diff options
Diffstat (limited to 'pkgs/applications/science')
17 files changed, 1556 insertions, 313 deletions
diff --git a/pkgs/applications/science/astronomy/gildas/default.nix b/pkgs/applications/science/astronomy/gildas/default.nix index 4bb3c7b34fe..cc6af8a17c0 100644 --- a/pkgs/applications/science/astronomy/gildas/default.nix +++ b/pkgs/applications/science/astronomy/gildas/default.nix @@ -1,14 +1,14 @@ -{ stdenv, fetchurl, gtk2-x11 , pkgconfig , python27 , gfortran , lesstif -, cfitsio , getopt , perl , groff , which, darwin +{ stdenv, fetchurl, gtk2-x11 , pkgconfig , python3 , gfortran , lesstif +, cfitsio , getopt , perl , groff , which, darwin, ncurses }: let - python27Env = python27.withPackages(ps: with ps; [ numpy ]); + python3Env = python3.withPackages(ps: with ps; [ numpy ]); in stdenv.mkDerivation rec { - srcVersion = "dec19a"; - version = "20191201_a"; + srcVersion = "jan20a"; + version = "20200101_a"; pname = "gildas"; src = fetchurl { @@ -16,17 +16,19 @@ stdenv.mkDerivation rec { # source code of the previous release to a different directory urls = [ "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.xz" "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.xz" ]; - sha256 = "0kwq5gzgzx5hkbabwvbrw2958pqz4m2s501k5cbllgxh4sqp86b1"; + sha256 = "12n08pax7gwg2z121ix3ah5prq3yswqnf2yc8jgs4i9rgkpbsfzz"; }; - enableParallelBuilding = true; + # Python scripts are not converted to Python 3 syntax when parallel + # building is turned on. Disable it until this is fixed upstream. + enableParallelBuilding = false; nativeBuildInputs = [ pkgconfig groff perl getopt gfortran which ]; - buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ] + buildInputs = [ gtk2-x11 lesstif cfitsio python3Env ncurses ] ++ stdenv.lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ CoreFoundation ]); - patches = [ ./wrapper.patch ./clang.patch ./aarch64.patch ]; + patches = [ ./wrapper.patch ./clang.patch ./aarch64.patch ./imager-py3.patch ]; NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.cc.isClang "-Wno-unused-command-line-argument"; @@ -34,7 +36,7 @@ stdenv.mkDerivation rec { configurePhase='' substituteInPlace admin/wrapper.sh --replace '%%OUT%%' $out - substituteInPlace admin/wrapper.sh --replace '%%PYTHONHOME%%' ${python27Env} + substituteInPlace admin/wrapper.sh --replace '%%PYTHONHOME%%' ${python3Env} substituteInPlace utilities/main/gag-makedepend.pl --replace '/usr/bin/perl' ${perl}/bin/perl source admin/gildas-env.sh -c gfortran -o openmp echo "gag_doc: $out/share/doc/" >> kernel/etc/gag.dico.lcl diff --git a/pkgs/applications/science/astronomy/gildas/imager-py3.patch b/pkgs/applications/science/astronomy/gildas/imager-py3.patch new file mode 100644 index 00000000000..71a129164ba --- /dev/null +++ b/pkgs/applications/science/astronomy/gildas/imager-py3.patch @@ -0,0 +1,12 @@ +diff -ruN gildas-src-jan20a.orig/contrib/imager/pro/define.ima gildas-src-jan20a/contrib/imager/pro/define.ima +--- gildas-src-jan20a.orig/contrib/imager/pro/define.ima 2020-01-01 02:15:16.000000000 +0100 ++++ gildas-src-jan20a/contrib/imager/pro/define.ima 2020-01-14 11:18:46.000000000 +0100 +@@ -9,7 +9,7 @@ + ! + ! Patch for a Bug on Mac-OS/X where Python blocks if activated first + ! from a script launched by a widget. +-python print "Starting Python" ++python print("Starting Python") + ! + ! INPUT, GO and UVT_CONVERT always defined by GreG + define command GO "@ p_go.ima" gag_pro:go_greg.hlp diff --git a/pkgs/applications/science/biology/bayescan/default.nix b/pkgs/applications/science/biology/bayescan/default.nix new file mode 100644 index 00000000000..4e216fbdbe6 --- /dev/null +++ b/pkgs/applications/science/biology/bayescan/default.nix @@ -0,0 +1,39 @@ +{ stdenv, fetchurl, unzip, llvmPackages }: + +stdenv.mkDerivation rec { + pname = "bayescan"; + version = "2.1"; + + src = fetchurl { + url = "http://cmpg.unibe.ch/software/BayeScan/files/BayeScan${version}.zip"; + sha256 = "0ismima8j8z0zj9yc267rpf7z90w57b2pbqzjnayhc3ab8mcbfy6"; + }; + + nativeBuildInputs = [ unzip ]; + buildInputs = stdenv.lib.optional stdenv.cc.isClang llvmPackages.openmp; + + # Disable FORTIFY_SOURCE or the binary fails with "buffer overflow" + hardeningDisable = [ "fortify" ]; + + sourceRoot = "BayeScan${version}/source"; + + postPatch = '' + substituteInPlace Makefile --replace "-static" "" \ + --replace "g++" "c++" + ''; + + installPhase = '' + mkdir -p $out/bin + mkdir -p $out/share/doc/bayescan + cp bayescan_${version} $out/bin + cp -r ../*pdf ../input_examples ../"R functions" $out/share/doc/bayescan + ''; + + meta = with stdenv.lib; { + description = "Detecting natural selection from population-based genetic data"; + homepage = "http://cmpg.unibe.ch/software/BayeScan"; + license = licenses.gpl3; + maintainers = [ maintainers.bzizou ]; + platforms = stdenv.lib.platforms.all; + }; +} diff --git a/pkgs/applications/science/biology/manta/default.nix b/pkgs/applications/science/biology/manta/default.nix new file mode 100644 index 00000000000..f0f0575e055 --- /dev/null +++ b/pkgs/applications/science/biology/manta/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, zlib, python2 }: + +stdenv.mkDerivation rec { + pname = "manta"; + version = "1.6.0"; + + src = fetchFromGitHub { + owner = "Illumina"; + repo = "manta"; + rev = "v${version}"; + sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib python2 ]; + postFixup = '' + sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py + sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py + sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py + ''; + doInstallCheck = true; + installCheckPhase = '' + rm $out/lib/python/**/*.pyc + PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript' + PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow' + ''; + + meta = with stdenv.lib; { + description = "Structural variant caller"; + license = licenses.gpl3; + homepage = "https://github.com/Illumina/manta"; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + }; +} diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index a67653c8437..44247f294aa 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.21.3"; + version = "2.21.6"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0s1gn2bkya41866kd8zj0g8xjbivs763jqmlzdpjz4c25h6xkhns"; + sha256 = "1vpyzhrs3bbviwk2n7k5296rnsw7g9ksvjsibl0gm7dawip9jb5s"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index daa2925de7c..f2c5e9f25be 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.9"; + version = "1.10"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"; + sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv"; }; nativeBuildInputs = [ perl ]; diff --git a/pkgs/applications/science/biology/xenomapper/default.nix b/pkgs/applications/science/biology/xenomapper/default.nix index cc235c4ca99..f5e538c7096 100644 --- a/pkgs/applications/science/biology/xenomapper/default.nix +++ b/pkgs/applications/science/biology/xenomapper/default.nix @@ -14,7 +14,7 @@ buildPythonPackage rec { propagatedBuildInputs = [ statistics ]; meta = with lib; { - homepage = "http://github.com/genomematt/xenomapper"; + homepage = "https://github.com/genomematt/xenomapper"; description = "A utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins"; license = licenses.gpl3; platforms = platforms.all; diff --git a/pkgs/applications/science/electronics/kicad/default.nix b/pkgs/applications/science/electronics/kicad/default.nix