVersion = "4.08"; @@ -36,13 +31,14 @@ buildDunePackage rec { nativeBuildInputs = [ menhir ]; propagatedBuildInputs = [ angstrom-unix - biocaml + biotk core gsl lacaml menhirLib ppx_deriving printbox-text + yojson ]; checkPhase = '' diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix index de27e8d83d8b..932ff6505b78 100644 --- a/pkgs/top-level/ocaml-packages.nix +++ b/pkgs/top-level/ocaml-packages.nix @@ -835,7 +835,6 @@ let phylogenetics = let angstrom = self.angstrom.override { inherit ppx_let; }; in callPackage ../development/ocaml-modules/phylogenetics { - inherit biocaml; ppx_deriving = self.ppx_deriving.override { inherit (jsDeps) ppxlib; }; angstrom-unix = self.angstrom-unix.override { inherit angstrom; }; };