From 3e7a2b9147fe78a229d5bd20849ce078e6b9ef71 Mon Sep 17 00:00:00 2001
From: Vincent Laporte <Vincent.Laporte@gmail.com>
Date: Mon, 13 Apr 2020 10:41:51 +0200
Subject: [PATCH] =?UTF-8?q?ocamlPackages.janeStreet:=200.12=20=E2=86=92=20?=
 =?UTF-8?q?0.13?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
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ocamlPackages.bistro: fix for core-0.13
ocamlPackages.phylogenetics: 2020-01-05 → 2020-01-25
---
 .../ocaml-modules/bistro/default.nix          |   8 +-
 .../ocaml-modules/janestreet/0.13.nix         | 503 ++++++++++++++++++
 .../janestreet/janePackage_0_13.nix           |  19 +
 .../ocaml-modules/phylogenetics/default.nix   |   6 +-
 pkgs/tools/misc/patdiff/default.nix           |   2 +-
 pkgs/top-level/ocaml-packages.nix             |  12 +-
 6 files changed, 543 insertions(+), 7 deletions(-)
 create mode 100644 pkgs/development/ocaml-modules/janestreet/0.13.nix
 create mode 100644 pkgs/development/ocaml-modules/janestreet/janePackage_0_13.nix

diff --git a/pkgs/development/ocaml-modules/bistro/default.nix b/pkgs/development/ocaml-modules/bistro/default.nix
index b141244f8c5..9603f283ee4 100644
--- a/pkgs/development/ocaml-modules/bistro/default.nix
+++ b/pkgs/development/ocaml-modules/bistro/default.nix
@@ -1,4 +1,4 @@
-{ lib, fetchFromGitHub, buildDunePackage
+{ lib, fetchFromGitHub, fetchpatch, buildDunePackage
 , base64, bos, core, lwt_react, ocamlgraph, rresult, tyxml
 }:
 
@@ -12,6 +12,12 @@ buildDunePackage rec {
     sha256 = "114gq48cpj2mvycypa9lfyqqb26wa2gkdfwkcqhnx7m6sdwv9a38";
   };
 
+  # The following patch adds support for core.v0.13
+  patches = [(fetchpatch {
+    url = "https://github.com/pveber/bistro/commit/0931db43a146ad7829dff5120161a775f732a878.patch";
+    sha256 = "06y0sxbbab1mssc1xfjjv12lpv4rny5iqv9qkdqyzrvzpl1bdvnd";
+  })];
+
   propagatedBuildInputs = [ base64 bos core lwt_react ocamlgraph rresult tyxml ];
 
   minimumOCamlVersion = "4.07";
diff --git a/pkgs/development/ocaml-modules/janestreet/0.13.nix b/pkgs/development/ocaml-modules/janestreet/0.13.nix
new file mode 100644
index 00000000000..4682a744d6f
--- /dev/null
+++ b/pkgs/development/ocaml-modules/janestreet/0.13.nix
@@ -0,0 +1,503 @@
+{ janePackage
+, ctypes
+, num
+, octavius
+, ppxlib
+, re
+, openssl
+}:
+
+rec {
+
+  ocaml-compiler-libs = janePackage {
+    pname = "ocaml-compiler-libs";
+    version = "0.12.1";
+    hash = "0hpk54fcsfcjp536fgwr80mjjf88hjk58q7jwnyrhk2ljd8xzgiv";
+    meta.description = "OCaml compiler libraries repackaged";
+  };
+
+  sexplib0 = janePackage {
+    pname = "sexplib0";
+    hash = "1b1bk0xs1hqa12qs5y4h1yl3mq6xml4ya2570dyhdn1j0fbw4g3y";
+    meta.description = "Library containing the definition of S-expressions and some base converters";
+  };
+
+  base = janePackage {
+    pname = "base";
+    version = "0.13.1";
+    hash = "08a5aymcgr5svvm8v0v20msd5cad64m6maakfbhz4172g7kd9jzw";
+    meta.description = "Full standard library replacement for OCaml";
+    propagatedBuildInputs = [ sexplib0 ];
+  };
+
+  stdio = janePackage {
+    pname = "stdio";
+    hash = "1hkj9vh8n8p3n5pvx7053xis1pfmqd8p7shjyp1n555xzimfxzgh";
+    meta.description = "Standard IO library for OCaml";
+    propagatedBuildInputs = [ base ];
+  };
+
+  ppx_sexp_conv = janePackage {
+    pname = "ppx_sexp_conv";
+    hash = "0jkhwmkrfq3ss6bv6i3m871alcr4xpngs6ci6bmzv3yfl7s8bwdf";
