Merge pull request NixOS#221957 from natsukium/dssp/update

dssp: 4.0.5 -> 4.2.2.1

pkgs/applications/science/biology/dssp/default.nix

@@ -1,19 +1,30 @@
-{ lib, stdenv, fetchFromGitHub, boost, cmake, libcifpp, zlib, }:
+{ lib, stdenv, fetchFromGitHub, cmake, libcifpp, libmcfp, zlib }:
+let
+  libcifpp' = libcifpp.overrideAttrs (oldAttrs:  rec {
+    # dssp 4.2.2.1 requires specific version "5.0.8" of libcifpp
+    version = "5.0.8";
+    src = fetchFromGitHub {
+      inherit (oldAttrs.src) owner repo;
+      rev = "v${version}";
+      sha256 = "sha256-KJGcopGhCWSl+ElG3BPJjBf/kvYJowOHxto6Ci1IMco=";
+    };
+  });
+in
 
 stdenv.mkDerivation rec {
   pname = "dssp";
-  version = "4.0.5";
+  version = "4.2.2.1";
 
   src = fetchFromGitHub {
     owner = "PDB-REDO";
     repo = pname;
     rev = "v${version}";
-    sha256 = "1x35rdcm4fch66pjbmy73lv0gdb6g9y3v023a66512a6nzsqjsir";
+    sha256 = "sha256-vmGvC5d8LTo+pcY9sxwj0d6JvH8Lyk+QSOZo5raBci4=";
   };
 
   nativeBuildInputs = [ cmake ];
 
-  buildInputs = [ boost libcifpp zlib ];
+  buildInputs = [ libcifpp' libmcfp zlib ];
 
   meta = with lib; {
     description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein";

pkgs/development/libraries/libcifpp/default.nix

@@ -1,19 +1,22 @@
-{ lib, stdenv, fetchFromGitHub, boost, cmake, }:
+{ lib, stdenv, fetchFromGitHub, boost, cmake, zlib }:
 
 stdenv.mkDerivation rec {
   pname = "libcifpp";
-  version = "4.2.2";
+  version = "5.0.8";
 
   src = fetchFromGitHub {
     owner = "PDB-REDO";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0mhplcpni4p8lavrq4fz9qq8mbxhvpnlxzy55yrz8y07d76ajg6y";
+    sha256 = "sha256-KJGcopGhCWSl+ElG3BPJjBf/kvYJowOHxto6Ci1IMco=";
   };
 
   nativeBuildInputs = [ cmake ];
 
-  buildInputs = [ boost ];
+  # disable network access
+  cmakeFlags = [ "-DCIFPP_DOWNLOAD_CCD=OFF" ];
+
+  buildInputs = [ boost zlib ];
 
   meta = with lib; {
     description = "Manipulate mmCIF and PDB files";

pkgs/development/libraries/libmcfp/default.nix

@@ -0,0 +1,23 @@
+{ lib, stdenv, fetchFromGitHub, cmake }:
+
+stdenv.mkDerivation rec {
+  pname = "libmcfp";
+  version = "1.2.3";
+
+  src = fetchFromGitHub {
+    owner = "mhekkel";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "sha256-Mi5nj8vR1j3V7fIMBrSyhD57emmlkCb0F08+5s7Usj0=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with lib; {
+    description = "Header only library that can collect configuration options from command line arguments";
+    homepage = "https://github.com/mhekkel/libmcfp";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+}

pkgs/top-level/all-packages.nix

@@ -21665,6 +21665,8 @@ with pkgs;
 
   libmaxminddb = callPackage ../development/libraries/libmaxminddb { };
 
+  libmcfp = callPackage ../development/libraries/libmcfp { };
+
   libmcrypt = callPackage ../development/libraries/libmcrypt { };
 
   libmediaart = callPackage ../development/libraries/libmediaart { };