From 8d8ce109cb72edb8abf2efd5438b4c5589400a80 Mon Sep 17 00:00:00 2001 From: Oleksii Filonenko Date: Mon, 6 Jan 2020 12:39:32 +0200 Subject: rink: 0.4.4 -> 0.4.5 --- .../science/misc/rink/cargo-lock.patch | 1400 ++++++++++++++++---- pkgs/applications/science/misc/rink/default.nix | 8 +- 2 files changed, 1157 insertions(+), 251 deletions(-) (limited to 'pkgs/applications/science') 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 = 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b/pkgs/applications/science/misc/rink/default.nix @@ -1,18 +1,18 @@ { stdenv, fetchFromGitHub, rustPlatform, openssl, pkgconfig, gmp, ncurses }: rustPlatform.buildRustPackage rec { - version = "0.4.4"; + version = "0.4.5"; pname = "rink"; src = fetchFromGitHub { owner = "tiffany352"; repo = "rink-rs"; rev = "v${version}"; - sha256 = "0rvck5ahg7s51fdlr2ch698cwnyc6qp84zhfgs3wkszj9r5j470k"; + sha256 = "0vl996y58a9b62d8sqrpfn2h8qkya7qbg5zqsmy7nxhph1vhbspj"; }; cargoPatches = [ ./cargo-lock.patch ]; - cargoSha256 = "1ijfvfhgjgzlpi1hjhy435m7vq568grh84bmkdlj3m83jxjcz874"; + cargoSha256 = "0q2g1hkqyzq9lsas4fhsbpk3jn5hikchh6i1jf9c08ca2xm136c2"; buildInputs = [ pkgconfig ]; propagatedBuildInputs = [ openssl gmp ncurses ]; @@ -22,7 +22,7 @@ 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 ]; }; -- cgit 1.4.1 From bc8dc2bd0a90c5ef0e11377caf6cc1a97485096d Mon Sep 17 00:00:00 2001 From: Oleksii Filonenko Date: Mon, 6 Jan 2020 12:41:19 +0200 Subject: rink: add filalex77 to maintainers --- pkgs/applications/science/misc/rink/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/misc/rink/default.nix b/pkgs/applications/science/misc/rink/default.nix index abdfb21ad35..dad1d245b10 100644 --- a/pkgs/applications/science/misc/rink/default.nix +++ b/pkgs/applications/science/misc/rink/default.nix @@ -24,6 +24,6 @@ rustPlatform.buildRustPackage rec { description = "Unit-aware calculator"; homepage = "http://rink.tiffnix.com"; license = with licenses; [ mpl20 gpl3 ]; - maintainers = [ maintainers.sb0 ]; + maintainers = with maintainers; [ sb0 filalex77 ]; }; } -- cgit 1.4.1 From 66156e04d55ce065ab69bd76a03eafcb01b46a8e Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 6 Jan 2020 06:33:28 -0800 Subject: gmsh: 4.4.1 -> 4.5.1 --- pkgs/applications/science/math/gmsh/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') 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 -- cgit 1.4.1 From 501f79aa9b4071502583d34d5ae4e370bf38fb23 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 6 Jan 2020 17:40:29 -0800 Subject: ngspice: 30 -> 31 --- pkgs/applications/science/electronics/ngspice/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') 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-${version}.tar.gz"; - sha256 = "15v0jdfy2a2zxp8dmy04fdp7w7a4vwvffcwa688r81b86wphxzh8"; + sha256 = "10n2lnfrpsv4vyrirkphr4jwjjhy7i617g6za78dwirfjq63npw4"; }; nativeBuildInputs = [ flex bison ]; -- cgit 1.4.1 From cc98c9fbb24e96a388ba31ea883b35263661c072 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 6 Jan 2020 19:47:54 -0800 Subject: pcb: 4.2.0 -> 4.2.1 --- pkgs/applications/science/electronics/pcb/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/electronics/pcb/default.nix b/pkgs/applications/science/electronics/pcb/default.nix index d68d4ace54b..ec47a37140f 100644 --- a/pkgs/applications/science/electronics/pcb/default.nix +++ b/pkgs/applications/science/electronics/pcb/default.nix @@ -21,11 +21,11 @@ stdenv.mkDerivation rec { pname = "pcb"; - version = "4.2.0"; + version = "4.2.1"; src = fetchurl { url = "mirror://sourceforge/pcb/${pname}-${version}.tar.gz"; - sha256 = "0hwsqmcrnk4wipbmfqx1yckmmgfn8vr37d1gh5srfy27czgkcjyd"; + sha256 = "1i9zvcj0vgwp2g2hkmvafdq0k39klj90jsdanqx9xl7gl70345cq"; }; nativeBuildInputs = [ -- cgit 1.4.1 From 