+    meta.description = "[@@deriving] plugin to generate S-expression conversion functions";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_here = janePackage {
+    pname = "ppx_here";
+    hash = "1ahidrrjsyi0al06bhv5h6aqmdk7ryz8dybfhqjsn1zp9q056q35";
+    meta.description = "Expands [%here] into its location";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_compare = janePackage {
+    pname = "ppx_compare";
+    hash = "14pnqa47gsvq93z1b8wb5pyq8zw90aaw71j4pwlyid4s86px454j";
+    meta.description = "Generation of comparison functions from types";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_cold = janePackage {
+    pname = "ppx_cold";
+    hash = "0wnfwsgbzk4i5aqjlcaqp6lkvrq5345vazryvx2klbbrd4759h9f";
+    meta.description = "Expands [@cold] into [@inline never][@specialise never][@local never]";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_assert = janePackage {
+    pname = "ppx_assert";
+    hash = "08dada2xcp3w5mir90z56qrdyd317lygml4qlfssj897534bwiqr";
+    meta.description = "Assert-like extension nodes that raise useful errors on failure";
+    propagatedBuildInputs = [ ppx_cold ppx_compare ppx_here ppx_sexp_conv ];
+  };
+
+  ppx_inline_test = janePackage {
+    pname = "ppx_inline_test";
+    hash = "135qzbhqy33lmigbq1rakr9i3y59y3pczh4laanqjyss9b9kfs60";
+    meta.description = "Syntax extension for writing in-line tests in ocaml code";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_custom_printf = janePackage {
+    pname = "ppx_custom_printf";
+    hash = "0kvfkdk4wg2z8x705bajvl1f8wiyy3aya203wdzc9425h73nqm5p";
+    meta.description = "Printf-style format-strings for user-defined string conversion";
+    propagatedBuildInputs = [ ppx_sexp_conv ];
+  };
+
+  fieldslib = janePackage {
+    pname = "fieldslib";
+    hash = "0nsl0i9vjk73pr70ksxqa65rd5v84jzdaazryfdy6i4a5sfg7bxa";
+    meta.description = "Syntax extension to define first class values representing record fields, to get and set record fields, iterate and fold over all fields of a record and create new record values";
+    propagatedBuildInputs = [ base ];
+  };
+
+  ppx_fields_conv = janePackage {
+    pname = "ppx_fields_conv";
+    hash = "0biw0fgphj522bj9wgjk263i2w92vnpaabzr5zn0grihp4yqy8w4";
+    meta.description = "Generation of accessor and iteration functions for ocaml records";
+    propagatedBuildInputs = [ fieldslib ppxlib ];
+  };
+
+  variantslib = janePackage {
+    pname = "variantslib";
+    hash = "04nps65v1n0nv9n1c1kj5k9jyqsfsxb6h2w3vf6cibhjr5m7z8xc";
+    meta.description = "Part of Jane Street's Core library";
+    propagatedBuildInputs = [ base ];
+  };
+
+  ppx_variants_conv = janePackage {
+    pname = "ppx_variants_conv";
+    hash = "1ssinizz11bws06qzjky486cj1zrflij1f7hi16d02j40qmyjz7b";
+    meta.description = "Generation of accessor and iteration functions for ocaml variant types";
+    propagatedBuildInputs = [ variantslib ppxlib ];
+  };
+
+  ppx_expect = janePackage {
+    pname = "ppx_expect";
+    hash = "1hhcga960wjvhcx5pk7rcywl1p9n2ycvqa294n24m8dhzqia6i47";
+    meta.description = "Cram like framework for OCaml";
+    propagatedBuildInputs = [ ppx_assert ppx_custom_printf ppx_fields_conv ppx_inline_test ppx_variants_conv re ];
+  };
+
+  ppx_enumerate = janePackage {
+    pname = "ppx_enumerate";
+    hash = "0hsg6f2nra1mb35jdgym5rf7spm642bs6qqifbikm9hg8f7z3ql4";
+    meta.description = "Generate a list containing all values of a finite type";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_hash = janePackage {
