diff options
Diffstat (limited to 'pkgs/applications/science')
214 files changed, 492 insertions, 300 deletions
diff --git a/pkgs/applications/science/astronomy/astrolog/default.nix b/pkgs/applications/science/astronomy/astrolog/default.nix index 743a58e9e053..7ad05e35e24e 100644 --- a/pkgs/applications/science/astronomy/astrolog/default.nix +++ b/pkgs/applications/science/astronomy/astrolog/default.nix @@ -58,6 +58,7 @@ stdenv.mkDerivation rec { maintainers = [ maintainers.kmein ]; homepage = "https://astrolog.org/astrolog.htm"; description = "Freeware astrology program"; + mainProgram = "astrolog"; platforms = platforms.linux; license = licenses.gpl2Plus; }; diff --git a/pkgs/applications/science/astronomy/celestia/default.nix b/pkgs/applications/science/astronomy/celestia/default.nix index d9130223e836..8b40196fdbff 100644 --- a/pkgs/applications/science/astronomy/celestia/default.nix +++ b/pkgs/applications/science/astronomy/celestia/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://celestia.space/"; description = "Real-time 3D simulation of space"; + mainProgram = "celestia"; changelog = "https://github.com/CelestiaProject/Celestia/releases/tag/${version}"; license = licenses.gpl2Plus; maintainers = with maintainers; [ hjones2199 ]; diff --git a/pkgs/applications/science/astronomy/gpredict/default.nix b/pkgs/applications/science/astronomy/gpredict/default.nix index 1fd2d4ac2adc..56c5a92460dd 100644 --- a/pkgs/applications/science/astronomy/gpredict/default.nix +++ b/pkgs/applications/science/astronomy/gpredict/default.nix @@ -29,6 +29,7 @@ in stdenv.mkDerivation { meta = with lib; { description = "Real time satellite tracking and orbit prediction"; + mainProgram = "gpredict"; longDescription = '' Gpredict is a real time satellite tracking and orbit prediction program written using the GTK widgets. Gpredict is targetted mainly towards ham radio diff --git a/pkgs/applications/science/astronomy/gravit/default.nix b/pkgs/applications/science/astronomy/gravit/default.nix index a957bfc988bc..36f58d8d18a1 100644 --- a/pkgs/applications/science/astronomy/gravit/default.nix +++ b/pkgs/applications/science/astronomy/gravit/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { broken = (stdenv.isLinux && stdenv.isAarch64); homepage = "https://github.com/gak/gravit"; description = "Beautiful OpenGL-based gravity simulator"; + mainProgram = "gravit"; license = lib.licenses.gpl2Plus; longDescription = '' diff --git a/pkgs/applications/science/astronomy/kstars/default.nix b/pkgs/applications/science/astronomy/kstars/default.nix index 14c684d432c4..ab141666c0aa 100644 --- a/pkgs/applications/science/astronomy/kstars/default.nix +++ b/pkgs/applications/science/astronomy/kstars/default.nix @@ -40,6 +40,7 @@ mkDerivation rec { meta = with lib; { description = "Virtual planetarium astronomy software"; + mainProgram = "kstars"; homepage = "https://kde.org/applications/education/org.kde.kstars"; longDescription = '' It provides an accurate graphical simulation of the night sky, from any location on Earth, at any date and time. diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index cad727c75fd6..59472c4b25ce 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -95,6 +95,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { description = "Free open-source planetarium"; + mainProgram = "stellarium"; homepage = "https://stellarium.org/"; license = lib.licenses.gpl2Plus; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/astronomy/xearth/default.nix b/pkgs/applications/science/astronomy/xearth/default.nix index 7fcc588658ae..6123f277fd12 100644 --- a/pkgs/applications/science/astronomy/xearth/default.nix +++ b/pkgs/applications/science/astronomy/xearth/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "sets the X root window to an image of the Earth"; + mainProgram = "xearth"; homepage = "https://xearth.org"; longDescription = '' Xearth sets the X root window to an image of the Earth, as seen from your favorite vantage point in space, diff --git a/pkgs/applications/science/astronomy/xplanet/default.nix b/pkgs/applications/science/astronomy/xplanet/default.nix index 94aa92a1b713..677bc0cdf077 100644 --- a/pkgs/applications/science/astronomy/xplanet/default.nix +++ b/pkgs/applications/science/astronomy/xplanet/default.nix @@ -30,6 +30,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Renders an image of the earth or other planets into the X root window"; + mainProgram = "xplanet"; homepage = "https://xplanet.sourceforge.net"; license = licenses.gpl2; maintainers = with maintainers; [ lassulus sander ]; diff --git a/pkgs/applications/science/biology/aragorn/default.nix b/pkgs/applications/science/biology/aragorn/default.nix index 4ee8501e8e13..3ec62ada04c9 100644 --- a/pkgs/applications/science/biology/aragorn/default.nix +++ b/pkgs/applications/science/biology/aragorn/default.nix @@ -44,6 +44,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences"; + mainProgram = "aragorn"; homepage = "http://www.ansikte.se/ARAGORN/"; license = licenses.gpl3Plus; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/astral/default.nix b/pkgs/applications/science/biology/astral/default.nix index 6a9513c6b817..34077949b97d 100644 --- a/pkgs/applications/science/biology/astral/default.nix +++ b/pkgs/applications/science/biology/astral/default.nix @@ -2,59 +2,78 @@ , stdenvNoCC , fetchFromGitHub , jdk8 -, makeWrapper , jre8 +, strip-nondeterminism +, makeWrapper , zip }: + let jdk = jdk8; jre = jre8; in -stdenvNoCC.mkDerivation rec { +stdenvNoCC.mkDerivation (finalAttrs: { pname = "astral"; version = "5.7.1"; src = fetchFromGitHub { owner = "smirarab"; repo = "ASTRAL"; - rev = "v${version}"; - sha256 = "043w2z6gbrisqirdid022f4b8jps1pp5syi344krv2bis1gjq5sn"; + rev = "v${finalAttrs.version}"; + hash = "sha256-VhcsX9BxiZ0nISN6Xe4N+kq0iBMCtNhyxDrm9cwXfBA="; }; - nativeBuildInputs = [ jdk makeWrapper jre zip ]; + patches = [ + # we can't use stripJavaArchivesHook here, because the build process puts a .jar file into a zip file + # this patch calls strip-nondeterminism manually + ./make-deterministic.patch + ]; + + nativeBuildInputs = [ + jdk + zip + strip-nondeterminism + makeWrapper + ]; buildPhase = '' + runHook preBuild patchShebangs ./make.sh ./make.sh + runHook postBuild ''; doCheck = true; checkPhase = '' runHook preCheck - java -jar astral.${version}.jar -i main/test_data/song_primates.424.gene.tre + java -jar astral.${finalAttrs.version}.jar -i main/test_data/song_primates.424.gene.tre runHook postCheck ''; installPhase = '' - mkdir -p $out/share/lib - mkdir -p $out/bin - mv astral.${version}.jar $out/share/ - mv lib/*.jar $out/share/lib - mv Astral.${version}.zip $out/share/ - cp -a main/test_data $out/share/ + runHook preInstall + + install -Dm644 astral.${finalAttrs.version}.jar -t $out/share + install -Dm644 lib/*.jar -t $out/share/lib + install -Dm644 Astral.${finalAttrs.version}.zip -t $out/share + cp -a main/test_data $out/share + makeWrapper ${jre}/bin/java $out/bin/astral \ - --add-flags "-jar $out/share/astral.${version}.jar" + --add-flags "-jar $out/share/astral.${finalAttrs.version}.jar" + + runHook postInstall ''; meta = with lib; { homepage = "https://github.com/smirarab/ASTRAL"; description = "Tool for estimating an unrooted species tree given a set of unrooted gene trees"; + mainProgram = "astral"; sourceProvenance = with sourceTypes; [ fromSource - binaryBytecode # source bundles dependencies as jars + binaryBytecode # source bundles dependencies as jars ]; license = licenses.asl20; - maintainers = with maintainers; [ bzizou ]; + maintainers = with maintainers; [ bzizou tomasajt ]; }; -} +}) diff --git a/pkgs/applications/science/biology/astral/make-deterministic.patch b/pkgs/applications/science/biology/astral/make-deterministic.patch new file mode 100644 index 000000000000..940182e2f49f --- /dev/null +++ b/pkgs/applications/science/biology/astral/make-deterministic.patch @@ -0,0 +1,21 @@ +diff --git a/make.sh b/make.sh +index 3ff6529..937b1a2 100644 +--- a/make.sh ++++ b/make.sh +@@ -17,6 +17,8 @@ jar cvfm ../astral.$version.jar ../manifest.text phylonet/util/BitSet.* phylonet + + cd .. + ++strip-nondeterminism --type jar astral.$version.jar ++ + chmod +x astral.$version.jar + sed -e "s/__astral.jar__/astral.$version.jar/g" -e "s/__astral.zip__/Astral.$version.zip/g" README.template.md > README.md + sed -e "s/__astral.jar__/astral.$version.jar/g" -e "s/__astral.zip__/Astral.$version.zip/g" astral-tutorial-template.md > astral-tutorial.md +@@ -32,6 +34,7 @@ ln -s ../astral-tutorial.pdf . + cd .. + rm -f Astral.$version.zip + zip -r Astral.$version.zip Astral ++strip-nondeterminism --type zip Astral.$version.zip + + set +x + echo " diff --git a/pkgs/applications/science/biology/bamtools/default.nix b/pkgs/applications/science/biology/bamtools/default.nix index 05373dafd381..602254e2966a 100644 --- a/pkgs/applications/science/biology/bamtools/default.nix +++ b/pkgs/applications/science/biology/bamtools/default.nix @@ -32,6 +32,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "C++ API & command-line toolkit for working with BAM data"; + mainProgram = "bamtools"; homepage = "https://github.com/pezmaster31/bamtools"; changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${finalAttrs.src.rev}"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/bioawk/default.nix b/pkgs/applications/science/biology/bioawk/default.nix index cfbb1a551fac..f7da30fc4f72 100644 --- a/pkgs/applications/science/biology/bioawk/default.nix +++ b/pkgs/applications/science/biology/bioawk/default.nix @@ -42,6 +42,7 @@ stdenv.mkDerivation { meta = with lib; { description = "BWK awk modified for biological data"; + mainProgram = "bioawk"; homepage = "https://github.com/lh3/bioawk"; license = licenses.hpnd; maintainers = with maintainers; [ natsukium ]; diff --git a/pkgs/applications/science/biology/bwa-mem2/default.nix b/pkgs/applications/science/biology/bwa-mem2/default.nix index b34b6dc8c90f..c339baf446d2 100644 --- a/pkgs/applications/science/biology/bwa-mem2/default.nix +++ b/pkgs/applications/science/biology/bwa-mem2/default.nix @@ -46,6 +46,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome"; + mainProgram = "bwa-mem2"; license = licenses.mit; homepage = "https://github.com/bwa-mem2/bwa-mem2/"; changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md"; diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index 4786f25beb50..8c883e2617bf 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation { meta = with lib; { description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; + mainProgram = "bwa"; license = licenses.gpl3Plus; homepage = "https://bio-bwa.sourceforge.net/"; maintainers = with maintainers; [ luispedro ]; diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index a131c6645499..d7d23dd2d46e 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Computational Morphometry Toolkit"; + mainProgram = "cmtk"; longDescription = ''A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O''; diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix index fe1c1f5511d1..d9092b9eeb11 100644 --- a/pkgs/applications/science/biology/conglomerate/default.nix +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -32,6 +32,6 @@ stdenv.mkDerivation rec { description = "More command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; - license = licenses.free; + license = licenses.hpndUc; }; } diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index 605ecaadf648..a7f30dbc075d 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -57,6 +57,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "DICOM to NIfTI converter"; + mainProgram = "dcm2niix"; longDescription = '' dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. ''; diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix index a7a1f77dfe90..2abd0825e6e3 100644 --- a/pkgs/applications/science/biology/deeptools/default.nix +++ b/pkgs/applications/science/biology/deeptools/default.nix @@ -5,14 +5,14 @@ python3.pkgs.buildPythonApplication rec { pname = "deeptools"; - version = "3.5.4"; + version = "3.5.5"; pyproject = true; src = fetchFromGitHub { owner = "deeptools"; repo = "deepTools"; - rev = version; - hash = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; + rev = "refs/tags/${version}"; + hash = "sha256-2kSlL7Y5f/FjVtStnmz+GlTw2oymrtxOCaXlqgbQ7FU="; }; nativeBuildInputs = with python3.pkgs; [ diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix index b483b3d57bef..34ea942b4f5c 100644 --- a/pkgs/applications/science/biology/delly/default.nix +++ b/pkgs/applications/science/biology/delly/default.nix @@ -54,6 +54,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Structural variant caller for mapped DNA sequenced data"; + mainProgram = "delly"; license = licenses.bsd3; maintainers = with maintainers; [ scalavision ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index 3349c0392d08..f3afff0f5eb7 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Accelerated BLAST compatible local sequence aligner"; + mainProgram = "diamond"; longDescription = '' DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: - Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 006b46db9974..6c7157a91764 100644 --- a/pkgs/applications/science/biology/dssp/default.nix +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -51,6 +51,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein"; + mainProgram = "mkdssp"; homepage = "https://github.com/PDB-REDO/dssp"; changelog = "https://github.com/PDB-REDO/libcifpp/releases/tag/${finalAttrs.src.rev}"; license = licenses.bsd2; diff --git a/pkgs/applications/science/biology/est-sfs/default.nix b/pkgs/applications/science/biology/est-sfs/default.nix index fe4a3e49930c..c306cfd71c39 100644 --- a/pkgs/applications/science/biology/est-sfs/default.nix +++ b/pkgs/applications/science/biology/est-sfs/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://sourceforge.net/projects/est-usfs"; description = "Estimate the unfolded site frequency spectrum and ancestral states"; + mainProgram = "est-sfs"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/fastp/default.nix b/pkgs/applications/science/biology/fastp/default.nix index e7fc0d4a35f1..0495da0e3c3d 100644 --- a/pkgs/applications/science/biology/fastp/default.nix +++ b/pkgs/applications/science/biology/fastp/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Ultra-fast all-in-one FASTQ preprocessor"; + mainProgram = "fastp"; license = licenses.mit; homepage = "https://github.com/OpenGene/fastp"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/febio-studio/default.nix b/pkgs/applications/science/biology/febio-studio/default.nix index 550d221c74eb..708bd0f4305a 100644 --- a/pkgs/applications/science/biology/febio-studio/default.nix +++ b/pkgs/applications/science/biology/febio-studio/default.nix @@ -53,6 +53,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "FEBio Suite Solver"; + mainProgram = "FEBioStudio"; license = with licenses; [ mit ]; homepage = "https://febio.org/"; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/flywheel-cli/default.nix b/pkgs/applications/science/biology/flywheel-cli/default.nix index 254a3c011d27..51600d31c513 100644 --- a/pkgs/applications/science/biology/flywheel-cli/default.nix +++ b/pkgs/applications/science/biology/flywheel-cli/default.nix @@ -41,6 +41,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Library and command line interface for interacting with a Flywheel site"; + mainProgram = "fw"; homepage = "https://gitlab.com/flywheel-io/public/python-cli"; sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.mit; diff --git a/pkgs/applications/science/biology/genmap/default.nix b/pkgs/applications/science/biology/genmap/default.nix index c6f9cf1fb193..235135cb6050 100644 --- a/pkgs/applications/science/biology/genmap/default.nix +++ b/pkgs/applications/science/biology/genmap/default.nix @@ -32,6 +32,7 @@ stdenv.mkDerivation rec { meta = { description = "Ultra-fast computation of genome mappability"; + mainProgram = "genmap"; license = lib.licenses.bsd3; homepage = "https://github.com/cpockrandt/genmap"; maintainers = with lib.maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/iqtree/default.nix b/pkgs/applications/science/biology/iqtree/default.nix index 37a8a58a92e1..17b2ba9f9bde 100644 --- a/pkgs/applications/science/biology/iqtree/default.nix +++ b/pkgs/applications/science/biology/iqtree/default.nix @@ -33,6 +33,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "http://www.iqtree.org/"; description = "Efficient and versatile phylogenomic software by maximum likelihood"; + mainProgram = "iqtree2"; license = licenses.lgpl2; maintainers = with maintainers; [ bzizou ]; platforms = [ "x86_64-linux" "x86_64-darwin" ]; diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix index 843f0df57924..366b4add2ed7 100644 --- a/pkgs/applications/science/biology/itsx/default.nix +++ b/pkgs/applications/science/biology/itsx/default.nix @@ -26,6 +26,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing"; + mainProgram = "ITSx"; homepage = "https://microbiology.se/software/itsx/"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 3ed6a885aa75..15694ae3e638 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -31,6 +31,7 @@ appimageTools.wrapType2 { meta = with lib; { description = "The next-generation genome browser"; + mainProgram = "jbrowse-desktop"; homepage = "https://jbrowse.org/jb2/"; license = licenses.asl20; maintainers = with maintainers; [ benwbooth ]; diff --git a/pkgs/applications/science/biology/kalign/default.nix b/pkgs/applications/science/biology/kalign/default.nix index 3ca83978d969..f26b679f799d 100644 --- a/pkgs/applications/science/biology/kalign/default.nix +++ b/pkgs/applications/science/biology/kalign/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { description = "A fast multiple sequence alignment program"; + mainProgram = "kalign"; homepage = "https://github.com/TimoLassmann/kalign"; changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${finalAttrs.src.rev}"; license = lib.licenses.gpl3Plus; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index a193fa59238f..55c555e387de 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -22,6 +22,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Program for quantifying abundances of transcripts from RNA-Seq data"; + mainProgram = "kallisto"; homepage = "https://pachterlab.github.io/kallisto"; license = licenses.bsd2; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/macs2/default.nix b/pkgs/applications/science/biology/macs2/default.nix index 8884d41d9064..73f12af6a605 100644 --- a/pkgs/applications/science/biology/macs2/default.nix +++ b/pkgs/applications/science/biology/macs2/default.nix @@ -46,6 +46,7 @@ python3.pkgs.buildPythonPackage rec { meta = with lib; { description = "Model-based Analysis for ChIP-Seq"; + mainProgram = "macs2"; homepage = "https://github.com/macs3-project/MACS/"; changelog = "https://github.com/macs3-project/MACS/releases/tag/v${version}"; license = licenses.bsd3; diff --git a/pkgs/applications/science/biology/macse/default.nix b/pkgs/applications/science/biology/macse/default.nix index 2ac09ca21ab6..06937f7e645e 100644 --- a/pkgs/applications/science/biology/macse/default.nix +++ b/pkgs/applications/science/biology/macse/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Multiple alignment of coding sequences"; + mainProgram = "macse"; homepage = "https://bioweb.supagro.inra.fr/macse/"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl2; diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix index e9acd1c88b66..f2e3ead2e913 100644 --- a/pkgs/applications/science/biology/mafft/default.nix +++ b/pkgs/applications/science/biology/mafft/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "mafft"; - version = "7.520"; + version = "7.525"; src = fetchFromGitLab { owner = "sysimm"; repo = pname; rev = "v${version}"; - sha256 = "sha256-H+EcKahJWwidAx+IUT4uCZEty+S8hUeMSB8VbTu5SmQ="; + sha256 = "sha256-ckBmvFssYAmYcBHAEftjQqBV0MB0theGfemaPx3XUws="; }; preBuild = '' diff --git a/pkgs/applications/science/biology/minia/default.nix b/pkgs/applications/science/biology/minia/default.nix index 023a05d7504f..3665639a2cd9 100644 --- a/pkgs/applications/science/biology/minia/default.nix +++ b/pkgs/applications/science/biology/minia/default.nix @@ -25,8 +25,9 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Short read genome assembler"; + mainProgram = "minia"; homepage = "https://github.com/GATB/minia"; - license = licenses.agpl3; + license = licenses.agpl3Plus; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 35c1b076d7eb..eeb31dee0538 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "minimap2"; - version = "2.26"; + version = "2.27"; src = fetchFromGitHub { repo = pname; owner = "lh3"; rev = "v${version}"; - sha256 = "sha256-vK8Z/j6Ndu1vMFYPPzViP4evtIhyVVFwsfTqNCYnXpQ="; + sha256 = "sha256-F6IJrYD2dk+5bKKVIahLiNnD/Hd/CjNQQd9zz0Gkans="; }; buildInputs = [ zlib ]; @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; + mainProgram = "minimap2"; homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/mmseqs2/default.nix b/pkgs/applications/science/biology/mmseqs2/default.nix index 3e39fcb2918b..18acee7a5f14 100644 --- a/pkgs/applications/science/biology/mmseqs2/default.nix +++ b/pkgs/applications/science/biology/mmseqs2/default.nix @@ -42,6 +42,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Ultra fast and sensitive sequence search and clustering suite"; + mainProgram = "mmseqs"; homepage = "https://mmseqs.com/"; license = licenses.gpl3; maintainers = with maintainers; [ natsukium ]; diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index e4c2bbe65652..54f5b9bbb370 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -13,6 +13,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Bayesian Inference of Phylogeny"; + mainProgram = "mb"; longDescription = '' Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix index 366d0278227d..cdcf6c7b50aa 100644 --- a/pkgs/applications/science/biology/muscle/default.nix +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Multiple sequence alignment with top benchmark scores scalable to thousands of sequences"; + mainProgram = "muscle"; license = licenses.gpl3Plus; homepage = "https://www.drive5.com/muscle/"; maintainers = with maintainers; [ unode thyol ]; diff --git a/pkgs/applications/science/biology/obitools/obitools3.nix b/pkgs/applications/science/biology/obitools/obitools3.nix index 9bf579a80c3b..f415c9c39141 100644 --- a/pkgs/applications/science/biology/obitools/obitools3.nix +++ b/pkgs/applications/science/biology/obitools/obitools3.nix @@ -27,6 +27,7 @@ python3Packages.buildPythonApplication rec { meta = with lib ; { description = "Management of analyses and data in DNA metabarcoding"; + mainProgram = "obi"; homepage = "https://git.metabarcoding.org/obitools/obitools3"; license = licenses.cecill20; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix index 0090ca82d6c3..c594108c6f47 100644 --- a/pkgs/applications/science/biology/octopus/default.nix +++ b/pkgs/applications/science/biology/octopus/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Bayesian haplotype-based mutation calling"; + mainProgram = "octopus"; license = licenses.mit; homepage = "https://github.com/luntergroup/octopus"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix index 00fd0ff0083e..0e65bed4cf3e 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -33,6 +33,7 @@ stdenv.mkDerivation rec { meta = { broken = (stdenv.isLinux && stdenv.isAarch64); description = "A comprehensive update to the PLINK association analysis toolset"; + mainProgram = "plink"; homepage = "https://www.cog-genomics.org/plink2"; license = lib.licenses.gpl3; platforms = lib.platforms.linux; diff --git a/pkgs/applications/science/biology/prodigal/default.nix b/pkgs/applications/science/biology/prodigal/default.nix index 28a21522c6b8..cd83a723f91e 100644 --- a/pkgs/applications/science/biology/prodigal/default.nix +++ b/pkgs/applications/science/biology/prodigal/default.nix @@ -18,6 +18,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Fast, reliable protein-coding gene prediction for prokaryotic genomes"; + mainProgram = "prodigal"; homepage = "https://github.com/hyattpd/Prodigal"; license = licenses.gpl3; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/repseek/default.nix b/pkgs/applications/science/biology/repseek/default.nix index 5966c83b7a5f..e5e0193f7911 100644 --- a/pkgs/applications/science/biology/repseek/default.nix +++ b/pkgs/applications/science/biology/repseek/default.nix @@ -19,6 +19,7 @@ stdenv.mkDerivation rec { meta = { description = "Tool to retrieve approximate repeats from large DNA sequences"; + mainProgram = "repseek"; homepage = "https://bioinfo.mnhn.fr/abi/public/RepSeek"; maintainers = [ lib.maintainers.bzizou ]; license = lib.licenses.lgpl21; diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix index e1722a7086d8..b6635f02aacd 100644 --- a/pkgs/applications/science/biology/sambamba/default.nix +++ b/pkgs/applications/science/biology/sambamba/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "SAM/BAM processing tool"; + mainProgram = "sambamba"; homepage = "https://lomereiter.github.io/sambamba/"; maintainers = with maintainers; [ jbedo ]; license = with licenses; gpl2; diff --git a/pkgs/applications/science/biology/samblaster/default.nix b/pkgs/applications/science/biology/samblaster/default.nix index 4315dd2767e1..f16d0e42d8ef 100644 --- a/pkgs/applications/science/biology/samblaster/default.nix +++ b/pkgs/applications/science/biology/samblaster/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files"; + mainProgram = "samblaster"; maintainers = with maintainers; [ jbedo ]; license = licenses.mit; homepage = "https://github.com/GregoryFaust/samblaster"; diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix index 2472e4976cad..edb3a9a9da5b 100644 --- a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix +++ b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; + mainProgram = "samtools"; license = licenses.mit; homepage = "https://samtools.sourceforge.net/"; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/seaview/default.nix b/pkgs/applications/science/biology/seaview/default.nix index 640d2f5ae416..06549748018d 100644 --- a/pkgs/applications/science/biology/seaview/default.nix +++ b/pkgs/applications/science/biology/seaview/default.nix @@ -16,6 +16,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "GUI for molecular phylogeny"; + mainProgram = "seaview"; longDescription = '' SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. - SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. diff --git a/pkgs/applications/science/biology/seqtk/default.nix b/pkgs/applications/science/biology/seqtk/default.nix index 90bd4bb3c65e..417bec9c062f 100644 --- a/pkgs/applications/science/biology/seqtk/default.nix +++ b/pkgs/applications/science/biology/seqtk/default.nix @@ -31,6 +31,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Toolkit for processing sequences in FASTA/Q formats"; + mainProgram = "seqtk"; license = licenses.mit; homepage = "https://github.com/lh3/seqtk"; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix index 034409cfb013..553725fb4566 100644 --- a/pkgs/applications/science/biology/somatic-sniper/default.nix +++ b/pkgs/applications/science/biology/somatic-sniper/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Identify single nucleotide positions that are different between tumor and normal"; + mainProgram = "bam-somaticsniper"; license = licenses.mit; homepage = "https://github.com/genome/somatic-sniper"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix index bfd6d20f1384..d47aae9ce665 100644 --- a/pkgs/applications/science/biology/sortmerna/default.nix +++ b/pkgs/applications/science/biology/sortmerna/default.nix @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data"; + mainProgram = "sortmerna"; license = licenses.lgpl3; platforms = platforms.x86_64; homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/"; diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix index d36c4b668ec3..fec5a5a3b92d 100644 --- a/pkgs/applications/science/biology/svaba/default.nix +++ b/pkgs/applications/science/biology/svaba/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation rec { meta = with lib; { broken = (stdenv.isLinux && stdenv.isAarch64); description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly"; + mainProgram = "svaba"; license = licenses.gpl3; homepage = "https://github.com/walaj/svaba"; maintainers = with maintainers; [ scalavision ]; diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix index a046aee1c6c3..879f9b95d846 100644 --- a/pkgs/applications/science/biology/tebreak/default.nix +++ b/pkgs/applications/science/biology/tebreak/default.nix @@ -40,6 +40,7 @@ python3.pkgs.buildPythonApplication rec { meta = with lib; { description = "Find and characterise transposable element insertions"; + mainProgram = "tebreak"; homepage = "https://github.com/adamewing/tebreak"; license = licenses.mit; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/trimmomatic/default.nix b/pkgs/applications/science/biology/trimmomatic/default.nix index 53cff76badce..db19278eaa47 100644 --- a/pkgs/applications/science/biology/trimmomatic/default.nix +++ b/pkgs/applications/science/biology/trimmomatic/default.nix @@ -5,7 +5,7 @@ , jdk , jre , makeWrapper -, canonicalize-jars-hook +, stripJavaArchivesHook }: stdenv.mkDerivation (finalAttrs: { @@ -29,7 +29,7 @@ stdenv.mkDerivation (finalAttrs: { ant jdk makeWrapper - canonicalize-jars-hook + stripJavaArchivesHook ]; buildPhase = '' diff --git a/pkgs/applications/science/biology/veryfasttree/default.nix b/pkgs/applications/science/biology/veryfasttree/default.nix index 63597a75d494..6c054fecd742 100644 --- a/pkgs/applications/science/biology/veryfasttree/default.nix +++ b/pkgs/applications/science/biology/veryfasttree/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { description = "Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies"; + mainProgram = "VeryFastTree"; homepage = "https://github.com/citiususc/veryfasttree"; license = lib.licenses.gpl3Plus; maintainers = with lib.maintainers; [ thyol ]; diff --git a/pkgs/applications/science/chemistry/apbs/default.nix b/pkgs/applications/science/chemistry/apbs/default.nix index 228c77ee5c0e..ec8f8e7ffbf6 100644 --- a/pkgs/applications/science/chemistry/apbs/default.nix +++ b/pkgs/applications/science/chemistry/apbs/default.nix @@ -104,6 +104,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Software for biomolecular electrostatics and solvation calculations"; + mainProgram = "apbs"; homepage = "https://www.poissonboltzmann.org/"; changelog = "https://github.com/Electrostatics/apbs/releases/tag/v${finalAttrs.version}"; license = licenses.bsd3; diff --git a/pkgs/applications/science/chemistry/avogadro2/default.nix b/pkgs/applications/science/chemistry/avogadro2/default.nix index 7b8d69681f46..7ee42c1a793c 100644 --- a/pkgs/applications/science/chemistry/avogadro2/default.nix +++ b/pkgs/applications/science/chemistry/avogadro2/default.nix @@ -41,6 +41,7 @@ in stdenv.mkDerivation rec { meta = with lib; { description = "Molecule editor and visualizer"; + mainProgram = "avogadro2"; maintainers = with maintainers; [ sheepforce ]; homepage = "https://github.com/OpenChemistry/avogadroapp"; platforms = platforms.mesaPlatforms; diff --git a/pkgs/applications/science/chemistry/d-seams/default.nix b/pkgs/applications/science/chemistry/d-seams/default.nix index 260b1e24a082..5b5d8cfbd9d4 100644 --- a/pkgs/applications/science/chemistry/d-seams/default.nix +++ b/pkgs/applications/science/chemistry/d-seams/default.nix @@ -25,6 +25,7 @@ clangStdenv.mkDerivation rec { meta = with lib; { description = "d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations"; + mainProgram = "yodaStruct"; longDescription = '' d-SEAMS, is a free and open-source postprocessing engine for the analysis of molecular dynamics trajectories, which is specifically able to diff --git a/pkgs/applications/science/chemistry/element/default.nix b/pkgs/applications/science/chemistry/element/default.nix index c18fc9a563b9..c3c4a0fe582e 100644 --- a/pkgs/applications/science/chemistry/element/default.nix +++ b/pkgs/applications/science/chemistry/element/default.nix @@ -15,6 +15,7 @@ buildGoModule rec { meta = with lib; { description = "The periodic table on the command line"; + mainProgram = "element"; homepage = "https://github.com/gennaro-tedesco/element"; license = licenses.asl20; maintainers = [ maintainers.j0hax ]; diff --git a/pkgs/applications/science/chemistry/ergoscf/default.nix b/pkgs/applications/science/chemistry/ergoscf/default.nix index 5343f102b249..3ee33cf19b74 100644 --- a/pkgs/applications/science/chemistry/ergoscf/default.nix +++ b/pkgs/applications/science/chemistry/ergoscf/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Quantum chemistry program for large-scale self-consistent field calculations"; + mainProgram = "ergo"; homepage = "http://www.ergoscf.org"; license = licenses.gpl3Plus; maintainers = [ maintainers.markuskowa ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index 0af60d240f69..ee3ab5f1f3a5 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -53,6 +53,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A Java 3D viewer for chemical structures"; + mainProgram = "jmol"; homepage = "https://sourceforge.net/projects/jmol"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.lgpl2; diff --git a/pkgs/applications/science/chemistry/nwchem/default.nix b/pkgs/applications/science/chemistry/nwchem/default.nix index a7d9462a7fbd..61266a9f0285 100644 --- a/pkgs/applications/science/chemistry/nwchem/default.nix +++ b/pkgs/applications/science/chemistry/nwchem/default.nix @@ -208,6 +208,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Open Source High-Performance Computational Chemistry"; + mainProgram = "nwchem"; platforms = [ "x86_64-linux" ]; maintainers = with maintainers; [ sheepforce markuskowa ]; homepage = "https://nwchemgit.github.io"; diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index 553e82eed8fb..0e4728dd65d6 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -71,6 +71,7 @@ python3Packages.buildPythonApplication rec { meta = with lib; { inherit description; + mainProgram = "pymol"; homepage = "https://www.pymol.org/"; license = licenses.mit; maintainers = with maintainers; [ samlich ]; diff --git a/pkgs/applications/science/chemistry/siesta/default.nix b/pkgs/applications/science/chemistry/siesta/default.nix index c0e0e874cbd6..02586dea2e29 100644 --- a/pkgs/applications/science/chemistry/siesta/default.nix +++ b/pkgs/applications/science/chemistry/siesta/default.nix @@ -64,6 +64,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A first-principles materials simulation code using DFT"; + mainProgram = "siesta"; longDescription = '' SIESTA is both a method and its computer program implementation, to perform efficient electronic structure diff --git a/pkgs/applications/science/chemistry/wxmacmolplt/default.nix b/pkgs/applications/science/chemistry/wxmacmolplt/default.nix index e2a4fdf0cb18..ae6c0df87905 100644 --- a/pkgs/applications/science/chemistry/wxmacmolplt/default.nix +++ b/pkgs/applications/science/chemistry/wxmacmolplt/default.nix @@ -35,6 +35,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Graphical user interface for GAMESS-US"; + mainProgram = "wxmacmolplt"; homepage = "https://brettbode.github.io/wxmacmolplt/"; license = licenses.gpl2Plus; platforms = platforms.linux; diff --git a/pkgs/applications/science/electronics/appcsxcad/default.nix b/pkgs/applications/science/electronics/appcsxcad/default.nix index 2e882aff361d..c401e150f35e 100644 --- a/pkgs/applications/science/electronics/appcsxcad/default.nix +++ b/pkgs/applications/science/electronics/appcsxcad/default.nix @@ -46,6 +46,7 @@ mkDerivation { meta = with lib; { description = "Minimal Application using the QCSXCAD library"; + mainProgram = "AppCSXCAD"; homepage = "https://github.com/thliebig/AppCSXCAD"; license = licenses.gpl3; maintainers = with maintainers; [ matthuszagh ]; diff --git a/pkgs/applications/science/electronics/archimedes/default.nix b/pkgs/applications/science/electronics/archimedes/default.nix index 631f44e80633..9d9498df00da 100644 --- a/pkgs/applications/science/electronics/archimedes/default.nix +++ b/pkgs/applications/science/electronics/archimedes/default.nix @@ -21,6 +21,7 @@ stdenv.mkDerivation rec { meta = { description = "GNU package for semiconductor device simulations"; + mainProgram = "archimedes"; homepage = "https://www.gnu.org/software/archimedes"; license = lib.licenses.gpl2Plus; platforms = with lib.platforms; linux; diff --git a/pkgs/applications/science/electronics/caneda/default.nix b/pkgs/applications/science/electronics/caneda/default.nix index 1adac4832a13..4a4cf61c7f65 100644 --- a/pkgs/applications/science/electronics/caneda/default.nix +++ b/pkgs/applications/science/electronics/caneda/default.nix @@ -16,6 +16,7 @@ mkDerivation rec { meta = { description = "Open source EDA software focused on easy of use and portability"; + mainProgram = "caneda"; homepage = "http://caneda.org"; license = lib.licenses.gpl2Plus; maintainers = with lib.maintainers; [viric]; diff --git a/pkgs/applications/science/electronics/dataexplorer/default.nix b/pkgs/applications/science/electronics/dataexplorer/default.nix index 8fd9dcc5eaa8..aa471d2bfcaf 100644 --- a/pkgs/applications/science/electronics/dataexplorer/default.nix +++ b/pkgs/applications/science/electronics/dataexplorer/default.nix @@ -8,11 +8,11 @@ stdenv.mkDerivation rec { pname = "dataexplorer"; - version = "3.8.3"; + version = "3.8.5"; src = fetchurl { url = "mirror://savannah/dataexplorer/dataexplorer-${version}-src.tar.gz"; - sha256 = "sha256-vU9klb6Mweg8yxnClsIdelG4uW92if64SJ7UHumYYbs="; + sha256 = "sha256-b68xIZNbzHdPyZwLngcnjcoBtI6AeTdrblz/qx/HbGQ="; }; nativeBuildInputs = [ ant makeWrapper ]; diff --git a/pkgs/applications/science/electronics/degate/default.nix b/pkgs/applications/science/electronics/degate/default.nix index 2aa20aec6503..30ded5d1354f 100644 --- a/pkgs/applications/science/electronics/degate/default.nix +++ b/pkgs/applications/science/electronics/degate/default.nix @@ -67,6 +67,7 @@ in stdenv.mkDerivation rec { meta = with lib; { description = "A modern and open-source cross-platform software for chips reverse engineering"; + mainProgram = "Degate"; homepage = "https://degate.readthedocs.io/"; license = licenses.gpl3; platforms = platforms.unix; diff --git a/pkgs/applications/science/electronics/digital/default.nix b/pkgs/applications/science/electronics/digital/default.nix index ed90b03dbc3e..41deecbb6224 100644 --- a/pkgs/applications/science/electronics/digital/default.nix +++ b/pkgs/applications/science/electronics/digital/default.nix @@ -60,6 +60,7 @@ maven.buildMavenPackage rec { meta = with lib; { homepage = "https://github.com/hneemann/Digital"; description = pkgDescription; + mainProgram = "digital"; license = licenses.gpl3Only; platforms = [ "x86_64-linux" "x86_64-darwin" ]; maintainers = with maintainers; [ Dettorer ]; diff --git a/pkgs/applications/science/electronics/diylc/default.nix b/pkgs/applications/science/electronics/diylc/default.nix index 8530e6927fe9..ced8c72d2155 100644 --- a/pkgs/applications/science/electronics/diylc/default.nix +++ b/pkgs/applications/science/electronics/diylc/default.nix @@ -67,6 +67,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Multi platform circuit layout and schematic drawing tool"; + mainProgram = "diylc"; homepage = "https://bancika.github.io/diy-layout-creator/"; changelog = "https://github.com/bancika/diy-layout-creator/releases"; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/electronics/dsview/default.nix b/pkgs/applications/science/electronics/dsview/default.nix index ec53e976aec5..3c8e7ad19064 100644 --- a/pkgs/applications/science/electronics/dsview/default.nix +++ b/pkgs/applications/science/electronics/dsview/default.nix @@ -30,6 +30,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc"; + mainProgram = "DSView"; homepage = "https://www.dreamsourcelab.com/"; license = licenses.gpl3Plus; platforms = platforms.unix; diff --git a/pkgs/applications/science/electronics/dwfv/default.nix b/pkgs/applications/science/electronics/dwfv/default.nix index ed340271f262..2d88e2647dfd 100644 --- a/pkgs/applications/science/electronics/dwfv/default.nix +++ b/pkgs/applications/science/electronics/dwfv/default.nix @@ -13,6 +13,7 @@ rustPlatform.buildRustPackage rec { meta = with lib; { description = "A simple digital waveform viewer with vi-like key bindings"; + mainProgram = "dwfv"; homepage = "https://github.com/psurply/dwfv"; license = licenses.mit; maintainers = with maintainers; [ newam ]; diff --git a/pkgs/applications/science/electronics/fped/default.nix b/pkgs/applications/science/electronics/fped/default.nix index 138d45c787cd..6d10426b298a 100644 --- a/pkgs/applications/science/electronics/fped/default.nix +++ b/pkgs/applications/science/electronics/fped/default.nix @@ -41,6 +41,7 @@ stdenv.mkDerivation { meta = { description = "An editor that allows the interactive creation of footprints electronic components"; + mainProgram = "fped"; homepage = "http://projects.qi-hardware.com/index.php/p/fped/"; license = licenses.gpl2; maintainers = with maintainers; [ expipiplus1 ]; diff --git a/pkgs/applications/science/electronics/gaw/default.nix b/pkgs/applications/science/electronics/gaw/default.nix index a54602de13f3..5dec368f454c 100644 --- a/pkgs/applications/science/electronics/gaw/default.nix +++ b/pkgs/applications/science/electronics/gaw/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Gtk Analog Wave viewer"; + mainProgram = "gaw"; longDescription = '' Gaw is a software tool for displaying analog waveforms from sampled datas, for example from the output of simulators or diff --git a/pkgs/applications/science/electronics/gerbv/default.nix b/pkgs/applications/science/electronics/gerbv/default.nix index 652a96617cbc..5f178e08280a 100644 --- a/pkgs/applications/science/electronics/gerbv/default.nix +++ b/pkgs/applications/science/electronics/gerbv/default.nix @@ -46,6 +46,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A Gerber (RS-274X) viewer"; + mainProgram = "gerbv"; homepage = "https://gerbv.github.io/"; changelog = "https://github.com/gerbv/gerbv/releases/tag/v${version}"; license = licenses.gpl2Plus; diff --git a/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix b/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix index 6bdc197269cc..4c3692266a5c 100644 --- a/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix +++ b/pkgs/applications/science/electronics/hal-hardware-analyzer/default.nix @@ -144,6 +144,7 @@ in stdenv.mkDerivation rec { meta = with lib; { description = "A comprehensive reverse engineering and manipulation framework for gate-level netlists"; + mainProgram = "hal"; homepage = "https://github.com/emsec/hal"; license = licenses.mit; platforms = platforms.unix; diff --git a/pkgs/applications/science/electronics/hyp2mat/default.nix b/pkgs/applications/science/electronics/hyp2mat/default.nix index 799af4c43086..71da4a259d54 100644 --- a/pkgs/applications/science/electronics/hyp2mat/default.nix +++ b/pkgs/applications/science/electronics/hyp2mat/default.nix @@ -45,6 +45,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Import Hyperlynx Boardsim files to openEMS, an open source 3D full-wave electromagnetic field solver"; + mainProgram = "hyp2mat"; homepage = "https://github.com/koendv/hyp2mat"; license = licenses.gpl3Plus; maintainers = with maintainers; [ matthuszagh ]; diff --git a/pkgs/applications/science/electronics/kicad/base.nix b/pkgs/applications/science/electronics/kicad/base.nix index bff63f3b2d7e..d884a60c984f 100644 --- a/pkgs/applications/science/electronics/kicad/base.nix +++ b/pkgs/applications/science/electronics/kicad/base.nix @@ -21,6 +21,10 @@ , libpthreadstubs , libXdmcp , unixODBC +, libgit2 +, libsecret +, libgcrypt +, libgpg-error , util-linux , libselinux @@ -92,12 +96,11 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-DKICAD_USE_EGL=ON" "-DOCC_INCLUDE_DIR=${opencascade-occt}/include/opencascade" + # https://gitlab.com/kicad/code/kicad/-/issues/17133 + "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;qa_spice'" ] - ++ optionals (stable) [ - # https://gitlab.com/kicad/code/kicad/-/issues/12491 - # should be resolved in the next major? release - "-DCMAKE_CTEST_ARGUMENTS='--exclude-regex;qa_eeschema'" - ] + ++ optional (stdenv.hostPlatform.system == "aarch64-linux") + "-DCMAKE_CTEST_ARGUMENTS=--exclude-regex;'qa_spice|qa_cli'" ++ optional (stable && !withNgspice) "-DKICAD_SPICE=OFF" ++ optionals (!withScripting) [ "-DKICAD_SCRIPTING_WXPYTHON=OFF" @@ -126,6 +129,10 @@ stdenv.mkDerivation rec { doxygen graphviz pkg-config + libgit2 + libsecret + libgcrypt + libgpg-error ] # wanted by configuration on linux, doesn't seem to affect performance # no effect on closure size @@ -180,13 +187,14 @@ stdenv.mkDerivation rec { doInstallCheck = !