2607c4b9f959adb526cda705ea99dfaaeb40fb6b Mon Sep 17 00:00:00 2001 From: Evils Date: Sat, 4 Jan 2020 11:34:52 +0100 Subject: kicad: split version.nix & add update.sh update.sh generates version.nix by default only updates kicad-unstable several options (can be combined) all, update to latest tag and master clean, generate versions.sh from scratch commit, make a git commit --- .../science/electronics/kicad/default.nix | 50 +----- .../science/electronics/kicad/update.sh | 191 +++++++++++++++++++++ .../science/electronics/kicad/versions.nix | 52 ++++++ 3 files changed, 251 insertions(+), 42 deletions(-) create mode 100755 pkgs/applications/science/electronics/kicad/update.sh create mode 100644 pkgs/applications/science/electronics/kicad/versions.nix (limited to 'pkgs/applications/science') 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"; + }; + }; + }; +} -- cgit 1.4.1 From f7a4e4a93a2a317fb76b9e09a97ea6246e477da2 Mon Sep 17 00:00:00 2001 From: Bruno Bzeznik Date: Thu, 9 Jan 2020 18:38:54 +0100 Subject: bayescan: init at 2.1 (#68191) Co-authored-by: Dmitry Kalinkin --- .../science/biology/bayescan/default.nix | 39 ++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 41 insertions(+) create mode 100644 pkgs/applications/science/biology/bayescan/default.nix (limited to 'pkgs/applications/science') 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/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6f7011fc874..5042a17c846 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -23701,6 +23701,8 @@ in stdenv = gcc49Stdenv; }; + bayescan = callPackage ../applications/science/biology/bayescan { }; + bedtools = callPackage ../applications/science/biology/bedtools { }; bcftools = callPackage ../applications/science/biology/bcftools { }; -- cgit 1.4.1 From 5961f211f3bcc28f878975489690013ee3e18be6 Mon Sep 17 00:00:00 2001 From: Jonathan Ringer Date: Fri, 10 Jan 2020 12:17:37 -0800 Subject: python.pkgs wide: fix problematic urls --- pkgs/applications/science/biology/xenomapper/default.nix | 2 +- pkgs/development/python-modules/Pygments/default.nix | 2 +- pkgs/development/python-modules/pastescript/default.nix | 2 +- pkgs/development/python-modules/pathos/default.nix | 2 +- pkgs/development/python-modules/pivy/default.nix | 2 +- pkgs/development/python-modules/pox/default.nix | 2 +- pkgs/development/python-modules/pvlib/default.nix | 2 +- pkgs/development/python-modules/pyenchant/default.nix | 2 +- pkgs/development/python-modules/pyftdi/default.nix | 2 +- pkgs/development/python-modules/pyparsing/default.nix | 2 +- pkgs/development/python-modules/pyramid_exclog/default.nix | 2 +- pkgs/development/python-modules/pysam/default.nix | 2 +- pkgs/development/python-modules/python-sql/default.nix | 4 +++- pkgs/development/python-modules/pyviz-comms/default.nix | 2 +- pkgs/development/python-modules/quantities/default.nix | 4 ++-- pkgs/development/python-modules/relatorio/default.nix | 5 ++++- pkgs/development/python-modules/robotframework/default.nix | 2 +- pkgs/development/python-modules/scikit-image/default.nix | 2 +- pkgs/development/python-modules/snakebite/default.nix | 2 +- pkgs/development/python-modules/sympy/default.nix | 2 +- pkgs/development/python-modules/threadpool/default.nix | 2 +- pkgs/development/python-modules/todoist/default.nix | 2 +- pkgs/development/python-modules/translationstring/default.nix | 2 +- pkgs/development/python-modules/wget/default.nix | 2 +- pkgs/development/python-modules/xstatic-bootstrap/default.nix | 2 +- pkgs/development/python-modules/xstatic-pygments/default.nix | 2 +- pkgs/development/python-modules/yattag/default.nix | 2 +- pkgs/development/python-modules/zope_filerepresentation/default.nix | 2 +- 28 files changed, 34 insertions(+), 29 deletions(-) (limited to 'pkgs/applications/science') 