+    pname = "ppx_hash";
+    hash = "1f7mfyx4wgk67hchi57w3142m61ka3vgy1969cbkwr3akv6ifly2";
+    meta.description = "A ppx rewriter that generates hash functions from type expressions and definitions";
+    propagatedBuildInputs = [ ppx_compare ppx_sexp_conv ];
+  };
+
+  ppx_js_style = janePackage {
+    pname = "ppx_js_style";
+    hash = "1zlhcn0an5k9xjymk5z5m2vqi8zajy6nvcbl5sdn19pjl3zv645x";
+    meta.description = "Code style checker for Jane Street Packages";
+    propagatedBuildInputs = [ octavius ppxlib ];
+  };
+
+  ppx_base = janePackage {
+    pname = "ppx_base";
+    hash = "0dkqc85x7bgbb6lgx9rghvj1q4dpdgy9qgjl88ywi4c8l9rgnnkz";
+    meta.description = "Base set of ppx rewriters";
+    propagatedBuildInputs = [ ppx_cold ppx_enumerate ppx_hash ppx_js_style ];
+  };
+
+  ppx_bench = janePackage {
+    pname = "ppx_bench";
+    hash = "0snmy05d3jgihmppixx3dzamkykijqa2v43vpd7q4z8dpnip620g";
+    meta.description = "Syntax extension for writing in-line benchmarks in ocaml code";
+    propagatedBuildInputs = [ ppx_inline_test ];
+  };
+
+  ppx_sexp_message = janePackage {
+    pname = "ppx_sexp_message";
+    hash = "03jhx3ajcv22iwxkg1jf1jjvd14gyrwi1yc6c5ryqi5ha0fywfw6";
+    meta.description = "A ppx rewriter for easy construction of s-expressions";
+    propagatedBuildInputs = [ ppx_here ppx_sexp_conv ];
+  };
+
+  splittable_random = janePackage {
+    pname = "splittable_random";
+    hash = "1kgcd6k31vsd7638g8ip77bp1b7vzgkbvgvij4jm2igl09132r85";
+    meta.description = "PRNG that can be split into independent streams";
+    propagatedBuildInputs = [ base ppx_assert ppx_bench ppx_sexp_message ];
+  };
+
+  ppx_let = janePackage {
+    pname = "ppx_let";
+    hash = "0qplsvbv10h7kwf6dhhgvi001gfphv1v66s83zjr5zbypyaarg5y";
+    meta.description = "Monadic let-bindings";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  base_quickcheck = janePackage {
+    pname = "base_quickcheck";
+    hash = "0ik8llm01m2xap4gia0vpsh7yq311hph7a2kf5109ag4988s8p0w";
+    meta.description = "Randomized testing framework, designed for compatibility with Base";
+    propagatedBuildInputs = [ ppx_base ppx_fields_conv ppx_let splittable_random ];
+  };
+
+  ppx_stable = janePackage {
+    pname = "ppx_stable";
+    hash = "0h7ls1bs0bsd8c4na4aj0nawwhvfy50ybm7sza7yz3qli9jammjk";
+    meta.description = "Stable types conversions generator";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  bin_prot = janePackage {
+    pname = "bin_prot";
+    hash = "1nnr21rljlfglmhiji27d7c1d6gg5fk4cc5rl3750m98w28mfdjw";
+    meta.description = "A binary protocol generator";
+    propagatedBuildInputs = [ ppx_compare ppx_custom_printf ppx_fields_conv ppx_variants_conv ];
+  };
+
+  ppx_bin_prot = janePackage {
+    pname = "ppx_bin_prot";
+    hash = "14nfjgqisdqqg8wg4qzvc859zil82y0qpr8fm4nhq05mgxp37iyc";
+    meta.description = "Generation of bin_prot readers and writers from types";
+    propagatedBuildInputs = [ bin_prot ppx_here ];
+  };
+
+  ppx_fail = janePackage {
+    pname = "ppx_fail";
+    hash = "165mikjg4a1lahq3n9q9y2h36jbln5g3l2hapx17irvf0l0c3vn5";
+    meta.description = "Add location to calls to failwiths";
+    propagatedBuildInputs = [ ppx_here ];
+  };
+
+  jst-config = janePackage {
+    pname = "jst-config";
+    hash = "15lj6f83hz555xhjy9aayl3adqwgl1blcjnja693a1ybi3ca8w0y";