(debug); installCheckTarget = "test"; - pythonForTests = python.withPackages(ps: with ps; [ - numpy - pytest - cairosvg - pytest-image-diff - ]); - nativeInstallCheckInputs = optional (!stable) pythonForTests; + nativeInstallCheckInputs = [ + (python.withPackages(ps: with ps; [ + numpy + pytest + cairosvg + pytest-image-diff + ])) + ]; dontStrip = debug; @@ -196,7 +204,7 @@ stdenv.mkDerivation rec { Just the build products, the libraries are passed via an env var in the wrapper, default.nix ''; homepage = "https://www.kicad.org/"; - license = lib.licenses.agpl3; + license = lib.licenses.agpl3Plus; platforms = lib.platforms.all; }; } diff --git a/pkgs/applications/science/electronics/kicad/default.nix b/pkgs/applications/science/electronics/kicad/default.nix index fa0c7ae7a75e..99670eee8a46 100644 --- a/pkgs/applications/science/electronics/kicad/default.nix +++ b/pkgs/applications/science/electronics/kicad/default.nix @@ -205,9 +205,9 @@ stdenv.mkDerivation rec { "--prefix GIO_EXTRA_MODULES : ${dconf}/lib/gio/modules" # required to open a bug report link in firefox-wayland "--set-default MOZ_DBUS_REMOTE 1" - "--set-default KICAD7_FOOTPRINT_DIR ${footprints}/share/kicad/footprints" - "--set-default KICAD7_SYMBOL_DIR ${symbols}/share/kicad/symbols" - "--set-default KICAD7_TEMPLATE_DIR ${template_dir}" + "--set-default KICAD8_FOOTPRINT_DIR ${footprints}/share/kicad/footprints" + "--set-default KICAD8_SYMBOL_DIR ${symbols}/share/kicad/symbols" + "--set-default KICAD8_TEMPLATE_DIR ${template_dir}" ] ++ optionals (addons != [ ]) ( let stockDataPath = symlinkJoin { @@ -218,11 +218,11 @@ stdenv.mkDerivation rec { ]; }; in - [ "--set-default NIX_KICAD7_STOCK_DATA_PATH ${stockDataPath}" ] + [ "--set-default NIX_KICAD8_STOCK_DATA_PATH ${stockDataPath}" ] ) ++ optionals (with3d) [ - "--set-default KICAD7_3DMODEL_DIR ${packages3d}/share/kicad/3dmodels" + "--set-default KICAD8_3DMODEL_DIR ${packages3d}/share/kicad/3dmodels" ] ++ optionals (withNgspice) [ "--prefix LD_LIBRARY_PATH : ${libngspice}/lib" ] diff --git a/pkgs/applications/science/electronics/kicad/runtime_stock_data_path.patch b/pkgs/applications/science/electronics/kicad/runtime_stock_data_path.patch index 16f7e493c623..43e99a531cf5 100644 --- a/pkgs/applications/science/electronics/kicad/runtime_stock_data_path.patch +++ b/pkgs/applications/science/electronics/kicad/runtime_stock_data_path.patch @@ -6,7 +6,7 @@ index a74cdd9..790cc58 100644 { wxString path; -+ if( wxGetEnv( wxT( "NIX_KICAD7_STOCK_DATA_PATH" ), &path ) ) { ++ if( wxGetEnv( wxT( "NIX_KICAD8_STOCK_DATA_PATH" ), &path ) ) { + return path; + } + diff --git a/pkgs/applications/science/electronics/kicad/versions.nix b/pkgs/applications/science/electronics/kicad/versions.nix index 11837638e1ab..36114fff73a3 100644 --- a/pkgs/applications/science/electronics/kicad/versions.nix +++ b/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,67 +3,67 @@ { "kicad" = { kicadVersion = { - version = "7.0.10"; + version = "8.0.1"; src = { - rev = "7daac78752749fc919e932be6156914aa83c926f"; - sha256 = "0z459yi0s02mwdgbr3xxw43gn9yjhvfkjnsxmns5mksgzsr5nmhh"; + rev = "20421d65e5a7ede894345d337ab47b469f5ba154"; + sha256 = "096kvmm96ccxir1rspgzzjkp6y2j80l3w2vphg9iv3drxmjp7qjv"; }; }; libVersion = { - version = "7.0.10"; + version = "8.0.1"; libSources = { - symbols.rev = "eedf6c9ddac2816023e817d4dc91032f9d7390b9"; - symbols.sha256 = "0nlgmxf9z1vf4g350dfkxql1dawgmw275wqxkgszsfxmhdfpmi9v"; - templates.rev = "9ce98cc45f3778e05c404edebf0f98de5c247ffe"; - templates.sha256 = "0mykfwwik7472i4r0isc5szj3dnmvd0538p0vlmzh4rcgj3pj3vm"; - footprints.rev = "7061fc9847ecc1b838e60dc6826db534028494f6"; - footprints.sha256 = "1az6fzh1lma71mj12bc4bblnmzjayrxhkb8w9rjvlhvvgv33cdmy"; - packages3d.rev = "d7345b34daaa23acf0d4506ed937fb424b5b18cd"; - packages3d.sha256 = "0xzyi4mgyifwc6dppdzh6jq294mkj0a71cwkqw2ymz1kfbksw626"; + symbols.rev = "d6aff3948edfca2bacf36900ff080f6b3f65fe4c"; + symbols.sha256 = "00xnvikmqd1zkg9p1f89kvryvkybl5f20baij6babqyc29nbzkwy"; + templates.rev = "0a6c4f798a68a5c639d54b4d3093460ab9267816"; + templates.sha256 = "0m9bggz3cm27kqpjjwxy19mqzk0c69bywcjkqcni7kafr21c6k4z"; + footprints.rev = "226b4f3d5c10a4126d88b895188bdab629fe60b0"; + footprints.sha256 = "1bb3mb2a7vkridgmqqm9ib3hv2m4zx1i14mglb11sribypy0ma5p"; + packages3d.rev = "49c1cd4017499b8a7f6dedbe7ede834d1713eb28"; + packages3d.sha256 = "0b5jwr5bbd0kzb75nj3028knjrv0872dk54sbsnxaz669q8zaxap"; }; }; }; "kicad-testing" = { kicadVersion = { - version = "7.0-2024-01-27"; + version = "8.0-2024-02-23"; src = { - rev = "13fcb571f7e5bf4bf142d151651fc577aca32053"; - sha256 = "0wvk3wx5lm2jvyip6b96ja464hdzp9klb7b7ng5i3mdldabh0jba"; + rev = "14d71c8ca6b48d2eb956bb069acf05a37b1b2652"; + sha256 = "0xqd0xbpnvsvba75526nwgzr8l2cfxy99sjmg13sjxfx7rq16kqi"; }; }; libVersion = { - version = "7.0-2024-01-27"; + version = "8.0-2024-02-23"; libSources = { - symbols.rev = "eedf6c9ddac2816023e817d4dc91032f9d7390b9"; - symbols.sha256 = "0nlgmxf9z1vf4g350dfkxql1dawgmw275wqxkgszsfxmhdfpmi9v"; - templates.rev = "9ce98cc45f3778e05c404edebf0f98de5c247ffe"; - templates.sha256 = "0mykfwwik7472i4r0isc5szj3dnmvd0538p0vlmzh4rcgj3pj3vm"; - footprints.rev = "7061fc9847ecc1b838e60dc6826db534028494f6"; - footprints.sha256 = "1az6fzh1lma71mj12bc4bblnmzjayrxhkb8w9rjvlhvvgv33cdmy"; - packages3d.rev = "d7345b34daaa23acf0d4506ed937fb424b5b18cd"; - packages3d.sha256 = "0xzyi4mgyifwc6dppdzh6jq294mkj0a71cwkqw2ymz1kfbksw626"; + symbols.rev = "e228d4e8b295364e90e36c57f4023d8285ba88cd"; + symbols.sha256 = "049h2a7yn6ks8sybppixa872dbvyd0rwf9r6nixvdg6d13fl6rwf"; + templates.rev = "2e00c233b67e35323f90d04c190bf70237a252f2"; + templates.sha256 = "0m9bggz3cm27kqpjjwxy19mqzk0c69bywcjkqcni7kafr21c6k4z"; + footprints.rev = "6e5329a6d4aaa81290e23af3eba88f505c2f61b0"; + footprints.sha256 = "0ypjlbmzmcl3pha3q2361va70c988b1drxy8320gm66jkzfc21a1"; + packages3d.rev = "d1e521228d9f5888836b1a6a35fb05fb925456fa"; + packages3d.sha256 = "0lcy1av7ixg1f7arflk50jllpc1749sfvf3h62hkxsz97wkr97xj"; }; }; }; "kicad-unstable" = { kicadVersion = { - version = "2023-08-15"; + version = "2024-02-23"; src = { - rev = "e0d4cf2d5b023a7e5b70d854452376aa3510acd8"; - sha256 = "0666j4q3vz24smcjw9m4ib3ca2dqiqgx2amhv7ys4rzqb6v2pvn2"; + rev = "b7b64d959f37f00bb0d14b007c3b3908196e1024"; + sha256 = "1gl7mjqpmqq4m55z6crwb77983g00gi2161ichsc7hsfhs4c8grh"; }; }; libVersion = { - version = "2023-08-15"; + version = "2024-02-23"; libSources = { - symbols.rev = "06d20a4b9f7e5375329194d141b096dcdcb7518a"; - symbols.sha256 = "1wr754m4ykidds3i14gqhvyrj3mbkchp2hkfnr0rjsdaqf4zmqdf"; - templates.rev = "867eef383a0f61015cb69677d5c632d78a2ea01a"; - templates.sha256 = "1qi20mrsfn4fxmr1fyphmil2i9p2nzmwk5rlfchc5aq2194nj3lq"; - footprints.rev = "5d2ac73ae72bfe8b8ee9eeb081a7851b2ca84c24"; - footprints.sha256 = "1qg016ysf0ddm3bd5bkjawlrc0z4r3zhmdjkqkwaaaydnpwp23qz"; - packages3d.rev = "f1dae9f95e59216f3b974f585e5b420db853da9e"; - packages3d.sha256 = "0ciri6lhnh0w9i00z167snj5acnjndi1rgmyls08p45zj4rma8y2"; + symbols.rev = "8b0c343d8694fe0a968e5c4af69fd161bacf7da1"; + symbols.sha256 = "049h2a7yn6ks8sybppixa872dbvyd0rwf9r6nixvdg6d13fl6rwf"; + templates.rev = "0a6c4f798a68a5c639d54b4d3093460ab9267816"; + templates.sha256 = "0m9bggz3cm27kqpjjwxy19mqzk0c69bywcjkqcni7kafr21c6k4z"; + footprints.rev = "ded6b053460faae5783c538a38e91e2b4bddcf2e"; + footprints.sha256 = "035bf37n4vrihaj4zfdncisdx9fly1vya7lhkxhlsbv5blpi4a5y"; + packages3d.rev = "984667325076d4e50dab14e755aeacf97f42194c"; + packages3d.sha256 = "0lkaxv02h4sxrnm8zr17wl9d07mazlisad78r35gry741i362cdg"; }; }; }; diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index 50be90716e09..5fc4b0036f9f 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.464"; + version = "8.3.465"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-ICXFskoB/mqKPgjWeIoJ81H2eg4dPSj0bHY7S5/A858="; + sha256 = "sha256-cb9A8rpjD3x3fJo+xexlyzn+/3M5iUJmSoBraom9zd8="; }; nativeBuildInputs = [ python3 ]; diff --git a/pkgs/applications/science/electronics/nanovna-saver/default.nix b/pkgs/applications/science/electronics/nanovna-saver/default.nix index 61788938e40a..d1b38d8b8e07 100644 --- a/pkgs/applications/science/electronics/nanovna-saver/default.nix +++ b/pkgs/applications/science/electronics/nanovna-saver/default.nix @@ -47,6 +47,7 @@ python3.pkgs.buildPythonApplication rec { homepage = "https://github.com/NanoVNA-Saver/nanovna-saver"; description = "A tool for reading, displaying and saving data from the NanoVNA"; + mainProgram = "NanoVNASaver"; longDescription = '' A multiplatform tool to save Touchstone files from the NanoVNA, sweep frequency spans in segments to gain more than 101 data points, and diff --git a/pkgs/applications/science/electronics/nvc/default.nix b/pkgs/applications/science/electronics/nvc/default.nix index 378daf9c498c..48c9b17816e9 100644 --- a/pkgs/applications/science/electronics/nvc/default.nix +++ b/pkgs/applications/science/electronics/nvc/default.nix @@ -57,6 +57,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "VHDL compiler and simulator"; + mainProgram = "nvc"; homepage = "https://www.nickg.me.uk/nvc/"; license = licenses.gpl3Plus; maintainers = with maintainers; [ wegank ]; diff --git a/pkgs/applications/science/electronics/openboardview/default.nix b/pkgs/applications/science/electronics/openboardview/default.nix index 9e498881d2e2..4eaf29133a44 100644 --- a/pkgs/applications/science/electronics/openboardview/default.nix +++ b/pkgs/applications/science/electronics/openboardview/default.nix @@ -67,6 +67,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Linux SDL/ImGui edition software for viewing .brd files"; + mainProgram = "openboardview"; homepage = "https://github.com/OpenBoardView/OpenBoardView"; license = licenses.mit; platforms = platforms.unix; diff --git a/pkgs/applications/science/electronics/openhantek6022/default.nix b/pkgs/applications/science/electronics/openhantek6022/default.nix index b6e5d89a3e97..ca0c651fad27 100644 --- a/pkgs/applications/science/electronics/openhantek6022/default.nix +++ b/pkgs/applications/science/electronics/openhantek6022/default.nix @@ -23,6 +23,7 @@ mkDerivation rec { meta = with lib; { description = "Free software for Hantek and compatible (Voltcraft/Darkwire/Protek/Acetech) USB digital signal oscilloscopes"; + mainProgram = "OpenHantek"; homepage = "https://github.com/OpenHantek/OpenHantek6022"; license = licenses.gpl3; maintainers = with maintainers; [ baracoder ]; diff --git a/pkgs/applications/science/electronics/pulseview/default.nix b/pkgs/applications/science/electronics/pulseview/default.nix index cab42731c336..52685f1df254 100644 --- a/pkgs/applications/science/electronics/pulseview/default.nix +++ b/pkgs/applications/science/electronics/pulseview/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Qt-based LA/scope/MSO GUI for sigrok (a signal analysis software suite)"; + mainProgram = "pulseview"; homepage = "https://sigrok.org/"; license = licenses.gpl3Plus; maintainers = with maintainers; [ bjornfor vifino ]; diff --git a/pkgs/applications/science/electronics/systemc/default.nix b/pkgs/applications/science/electronics/systemc/default.nix index dc6186841f47..4e14d08e63bf 100644 --- a/pkgs/applications/science/electronics/systemc/default.nix +++ b/pkgs/applications/science/electronics/systemc/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, autoreconfHook }: +{ lib, stdenv, fetchFromGitHub, cmake }: stdenv.mkDerivation rec { pname = "systemc"; @@ -11,16 +11,21 @@ stdenv.mkDerivation rec { sha256 = "0sj8wlkp68cjhmkd9c9lvm3lk3sckczpz7w9vby64inc1f9fnf0b"; }; - enableParallelBuilding = true; - nativeBuildInputs = [ autoreconfHook ]; + nativeBuildInputs = [ cmake ]; - configureFlags = [ "--with-unix-layout" ]; + cmakeFlags = [ + # Undefined reference to the sc_core::sc_api_version_2_3_4_XXX + # https://github.com/accellera-official/systemc/issues/21 + "-DCMAKE_CXX_STANDARD=17" + ]; + + doCheck = stdenv.buildPlatform.canExecute stdenv.hostPlatform; meta = with lib; { description = "The language for System-level design, modeling and verification"; homepage = "https://systemc.org/"; license = licenses.asl20; - platforms = platforms.linux; + platforms = platforms.unix; maintainers = with maintainers; [ victormignot amiloradovsky ]; }; } diff --git a/pkgs/applications/science/electronics/tkgate/1.x.nix b/pkgs/applications/science/electronics/tkgate/1.x.nix index f8741cd8d180..f20ce5e0acd0 100644 --- a/pkgs/applications/science/electronics/tkgate/1.x.nix +++ b/pkgs/applications/science/electronics/tkgate/1.x.nix @@ -35,6 +35,7 @@ stdenv.mkDerivation rec { meta = { description = "Event driven digital circuit simulator with a TCL/TK-based graphical editor"; + mainProgram = "gmac"; homepage = "http://www.tkgate.org/"; license = lib.licenses.gpl2Plus; hydraPlatforms = lib.platforms.linux; diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix index 062ba93ca420..92f8fa52b91f 100644 --- a/pkgs/applications/science/electronics/verilator/default.nix +++ b/pkgs/applications/science/electronics/verilator/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, perl, flex, bison, python3, autoconf, +{ lib, stdenv, fetchFromGitHub, fetchpatch, perl, flex, bison, python3, autoconf, which, cmake, ccache, help2man, makeWrapper, glibcLocales, systemc, git, numactl }: @@ -13,6 +13,15 @@ stdenv.mkDerivation rec { hash = "sha256-Ya3lqK8BfvMVLZUrD2Et6OmptteWXp5VmZb2x2G/V/E="; }; + patches = [ + (fetchpatch { + # Fix try-lock spuriously fail in V3ThreadPool destructor + # https://github.com/verilator/verilator/pull/4938 + url = "https://github.com/verilator/verilator/commit/4b9cce4369c78423779238e585ed693c456d464e.patch"; + hash = "sha256-sGrk/pxqZqUcmJdzQoPlzXMmYqHCOmd9Y2n6ieVNg1U="; + }) + ]; + enableParallelBuilding = true; buildInputs = [ perl python3 systemc ]; # ccache nativeBuildInputs = [ makeWrapper flex bison autoconf help2man git ]; @@ -37,6 +46,11 @@ stdenv.mkDerivation rec { done ''; + env = { + SYSTEMC_INCLUDE = "${lib.getDev systemc}/include"; + SYSTEMC_LIBDIR = "${lib.getLib systemc}/lib"; + }; + meta = with lib; { description = "Fast and robust (System)Verilog simulator/compiler and linter"; homepage = "https://www.veripool.org/verilator"; diff --git a/pkgs/applications/science/electronics/vhd2vl/default.nix b/pkgs/applications/science/electronics/vhd2vl/default.nix index 0ec14d282b4a..d56a8aa6ce84 100644 --- a/pkgs/applications/science/electronics/vhd2vl/default.nix +++ b/pkgs/applications/science/electronics/vhd2vl/default.nix @@ -44,6 +44,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "VHDL to Verilog converter"; + mainProgram = "vhd2vl"; homepage = "https://github.com/ldoolitt/vhd2vl"; license = licenses.gpl2Plus; maintainers = with maintainers; [ matthuszagh ]; diff --git a/pkgs/applications/science/electronics/xcircuit/default.nix b/pkgs/applications/science/electronics/xcircuit/default.nix index 61b63ff1d7a4..c51156d2c1ab 100644 --- a/pkgs/applications/science/electronics/xcircuit/default.nix +++ b/pkgs/applications/science/electronics/xcircuit/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Generic drawing program tailored to circuit diagrams"; + mainProgram = "xcircuit"; homepage = "http://opencircuitdesign.com/xcircuit"; license = licenses.gpl2; platforms = platforms.linux; diff --git a/pkgs/applications/science/electronics/xoscope/default.nix b/pkgs/applications/science/electronics/xoscope/default.nix index 9f9224b5543c..0fa0c1bc79bf 100644 --- a/pkgs/applications/science/electronics/xoscope/default.nix +++ b/pkgs/applications/science/electronics/xoscope/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = { description = "Oscilloscope through the sound card"; + mainProgram = "xoscope"; homepage = "https://xoscope.sourceforge.net"; license = lib.licenses.gpl2Plus; maintainers = with lib.maintainers; [viric]; diff --git a/pkgs/applications/science/engineering/brmodelo/default.nix b/pkgs/applications/science/engineering/brmodelo/default.nix index c0573ae131d3..c484260d25f3 100644 --- a/pkgs/applications/science/engineering/brmodelo/default.nix +++ b/pkgs/applications/science/engineering/brmodelo/default.nix @@ -102,6 +102,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Entity-relationship diagram tool for making conceptual and logical database models"; + mainProgram = "brmodelo"; homepage = "https://github.com/chcandido/brModelo"; license = licenses.gpl3; maintainers = with maintainers; [ yuu ]; diff --git a/pkgs/applications/science/engineering/strictdoc/default.nix b/pkgs/applications/science/engineering/strictdoc/default.nix deleted file mode 100644 index 5097a936caaa..000000000000 --- a/pkgs/applications/science/engineering/strictdoc/default.nix +++ /dev/null @@ -1,75 +0,0 @@ -{ lib -, fetchFromGitHub -, python3 -}: - -python3.pkgs.buildPythonApplication rec { - pname = "strictdoc"; - version = "0.0.40"; - pyproject = true; - - src = fetchFromGitHub { - owner = "strictdoc-project"; - repo = "strictdoc"; - rev = "refs/tags/${version}"; - hash = "sha256-kZ8qVhroSPSGAcgUFZb1vRI6JoFyjeg/0qYosbRnwyc="; - }; - - pythonRelaxDeps = true; - - nativeBuildInputs = with python3.pkgs; [ - hatchling - pythonRelaxDepsHook - ]; - - propagatedBuildInputs = with python3.pkgs; [ - beautifulsoup4 - datauri - docutils - fastapi - html5lib - jinja2 - lxml - markupsafe - pybtex - pygments - python-multipart - reqif - selenium - setuptools - spdx-tools - textx - toml - uvicorn - webdriver-manager - websockets - xlrd - xlsxwriter - ] ++ uvicorn.optional-dependencies.standard; - - nativeCheckInputs = with python3.pkgs; [ - httpx - pytestCheckHook - ]; - - pythonImportsCheck = [ - "strictdoc" - ]; - - disabledTests = [ - # fixture 'fs' not found - "test_001_load_from_files" - ]; - - disabledTestPaths = [ - "tests/end2end/" - ]; - - meta = with lib; { - description = "Software requirements specification tool"; - homepage = "https://github.com/strictdoc-project/strictdoc"; - changelog = "https://github.com/strictdoc-project/strictdoc/releases/tag/${version}"; - license = licenses.asl20; - maintainers = with maintainers; [ yuu ]; - }; -} diff --git a/pkgs/applications/science/geometry/tetgen/1.4.nix b/pkgs/applications/science/geometry/tetgen/1.4.nix index 684f5913f79f..f67bf198443a 100644 --- a/pkgs/applications/science/geometry/tetgen/1.4.nix +++ b/pkgs/applications/science/geometry/tetgen/1.4.nix @@ -16,6 +16,7 @@ stdenv.mkDerivation rec { meta = { description = "Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator"; + mainProgram = "tetgen"; homepage = "http://tetgen.org/"; license = lib.licenses.mit; platforms = lib.platforms.linux; diff --git a/pkgs/applications/science/geometry/tetgen/default.nix b/pkgs/applications/science/geometry/tetgen/default.nix index ff2b211b34d2..dce56dc4e17d 100644 --- a/pkgs/applications/science/geometry/tetgen/default.nix +++ b/pkgs/applications/science/geometry/tetgen/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = { description = "Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator"; + mainProgram = "tetgen"; homepage = "http://tetgen.org/"; license = lib.licenses.agpl3Plus; platforms = lib.platforms.linux; diff --git a/pkgs/applications/science/logic/abella/default.nix b/pkgs/applications/science/logic/abella/default.nix index 4483b8ad4756..7878626d6e9a 100644 --- a/pkgs/applications/science/logic/abella/default.nix +++ b/pkgs/applications/science/logic/abella/default.nix @@ -27,6 +27,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { description = "Interactive theorem prover"; + mainProgram = "abella"; longDescription = '' Abella is an interactive theorem prover based on lambda-tree syntax. This means that Abella is well-suited for reasoning about the meta-theory diff --git a/pkgs/applications/science/logic/anders/default.nix b/pkgs/applications/science/logic/anders/default.nix index eb2be71f1681..dff6c86703d4 100644 --- a/pkgs/applications/science/logic/anders/default.nix +++ b/pkgs/applications/science/logic/anders/default.nix @@ -20,6 +20,7 @@ ocamlPackages.buildDunePackage rec { meta = with lib; { description = "Modal Homotopy Type System"; + mainProgram = "anders"; homepage = "https://homotopy.dev/"; license = licenses.isc; maintainers = [ maintainers.suhr ]; diff --git a/pkgs/applications/science/logic/bitwuzla/default.nix b/pkgs/applications/science/logic/bitwuzla/default.nix index 4af4058339d9..bacf8620e5fd 100644 --- a/pkgs/applications/science/logic/bitwuzla/default.nix +++ b/pkgs/applications/science/logic/bitwuzla/default.nix @@ -61,6 +61,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A SMT solver