index 47222fe4a96..0b627dbb23a 100644 --- a/pkgs/applications/science/electronics/kicad/default.nix +++ b/pkgs/applications/science/electronics/kicad/default.nix @@ -21,48 +21,7 @@ let stable = pname != "kicad-unstable"; baseName = if (stable) then "kicad" else "kicad-unstable"; - versions = { - "kicad" = { - kicadVersion = { - version = "5.1.5"; - src.sha256 = "15h3rwisjss3fdc9bam9n2wq94slhacc3fbg14bnzf4n5agsnv5b"; - }; - libVersion = { - version = "5.1.5"; - libSources = { - i18n.sha256 = "1rfpifl8vky1gba2angizlb2n7mwmsiai3r6ip6qma60wdj8sbd3"; - symbols.sha256 = "048b07ffsaav1ssrchw2p870lvb4rsyb5vnniy670k7q9p16qq6h"; - templates.sha256 = "0cs3bm3zb5ngw5ldn0lzw5bvqm4kvcidyrn76438alffwiz2b15g"; - footprints.sha256 = "1c4whgn14qhz4yqkl46w13p6rpv1k0hsc9s9h9368fxfcz9knb2j"; - packages3d.sha256 = "0cff2ms1bsw530kqb1fr1m2pjixyxzwa81mxgac3qpbcf8fnpvaz"; - }; - }; - }; - "kicad-unstable" = { - kicadVersion = { - version = "2019-12-31"; - src = { - rev = "eaaa4eb63acb289047dfbb6cc275579dea58f12b"; - sha256 = "1v2hf2slphjdh14y56pmzlpi6mqidrd8198if1fi0cch72v37zch"; - }; - }; - libVersion = { - version = "unstable"; - libSources = { - i18n.rev = "e7439fd76f27cfc26e269c4e6c4d56245345c28b"; - i18n.sha256 = "1nqm1kx5b4f7s0f9q8bg4rdhqnp0128yp6bgnrkia1kwmfnf5gmy"; - symbols.rev = "1bc5ff11c76bcbfda227e534b0acf737edddde8f"; - symbols.sha256 = "05kv93790wi4dpbn2488p587b83yz1zw9h62lkv41h7vn2r1mmb7"; - templates.rev = "0c0490897f803ab8b7c3dad438b7eb1f80e0417c"; - templates.sha256 = "0cs3bm3zb5ngw5ldn0lzw5bvqm4kvcidyrn76438alffwiz2b15g"; - footprints.rev = "454126c125edd3fa8633f301421a7d9c4de61b77"; - footprints.sha256 = "00nli4kx2i68bk852rivbirzcgpsdlpdk34g1q892952jsbh7fy6"; - packages3d.rev = "c2b92a411adc93ddeeed74b36b542e1057f81a2a"; - packages3d.sha256 = "05znc6y2lc31iafspg308cxdda94zg6c7mwslmys76npih1pb8qc"; - }; - }; - }; - }; + versions = import ./versions.nix; versionConfig = versions.${baseName}; wxGTK = if (stable) @@ -157,6 +116,13 @@ stdenv.mkDerivation rec { '' ; + # can't run this for each pname + # stable and unstable are in the same versions.nix + # and kicad-small reuses stable + # with "all" it updates both, run it manually if you don't want that + # and can't git commit if this could be running in parallel with other scripts + passthru.updateScript = [ ./update.sh "all" ]; + meta = { description = if (stable) then "Open Source Electronics Design Automation Suite" diff --git a/pkgs/applications/science/electronics/kicad/update.sh b/pkgs/applications/science/electronics/kicad/update.sh new file mode 100755 index 00000000000..b4f744c47ef --- /dev/null +++ b/pkgs/applications/science/electronics/kicad/update.sh @@ -0,0 +1,191 @@ +#!/usr/bin/env nix-shell +#!nix-shell -i bash -p coreutils git nix curl + +# this script will generate versions.nix in the right location +# this should contain the versions' revs and hashes +# the stable revs are stored only for ease of skipping + +# if you get something like "tar: no space left on device" +# you may need a bigger tmpfs, this can be set as such +# services.logind.extraConfig = "RuntimeDirectorySize=8G"; +# this is most likely only needed for the packages3d +# this can be checked without that config by manual TOFU +# copy the generated items from ,versions.nix to versions.nix +# then nix-build and see what it actually gets + +# if something goes unrepairably wrong, run 'update.sh all clean' + +# TODO +# support parallel instances for each pname +# currently risks reusing old data +# no getting around manually checking if the build product works... +# if there is, default to commiting +# remove items left in /nix/store? + +# get the latest tag that isn't an RC or *.99 +latest_tag="$(git ls-remote --tags --sort -version:refname \ + https://gitlab.com/kicad/code/kicad.git \ + | grep -o 'refs/tags/[0-9]*\.