+    meta.description = "Compile-time configuration for Jane Street libraries";
+    buildInputs = [ ppx_assert ];
+  };
+
+  ppx_optcomp = janePackage {
+    pname = "ppx_optcomp";
+    hash = "13db395swqf7v87pgl9qiyj4igmvj57hpl8blx3kkrzj6ddh38a8";
+    meta.description = "Optional compilation for OCaml";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  jane-street-headers = janePackage {
+    pname = "jane-street-headers";
+    hash = "1qjg2ari0xn40dlbk0h9xkwr37k97ldkxpkv792fbl6wc2jlv3x5";
+    meta.description = "Jane Street C header files";
+  };
+
+  time_now = janePackage {
+    pname = "time_now";
+    hash = "1if234kz1ssmv22c0vh1cwhbivab6yy3xvy37ny1q4k5ibjc3v0n";
+    meta.description = "Reports the current time";
+    buildInputs = [ jst-config ppx_optcomp ];
+    propagatedBuildInputs = [ jane-street-headers base ppx_base ];
+  };
+
+  ppx_module_timer = janePackage {
+    pname = "ppx_module_timer";
+    hash = "13kv5fzwf41wsaksj41hnvcpx8pnbmzcainlq6f5shj9671hpnhb";
+    meta.description = "Ppx rewriter that records top-level module startup times";
+    propagatedBuildInputs = [ time_now ];
+  };
+
+  ppx_optional = janePackage {
+    pname = "ppx_optional";
+    hash = "1nwb9jvmszxddj9wxgv9g02qhr10yymm2q1w1gjfqd97m2m1mx4n";
+    meta.description = "Pattern matching on flat options";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_pipebang = janePackage {
+    pname = "ppx_pipebang";
+    hash = "0ybj0flsi95pf13ayzz1lcrqhqvkv1lm2dz6y8w49f12583496mc";
+    meta.description = "A ppx rewriter that inlines reverse application operators `|>` and `|!`";
+    propagatedBuildInputs = [ ppxlib ];
+  };
+
+  ppx_sexp_value = janePackage {
+    pname = "ppx_sexp_value";
+    hash = "18k5015awv9yjl44cvdmp3pn894cgsxmn5s7picxapm9675xqcg9";
+    meta.description = "A ppx rewriter that simplifies building s-expressions from ocaml values";
+    propagatedBuildInputs = [ ppx_here ppx_sexp_conv ];
+  };
+
+  typerep = janePackage {
+    pname = "typerep";
+    hash = "116hlifww2cqq1i9vwpl7ziwkc1na7p9icqi9srpdxnvn8ibcsas";
+    meta.description = "Typerep is a library for runtime types";
+    propagatedBuildInputs = [ base ];
+  };
+
+  ppx_typerep_conv = janePackage {
+    pname = "ppx_typerep_conv";
+    hash = "1jlmga9i79inr412l19n4vvmgafzp1bznqxwhy42x309wblbhxx9";
+    meta.description = "Generation of runtime types from type declarations";
+    propagatedBuildInputs = [ ppxlib typerep ];
+  };
+
+  ppx_jane = janePackage {
+    pname = "ppx_jane";
+    hash = "1a86rvnry8lvjhsg2k73f5bgz7l2962k5i49yzmzn8w66kj0yz60";
+    meta.description = "Standard Jane Street ppx rewriters";
+    propagatedBuildInputs = [ base_quickcheck ppx_bench ppx_bin_prot ppx_expect ppx_fail ppx_module_timer ppx_optcomp ppx_optional ppx_pipebang ppx_sexp_value ppx_stable ppx_typerep_conv ];
+  };
+
+  base_bigstring = janePackage {
+    pname = "base_bigstring";
+    hash = "1i3zr8bn71l442vl5rrvjpwphx20frp2vaw1qc05d348j76sxfp7";
+    meta.description = "String type based on [Bigarray], for use in I/O and C-bindings";
+    propagatedBuildInputs = [ ppx_jane ];
+  };
+
+  parsexp = janePackage {
+    pname = "parsexp";
+    hash = "0fsxy5lpsvfadj8m2337j8iprs294dfikqxjcas7si74nskx6l38";
+    meta.description = "S-expression parsing library";
+    propagatedBuildInputs = [ base sexplib0 ];
+  };
+
+  sexplib = janePackage {
+    pname = "sexplib";
+    hash = "059ypcyirw00x6dqa33x49930pwxcr3i72qz5pf220js2ai2nzhn";
