diff options
Diffstat (limited to 'pkgs/applications/science')
10 files changed, 227 insertions, 68 deletions
diff --git a/pkgs/applications/science/biology/blast/bin.nix b/pkgs/applications/science/biology/blast/bin.nix new file mode 100644 index 0000000000000..03e61bdcbe867 --- /dev/null +++ b/pkgs/applications/science/biology/blast/bin.nix @@ -0,0 +1,60 @@ +{ lib +, stdenv +, fetchurl +, python3 +, perl +, blast +, autoPatchelfHook +, zlib +, bzip2 +, glib +, libxml2 +, coreutils +}: +let + pname = "blast-bin"; + version = "2.13.0"; + + srcs = rec { + x86_64-linux = fetchurl { + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-linux.tar.gz"; + hash = "sha256-QPK3OdT++GoNI1NHyEpu2/hB2hqHYPQ/vNXFAVCwVEc="; + }; + aarch64-linux = fetchurl { + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-arm-linux.tar.gz"; + hash = "sha256-vY8K66k7KunpBUjFsJTTb+ur5n1XmU0/mYxhZsi9ycs="; + }; + x86_64-darwin = fetchurl { + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-macosx.tar.gz"; + hash = "sha256-Y0JlOUl9Ego6LTxTCNny3P5c1H3fApPXQm7Z6Zhq9RA="; + }; + aarch64-darwin = x86_64-darwin; + }; + src = srcs.${stdenv.hostPlatform.system}; +in +stdenv.mkDerivation { + inherit pname version src; + + nativeBuildInputs = lib.optional stdenv.isLinux [ autoPatchelfHook ]; + + buildInputs = [ python3 perl ] ++ lib.optionals stdenv.isLinux [ zlib bzip2 glib libxml2 ]; + + installPhase = '' + runHook preInstall + + install -Dm755 bin/* -t $out/bin + + runHook postInstall + ''; + + preFixup = '' + substituteInPlace $out/bin/get_species_taxids.sh \ + --replace /bin/rm ${coreutils}/bin/rm + ''; + + meta = with lib; { + inherit (blast.meta) description homepage license; + platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ]; + maintainers = with maintainers; [ natsukium ]; + }; +} diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 0104a5506bc6a..7b6689a358a8a 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1447"; + version = "1453"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-zts1F2tFeBP7CQifpc2M4i6duK8FA7hQXTOizv8/kWM="; + hash = "sha256-r8bWk1+weSyQ5QPGKKwdAzMkzh3DgzTUr5YCMUq5UUM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 15a1e3158233f..155d521549e3b 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -70,7 +70,6 @@ python3Packages.buildPythonApplication rec { ''; meta = with lib; { - broken = stdenv.isDarwin; inherit description; homepage = "https://www.pymol.org/"; license = licenses.mit; diff --git a/pkgs/applications/science/electronics/kicad/base.nix b/pkgs/applications/science/electronics/kicad/base.nix index 697c27842081d..eb65b6881ae20 100644 --- a/pkgs/applications/science/electronics/kicad/base.nix +++ b/pkgs/applications/science/electronics/kicad/base.nix @@ -20,9 +20,7 @@ , pcre , libpthreadstubs , libXdmcp -, lndir , unixODBC -, fetchpatch , util-linux , libselinux @@ -48,7 +46,6 @@ , baseName , kicadSrc , kicadVersion -, withOCC , withNgspice , withScripting , withI18n @@ -72,19 +69,6 @@ stdenv.mkDerivation rec { patches = [ # upstream issue 12941 (attempted to upstream, but appreciably unacceptable) ./writable.patch - ] - ++ optionals (stable) # the 2 wxGTK ones should in the next stable point release - [ - (fetchpatch { # for wxGTK 3.2.2.1's .1 field - name = "support wxWidgets subrelease field"; - url = "https://gitlab.com/kicad/code/kicad/-/commit/b536580119c59fde78e38d8d6388f2540ecb6cf9.diff"; - hash = "sha256-F+J5oZO0BsT1VWKpx0KGA7ecn5/PBgCw8uiScihM+54="; - }) - (fetchpatch { # for wxGTK 3.2.2.1's .1 field, but for wxPython - name = "relax wxPython check to just major.minor"; - url = "https://gitlab.com/kicad/code/kicad/-/commit/1e8cc6855d6a8fc1f9dfc933224c3a10fb759f9c.diff"; - hash = "sha256-CGNgxZ7QiVLkaauNl7Pmcl152lwyDZqA/HSyFdOswwU="; - }) ]; # tagged releases don't have "unknown" @@ -97,40 +81,42 @@ stdenv.mkDerivation rec { makeFlags = optionals (debug) [ "CFLAGS+=-Og" "CFLAGS+=-ggdb" ]; + # some ngspice tests attempt to write to $HOME/.cache/ + XDG_CACHE_HOME = "$TMP"; + # failing tests still attempt to create $HOME though + cmakeFlags = [ - # RPATH of binary /nix/store/.../bin/... contains a forbidden reference to /build/ - "-DCMAKE_SKIP_BUILD_RPATH=ON" "-DKICAD_USE_EGL=ON" - "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;qa_eeschema'" # upstream issue 12491 + "-DOCC_INCLUDE_DIR=${opencascade-occt}/include/opencascade" + ] + ++ optionals (stable) [ + # https://gitlab.com/kicad/code/kicad/-/issues/12491 + # should be resolved in the next release + "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;qa_eeschema'" ] - ++ optionals (withScripting) [ - "-DKICAD_SCRIPTING_WXPYTHON=ON" + ++ optionals (!stable) [ # workaround for https://gitlab.com/kicad/code/kicad/-/issues/14346 + "-DPYTHON_SITE_PACKAGE_PATH=${placeholder "out"}/${python.sitePackages}/" ] + ++ optional (stable && !withNgspice) "-DKICAD_SPICE=OFF" ++ optionals (!withScripting) [ "-DKICAD_SCRIPTING_WXPYTHON=OFF" ] - ++ optional (!withNgspice) "-DKICAD_SPICE=OFF" - ++ optional (!withOCC) "-DKICAD_USE_OCC=OFF" - ++ optionals (withOCC) [ - "-DKICAD_USE_OCC=ON" - "-DOCC_INCLUDE_DIR=${opencascade-occt}/include/opencascade" + ++ optionals (withI18n) [ + "-DKICAD_BUILD_I18N=ON" + ] + ++ optionals (!doInstallCheck) [ + "-DKICAD_BUILD_QA_TESTS=OFF" ] ++ optionals (debug) [ "-DCMAKE_BUILD_TYPE=Debug" "-DKICAD_STDLIB_DEBUG=ON" "-DKICAD_USE_VALGRIND=ON" ] - ++ optionals (!doInstallCheck) [ - "-DKICAD_BUILD_QA_TESTS=OFF" - ] ++ optionals (sanitizeAddress) [ "-DKICAD_SANITIZE_ADDRESS=ON" ] ++ optionals (sanitizeThreads) [ "-DKICAD_SANITIZE_THREADS=ON" - ] - ++ optionals (withI18n) [ - "-DKICAD_BUILD_I18N=ON" ]; nativeBuildInputs = [ @@ -138,7 +124,6 @@ stdenv.mkDerivation rec { doxygen graphviz pkg-config - lndir ] # wanted by configuration on linux, doesn't seem to affect performance # no effect on closure size @@ -177,10 +162,10 @@ stdenv.mkDerivation rec { python unixODBC libdeflate + opencascade-occt ] ++ optional (withScripting) wxPython ++ optional (withNgspice) libngspice - ++ optional (withOCC) opencascade-occt ++ optional (debug) valgrind; # debug builds fail all but the python test diff --git a/pkgs/applications/science/electronics/kicad/default.nix b/pkgs/applications/science/electronics/kicad/default.nix index c7eb9d69522c9..50628a3e1f019 100644 --- a/pkgs/applications/science/electronics/kicad/default.nix +++ b/pkgs/applications/science/electronics/kicad/default.nix @@ -14,7 +14,6 @@ , pname ? "kicad" , stable ? true -, withOCC ? true , withNgspice ? !stdenv.isDarwin , libngspice , withScripting ? true @@ -117,7 +116,7 @@ stdenv.mkDerivation rec { inherit stable baseName; inherit kicadSrc kicadVersion; inherit wxGTK python wxPython; - inherit withOCC withNgspice withScripting withI18n; + inherit withNgspice withScripting withI18n; inherit debug sanitizeAddress sanitizeThreads; }; @@ -131,7 +130,7 @@ stdenv.mkDerivation rec { dontFixup = true; pythonPath = optionals (withScripting) - [ wxPython python.pkgs.six ]; + [ wxPython python.pkgs.six python.pkgs.requests ]; nativeBuildInputs = [ makeWrapper ] ++ optionals (withScripting) diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index 4562e8447624f..b102da24a3d40 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,45 +3,45 @@ { "kicad" = { kicadVersion = { - version = "7.0.0"; + version = "7.0.1"; src = { - rev = "da2b9df05c3ccd5ec104cf8cd8ded34f5dd25216"; - sha256 = "1zgpj1rvf97qv36hg4dja46pbzyixlh2g04wlh7cizcrs16b9mzw"; + rev = "3b83917a115be1ce2f33a73039f59f8784b5c2e7"; + sha256 = "021safxvyq9qzs08jy3jvpazmhvix4kyl05s9y9hwmyzdmdl2smn"; }; }; libVersion = { - version = "7.0.0"; + version = "7.0.1"; libSources = { - symbols.rev = "08a25991d07924b263cbf87c6e513feac2b2169f"; - symbols.sha256 = "1r87xr1453dpfglkg1m4p5d7kcv9gxls1anwk3vp2yppnwz24ydm"; + symbols.rev = "adfe3c06b5750d81580ed44e669b578f49c205eb"; + symbols.sha256 = "14c5gci13m30xv0cmic5jxsmfx9lq3fnd8hyq3mmgkrw7443zy30"; templates.rev = "66d76556d9e81f8a5be74457686d211c666ed200"; templates.sha256 = "02i279269mhq7wjhb1yqk90820ncssxl9n7b20qr2r4fmm7jpvxv"; - footprints.rev = "a0388d07e4a37e8db13a716efb3ad4750c839f9c"; - footprints.sha256 = "1akhifnjm8jvqsvscn2rr1wpzrls73bpdc6sk40355r1in2djmry"; - packages3d.rev = "bbee2295519bcf469d97f5e06bcf7175cddd2037"; - packages3d.sha256 = "1qw5xm0wbhv6gqvd8mn0jp4abjbizrkx79r6y8f6911mkzi47r6n"; + footprints.rev = "1cf5a1d979cffebd62464c1bb0d7b09c5ee3b8c3"; + footprints.sha256 = "0k0z40wmaq665hjxb6kp1yl3v7clxz49r6ki0chyphsxv1cnixmy"; + packages3d.rev = "e54b5b6368d03f396098448bcce37f2e432dac33"; + packages3d.sha256 = "0nzi7ijfb3rjm98kaa9va2mkh0nfzpq4vfhxkq8j18qhx24h5c8v"; }; }; }; "kicad-unstable" = { kicadVersion = { - version = "2023-02-14"; + version = "2023-03-29"; src = { - rev = "29c4482bc898f627cebcd5f64e063e8a813a5445"; - sha256 = "1hs1p79skmrn2k7qrpnkynzkk2g8ry20lqivzfqg87c56rd1522y"; + rev = "d5bc223ff2cd1fbf4e923e23b5bb442bb54faa95"; + sha256 = "0pbzmv9vh4bzhsxj46gjkgh7kk6a0v8gijvkmb56fy5i8xv2ixkn"; }; }; libVersion = { - version = "2023-02-14"; + version = "2023-03-29"; libSources = { - symbols.rev = "3ad8b98287ddf528ce8ff07bbe70aed85cb4410a"; - symbols.sha256 = "1p0wa3bhw2qgdvb5vzwvrbhkb6sqpc93d754rbcs2xh79d75l9nn"; + symbols.rev = "36fc1c88921bf32ebf667e027dfe63cca649fd95"; + symbols.sha256 = "177mqvjf3knldnl7pf1abv4pmlgi5cg02ggfwbc655jq4x6x8fkz"; templates.rev = "867eef383a0f61015cb69677d5c632d78a2ea01a"; templates.sha256 = "1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq"; - footprints.rev = "a168dd18ea63c2df948c2de3026dc19730cb70cf"; - footprints.sha256 = "0y3cl9fcyi8z4yrn0kfgfy28gn9ngrdvnpgbpwykbbp8fpx401nk"; - packages3d.rev = "a0919e5e805157bccd65af313806de3833c1673e"; - packages3d.sha256 = "1yizw9g3skz7i9x9iwbnn3gk3lnh10krf6xg32plb2plxfynz3cw"; + footprints.rev = "dc4574eb65136d95a7775d09412d5159f8d7832c"; + footprints.sha256 = "1iz4wyiysdii378c3pjgkgwh1cssxbh5jkbhvj7rmi2vmgngl6nc"; + packages3d.rev = "e54b5b6368d03f396098448bcce37f2e432dac33"; + packages3d.sha256 = "0nzi7ijfb3rjm98kaa9va2mkh0nfzpq4vfhxkq8j18qhx24h5c8v"; }; }; }; diff --git a/pkgs/applications/science/electronics/openroad/0001-Fix-string-formatting-in-tests.patch b/pkgs/applications/science/electronics/openroad/0001-Fix-string-formatting-in-tests.patch new file mode 100644 index 0000000000000..0332ade17dc70 --- /dev/null +++ b/pkgs/applications/science/electronics/openroad/0001-Fix-string-formatting-in-tests.patch @@ -0,0 +1,53 @@ +From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001 +From: Nicolas Benes <nbenes.gh@xandea.de> +Date: Sun, 2 Apr 2023 01:24:51 +0200 +Subject: [PATCH] Fix string formatting in tests + +Hide