[0-9]*\.[0-9]*$' \ + | grep -v ".99" | head -n 1 | cut -d '/' -f 3)" + +all_versions=( "${latest_tag}" master ) + +prefetch="nix-prefetch-url --unpack --quiet" + +clean="" +check_stable="" +check_unstable=1 +commit="" + +for arg in "$@"; do + case "${arg}" in + help|-h|--help) echo "Read me!" >&2; exit 1; ;; + kicad|release|tag|stable|*small|5*|6*) check_stable=1; check_unstable="" ;; + all|both|full) check_stable=1; check_unstable=1 ;; + commit) commit=1 ;; + clean|fix|*fuck) check_stable=1; check_unstable=1; clean=1 ;; + master|*unstable|latest|now|today) check_unstable=1 ;; + *) ;; + esac +done + +here="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )" +now=$(date --iso-8601) + +file="${here}/versions.nix" +# just in case this runs in parallel +rand="$(head -c 3 /dev/urandom | base64)" +tmp="${here}/,versions.nix.${rand}" + +# libraries currently on github, move to $gitlab/libraries planned +libs=( symbols templates footprints packages3d ) + +get_rev="git ls-remote --heads --tags" + +gitlab="https://gitlab.com/kicad" +# append commit hash or tag +gitlab_pre="https://gitlab.com/api/v4/projects/kicad%2Fcode%2Fkicad/repository/archive.tar.gz?sha=" + +# append "-$lib/archive/[hash or tag].tar.gz +github="https://github.com/kicad/kicad" + +# not a lib, but separate and already moved to gitlab +i18n="${gitlab}/code/kicad-i18n.git" +i18n_pre="https://gitlab.com/api/v4/projects/kicad%2Fcode%2Fkicad-i18n/repository/archive.tar.gz?sha=" + +count=0 + +printf "Latest tag is\t%s\n" "${latest_tag}" >&2 + +if [[ ! -f ${file} ]]; then + echo "No existing file, generating from scratch" >&2 + check_stable=1; check_unstable=1; clean=1 +fi + +printf "Writing %s\n" "${tmp}" >&2 + +# not a dangling brace, grouping the output to redirect to file +{ + +printf "# This file was generated by update.sh\n\n" +printf "{\n" + +for version in "${all_versions[@]}"; do + + if [[ ${version} == "master" ]]; then + pname="kicad-unstable" + today="${now}" + else + pname="kicad" + today="${version}" + fi + # skip a version if we don't want to check it + if [[ (${version} != "master" && -n ${check_stable}) \ + || (${version} == "master" && -n ${check_unstable}) ]]; then + + printf "\nChecking %s\n" "${pname}" >&2 + + printf "%2s\"%s\" = {\n" "" "${pname}" + printf "%4skicadVersion = {\n" "" + printf "%6sversion =\t\t\t\"%s\";\n" "" "${today}" + printf "%6ssrc = {\n" "" + + echo "Checking src" >&2 + src_rev="$(${get_rev} "${gitlab}"/code/kicad.git "${version}" | cut -f1)" + ret="$(grep -sm 1 "\"${pname}\"" -A 4 "${file}" | grep -sm 1 "${src_rev}")" + has_hash="$(grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "sha256")" + if [[ -n ${ret} && -n ${has_hash} && -z ${clean} ]]; then + echo "Reusing old ${pname}.src.sha256, already latest .rev" >&2 + grep -sm 1 "\"${pname}\"" -A 5 "${file}" | grep -sm 1 "rev" -A 1 + else + printf "%8srev =\t\t\t\"%s\";\n" "" "${src_rev}" + printf "%8ssha256 =\t\t\"%s\";\n" \ + "" "$(${prefetch} "${gitlab_pre}${src_rev}")" + (( count++ )) + fi + printf "%6s};\n" "" + printf "%4s};\n" "" + + printf "%4slibVersion = {\n" "" + printf "%6sversion =\t\t\t\"%s\";\n" "" "${today}" + printf "%6slibSources = {\n" "" + + echo "Checking i18n" >&2 + i18n_rev="$(${get_rev} "${i18n}" "${version}" | cut -f1)" + ret="$(grep -sm 1 "\"${pname}\"" -A 11 "${file}" | grep -sm 1 "${i18n_rev}")" + has_hash="$(grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n.sha256")" + if [[ -n ${ret} && -n ${has_hash} && -z ${clean} ]]; then + echo "Reusing old kicad-i18n-${today}.src.sha256, already latest .rev" >&2 + grep -sm 1 "\"${pname}\"" -A 12 "${file}" | grep -sm 1 "i18n" -A 1 + else + printf "%8si18n.rev =\t\t\"%s\";\n" "" "${i18n_rev}" + printf "%8si18n.sha256 =\t\t\"%s\";\n" "" \ + "$(${prefetch} "${i18n_pre}${i18n_rev}")" + (( count++ )) + fi + + for lib in "${libs[@]}"; do + echo "Checking ${lib}" >&2 + url="${github}-${lib}.git" + lib_rev="$(${get_rev} "${url}" "${version}" | cut -f1)" + ret="$(grep -sm 1 "\"${pname}\"" -A 19 "${file}" | grep -sm 1 "${lib_rev}" -A 1)" + has_hash="$(grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}.sha256")" + if [[ -n ${ret} && -n ${has_hash} && -z ${clean} ]]; then + echo "Reusing old kicad-${lib}-${today}.src.sha256, already latest .rev" >&2 + grep -sm 1 "\"${pname}\"" -A 20 "${file}" | grep -sm 1 "${lib}" -A 1 + else + printf "%8s%s.rev =\t" "" "${lib}" + case "${lib}" in + symbols|templates) printf "\t" ;; *) ;; + esac + printf "\"%s\";\n" "${lib_rev}" + printf "%8s%s.sha256 =\t\"%s\";\n" "" \ + "${lib}" "$(${prefetch} "${github}-${lib}/archive/${lib_rev}.tar.gz")" + (( count++ )) + fi + done + printf "%6s};\n" "" + printf "%4s};\n" "" + printf "%2s};\n" "" + else + printf "\nReusing old %s\n" "${pname}" >&2 + grep -sm 1 "\"${pname}\"" -A 23 "${file}" + fi +done +printf "}\n" +} > "${tmp}" + +mv "${tmp}" "${file}" + +printf "\nFinished\nMoved output to %s\n\n" "${file}" >&2 + +if [[ ${count} -gt 0 ]]; then + if [[ ${count} -gt 1 ]]; then s="s"; else s=""; fi + echo "${count} revision${s} changed" >&2 + if [[ -n ${commit} ]]; then + git commit -am "$(printf "kicad: automatic update of %s item%s\n" "${count}" "${s}")" + fi + echo "Please confirm the new versions.nix works before making a PR." >&2 +else + echo "No changes, those checked are up to date" >&2 +fi diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix new file mode 100644 index 00000000000..ac273a1265c --- /dev/null +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -0,0 +1,52 @@ +# This file was generated by update.sh + +{ + "kicad" = { + kicadVersion = { + version = "5.1.5"; + src = { + rev = "52549c5d09cbfb0e807fcbcb07819bc9f7861544"; + sha256 = "15h3rwisjss3fdc9bam9n2wq94slhacc3fbg14bnzf4n5agsnv5b"; + }; + }; + libVersion = { + version = "5.1.5"; + libSources = { + i18n.rev = "5122cbec6563fb7c8d6f960a639ac470353af91b"; + i18n.sha256 = "1rfpifl8vky1gba2angizlb2n7mwmsiai3r6ip6qma60wdj8sbd3"; + symbols.rev = "dd122ec170b49e032179511c9d263126f52f4020"; + symbols.sha256 = "048b07ffsaav1ssrchw2p870lvb4rsyb5vnniy670k7q9p16qq6h"; + templates.rev = "94761f10d06582b33cd55ea2149d72f269f65580"; + templates.sha256 = "0cs3bm3zb5ngw5ldn0lzw5bvqm4kvcidyrn76438alffwiz2b15g"; + footprints.rev = "e076f8f271f8db96d5fec45616b7554caebb7ef7"; + footprints.sha256 = "1c4whgn14qhz4yqkl46w13p6rpv1k0hsc9s9h9368fxfcz9knb2j"; + packages3d.rev = "8d233cdcb109aa1c3b8ba4c934ee31f6a3b6e1f4"; + packages3d.sha256 = "0cff2ms1bsw530kqb1fr1m2pjixyxzwa81mxgac3qpbcf8fnpvaz"; + }; + }; + }; + "kicad-unstable" = { + kicadVersion = { + version = "2020-01-08"; + src = { + rev = "ca34ade00c554157f106fde97af5f08a202808ef"; + sha256 = "0xx5qkc5pi3qdrdikgq3902ws8zilv2476fb4bbgh95d9wpgr35v"; + }; + }; + libVersion = { + version = "2020-01-08"; + libSources = { + i18n.rev = "e7439fd76f27cfc26e269c4e6c4d56245345c28b"; + i18n.sha256 = "1nqm1kx5b4f7s0f9q8bg4rdhqnp0128yp6bgnrkia1kwmfnf5gmy"; + symbols.rev = "ad58768b88d564fd188c6667841adec436da53f2"; + symbols.sha256 = "1rdplf04bff0hmgjwr81fbcr9nkqi21n0n88nzs5fdp73mqiywcy"; + templates.rev = "0c0490897f803ab8b7c3dad438b7eb1f80e0417c"; + templates.sha256 = "0cs3bm3zb5ngw5ldn0lzw5bvqm4kvcidyrn76438alffwiz2b15g"; + footprints.rev = "973867de7f33f202e9fd1b3455bd1f7e7fe4a074"; + footprints.sha256 = "0yvidpnqbfxjdwaiscl5bdchsg0l4d769vp456dc8h0f3802mibi"; + packages3d.rev = "c2b92a411adc93ddeeed74b36b542e1057f81a2a"; + packages3d.sha256 = "05znc6y2lc31iafspg308cxdda94zg6c7mwslmys76npih1pb8qc"; + }; + }; + }; +} diff --git a/pkgs/applications/science/electronics/ngspice/default.nix b/pkgs/applications/science/electronics/ngspice/default.nix index 78240a40bac..f044f1d88e7 100644 --- a/pkgs/applications/science/electronics/ngspice/default.nix +++ b/pkgs/applications/science/electronics/ngspice/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { pname = "ngspice"; - version = "30"; + version = "31"; src = fetchurl { url = "mirror://sourceforge/ngspice/ngspice-${version}.tar.gz"; - sha256 = "15v0jdfy2a2zxp8dmy04fdp7w7a4vwvffcwa688r81b86wphxzh8"; + sha256 = "10n2lnfrpsv4vyrirkphr4jwjjhy7i617g6za78dwirfjq63npw4"; }; nativeBuildInputs = [ flex bison ]; diff --git a/pkgs/applications/science/electronics/pcb/default.nix b/pkgs/applications/science/electronics/pcb/default.nix index d68d4ace54b..ec47a37140f 100644 --- a/pkgs/applications/science/electronics/pcb/default.nix +++ b/pkgs/applications/science/electronics/pcb/default.nix @@ -21,11 +21,11 @@ stdenv.mkDerivation rec { pname = "pcb"; - version = "4.2.0"; + version = "4.2.1"; src = fetchurl { url = "mirror://sourceforge/pcb/${pname}-${version}.tar.gz"; - sha256 = "0hwsqmcrnk4wipbmfqx1yckmmgfn8vr37d1gh5srfy27czgkcjyd"; + sha256 = "1i9zvcj0vgwp2g2hkmvafdq0k39klj90jsdanqx9xl7gl70345cq"; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/logic/cubicle/default.nix b/pkgs/applications/science/logic/cubicle/default.nix index cd41e1ca64b..d198de41f9b 100644 --- a/pkgs/applications/science/logic/cubicle/default.nix +++ b/pkgs/applications/science/logic/cubicle/default.nix @@ -19,6 +19,6 @@ stdenv.mkDerivation rec { homepage = http://cubicle.lri.fr/; license = licenses.asl20; platforms = platforms.unix; - maintainers = with maintainers; [ lucas8 ]; + maintainers = with maintainers; [ dwarfmaster ]; }; } diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 66c41bb073a..07ec466e000 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { pname = "gmsh"; - version = "4.4.1"; + version = "4.5.1"; src = fetchurl { url = "http://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "1p7hibmsgv961lfkzdxlgcvmcb0q155m2sp60r97cjsfzhw68g45"; + sha256 = "0rjwxpz5qwq6dj7ka53mhxlgnp9bs5jphhsamlb0nk3h8kzckisq"; }; buildInputs = [ openblasCompat gmm fltk libjpeg zlib libGLU libGL diff --git a/pkgs/applications/science/math/nota/default.nix b/pkgs/applications/science/math/nota/default.nix new file mode 100644 index 00000000000..897785ef6e8 --- /dev/null +++ b/pkgs/applications/science/math/nota/default.nix @@ -0,0 +1,40 @@ +{ mkDerivation, haskellPackages, fetchurl, lib }: + +mkDerivation rec { + pname = "nota"; + version = "1.0"; + + # Can't use fetchFromGitLab since codes.kary.us doesn't support https + src = fetchurl { + url = "http://codes.kary.us/nota/nota/-/archive/V${version}/nota-V${version}.tar.bz2"; + sha256 = "0bbs6bm9p852hvqadmqs428ir7m65h2prwyma238iirv42pk04v8"; + }; + + postUnpack = '' + export sourceRoot=$sourceRoot/source + ''; + + isLibrary = false; + isExecutable = true; + + libraryHaskellDepends = with haskellPackages; [ + base + bytestring + array + split + scientific + parsec + ansi-terminal + regex-compat + containers + terminal-size + numbers + text + time + ]; + + description = "The most beautiful command line calculator"; + homepage = "https://kary.us/nota"; + license = lib.licenses.mpl20; + maintainers = with lib.maintainers; [ dtzWill ]; +} diff --git a/pkgs/applications/science/misc/rink/cargo-lock.patch b/pkgs/applications/science/misc/rink/cargo-lock.patch index 39029713430..1fb3c2f4b56 100644 --- a/pkgs/applications/science/misc/rink/cargo-lock.patch +++ b/pkgs/applications/science/misc/rink/cargo-lock.patch @@ -1,42 +1,64 @@ diff --git a/Cargo.lock b/Cargo.lock new file mode 100644 -index 0000000..c67e9ed +index 0000000..17d0ae9 --- /dev/null +++ b/Cargo.lock -@@ -0,0 +1,1719 @@ +@@ -0,0 +1,2625 @@ ++# This file is automatically @generated by Cargo. ++# It is not intended for manual editing. +[[package]] -+name = "MacTypes-sys" -+version = "2.1.0" ++name = "adler32" ++version = "1.