+    meta.description = "Library for serializing OCaml values to and from S-expressions";
+    propagatedBuildInputs = [ num parsexp ];
+  };
+
+  core_kernel = janePackage {
+    version = "0.13.1";
+    pname = "core_kernel";
+    hash = "1ynyz6jkf23q0cwbn6kv06mgyjd644qxb0qkrydq0cglcaa4kjhp";
+    meta.description = "System-independent part of Core";
+    buildInputs = [ jst-config ];
+    propagatedBuildInputs = [ base_bigstring sexplib ];
+  };
+
+  spawn = janePackage {
+    pname = "spawn";
+    hash = "1w003k1kw1lmyiqlk58gkxx8rac7dchiqlz6ah7aj7bh49b36ppf";
+    meta.description = "Spawning sub-processes";
+    buildInputs = [ ppx_expect ];
+  };
+
+  core = janePackage {
+    pname = "core";
+    hash = "1i5z9myl6i7axd8dz4b71gdsz9la6k07ib9njr4bn12yn0y76b1m";
+    meta.description = "System-independent part of Core";
+    buildInputs = [ jst-config ];
+    propagatedBuildInputs = [ core_kernel spawn ];
+  };
+
+  async_kernel = janePackage {
+    pname = "async_kernel";
+    hash = "1rrbyy3pyh31qwv0jiarhpgdyq2z2gx6axmaplgpxshk4qx6gsld";
+    meta.description = "Monadic concurrency library";
+    propagatedBuildInputs = [ core_kernel ];
+  };
+
+  protocol_version_header = janePackage {
+    pname = "protocol_version_header";
+    hash = "19wscd81jlj355f9din1sg21m3af456a0id2a37bx38r390wrghc";
+    meta.description = "Protocol versioning";
+    propagatedBuildInputs = [ core_kernel ];
+  };
+
+  async_rpc_kernel = janePackage {
+    pname = "async_rpc_kernel";
+    hash = "1k3f2psyd1xcf7nkk0q1fq57yyhfqbzyynsz821n7mrnm37simac";
+    meta.description = "Platform-independent core of Async RPC library";
+    propagatedBuildInputs = [ async_kernel protocol_version_header ];
+  };
+
+  async_unix = janePackage {
+    pname = "async_unix";
+    hash = "0n3jz3qjlphyhkqgnbjbwf2fqxaksws82dx1mk4m4wnw3275gdi5";
+    meta.description = "Monadic concurrency library";
+    propagatedBuildInputs = [ async_kernel core ];
+  };
+
+  async_extra = janePackage {
+    pname = "async_extra";
+    hash = "06q1farx7dwi4h490xi1azq7ym57ih2d23sq17g2jfvw889kf4n1";
+    meta.description = "Monadic concurrency library";
+    propagatedBuildInputs = [ async_rpc_kernel async_unix ];
+  };
+
+  textutils = janePackage {
+    pname = "textutils";
+    hash = "1wnyqj9dzfgl0kddmdl4n9rkl16hwy432dd2i4ksvk2z5g9kkb0d";
+    meta.description = "Text output utilities";
+    propagatedBuildInputs = [ core ];
+  };
+
+  async = janePackage {
+    pname = "async";
+    hash = "002j9yxpw0ghi12a84163vaqa3n9h8j35f4i72nbxnilxwvy95sr";
+    meta.description = "Monadic concurrency library";
+    propagatedBuildInputs = [ async_rpc_kernel async_unix textutils ];
+  };
+
+  async_find = janePackage {
+    pname = "async_find";
+    hash = "0l8cfhyrx2rb2avdcfx5m70aj6rx2d57qxqvfycad5afqz4xx2n9";
+    meta.description = "Directory traversal with Async";
+    propagatedBuildInputs = [ async ];
+  };
+
+  re2 = janePackage {
+    pname = "re2";
+    hash = "0hmizznlzilynn5kh6149bbpkfw2l0xi7zi1y1fxfww2ma3wpim0";
+    meta.description = "OCaml bindings for RE2, Google's regular expression library";
+    propagatedBuildInputs = [ core_kernel ];
+    prePatch = ''
+      substituteInPlace src/re2_c/dune --replace 'CXX=g++' 'CXX=c++'
+      substituteInPlace src/dune --replace '(cxx_flags (:standard \ -pedantic) (-I re2_c/libre2))' '(cxx_flags (:standard \ -pedantic) (-I re2_c/libre2) (-x c++))'
+    '';
+  };
+
