From 5e765ecc68a02fbad7ae1626558f5a58a8825764 Mon Sep 17 00:00:00 2001 From: thyol Date: Wed, 13 Jul 2022 11:58:02 +0200 Subject: [PATCH 1/5] diamond: 0.8.36 -> 2.0.15 --- pkgs/applications/science/biology/diamond/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index 86b239c93843..c0e59fbaf066 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "diamond"; - version = "0.8.36"; + version = "2.0.15"; src = fetchFromGitHub { owner = "bbuchfink"; repo = "diamond"; rev = "v${version}"; - sha256 = "sha256-7uqOQOzkYN0RNwKBGUZ/Ny5NVZMoGByOk+GUvjdBzck="; + sha256 = "17z9vwj58i1zc22gv4qscx0dk3nxf5ix443gxsibh3a5zsnc6dkg"; }; patches = [ From 4e79b5e370d92197d53713e49884ab3f6045711c Mon Sep 17 00:00:00 2001 From: thyol Date: Wed, 13 Jul 2022 11:58:39 +0200 Subject: [PATCH 2/5] diamond: remove patch --- .../science/biology/diamond/default.nix | 3 --- .../diamond/diamond-0.8.36-no-warning.patch | 20 ------------------- 2 files changed, 23 deletions(-) delete mode 100644 pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index c0e59fbaf066..d287ab8a4848 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -11,9 +11,6 @@ stdenv.mkDerivation rec { sha256 = "17z9vwj58i1zc22gv4qscx0dk3nxf5ix443gxsibh3a5zsnc6dkg"; }; - patches = [ - ./diamond-0.8.36-no-warning.patch - ]; nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; diff --git a/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch b/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch deleted file mode 100644 index a16d475c5564..000000000000 --- a/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff -u -r diamond-0.8.36/src/dp/scalar_traceback.h diamond-0.8.36-patched/src/dp/scalar_traceback.h ---- diamond-0.8.36/src/dp/scalar_traceback.h 2017-02-06 16:32:05.000000000 +0100 -+++ diamond-0.8.36-patched/src/dp/scalar_traceback.h 2017-02-23 15:13:24.000000000 +0100 -@@ -19,6 +19,7 @@ - #ifndef SCALAR_TRACEBACK_H_ - #define SCALAR_TRACEBACK_H_ - -+#include - #include - #include "../basic/score_matrix.h" - -@@ -31,7 +32,7 @@ - template<> - inline bool almost_equal(float x, float y) - { -- return abs(x - y) < 0.001f; -+ return std::abs(x - y) < 0.001f; - } - - template From 55853ae09676ecd78170f514d4d8961908d2adbe Mon Sep 17 00:00:00 2001 From: thyol Date: Wed, 13 Jul 2022 12:01:14 +0200 Subject: [PATCH 3/5] maintainers: add thyol --- maintainers/maintainer-list.nix | 6 ++++++ pkgs/applications/science/biology/diamond/default.nix | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index 6d9da62e2ddf..52bf46e86671 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -12694,6 +12694,12 @@ githubId = 3268082; name = "Thibaut Marty"; }; + thyol = { + name = "thyol"; + email = "thyol@pm.me"; + github = "thyol"; + githubId = 81481634; + }; thmzlt = { email = "git@thomazleite.com"; github = "thmzlt"; diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index d287ab8a4848..fc3721dc66eb 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -36,6 +36,6 @@ stdenv.mkDerivation rec { fullName = "University of Tuebingen, Benjamin Buchfink"; url = "https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING"; }; - maintainers = [ ]; + maintainers = with lib.maintainers; [ thyol ]; }; } From 0d6e3afdba59da87eecc3aed8b1bef73a78f38fd Mon Sep 17 00:00:00 2001 From: thyol Date: Wed, 13 Jul 2022 12:03:05 +0200 Subject: [PATCH 4/5] diamond: update metadata --- .../science/biology/diamond/default.nix | 23 +++++++------------ 1 file changed, 8 insertions(+), 15 deletions(-) diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index fc3721dc66eb..8073b1bea163 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -18,24 +18,17 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Accelerated BLAST compatible local sequence aligner"; longDescription = '' - A sequence aligner for protein and translated DNA - searches and functions as a drop-in replacement for the NCBI BLAST - software tools. It is suitable for protein-protein search as well as - DNA-protein search on short reads and longer sequences including contigs - and assemblies, providing a speedup of BLAST ranging up to x20,000. + DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: + - Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. + - Frameshift alignments for long read analysis. + - Low resource requirements and suitable for running on standard desktops or laptops. + - Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification. - DIAMOND is developed by Benjamin Buchfink. Feel free to contact him for support (Email Twitter). - - If you use DIAMOND in published research, please cite - B. Buchfink, Xie C., D. Huson, - "Fast and sensitive protein alignment using DIAMOND", - Nature Methods 12, 59-60 (2015). + When using the tool in published research, please cite: + - Buchfink B, Reuter K, Drost HG, "Sensitive protein alignments at tree-of-life scale using DIAMOND", Nature Methods 18, 366–368 (2021). doi:10.1038/s41592-021-01101-x ''; homepage = "https://github.com/bbuchfink/diamond"; - license = { - fullName = "University of Tuebingen, Benjamin Buchfink"; - url = "https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING"; - }; + license = lib.licenses.gpl3Plus; maintainers = with lib.maintainers; [ thyol ]; }; } From bb3ed09b06bd4ac113b6192b45f3f993cf28be84 Mon Sep 17 00:00:00 2001 From: thyol Date: Wed, 13 Jul 2022 12:18:08 +0200 Subject: [PATCH 5/5] diamond: add release notes --- .../doc/manual/from_md/release-notes/rl-2211.section.xml | 8 ++++++++ nixos/doc/manual/release-notes/rl-2211.section.md | 2 ++ 2 files changed, 10 insertions(+) diff --git a/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml b/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml index 550dddfaf352..57df5483a0a7 100644 --- a/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml +++ b/nixos/doc/manual/from_md/release-notes/rl-2211.section.xml @@ -320,6 +320,14 @@ and require manual remediation. + + + The diamond package has been update from + 0.8.36 to 2.0.15. See the + upstream + release notes for more details. + + dockerTools.buildImage deprecates the diff --git a/nixos/doc/manual/release-notes/rl-2211.section.md b/nixos/doc/manual/release-notes/rl-2211.section.md index b652419bcf16..028b5a5b7774 100644 --- a/nixos/doc/manual/release-notes/rl-2211.section.md +++ b/nixos/doc/manual/release-notes/rl-2211.section.md @@ -121,6 +121,8 @@ Use `configure.packages` instead. - Matrix Synapse now requires entries in the `state_group_edges` table to be unique, in order to prevent accidentally introducing duplicate information (for example, because a database backup was restored multiple times). If your Synapse database already has duplicate rows in this table, this could fail with an error and require manual remediation. +- The `diamond` package has been update from 0.8.36 to 2.0.15. See the [upstream release notes](https://github.com/bbuchfink/diamond/releases) for more details. + - `dockerTools.buildImage` deprecates the misunderstood `contents` parameter, in favor of `copyToRoot`. Use `copyToRoot = buildEnv { ... };` or similar if you intend to add packages to `/bin`.