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" -+dependencies = [ -+ "libc 0.2.48 (registry+https://github.com/rust-lang/crates.io-index)", -+] + +[[package]] +name = "aho-corasick" -+version = "0.6.9" ++version = "0.6.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +dependencies = [ -+ "memchr 2.1.3 (registry+https://github.com/rust-lang/crates.io-index)", ++ "memchr 2.2.1 (registry+https://github.com/rust-lang/crates.io-index)", +] + +[[package]] -+name = "antidote" -+version = "1.0.0" ++name = "autocfg" ++version = "0.1.7" +source = "registry+https://github.com/rust-lang/crates.io-index" + +[[package]] -+name = "autocfg" -+version = "0.1.2" ++name = "backtrace" ++version = "0.3.40" +source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "backtrace-sys 0.1.32 (registry+https://github.com/rust-lang/crates.io-index)", ++ "cfg-if 0.1.10 (registry+https://github.com/rust-lang/crates.io-index)", ++ "libc 0.2.66 (registry+https://github.com/rust-lang/crates.io-index)", ++ "rustc-demangle 0.1.16 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] ++name = "backtrace-sys" ++version = "0.1.32" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "cc 1.0.48 (registry+https://github.com/rust-lang/crates.io-index)", ++ "libc 0.2.66 (registry+https://github.com/rust-lang/crates.io-index)", ++] + +[[package]] +name = "base64" +version = "0.9.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +dependencies = [ -+ "byteorder 1.3.1 (registry+https://github.com/rust-lang/crates.io-index)", -+ "safemem 0.3.0 (registry+https://github.com/rust-lang/crates.io-index)", ++ "byteorder 1.3.2 (registry+https://github.com/rust-lang/crates.io-index)", ++ "safemem 0.3.3 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] ++name = "base64" ++version = "0.10.1" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "byteorder 1.3.2 (registry+https://github.com/rust-lang/crates.io-index)", +] + +[[package]] @@ -44,7 +66,7 @@ index 0000000..c67e9ed +version = "0.6.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +dependencies = [ -+ "byteorder 1.3.1 (registry+https://github.com/rust-lang/crates.io-index)", ++ "byteorder 1.3.2 (registry+https://github.com/rust-lang/crates.io-index)", + "num-traits 0.1.43 (registry+https://github.com/rust-lang/crates.io-index)", + "rustc-serialize 0.3.24 (registry+https://github.com/rust-lang/crates.io-index)", + "serde 0.8.23 (registry+https://github.com/rust-lang/crates.io-index)", @@ -62,7 +84,7 @@ index 0000000..c67e9ed + +[[package]] +name = "bitflags" -+version = "1.0.4" ++version = "1.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" + +[[package]] @@ -84,7 +106,7 @@ index 0000000..c67e9ed + +[[package]] +name = "byteorder" -+version = "1.3.1" ++version = "1.