+  shell = janePackage {
+    pname = "shell";
+    hash = "190ymhm0z9b7hngbcpg88wwrfxwfcdh339d7rd2xhmrhi4z99r18";
+    meta.description = "Yet another implementation of fork&exec and related functionality";
+    buildInputs = [ jst-config ];
+    propagatedBuildInputs = [ re2 textutils ];
+  };
+
+  async_shell = janePackage {
+    pname = "async_shell";
+    hash = "0bfxyvdmyv23zfr49pb4c3bgfkjr4s3nb3z07xrw6szia3j1kp4j";
+    meta.description = "Shell helpers for Async";
+    propagatedBuildInputs = [ async shell ];
+  };
+
+  core_bench = janePackage {
+    pname = "core_bench";
+    hash = "1nk0i3z8rqrljbf4bc7ljp71g0a4361nh85s2ang0lgxri74zacm";
+    meta.description = "Benchmarking library";
+    propagatedBuildInputs = [ textutils ];
+  };
+
+  core_extended = janePackage {
+    pname = "core_extended";
+    hash = "0zh1wwkg5cxkz633dl9zbbl65aksvzb5mss1q8f7w6i1sv3n0135";
+    meta.description = "Extra components that are not as closely vetted or as stable as Core";
+    propagatedBuildInputs = [ core ];
+  };
+
+  sexp_pretty = janePackage {
+    pname = "sexp_pretty";
+    hash = "1a59xc9frmvi7n0i32dzs8gpf5ral80xkwv97a13zv5cyg8l6216";
+    meta.description = "S-expression pretty-printer";
+    propagatedBuildInputs = [ ppx_base re sexplib ];
+  };
+
+  expect_test_helpers_kernel = janePackage {
+    pname = "expect_test_helpers_kernel";
+    hash = "11m0i7mj6b1cmqnwhmsrqdc814s0lk3sip8rh97k75grngazmjvn";
+    meta.description = "Helpers for writing expectation tests";
+    buildInputs = [ ppx_jane ];
+    propagatedBuildInputs = [ core_kernel sexp_pretty ];
+  };
+
+  expect_test_helpers = janePackage {
+    pname = "expect_test_helpers";
+    hash = "0sw9yam8d9hdam8p194q0hgc4i26vvwj5qi2cba1jxfhdzhy8jdd";
+    meta.description = "Async helpers for writing expectation tests";
+    propagatedBuildInputs = [ async expect_test_helpers_kernel ];
+  };
+
+  patience_diff = janePackage {
+    pname = "patience_diff";
+    hash = "012rlbnw21yq2lsbfk3f7l4m4qq3jdx238146z36v54vnhhs6r2r";
+    meta.description = "Diff library using Bram Cohen's patience diff algorithm";
+    propagatedBuildInputs = [ core_kernel ];
+  };
+
+  ecaml = janePackage {
+    pname = "ecaml";
+    hash = "0jmmsi1m7d4cl5mnw6v9h4ng29anwxy73a6qfi28lgpzafn452bc";
+    meta.description = "Library for writing Emacs plugin in OCaml";
+    propagatedBuildInputs = [ async expect_test_helpers_kernel ];
+  };
+
+  ### Packages at version 0.11, with dependencies at version 0.12
+
+  configurator = janePackage {
+    pname = "configurator";
+    version = "0.11.0";
+    hash = "0h686630cscav7pil8c3w0gbh6rj4b41dvbnwmicmlkc746q5bfk";
+    propagatedBuildInputs = [ stdio ];
+    meta.description = "Helper library for gathering system configuration";
+  };
+
+  ppx_core = janePackage {
+    pname = "ppx_core";
+    version = "0.11.0";
+    hash = "11hgm9mxig4cm3c827f6dns9mjv3pf8g6skf10x0gw9xnp1dmzmx";
+    propagatedBuildInputs = [ ppxlib ];
+    meta.description = "Deprecated (see ppxlib)";
+  };
+
+  ppx_driver = janePackage {
+    pname = "ppx_driver";
+    version = "0.11.0";
+    hash = "00kfx6js2kxk57k4v7hiqvwk7h35whgjihnxf75m82rnaf4yzvfi";
+    propagatedBuildInputs = [ ppxlib ];
+    meta.description = "Deprecated (see ppxlib)";
+  };
+
+  ppx_type_conv = janePackage {
+    pname = "ppx_type_conv";
+    version = "0.11.0";
+    hash = "04dbrglqqhkas25cpjz8xhjcbpk141c35qggzw66bn69izczfmaf";