the decimal point and digits after the decimal point when they are +not needed. + +diff --git a/src/par/test/partition_gcd.ok b/src/par/test/partition_gcd.ok +index 6c40c14..b9a42f6 100644 +--- a/src/par/test/partition_gcd.ok ++++ b/src/par/test/partition_gcd.ok +@@ -9,7 +9,7 @@ + ======================================== + [INFO] Partitioning parameters**** + [PARAM] Number of partitions = 2 +-[PARAM] UBfactor = 1.0 ++[PARAM] UBfactor = 1 + [PARAM] Vertex dimensions = 1 + [PARAM] Hyperedge dimensions = 1 + ======================================== +@@ -118,7 +118,7 @@ After Hyperedge Reduction : num_vertices = 137, num_hyperedges = 251 + [V-Refine] Level 2 :: 207, 301, 154.65254 + [V-Refine] Level 3 :: 312, 370, 154.65254 + [V-Refine] Level 4 :: 469, 451, 154.65254 +-[INFO] V-cycle refinement 1 delta cost 0.0 ++[INFO] V-cycle refinement 1 delta cost 0 + ========================================= + [STATUS] Running FC multilevel coarsening + ========================================= +@@ -133,7 +133,7 @@ After Hyperedge Reduction : num_vertices = 137, num_hyperedges = 251 + [V-Refine] Level 2 :: 207, 301, 154.65254 + [V-Refine] Level 3 :: 312, 370, 154.65254 + [V-Refine] Level 4 :: 469, 451, 154.65254 +-[INFO] V-cycle refinement 2 delta cost 0.0 ++[INFO] V-cycle refinement 2 delta cost 0 + [Cutcost of partition : 154.65254] + [Vertex balance of block_0 : 0.59249 ( 327.17993 ) + [Vertex balance of block_1 : 0.40751 ( 225.03609 ) +diff --git a/src/pdn/test/design_width.ok b/src/pdn/test/design_width.ok +index 381dca1..a102974 100644 +--- a/src/pdn/test/design_width.ok ++++ b/src/pdn/test/design_width.ok +@@ -9,5 +9,5 @@ + [INFO ODB-0130] Created 54 pins. + [INFO ODB-0131] Created 406 components and 1816 component-terminals. + [INFO ODB-0133] Created 361 nets and 1004 connections. +-[ERROR PDN-0185] Insufficient width (14.04 um) to add straps on layer M8 in grid "Core" with total strap width 6.0 um and offset 10.0 um. ++[ERROR PDN-0185] Insufficient width (14.04 um) to add straps on layer M8 in grid "Core" with total strap width 6 um and offset 10 um. + PDN-0185 +-- +2.38.4 + diff --git a/pkgs/applications/science/electronics/openroad/0002-Ignore-warning-on-stderr.patch b/pkgs/applications/science/electronics/openroad/0002-Ignore-warning-on-stderr.patch new file mode 100644 index 0000000000000..f0b0666789a79 --- /dev/null +++ b/pkgs/applications/science/electronics/openroad/0002-Ignore-warning-on-stderr.patch @@ -0,0 +1,41 @@ +From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001 +From: Nicolas Benes <nbenes.gh@xandea.de> +Date: Sun, 2 Apr 2023 04:57:17 +0200 +Subject: [PATCH] Ignore warning on stderr + +The following warning is written to stderr, which causes the overall +test to fail: + +``` +sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8) +``` + +diff --git a/src/dst/test/cpp_tests.tcl b/src/dst/test/cpp_tests.tcl +index 9087c2c..63d0cb7 100644 +--- a/src/dst/test/cpp_tests.tcl ++++ b/src/dst/test/cpp_tests.tcl +@@ -4,7 +4,7 @@ set test_dir [pwd] + set openroad_dir [file dirname [file dirname [file dirname $test_dir]]] + set tests_path [file join $openroad_dir "build" "src" "dst" "test" "cpp"] + +-set tests_list [split [exec sh -c "find $tests_path -maxdepth 1 -name 'Test*'"] \n] ++set tests_list [split [exec -ignorestderr sh -c "find $tests_path -maxdepth 1 -name 'Test*'"] \n] + + foreach test $tests_list { + set test_name [file tail $test] +diff --git a/src/odb/test/cpp_tests.tcl b/src/odb/test/cpp_tests.tcl +index 091d576..6811760 100644 +--- a/src/odb/test/cpp_tests.tcl ++++ b/src/odb/test/cpp_tests.tcl +@@ -4,7 +4,7 @@ set test_dir [pwd] + set openroad_dir [file dirname [file dirname [file dirname $test_dir]]] + set tests_path [file join $openroad_dir "build" "src" "odb" "test" "cpp"] + +-set tests_list [split [exec sh -c "find $tests_path -maxdepth 1 -name 'Test*' ! -name '*.cmake'"] \n] ++set tests_list [split [exec -ignorestderr sh -c "find $tests_path -maxdepth 1 -name 'Test*' ! -name '*.cmake'"] \n] + + foreach test $tests_list { + set test_name [file tail $test] +-- +2.38.4 + diff --git a/pkgs/applications/science/electronics/openroad/default.nix b/pkgs/applications/science/electronics/openroad/default.nix index 636caec6902a1..68e079e2f89b6 100644 --- a/pkgs/applications/science/electronics/openroad/default.nix +++ b/pkgs/applications/science/electronics/openroad/default.nix @@ -9,13 +9,20 @@ , python3 , swig4 , boost17x +, cbc # for clp , cimg +, clp # for or-tools , eigen +, glpk +, gtest , lcov , lemon-graph , libjpeg +, or-tools , pcre +, pkg-config , qtbase +, re2 # for or-tools , readline , spdlog , tcl @@ -27,14 +34,14 @@ mkDerivation rec { pname = "openroad"; - version = "unstable-2022-07-19"; + version = "unstable-2023-03-31"; src = fetchFromGitHub { owner = "The-OpenROAD-Project"; repo = "OpenROAD"; - rev = "2610b3953ef62651825d89fb96917cf5d20af0f1"; + rev = "cd03c5cf8a8eb78c0e07fe33a56b8e9d64672efe"; fetchSubmodules = true; - sha256 = "sha256-BP0JSnxl1XyqHzDY4eITaGHevqd+rbjWZy/LAfDfELs="; + hash = "sha256-BWUvFCuWKWQpifErpak03J+A7ni0jZWIrCMhMdKIbD0="; }; nativeBuildInputs = [ @@ -43,19 +50,25 @@ mkDerivation rec { doxygen flex git + pkg-config swig4 ]; buildInputs = [ boost17x + cbc cimg + clp eigen + glpk lcov lemon-graph libjpeg + or-tools pcre python3 qtbase + re2 readline spdlog tcl @@ -65,6 +78,11 @@ mkDerivation rec { zlib ]; + patches = [ + ./0001-Fix-string-formatting-in-tests.patch + ./0002-Ignore-warning-on-stderr.patch + ]; + postPatch = '' patchShebangs --build etc/find_messages.py ''; @@ -74,18 +92,22 @@ mkDerivation rec { "-DUSE_SYSTEM_BOOST=ON" "-DUSE_CIMG_LIB=ON" "-DOPENROAD_VERSION=${src.rev}" + + # 2023-03-31: see discussion on fmt workaround in + # https://github.com/The-OpenROAD-Project/OpenROAD/pull/2696 + "-DCMAKE_CXX_FLAGS=-DFMT_DEPRECATED_OSTREAM" ]; # Resynthesis needs access to the Yosys binaries. qtWrapperArgs = [ "--prefix PATH : ${lib.makeBinPath [ yosys ]}" ]; + checkInputs = [ gtest ]; + # Upstream uses vendored package versions for some dependencies, so regression testing is prudent # to see if there are any breaking changes in unstable that should be vendored as well. - doCheck = false; # Disabled pending upstream release with fix for rcx log file creation. + doCheck = true; checkPhase = '' - # Regression tests must be run from the project root not from within the CMake build directory. - cd .. - test/regression + ../test/regression ''; doInstallCheck = true; diff --git a/pkgs/applications/science/math/scalp/default.nix b/pkgs/applications/science/math/scalp/default.nix index 05261701fc287..4145407d7aaaa 100644 --- a/pkgs/applications/science/math/scalp/default.nix +++ b/pkgs/applications/science/math/scalp/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { src = fetchgit { url = "https://digidev.digi.e-technik.uni-kassel.de/git/scalp.git"; - # mirrored at https://github.com/wegank/scalp.git + # mirrored at https://git.sr.ht/~weijia/scalp rev = "185b84e4ff967f42cf2de5db4db4e6fa0cc18fb8"; sha256 = "sha256-NyMZdJwdD3FR6uweYCclJjfcf3Y24Bns1ViwsmJ5izg="; }; |