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/development/python-modules/Pygments/default.nix b/pkgs/development/python-modules/Pygments/default.nix index 38636c9e31d..ca9181fc068 100644 --- a/pkgs/development/python-modules/Pygments/default.nix +++ b/pkgs/development/python-modules/Pygments/default.nix @@ -19,7 +19,7 @@ buildPythonPackage rec { doCheck = false; meta = { - homepage = http://pygments.org/; + homepage = https://pygments.org/; description = "A generic syntax highlighter"; license = lib.licenses.bsd2; maintainers = with lib.maintainers; [ ]; diff --git a/pkgs/development/python-modules/pastescript/default.nix b/pkgs/development/python-modules/pastescript/default.nix index c7a863ea0f5..dd93bd404d0 100644 --- a/pkgs/development/python-modules/pastescript/default.nix +++ b/pkgs/development/python-modules/pastescript/default.nix @@ -24,7 +24,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "A pluggable command-line frontend, including commands to setup package file layouts"; - homepage = http://pythonpaste.org/script/; + homepage = https://github.com/cdent/pastescript/; license = licenses.mit; }; diff --git a/pkgs/development/python-modules/pathos/default.nix b/pkgs/development/python-modules/pathos/default.nix index b121176c31b..e575aa333eb 100644 --- a/pkgs/development/python-modules/pathos/default.nix +++ b/pkgs/development/python-modules/pathos/default.nix @@ -23,7 +23,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "Parallel graph management and execution in heterogeneous computing"; - homepage = http://www.cacr.caltech.edu/~mmckerns/pathos.htm; + homepage = https://github.com/uqfoundation/pathos/; license = licenses.bsd3; }; diff --git a/pkgs/development/python-modules/pivy/default.nix b/pkgs/development/python-modules/pivy/default.nix index f7ec55bba05..4206b58032f 100644 --- a/pkgs/development/python-modules/pivy/default.nix +++ b/pkgs/development/python-modules/pivy/default.nix @@ -39,7 +39,7 @@ buildPythonPackage rec { ''; meta = with stdenv.lib; { - homepage = http://pivy.coin3d.org/; + homepage = https://github.com/coin3d/pivy/; description = "A Python binding for Coin"; license = licenses.bsd0; maintainers = with maintainers; [ gebner ]; diff --git a/pkgs/development/python-modules/pox/default.nix b/pkgs/development/python-modules/pox/default.nix index 4b0e292ce78..3ae276ca28e 100644 --- a/pkgs/development/python-modules/pox/default.nix +++ b/pkgs/development/python-modules/pox/default.nix @@ -15,7 +15,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "Utilities for filesystem exploration and automated builds"; license = licenses.bsd3; - homepage = http://www.cacr.caltech.edu/~mmckerns/pox.htm; + homepage = https://github.com/uqfoundation/pox/; }; } diff --git a/pkgs/development/python-modules/pvlib/default.nix b/pkgs/development/python-modules/pvlib/default.nix index 7e561089a18..e04a2a62d49 100644 --- a/pkgs/development/python-modules/pvlib/default.nix +++ b/pkgs/development/python-modules/pvlib/default.nix @@ -26,7 +26,7 @@ buildPythonPackage rec { ''; meta = with stdenv.lib; { - homepage = http://pvlib-python.readthedocs.io; + homepage = https://pvlib-python.readthedocs.io; description = "Simulate the performance of photovoltaic energy systems"; license = licenses.bsd3; maintainers = with maintainers; [ jluttine ]; diff --git a/pkgs/development/python-modules/pyenchant/default.nix b/pkgs/development/python-modules/pyenchant/default.nix index 8c240261463..cd645a8d89b 100644 --- a/pkgs/development/python-modules/pyenchant/default.nix +++ b/pkgs/development/python-modules/pyenchant/default.nix @@ -29,7 +29,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "pyenchant: Python bindings for the Enchant spellchecker"; - homepage = https://pythonhosted.org/pyenchant/; + homepage = https://github.com/pyenchant/pyenchant; license = licenses.lgpl21; badPlatforms = [ "x86_64-darwin" ]; }; diff --git a/pkgs/development/python-modules/pyftdi/default.nix b/pkgs/development/python-modules/pyftdi/default.nix index 09cb17098dd..76c7ea9b5bc 100644 --- a/pkgs/development/python-modules/pyftdi/default.nix +++ b/pkgs/development/python-modules/pyftdi/default.nix @@ -20,7 +20,7 @@ buildPythonPackage rec { meta = { description = "User-space driver for modern FTDI devices"; - homepage = "http://github.com/eblot/pyftdi"; + homepage = "https://github.com/eblot/pyftdi"; license = lib.licenses.lgpl2; }; } diff --git a/pkgs/development/python-modules/pyparsing/default.nix b/pkgs/development/python-modules/pyparsing/default.nix index a47c271b76f..f1f43a5f495 100644 --- a/pkgs/development/python-modules/pyparsing/default.nix +++ b/pkgs/development/python-modules/pyparsing/default.nix @@ -12,7 +12,7 @@ buildPythonPackage rec { doCheck = false; meta = with stdenv.lib; { - homepage = http://pyparsing.wikispaces.com/; + homepage = https://pyparsing.wikispaces.com/; description = "An alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions"; license = licenses.mit; }; diff --git a/pkgs/development/python-modules/pyramid_exclog/default.nix b/pkgs/development/python-modules/pyramid_exclog/default.nix index 152b12a935a..912fb06c11b 100644 --- a/pkgs/development/python-modules/pyramid_exclog/default.nix +++ b/pkgs/development/python-modules/pyramid_exclog/default.nix @@ -17,7 +17,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "A package which logs to a Python logger when an exception is raised by a Pyramid application"; - homepage = http://docs.pylonsproject.org/; + homepage = https://docs.pylonsproject.org/; license = licenses.bsd0; maintainers = with maintainers; [ domenkozar ]; }; diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix index e5cc2cf9da0..46dd54c62e2 100644 --- a/pkgs/development/python-modules/pysam/default.nix +++ b/pkgs/development/python-modules/pysam/default.nix @@ -39,7 +39,7 @@ buildPythonPackage rec { ''; meta = { - homepage = http://pysam.readthedocs.io/; + homepage = https://pysam.readthedocs.io/; description = "A python module for reading, manipulating and writing genome data sets"; maintainers = with lib.maintainers; [ unode ]; license = lib.licenses.mit; diff --git a/pkgs/development/python-modules/python-sql/default.nix b/pkgs/development/python-modules/python-sql/default.nix index 451138fa38d..54cb815bf3d 100644 --- a/pkgs/development/python-modules/python-sql/default.nix +++ b/pkgs/development/python-modules/python-sql/default.nix @@ -3,12 +3,14 @@ buildPythonPackage rec { pname = "python-sql"; version = "1.0.0"; + src = fetchPypi { inherit pname version; sha256 = "05ni936y0ia9xmryl7mlhbj9i80nnvq1bi4zxhb96rv7yvpb3fqb"; }; + meta = { - homepage = http://python-sql.tryton.org/; + homepage = https://python-sql.tryton.org/; description = "A library to write SQL queries in a pythonic way"; maintainers = with lib.maintainers; [ johbo ]; license = lib.licenses.bsd3; diff --git a/pkgs/development/python-modules/pyviz-comms/default.nix b/pkgs/development/python-modules/pyviz-comms/default.nix index 422e2896082..f83ee05bc26 100644 --- a/pkgs/development/python-modules/pyviz-comms/default.nix +++ b/pkgs/development/python-modules/pyviz-comms/default.nix @@ -20,7 +20,7 @@ buildPythonPackage rec { meta = with lib; { description = "Launch jobs, organize the output, and dissect the results"; - homepage = http://pyviz.org/; + homepage = https://pyviz.org/; license = licenses.bsd3; maintainers = [ maintainers.costrouc ]; }; diff --git a/pkgs/development/python-modules/quantities/default.nix b/pkgs/development/python-modules/quantities/default.nix index bc778984493..83cce4ad4ba 100644 --- a/pkgs/development/python-modules/quantities/default.nix +++ b/pkgs/development/python-modules/quantities/default.nix @@ -22,7 +22,7 @@ buildPythonPackage rec { meta = { description = "Quantities is designed to handle arithmetic and"; - homepage = http://python-quantities.readthedocs.io/; + homepage = https://python-quantities.readthedocs.io/; license = lib.licenses.bsd2; }; -} \ No newline at end of file +} diff --git a/pkgs/development/python-modules/relatorio/default.nix b/pkgs/development/python-modules/relatorio/default.nix index 13a41d14f02..ce9a4888eb9 100644 --- a/pkgs/development/python-modules/relatorio/default.nix +++ b/pkgs/development/python-modules/relatorio/default.nix @@ -3,17 +3,20 @@ buildPythonPackage rec { pname = "relatorio"; version = "0.9.0"; + src = fetchPypi { inherit pname version; sha256 = "0q93sl7ppfvjxylgq9m5n4xdgv4af7d69yxd84zszq10vjmpsg6k"; }; + propagatedBuildInputs = [ genshi lxml python_magic ]; + meta = { - homepage = http://relatorio.tryton.org/; + homepage = https://relatorio.tryton.org/; description = "A templating library able to output odt and pdf files"; maintainers = with lib.maintainers; [ johbo ]; license = lib.licenses.gpl3; diff --git a/pkgs/development/python-modules/robotframework/default.nix b/pkgs/development/python-modules/robotframework/default.nix index 09d98c91203..bd96da28964 100644 --- a/pkgs/development/python-modules/robotframework/default.nix +++ b/pkgs/development/python-modules/robotframework/default.nix @@ -12,7 +12,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "Generic test automation framework"; - homepage = http://robotframework.org/; + homepage = https://robotframework.org/; license = licenses.asl20; maintainers = with maintainers; [ bjornfor ]; }; diff --git a/pkgs/development/python-modules/scikit-image/default.nix b/pkgs/development/python-modules/scikit-image/default.nix index ced53a13490..fa6ced432f7 100644 --- a/pkgs/development/python-modules/scikit-image/default.nix +++ b/pkgs/development/python-modules/scikit-image/default.nix @@ -35,7 +35,7 @@ buildPythonPackage rec { meta = { description = "Image processing routines for SciPy"; - homepage = http://scikit-image.org; + homepage = https://scikit-image.org; license = lib.licenses.bsd3; }; } diff --git a/pkgs/development/python-modules/snakebite/default.nix b/pkgs/development/python-modules/snakebite/default.nix index 1d08570d727..09945a094c7 100644 --- a/pkgs/development/python-modules/snakebite/default.nix +++ b/pkgs/development/python-modules/snakebite/default.nix @@ -34,7 +34,7 @@ buildPythonPackage rec { meta = with lib; { description = "Pure Python HDFS client"; - homepage = http://github.com/spotify/snakebite; + homepage = https://github.com/spotify/snakebite; license = licenses.asl20; maintainers = [ maintainers.costrouc ]; }; diff --git a/pkgs/development/python-modules/sympy/default.nix b/pkgs/development/python-modules/sympy/default.nix index 87ef13bba0f..2128be1a3c0 100644 --- a/pkgs/development/python-modules/sympy/default.nix +++ b/pkgs/development/python-modules/sympy/default.nix @@ -28,7 +28,7 @@ buildPythonPackage rec { meta = { description = "A Python library for symbolic mathematics"; - homepage = http://www.sympy.org/; + homepage = https://www.sympy.org/; license = lib.licenses.bsd3; maintainers = with lib.maintainers; [ lovek323 timokau ]; }; diff --git a/pkgs/development/python-modules/threadpool/default.nix b/pkgs/development/python-modules/threadpool/default.nix index b3d7f58c66d..a604302add1 100644 --- a/pkgs/development/python-modules/threadpool/default.nix +++ b/pkgs/development/python-modules/threadpool/default.nix @@ -13,7 +13,7 @@ buildPythonPackage rec { }; meta = with stdenv.lib; { - homepage = http://chrisarndt.de/projects/threadpool/; + homepage = https://chrisarndt.de/projects/threadpool/; description = "Easy to use object-oriented thread pool framework"; license = licenses.mit; }; diff --git a/pkgs/development/python-modules/todoist/default.nix b/pkgs/development/python-modules/todoist/default.nix index 08ea37f4ba1..6ad6a62861d 100644 --- a/pkgs/development/python-modules/todoist/default.nix +++ b/pkgs/development/python-modules/todoist/default.nix @@ -14,7 +14,7 @@ buildPythonPackage rec { meta = { description = "The official Todoist Python API library"; - homepage = http://todoist-python.readthedocs.io/en/latest/; + homepage = https://todoist-python.readthedocs.io/en/latest/; license = stdenv.lib.licenses.mit; maintainers = with stdenv.lib.maintainers; [ the-kenny ]; }; diff --git a/pkgs/development/python-modules/translationstring/default.nix b/pkgs/development/python-modules/translationstring/default.nix index 91ac8f06256..53f88188083 100644 --- a/pkgs/development/python-modules/translationstring/default.nix +++ b/pkgs/development/python-modules/translationstring/default.nix @@ -13,7 +13,7 @@ buildPythonPackage rec { }; meta = with stdenv.lib; { - homepage = http://pylonsproject.org/; + homepage = https://pylonsproject.org/; description = "Utility library for i18n relied on by various Repoze and Pyramid packages"; license = licenses.bsd0; maintainers = with maintainers; [ domenkozar ]; diff --git a/pkgs/development/python-modules/wget/default.nix b/pkgs/development/python-modules/wget/default.nix index 502c7f64b86..2ffd747d04d 100644 --- a/pkgs/development/python-modules/wget/default.nix +++ b/pkgs/development/python-modules/wget/default.nix @@ -15,7 +15,7 @@ buildPythonPackage rec { meta = { description = "Pure python download utility"; - homepage = http://bitbucket.org/techtonik/python-wget/; + homepage = https://bitbucket.org/techtonik/python-wget/; license = with lib.licenses; [ unlicense ]; maintainers = with lib.maintainers; [ prusnak ]; }; diff --git a/pkgs/development/python-modules/xstatic-bootstrap/default.nix b/pkgs/development/python-modules/xstatic-bootstrap/default.nix index a1e2c1a4e7b..9abc9b273a2 100644 --- a/pkgs/development/python-modules/xstatic-bootstrap/default.nix +++ b/pkgs/development/python-modules/xstatic-bootstrap/default.nix @@ -16,7 +16,7 @@ buildPythonPackage rec { doCheck = false; meta = with lib;{ - homepage = http://getbootstrap.com; + homepage = https://getbootstrap.com; description = "Bootstrap packaged static files for python"; license = licenses.mit; maintainers = with maintainers; [ makefu ]; diff --git a/pkgs/development/python-modules/xstatic-pygments/default.nix b/pkgs/development/python-modules/xstatic-pygments/default.nix index 956d331e7b8..919d262c50d 100644 --- a/pkgs/development/python-modules/xstatic-pygments/default.nix +++ b/pkgs/development/python-modules/xstatic-pygments/default.nix @@ -16,7 +16,7 @@ buildPythonPackage rec { doCheck = false; meta = with lib;{ - homepage = http://pygments.org; + homepage = https://pygments.org; description = "pygments packaged static files for python"; license = licenses.mit; maintainers = with maintainers; [ makefu ]; diff --git a/pkgs/development/python-modules/yattag/default.nix b/pkgs/development/python-modules/yattag/default.nix index 30518a19399..8f97a374df6 100644 --- a/pkgs/development/python-modules/yattag/default.nix +++ b/pkgs/development/python-modules/yattag/default.nix @@ -12,6 +12,6 @@ buildPythonPackage rec { meta = with lib; { description = "Generate HTML or XML in a pythonic way. Pure python alternative to web template engines. Can fill HTML forms with default values and error messages."; license = [ licenses.lgpl21 ]; - homepage = http://www.yattag.org/; + homepage = https://www.yattag.org/; }; } diff --git a/pkgs/development/python-modules/zope_filerepresentation/default.nix