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" + +[[package]] @@ -93,13 +115,31 @@ index 0000000..c67e9ed +source = "registry+https://github.com/rust-lang/crates.io-index" + +[[package]] ++name = "bytes" ++version = "0.4.12" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "byteorder 1.3.2 (registry+https://github.com/rust-lang/crates.io-index)", ++ "either 1.5.3 (registry+https://github.com/rust-lang/crates.io-index)", ++ "iovec 0.1.4 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] ++name = "c2-chacha" ++version = "0.2.3" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "ppv-lite86 0.2.6 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] +name = "cc" -+version = "1.0.28" ++version = "1.0.48" +source = "registry+https://github.com/rust-lang/crates.io-index" + +[[package]] +name = "cfg-if" -+version = "0.1.6" ++version = "0.1.10" +source = "registry+https://github.com/rust-lang/crates.io-index" + +[[package]] @@ -113,12 +153,12 @@ index 0000000..c67e9ed + +[[package]] +name = "chrono" -+version = "0.4.6" ++version = "0.4.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +dependencies = [ -+ "num-integer 0.1.39 (registry+https://github.com/rust-lang/crates.io-index)", -+ "num-traits 0.2.6 (registry+https://github.com/rust-lang/crates.io-index)", -+ "serde 1.0.85 (registry+https://github.com/rust-lang/crates.io-index)", ++ "num-integer 0.1.41 (registry+https://github.com/rust-lang/crates.io-index)", ++ "num-traits 0.2.10 (registry+https://github.com/rust-lang/crates.io-index)", ++ "serde 1.0.104 (registry+https://github.com/rust-lang/crates.io-index)", + "time 0.1.42 (registry+https://github.com/rust-lang/crates.io-index)", +] + @@ -144,7 +184,7 @@ index 0000000..c67e9ed +version = "0.0.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +dependencies = [ -+ "bitflags 1.0.4 (registry+https://github.com/rust-lang/crates.io-index)", ++ "bitflags 1.2.1 (registry+https://github.com/rust-lang/crates.io-index)", +] + +[[package]] @@ -156,20 +196,100 @@ index 0000000..c67e9ed +] + +[[package]] ++name = "cookie" ++version = "0.12.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "time 0.1.42 (registry+https://github.com/rust-lang/crates.io-index)", ++ "url 1.7.2 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] ++name = "cookie_store" ++version = "0.7.0" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "cookie 0.12.0 (registry+https://github.com/rust-lang/crates.io-index)", ++ "failure 0.1.6 (registry+https://github.com/rust-lang/crates.io-index)", ++ "idna 0.1.5 (registry+https://github.com/rust-lang/crates.io-index)", ++ "log 0.4.8 (registry+https://github.com/rust-lang/crates.io-index)", ++ "publicsuffix 1.5.4 (registry+https://github.com/rust-lang/crates.io-index)", ++ "serde 1.0.104 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= "registry+https://github.com/rust-lang/crates.io-index" @@ -1294,6 +1898,14 @@ index 0000000..c67e9ed +] + +[[package]] ++name = "string" ++version = "0.2.1" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "bytes 0.4.12 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] +name = "strsim" +version = "0.5.2" +source = "registry+https://github.com/rust-lang/crates.io-index" @@ -1308,25 +1920,46 @@ index 0000000..c67e9ed +] + +[[package]] ++name = "syn" ++version = "1.0.13" ++source = "registry+https://github.com/rust-lang/crates.io-index" ++dependencies = [ ++ "proc-macro2 1.0.7 (registry+https://github.com/rust-lang/crates.io-index)", ++ "quote 1.0.2 (registry+https://github.com/rust-lang/crates.io-index)", ++ "unicode-xid 0.2.0 (registry+https://github.com/rust-lang/crates.io-index)", ++] ++ ++[[package]] ++name = "synstructure" ++version = "0.12.3" ++source = "registry+https://github.com/rust-lang/crates.io-index" 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-22,8 +22,8 @@ rustPlatform.buildRustPackage rec { meta = with stdenv.lib; { description = "Unit-aware calculator"; - homepage = http://rink.tiffnix.com; + homepage = "http://rink.tiffnix.com"; license = with licenses; [ mpl20 gpl3 ]; - maintainers = [ maintainers.sb0 ]; + maintainers = with maintainers; [ sb0 filalex77 ]; }; } |