+    propagatedBuildInputs = [ ppxlib ];
+    meta.description = "Deprecated (see ppxlib)";
+  };
+
+}
diff --git a/pkgs/development/ocaml-modules/janestreet/janePackage_0_13.nix b/pkgs/development/ocaml-modules/janestreet/janePackage_0_13.nix
new file mode 100644
index 00000000000..b92bcead95c
--- /dev/null
+++ b/pkgs/development/ocaml-modules/janestreet/janePackage_0_13.nix
@@ -0,0 +1,19 @@
+{ lib, fetchFromGitHub, buildDunePackage, defaultVersion ? "0.13.0" }:
+
+{ pname, version ? defaultVersion, hash, ...}@args:
+
+buildDunePackage (args // {
+  inherit version;
+
+  minimumOCamlVersion = "4.08";
+
+  src = fetchFromGitHub {
+    owner = "janestreet";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = hash;
+  };
+
+  meta.license = lib.licenses.mit;
+  meta.homepage = "https://github.com/janestreet/${pname}";
+})
diff --git a/pkgs/development/ocaml-modules/phylogenetics/default.nix b/pkgs/development/ocaml-modules/phylogenetics/default.nix
index 916be9b3d38..1873a4e0c58 100644
--- a/pkgs/development/ocaml-modules/phylogenetics/default.nix
+++ b/pkgs/development/ocaml-modules/phylogenetics/default.nix
@@ -3,15 +3,15 @@
 
 buildDunePackage rec {
   pname = "phylogenetics";
-  version = "unstable-2020-01-05";
+  version = "unstable-2020-01-25";
 
   useDune2 = true;
 
   src = fetchFromGitHub {
     owner  = "biocaml";
     repo   = pname;
-    rev    = "b55ef7d7322bd822be26d21339945d45487fb547";
-    sha256 = "0hzfjhs5w3a7hlzxs739k5ik3k1xn3dzyzziid765s74f638n4hj";
+    rev    = "752a7d0324709ba919ef43630a270afd45d6b734";
+    sha256 = "1zsxpl1yjbw6y6n1q7qk3h0l7c0lxhh8yp8bkxlwnpzlkqq28ycg";
   };
 
   minimumOCamlVersion = "4.08";  # e.g., uses Float.min
diff --git a/pkgs/tools/misc/patdiff/default.nix b/pkgs/tools/misc/patdiff/default.nix
index 1c5e5b04474..e0b54e56081 100644
--- a/pkgs/tools/misc/patdiff/default.nix
+++ b/pkgs/tools/misc/patdiff/default.nix
@@ -4,7 +4,7 @@ with ocamlPackages;
 
 janePackage {
   pname = "patdiff";
-  hash = "04krzn6rj2r81z55pms5ayk6bxhlxrm006cbhy0m6rc69a0h00lh";
+  hash = "1yqvxdmkgcwgx3npgncpdqwkpdxiqr1q41wci7589s8z7xi5nwyz";
   buildInputs = [ core_extended expect_test_helpers patience_diff ocaml_pcre shell ];
   meta = {
     description = "File Diff using the Patience Diff algorithm";
diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix
index 160adc015f8..b5d8abade09 100644
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@@ -980,12 +980,20 @@ let
     # Jane Street
 
     janePackage =
-      if lib.versionOlder "4.07" ocaml.version
+      if lib.versionOlder "4.08" ocaml.version
+      then callPackage ../development/ocaml-modules/janestreet/janePackage_0_13.nix {}
+      else if lib.versionOlder "4.07" ocaml.version
       then callPackage ../development/ocaml-modules/janestreet/janePackage_0_12.nix {}
       else callPackage ../development/ocaml-modules/janestreet/janePackage.nix {};
 
     janeStreet =
-    if lib.versionOlder "4.07" ocaml.version
+    if lib.versionOlder "4.08" ocaml.version
+    then import ../development/ocaml-modules/janestreet/0.13.nix {
+      inherit ctypes janePackage num octavius re;
+      inherit (pkgs) openssl;
+      ppxlib = ppxlib.override { version = "0.12.0"; };
+    }
+    else if lib.versionOlder "4.07" ocaml.version
     then import ../development/ocaml-modules/janestreet/0.12.nix {
       inherit ctypes janePackage num octavius ppxlib re;
       inherit (pkgs) openssl;