b/pkgs/development/python-modules/zope_filerepresentation/default.nix index 36d664efd1a..e9104a1b939 100644 --- a/pkgs/development/python-modules/zope_filerepresentation/default.nix +++ b/pkgs/development/python-modules/zope_filerepresentation/default.nix @@ -16,7 +16,7 @@ buildPythonPackage rec { propagatedBuildInputs = [ zope_schema ]; meta = with stdenv.lib; { - homepage = http://zopefilerepresentation.readthedocs.io/; + homepage = https://zopefilerepresentation.readthedocs.io/; description = "File-system Representation Interfaces"; license = licenses.zpl20; maintainers = with maintainers; [ goibhniu ]; -- cgit 1.4.1 From 0956fcab16e5f993c0468a84373546c3a9334f08 Mon Sep 17 00:00:00 2001 From: Sébastien Maret Date: Tue, 7 Jan 2020 14:43:36 +0100 Subject: gildas: 20191201_a -> 20200101_a --- .../science/astronomy/gildas/default.nix | 22 ++++++++++++---------- .../science/astronomy/gildas/imager-py3.patch | 12 ++++++++++++ 2 files changed, 24 insertions(+), 10 deletions(-) create mode 100644 pkgs/applications/science/astronomy/gildas/imager-py3.patch (limited to 'pkgs/applications/science') 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: $out/share/doc/" >> kernel/etc/gag.dico.lcl diff --git a/pkgs/applications/science/astronomy/gildas/imager-py3.patch b/pkgs/applications/science/astronomy/gildas/imager-py3.patch new file mode 100644 index 00000000000..71a129164ba --- /dev/null +++ b/pkgs/applications/science/astronomy/gildas/imager-py3.patch @@ -0,0 +1,12 @@ +diff -ruN gildas-src-jan20a.orig/contrib/imager/pro/define.ima gildas-src-jan20a/contrib/imager/pro/define.ima +--- gildas-src-jan20a.orig/contrib/imager/pro/define.ima 2020-01-01 02:15:16.000000000 +0100 ++++ gildas-src-jan20a/contrib/imager/pro/define.ima 2020-01-14 11:18:46.000000000 +0100 +@@ -9,7 +9,7 @@ + ! + ! Patch for a Bug on Mac-OS/X where Python blocks if activated first + ! from a script launched by a widget. +-python print "Starting Python" ++python print("Starting Python") + ! + ! INPUT, GO and UVT_CONVERT always defined by GreG + define command GO "@ p_go.ima" gag_pro:go_greg.hlp -- cgit 1.4.1 From afe905246d890edf4026a565de3ca340a601de2a Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Tue, 14 Jan 2020 15:54:19 -0600 Subject: nota: init at 1.0 Fixes #77590. --- pkgs/applications/science/math/nota/default.nix | 40 +++++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 3 +- 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 pkgs/applications/science/math/nota/default.nix (limited to 'pkgs/applications/science') diff --git a/pkgs/applications/science/math/nota/default.nix b/pkgs/applications/science/math/nota/default.nix new file mode 100644 index 00000000000..897785ef6e8 --- /dev/null +++ b/pkgs/applications/science/math/nota/default.nix @@ -0,0 +1,40 @@ +{ mkDerivation, haskellPackages, fetchurl, lib }: + +mkDerivation rec { + pname = "nota"; + version = "1.0"; + + # Can't use fetchFromGitLab since codes.kary.us doesn't support https + src = fetchurl { + url = "http://codes.kary.us/nota/nota/-/archive/V${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/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index d84f18969f0..fe85cc25f4f 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -23915,6 +23915,8 @@ in nasc = callPackage ../applications/science/math/nasc { }; + nota = haskellPackages.callPackage ../applications/science/math/nota { }; + openblas = callPackage ../development/libraries/science/math/openblas { }; # A version of OpenBLAS using 32-bit integers on all platforms for compatibility with @@ -25799,5 +25801,4 @@ in sentencepiece = callPackage ../development/libraries/sentencepiece {}; kcli = callPackage ../development/tools/kcli {}; - } -- cgit 1.4.1 From 4de137a77d9bec92d23f36d60990e70bc101732c Mon Sep 17 00:00:00 2001 From: Jonathan Ringer Date: Mon, 13 Jan 2020 17:52:33 -0800 Subject: samtools: 1.9 -> 1.10 --- pkgs/applications/science/biology/samtools/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') 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 ]; -- cgit 1.4.1 From 227a3f438300a20c88e2017109ffb3d1ac0f7a58 Mon Sep 17 00:00:00 2001 From: DwarfMaster Date: Tue, 21 Jan 2020 16:39:52 +1000 Subject: Renamed maintainer lucas8 -> dwarfmaster --- maintainers/maintainer-list.nix | 12 ++++++------ pkgs/applications/graphics/imlibsetroot/default.nix | 2 +- pkgs/applications/science/logic/cubicle/default.nix | 2 +- pkgs/tools/text/fanficfare/default.nix | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) (limited to 'pkgs/applications/science') diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index dc032e5edcd..844ed91360d 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -1919,6 +1919,12 @@ fingerprint = "5DD7 C6F6 0630 F08E DAE7 4711 1525 585D 1B43 C62A"; }]; }; + dwarfmaster = { + email = "nixpkgs@dwarfmaster.net"; + github = "dwarfmaster"; + githubId = 2025623; + name = "Luc Chabassier"; + }; dxf = { email = "dingxiangfei2009@gmail.com"; github = "dingxiangfei2009"; @@ -4169,12 +4175,6 @@ github = "ltavard"; name = "Laure Tavard"; }; - lucas8 = { - email = "luc.linux@mailoo.org"; - github = "lucas8"; - githubId = 2025623; - name = "Luc Chabassier"; - }; lucus16 = { email = "lars.jellema@gmail.com"; github = "Lucus16"; diff --git a/pkgs/applications/graphics/imlibsetroot/default.nix b/pkgs/applications/graphics/imlibsetroot/default.nix index 49868bbd831..8ca4d71bb56 100644 --- a/pkgs/applications/graphics/imlibsetroot/default.nix +++ b/pkgs/applications/graphics/imlibsetroot/default.nix @@ -24,6 +24,6 @@ stdenv.mkDerivation { homepage = http://robotmonkeys.net/2010/03/30/imlibsetroot/; license = licenses.gpl2; platforms = platforms.linux; - maintainers = with maintainers; [ lucas8 ]; + maintainers = with maintainers; [ dwarfmaster ]; }; } 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/tools/text/fanficfare/default.nix b/pkgs/tools/text/fanficfare/default.nix index b01317a532f..31952cb1b1b 100644 --- a/pkgs/tools/text/fanficfare/default.nix +++ b/pkgs/tools/text/fanficfare/default.nix @@ -23,7 +23,7 @@ python3Packages.buildPythonApplication rec { homepage = https://github.com/JimmXinu/FanFicFare; license = licenses.gpl3; platforms = platforms.linux; - maintainers = with maintainers; [ lucas8 ]; + maintainers = with maintainers; [ dwarfmaster ]; inherit version; }; } -- cgit 1.4.1 From fff7a7a8620c195cfbac227e33d1c1263ba38dee Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Wed, 22 Jan 2020 10:12:28 +0000 Subject: picard-tools: 2.21.3 -> 2.21.6 --- pkgs/applications/science/biology/picard-tools/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'pkgs/applications/science') 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 ]; -- cgit 1.4.1 From 7f142260d38e586fe1e182a650fa32e199a96370 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 16 Dec 2019 16:31:09 +1100 Subject: manta: init 1.6.0 --- .../applications/science/biology/manta/default.nix | 35 ++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 37 insertions(+) create mode 100644 pkgs/applications/science/biology/manta/default.nix (limited to 'pkgs/applications/science') 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/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 59492df5236..fed4a37a88f 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -23907,6 +23907,8 @@ in niftyseg = callPackage ../applications/science/biology/niftyseg { }; + manta = callPackage ../applications/science/biology/manta { }; + octopus-caller = callPackage ../applications/science/biology/octopus { }; paml = callPackage ../applications/science/biology/paml { }; -- cgit 1.4.1