for fixed-size bit-vectors, floating-point arithmetic, arrays, and uninterpreted functions"; + mainProgram = "bitwuzla"; homepage = "https://bitwuzla.github.io"; license = licenses.mit; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/celf/default.nix b/pkgs/applications/science/logic/celf/default.nix index 044a6f3ca1c4..e1f0c237f673 100644 --- a/pkgs/applications/science/logic/celf/default.nix +++ b/pkgs/applications/science/logic/celf/default.nix @@ -28,6 +28,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Linear logic programming system"; + mainProgram = "celf"; homepage = "https://github.com/clf/celf"; license = licenses.gpl3; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/logic/clprover/clprover.nix b/pkgs/applications/science/logic/clprover/clprover.nix index 2a8c058a80bb..543c6cb4310b 100644 --- a/pkgs/applications/science/logic/clprover/clprover.nix +++ b/pkgs/applications/science/logic/clprover/clprover.nix @@ -19,6 +19,7 @@ stdenv.mkDerivation { meta = with lib; { description = "Resolution-based theorem prover for Coalition Logic implemented in C++"; + mainProgram = "CLProver++"; homepage = "https://cgi.csc.liv.ac.uk/~ullrich/CLProver++/"; license = licenses.gpl3; # Note that while the website states that it is GPLv2 but the file in the zip as well as the comments in the source state it is GPLv3 maintainers = with maintainers; [ mgttlinger ]; diff --git a/pkgs/applications/science/logic/cryptominisat/default.nix b/pkgs/applications/science/logic/cryptominisat/default.nix index f2e3eaab91dc..4be57a194635 100644 --- a/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/pkgs/applications/science/logic/cryptominisat/default.nix @@ -22,6 +22,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An advanced SAT Solver"; + mainProgram = "cryptominisat5"; homepage = "https://github.com/msoos/cryptominisat"; license = licenses.mit; maintainers = with maintainers; [ mic92 ]; diff --git a/pkgs/applications/science/logic/cryptoverif/default.nix b/pkgs/applications/science/logic/cryptoverif/default.nix index 5c15b8a17241..4b74cdd518ca 100644 --- a/pkgs/applications/science/logic/cryptoverif/default.nix +++ b/pkgs/applications/science/logic/cryptoverif/default.nix @@ -42,6 +42,7 @@ stdenv.mkDerivation rec { meta = { description = "Cryptographic protocol verifier in the computational model"; + mainProgram = "cryptoverif"; homepage = "https://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/"; license = lib.licenses.cecill-b; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/logic/cubicle/default.nix b/pkgs/applications/science/logic/cubicle/default.nix index c9382c5d0f1a..03409e68ea33 100644 --- a/pkgs/applications/science/logic/cubicle/default.nix +++ b/pkgs/applications/science/logic/cubicle/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An open source model checker for verifying safety properties of array-based systems"; + mainProgram = "cubicle"; homepage = "https://cubicle.lri.fr/"; license = licenses.asl20; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/cvc3/default.nix b/pkgs/applications/science/logic/cvc3/default.nix index 0385909610e6..bec5a89cc691 100644 --- a/pkgs/applications/science/logic/cvc3/default.nix +++ b/pkgs/applications/science/logic/cvc3/default.nix @@ -28,6 +28,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A prover for satisfiability modulo theory (SMT)"; + mainProgram = "cvc3"; maintainers = with maintainers; [ raskin ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/cvc4/default.nix b/pkgs/applications/science/logic/cvc4/default.nix index 1513c7477985..ac45db8cb312 100644 --- a/pkgs/applications/science/logic/cvc4/default.nix +++ b/pkgs/applications/science/logic/cvc4/default.nix @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A high-performance theorem prover and SMT solver"; + mainProgram = "cvc4"; homepage = "http://cvc4.cs.stanford.edu/web/"; license = licenses.gpl3; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/cvc5/default.nix b/pkgs/applications/science/logic/cvc5/default.nix index 2dff344e4edb..d34b29337296 100644 --- a/pkgs/applications/science/logic/cvc5/default.nix +++ b/pkgs/applications/science/logic/cvc5/default.nix @@ -30,6 +30,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A high-performance theorem prover and SMT solver"; + mainProgram = "cvc5"; homepage = "https://cvc5.github.io"; license = licenses.gpl3Only; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/dafny/default.nix b/pkgs/applications/science/logic/dafny/default.nix index 5f56d612ab24..83d472c1abb1 100644 --- a/pkgs/applications/science/logic/dafny/default.nix +++ b/pkgs/applications/science/logic/dafny/default.nix @@ -8,13 +8,13 @@ buildDotnetModule rec { pname = "Dafny"; - version = "4.4.0"; + version = "4.5.0"; src = fetchFromGitHub { owner = "dafny-lang"; repo = "dafny"; rev = "v${version}"; - hash = "sha256-rnPZms60vRtefEV+3IeVXoZJU9WMjVxPVioRaEcyw/o="; + hash = "sha256-NsQhJY++IaLyFc5jqo7TyZBcz0P8VUizGLxdIe9KEO4="; }; postPatch = '' diff --git a/pkgs/applications/science/logic/dafny/deps.nix b/pkgs/applications/science/logic/dafny/deps.nix index a786d8b3d6fd..91fe5624ac7f 100644 --- a/pkgs/applications/science/logic/dafny/deps.nix +++ b/pkgs/applications/science/logic/dafny/deps.nix @@ -2,19 +2,19 @@ # Please dont edit it manually, your changes might get overwritten! { fetchNuGet }: [ - (fetchNuGet { pname = "Boogie"; version = "3.0.9"; sha256 = "12700rvm3zj73pkkjaypfa72fvqz8bp78hi3jkh89dqavhg3l7p5"; }) - (fetchNuGet { pname = "Boogie.AbstractInterpretation"; version = "3.0.9"; sha256 = "1612d1x7smhcczmk21z9kswjjvq3h0r5mlf1zb8mznyx0154pckg"; }) - (fetchNuGet { pname = "Boogie.BaseTypes"; version = "3.0.9"; sha256 = "0v6x8k61rl6bvp1zbvbhnlpkakbw11c2mf8glafmf4znrakwil23"; }) - (fetchNuGet { pname = "Boogie.CodeContractsExtender"; version = "3.0.9"; sha256 = "045z0j7bhsb8fypzkz8spixfqdchcpsq3bb9bfwb95if2mna4zx2"; }) - (fetchNuGet { pname = "Boogie.Concurrency"; version = "3.0.9"; sha256 = "00k08qh614vciadzk7lr1dcwsvrcfpslvs342amq12c25rxh3125"; }) - (fetchNuGet { pname = "Boogie.Core"; version = "3.0.9"; sha256 = "03fip919iw7y3vwk5nj53jj73ry43z9fpn752j5fbgygkl2zbx4q"; }) - (fetchNuGet { pname = "Boogie.ExecutionEngine"; version = "3.0.9"; sha256 = "098l1qmya021raqgdapxvwq3pra4v7wpv7j3dmmhsnpg8zs30jgi"; }) - (fetchNuGet { pname = "Boogie.Graph"; version = "3.0.9"; sha256 = "1y8aai7wmsyh2pn9bl1rp2nifs3k9b8kb2lqx5rgs1fdiyk2q24j"; }) - (fetchNuGet { pname = "Boogie.Houdini"; version = "3.0.9"; sha256 = "1ssr82swqmjsap6v344v2kwkfsv70gx082dk54x7vpapr56f1fgp"; }) - (fetchNuGet { pname = "Boogie.Model"; version = "3.0.9"; sha256 = "1cy04a7dr1z7dxfkx6l9kfm30rx5wsn7g50b0wyzp4ns6sbkh47f"; }) - (fetchNuGet { pname = "Boogie.Provers.SMTLib"; version = "3.0.9"; sha256 = "1ijzn67wl82ycr1k7gbh8dhq99zxqqjdc48glf4ld832l7sp3vam"; }) - (fetchNuGet { pname = "Boogie.VCExpr"; version = "3.0.9"; sha256 = "0hivg31c8v9ix5b8mici6mxz1yzydwiyvgb510bnghxciwbnd4gp"; }) - (fetchNuGet { pname = "Boogie.VCGeneration"; version = "3.0.9"; sha256 = "1j9853vixzpgdfd60c3hr5padfdj3sbrbhmr6jg9a0cr3afk72sm"; }) + (fetchNuGet { pname = "Boogie"; version = "3.1.3"; sha256 = "0xzc7s0rjb8dhdkdf71g6pdsnyhbl534xpwd8gbx6g16a87iqx6i"; }) + (fetchNuGet { pname = "Boogie.AbstractInterpretation"; version = "3.1.3"; sha256 = "0a7v2jkkbh59pyc5nz4avszm3dbmp4amkmr6lvn0gyc3hxgn8d3k"; }) + (fetchNuGet { pname = "Boogie.BaseTypes"; version = "3.1.3"; sha256 = "1h94yl4ymhd2g14i5w8lnnh2zw7gx65qydzvv8cm8d5yn64gch63"; }) + (fetchNuGet { pname = "Boogie.CodeContractsExtender"; version = "3.1.3"; sha256 = "0b1h1lz997lgyq34bx3ngnhgcrw8j4qvsa6iygb6bydxz7rirrf4"; }) + (fetchNuGet { pname = "Boogie.Concurrency"; version = "3.1.3"; sha256 = "1aq0gdz1xkmp82c67vrmyvkncfbbj5zxrsg78lsmmi22h9qbkzm3"; }) + (fetchNuGet { pname = "Boogie.Core"; version = "3.1.3"; sha256 = "0yhl272lv9lncjval2z7zl9wavlxx8bivj467zl2zzbrxw2k5wz8"; }) + (fetchNuGet { pname = "Boogie.ExecutionEngine"; version = "3.1.3"; sha256 = "0p0zp329h6mddbswm3pdcyvy03y69vyznv11ph6bkpya21lsxqy7"; }) + (fetchNuGet { pname = "Boogie.Graph"; version = "3.1.3"; sha256 = "1p8vb4x4iy7f0ycwb8f71j9a2ci8irwg3rvad2hg3rgbihbwp1qj"; }) + (fetchNuGet { pname = "Boogie.Houdini"; version = "3.1.3"; sha256 = "06qlgi9f70r2w7w6h9qw3lx9dd4pbddpdplqjxi090rpry6dhrbz"; }) + (fetchNuGet { pname = "Boogie.Model"; version = "3.1.3"; sha256 = "0fbvnrghaq17fdpjx12axxrrjp1mh99skaznmvxd1ylsqqnn4cbk"; }) + (fetchNuGet { pname = "Boogie.Provers.SMTLib"; version = "3.1.3"; sha256 = "0x7gpc7m04in2gzdn4jgjphd2xjqrdfmh84wzwnwpvi5wyn869jc"; }) + (fetchNuGet { pname = "Boogie.VCExpr"; version = "3.1.3"; sha256 = "0dyndhqz1yf9qnq9mw73g53rnz0xfbdbi3yk6pg7fdm1m3363h5p"; }) + (fetchNuGet { pname = "Boogie.VCGeneration"; version = "3.1.3"; sha256 = "1bl83727zc1rhskx548p5pa27804n3f5i9n233jvcz6n6bfjn74k"; }) (fetchNuGet { pname = "CocoR"; version = "2014.12.24"; sha256 = "0ps8h7aawkcc1910qnh13llzb01pvgsjmg862pxp0p4wca2dn7a2"; }) (fetchNuGet { pname = "JetBrains.Annotations"; version = "2021.1.0"; sha256 = "07pnhxxlgx8spmwmakz37nmbvgyb6yjrbrhad5rrn6y767z5r1gb"; }) (fetchNuGet { pname = "MediatR"; version = "8.1.0"; sha256 = "0cqx7yfh998xhsfk5pr6229lcjcs1jxxyqz7dwskc9jddl6a2akp"; }) @@ -40,6 +40,7 @@ (fetchNuGet { pname = "Microsoft.Extensions.FileProviders.Abstractions"; version = "5.0.0"; sha256 = "01ahgd0b2z2zycrr2lcsq2cl59fn04bh51hdwdp9dcsdkpvnasj1"; }) (fetchNuGet { pname = "Microsoft.Extensions.FileProviders.Physical"; version = "5.0.0"; sha256 = "00vii8148a6pk12l9jl0rhjp7apil5q5qcy7v1smnv17lj4p8szd"; }) (fetchNuGet { pname = "Microsoft.Extensions.FileSystemGlobbing"; version = "5.0.0"; sha256 = "0lm6n9vbyjh0l17qcc2y9qwn1cns3dyjmkvbxjp0g9sll32kjpmb"; }) + (fetchNuGet { pname = "Microsoft.Extensions.Logging"; version = "2.0.0"; sha256 = "1jkwjcq1ld9znz1haazk8ili2g4pzfdp6i7r7rki4hg3jcadn386"; }) (fetchNuGet { pname = "Microsoft.Extensions.Logging"; version = "5.0.0"; sha256 = "1qa1l18q2jh9azya8gv1p8anzcdirjzd9dxxisb4911i9m1648i3"; }) (fetchNuGet { pname = "Microsoft.Extensions.Logging.Abstractions"; version = "5.0.0"; sha256 = "1yza38675dbv1qqnnhqm23alv2bbaqxp0pb7zinjmw8j2mr5r6wc"; }) (fetchNuGet { pname = "Microsoft.Extensions.Options"; version = "2.0.0"; sha256 = "0g4zadlg73f507krilhaaa7h0jdga216syrzjlyf5fdk25gxmjqh"; }) @@ -53,10 +54,9 @@ (fetchNuGet { pname = "Microsoft.NETCore.Platforms"; version = "3.0.0"; sha256 = "1bk8r4r3ihmi6322jmcag14jmw11mjqys202azqjzglcx59pxh51"; }) (fetchNuGet { pname = "Microsoft.NETCore.Targets"; version = "1.0.1"; sha256 = "0ppdkwy6s9p7x9jix3v4402wb171cdiibq7js7i13nxpdky7074p"; }) (fetchNuGet { pname = "Microsoft.NETCore.Targets"; version = "1.1.0"; sha256 = "193xwf33fbm0ni3idxzbr5fdq3i2dlfgihsac9jj7whj0gd902nh"; }) - (fetchNuGet { pname = "Microsoft.TestPlatform.Extensions.TrxLogger"; version = "17.0.0"; sha256 = "067vpfk5690j0d01lfy8mry42pkzz79l873cp2dby0hi8skfklaq"; }) - (fetchNuGet { pname = "Microsoft.TestPlatform.ObjectModel"; version = "16.11.0"; sha256 = "1fc0ghk1cny4i8w43b94pxhl0srxisv6kaflkkp30ncsa9szhkxh"; }) - (fetchNuGet { pname = "Microsoft.TestPlatform.ObjectModel"; version = "17.0.0"; sha256 = "1bh5scbvl6ndldqv20sl34h4y257irm9ziv2wyfc3hka6912fhn7"; }) - (fetchNuGet { pname = "Microsoft.TestPlatform.TestHost"; version = "16.11.0"; sha256 = "0hp1vndf2jhyg1f3miq4g2068z5kpfzy6nmswm25vymghxp1ws4k"; }) + (fetchNuGet { pname = "Microsoft.TestPlatform.Extensions.TrxLogger"; version = "17.9.0"; sha256 = "0wn38vj9i4gjw5zsl4wcivpqrmp1h5n6m1zxcfwj7yjn9hf45rz9"; }) + (fetchNuGet { pname = "Microsoft.TestPlatform.ObjectModel"; version = "17.9.0"; sha256 = "1kgsl9w9fganbm9wvlkqgk0ag9hfi58z88rkfybc6kvg78bx89ca"; }) + (fetchNuGet { pname = "Microsoft.TestPlatform.TestHost"; version = "17.9.0"; sha256 = "19ffh31a1jxzn8j69m1vnk5hyfz3dbxmflq77b8x82zybiilh5nl"; }) (fetchNuGet { pname = "Microsoft.VisualStudio.Threading"; version = "16.7.56"; sha256 = "13x0xrsjxd86clf9cjjwmpzlyp8pkrf13riya7igs8zy93zw2qap"; }) (fetchNuGet { pname = "Microsoft.VisualStudio.Threading.Analyzers"; version = "16.7.56"; sha256 = "04v9df0k7bsc0rzgkw4mnvi43pdrh42vk6xdcwn9m6im33m0nnz2"; }) (fetchNuGet { pname = "Microsoft.VisualStudio.Validation"; version = "15.5.31"; sha256 = "1ah99rn922qa0sd2k3h64m324f2r32pw8cn4cfihgvwx4qdrpmgw"; }) @@ -64,8 +64,8 @@ (fetchNuGet { pname = "Microsoft.Win32.Registry"; version = "4.6.0"; sha256 = "0i4y782yrqqyx85pg597m20gm0v126w0j9ddk5z7xb3crx4z9f2s"; }) (fetchNuGet { pname = "Microsoft.Win32.SystemEvents"; version = "6.0.0"; sha256 = "0c6pcj088g1yd1vs529q3ybgsd2vjlk5y1ic6dkmbhvrp5jibl9p"; }) (fetchNuGet { pname = "Nerdbank.Streams"; version = "2.6.81"; sha256 = "06wihcaga8537ibh0mkj28m720m6vzkqk562zkynhca85nd236yi"; }) + (fetchNuGet { pname = "Newtonsoft.Json"; version = "11.0.2"; sha256 = "1784xi44f4k8v1fr696hsccmwpy94bz7kixxqlri98zhcxn406b2"; }) (fetchNuGet { pname = "Newtonsoft.Json"; version = "13.0.1"; sha256 = "0fijg0w6iwap8gvzyjnndds0q4b8anwxxvik7y8vgq97dram4srb"; }) - (fetchNuGet { pname = "NuGet.Frameworks"; version = "5.0.0"; sha256 = "18ijvmj13cwjdrrm52c8fpq021531zaz4mj4b4zapxaqzzxf2qjr"; }) (fetchNuGet { pname = "OmniSharp.Extensions.JsonRpc"; version = "0.19.5"; sha256 = "0ilcv3cxcvjkd8ngiydi69pzll07rhqdv5nq9yjnhyj142ynw2cb"; }) (fetchNuGet { pname = "OmniSharp.Extensions.JsonRpc.Generators"; version = "0.19.5"; sha256 = "1mac4yx29ld8fyirg7n0vqn81hzdvcrl8w0l9w5xhnnm6bcd42v8"; }) (fetchNuGet { pname = "OmniSharp.Extensions.LanguageProtocol"; version = "0.19.5"; sha256 = "1clgrbw6dlh46iiiqhavwh15xqar41az352mb5r4ln8ql3wnmk1i"; }) @@ -104,7 +104,7 @@ (fetchNuGet { pname = "runtime.unix.System.IO.FileSystem"; version = "4.3.0"; sha256 = "14nbkhvs7sji5r1saj2x8daz82rnf9kx28d3v2qss34qbr32dzix"; }) (fetchNuGet { pname = "runtime.unix.System.Private.Uri"; version = "4.3.0"; sha256 = "1jx02q6kiwlvfksq1q9qr17fj78y5v6mwsszav4qcz9z25d5g6vk"; }) (fetchNuGet { pname = "runtime.unix.System.Runtime.Extensions"; version = "4.3.0"; sha256 = "0pnxxmm8whx38dp6yvwgmh22smknxmqs5n513fc7m4wxvs1bvi4p"; }) - (fetchNuGet { pname = "Serilog"; version = "2.10.0"; sha256 = "08bih205i632ywryn3zxkhb15dwgyaxbhmm1z3b5nmby9fb25k7v"; }) + (fetchNuGet { pname = "Serilog"; version = "2.12.0"; sha256 = "0lqxpc96qcjkv9pr1rln7mi4y7n7jdi4vb36c2fv3845w1vswgr4"; }) (fetchNuGet { pname = "Serilog.Extensions.Logging"; version = "3.0.1"; sha256 = "069qy7dm5nxb372ij112ppa6m99b4iaimj3sji74m659fwrcrl9a"; }) (fetchNuGet { pname = "Serilog.Settings.Configuration"; version = "3.1.0"; sha256 = "1cj5am4n073331gbfm2ylqb9cadl4q3ppzgwmm5c8m1drxpiwkb5"; }) (fetchNuGet { pname = "Serilog.Sinks.Debug"; version = "2.0.0"; sha256 = "1i7j870l47gan3gpnnlzkccn5lbm7518cnkp25a3g5gp9l0dbwpw"; }) @@ -114,8 +114,6 @@ (fetchNuGet { pname = "System.Collections"; version = "4.3.0"; sha256 = "19r4y64dqyrq6k4706dnyhhw7fs24kpp3awak7whzss39dakpxk9"; }) (fetchNuGet { pname = "System.Collections.Immutable"; version = "1.7.0"; sha256 = "1gik4sn9jsi1wcy1pyyp0r4sn2g17cwrsh24b2d52vif8p2h24zx"; }) (fetchNuGet { pname = "System.Collections.Immutable"; version = "1.7.1"; sha256 = "1nh4nlxfc7lbnbl86wwk1a3jwl6myz5j6hvgh5sp4krim9901hsq"; }) - (fetchNuGet { pname = "System.Collections.NonGeneric"; version = "4.0.1"; sha256 = "19994r5y5bpdhj7di6w047apvil8lh06lh2c2yv9zc4fc5g9bl4d"; }) - (fetchNuGet { pname = "System.Collections.Specialized"; version = "4.0.1"; sha256 = "1wbv7y686p5x169rnaim7sln67ivmv6r57falrnx8aap9y33mam9"; }) (fetchNuGet { pname = "System.CommandLine"; version = "2.0.0-beta4.22272.1"; sha256 = "1iy5hwwgvx911g3yq65p4zsgpy08w4qz9j3h0igcf7yci44vw8yd"; }) (fetchNuGet { pname = "System.Configuration.ConfigurationManager"; version = "6.0.0"; sha256 = "0sqapr697jbb4ljkq46msg0xx1qpmc31ivva6llyz2wzq3mpmxbw"; }) (fetchNuGet { pname = "System.Diagnostics.Debug"; version = "4.3.0"; sha256 = "00yjlf19wjydyr6cfviaph3vsjzg3d5nvnya26i2fvfg53sknh3y"; }) @@ -124,7 +122,6 @@ (fetchNuGet { pname = "System.Dynamic.Runtime"; version = "4.0.11"; sha256 = "1pla2dx8gkidf7xkciig6nifdsb494axjvzvann8g2lp3dbqasm9"; }) (fetchNuGet { pname = "System.Globalization"; version = "4.0.11"; sha256 = "070c5jbas2v7smm660zaf1gh0489xanjqymkvafcs4f8cdrs1d5d"; }) (fetchNuGet { pname = "System.Globalization"; version = "4.3.0"; sha256 = "1cp68vv683n6ic2zqh2s1fn4c2sd87g5hpp6l4d4nj4536jz98ki"; }) - (fetchNuGet { pname = "System.Globalization.Extensions"; version = "4.0.1"; sha256 = "0hjhdb5ri8z9l93bw04s7ynwrjrhx2n0p34sf33a9hl9phz69fyc"; }) (fetchNuGet { pname = "System.IO"; version = "4.1.0"; sha256 = "1g0yb8p11vfd0kbkyzlfsbsp5z44lwsvyc0h3dpw6vqnbi035ajp"; }) (fetchNuGet { pname = "System.IO"; version = "4.3.0"; sha256 = "05l9qdrzhm4s5dixmx68kxwif4l99ll5gqmh7rqgw554fx0agv5f"; }) (fetchNuGet { pname = "System.IO.FileSystem"; version = "4.0.1"; sha256 = "0kgfpw6w4djqra3w5crrg8xivbanh1w9dh3qapb28q060wb9flp1"; }) diff --git a/pkgs/applications/science/logic/easycrypt/default.nix b/pkgs/applications/science/logic/easycrypt/default.nix index 2869bcd6e1e3..782d15d61559 100644 --- a/pkgs/applications/science/logic/easycrypt/default.nix +++ b/pkgs/applications/science/logic/easycrypt/default.nix @@ -51,5 +51,6 @@ stdenv.mkDerivation rec { platforms = lib.platforms.all; homepage = "https://easycrypt.info/"; description = "Computer-Aided Cryptographic Proofs"; + mainProgram = "easycrypt"; }; } diff --git a/pkgs/applications/science/logic/easycrypt/runtest.nix b/pkgs/applications/science/logic/easycrypt/runtest.nix index c0d72d96e1d1..b714dc14991b 100644 --- a/pkgs/applications/science/logic/easycrypt/runtest.nix +++ b/pkgs/applications/science/logic/easycrypt/runtest.nix @@ -21,5 +21,6 @@ python3Packages.buildPythonApplication rec { meta = easycrypt.meta // { description = "Testing program for EasyCrypt formalizations"; + mainProgram = "ec-runtest"; }; } diff --git a/pkgs/applications/science/logic/egglog/default.nix b/pkgs/applications/science/logic/egglog/default.nix index ab5653b50912..8b94c449c6be 100644 --- a/pkgs/applications/science/logic/egglog/default.nix +++ b/pkgs/applications/science/logic/egglog/default.nix @@ -25,6 +25,7 @@ rustPlatform.buildRustPackage { meta = with lib; { description = "A fixpoint reasoning system that unifies Datalog and equality saturation"; + mainProgram = "egglog"; homepage = "https://github.com/egraphs-good/egglog"; license = licenses.mit; maintainers = with maintainers; [ figsoda ]; diff --git a/pkgs/applications/science/logic/fast-downward/default.nix b/pkgs/applications/science/logic/fast-downward/default.nix index a73d141f45b8..77b538d1cbd8 100644 --- a/pkgs/applications/science/logic/fast-downward/default.nix +++ b/pkgs/applications/science/logic/fast-downward/default.nix @@ -59,6 +59,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A domain-independent planning system"; + mainProgram = "fast-downward"; homepage = "https://www.fast-downward.org/"; license = licenses.gpl3Plus; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/gappa/default.nix b/pkgs/applications/science/logic/gappa/default.nix index af6673caa54f..2eb8567aaa4c 100644 --- a/pkgs/applications/science/logic/gappa/default.nix +++ b/pkgs/applications/science/logic/gappa/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = { homepage = "http://gappa.gforge.inria.fr/"; description = "Verifying and formally proving properties on numerical programs dealing with floating-point or fixed-point arithmetic"; + mainProgram = "gappa"; license = with lib.licenses; [ cecill20 gpl2 ]; maintainers = with lib.maintainers; [ vbgl ]; platforms = lib.platforms.all; diff --git a/pkgs/applications/science/logic/glucose/default.nix b/pkgs/applications/science/logic/glucose/default.nix index 512f0414f1c6..a2392ef39861 100644 --- a/pkgs/applications/science/logic/glucose/default.nix +++ b/pkgs/applications/science/logic/glucose/default.nix @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Modern, parallel SAT solver (${if enableUnfree then "parallel" else "sequential"} version)"; + mainProgram = "glucose"; homepage = "https://www.labri.fr/perso/lsimon/research/glucose/"; license = if enableUnfree then licenses.unfreeRedistributable else licenses.mit; platforms = platforms.unix; diff --git a/pkgs/applications/science/logic/kissat/default.nix b/pkgs/applications/science/logic/kissat/default.nix index d1703340527b..65bcebdc6b1a 100644 --- a/pkgs/applications/science/logic/kissat/default.nix +++ b/pkgs/applications/science/logic/kissat/default.nix @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A 'keep it simple and clean bare metal SAT solver' written in C"; + mainProgram = "kissat"; longDescription = '' Kissat is a "keep it simple and clean bare metal SAT solver" written in C. It is a port of CaDiCaL back to C with improved data structures, diff --git a/pkgs/applications/science/logic/lci/default.nix b/pkgs/applications/science/logic/lci/default.nix index 593b2c54c5cf..659855c23fb2 100644 --- a/pkgs/applications/science/logic/lci/default.nix +++ b/pkgs/applications/science/logic/lci/default.nix @@ -9,6 +9,7 @@ stdenv.mkDerivation rec { buildInputs = [readline]; meta = { description = "Lambda calculus interpreter"; + mainProgram = "lci"; maintainers = with lib.maintainers; [raskin]; platforms = with lib.platforms; linux; license = lib.licenses.gpl3; diff --git a/pkgs/applications/science/logic/lean4/default.nix b/pkgs/applications/science/logic/lean4/default.nix index fbc41a67d73b..dca55d969db4 100644 --- a/pkgs/applications/science/logic/lean4/default.nix +++ b/pkgs/applications/science/logic/lean4/default.nix @@ -50,11 +50,6 @@ stdenv.mkDerivation (finalAttrs: { "-DINSTALL_LICENSE=OFF" ]; - # Work around https://github.com/NixOS/nixpkgs/issues/166205. - env = lib.optionalAttrs stdenv.cc.isClang { - NIX_LDFLAGS = "-l${stdenv.cc.libcxx.cxxabi.libName}"; - }; - passthru.tests = { version = testers.testVersion { package = finalAttrs.finalPackage; diff --git a/pkgs/applications/science/logic/leo2/default.nix b/pkgs/applications/science/logic/leo2/default.nix index a72444adbba0..dcf2d5b7c33c 100644 --- a/pkgs/applications/science/logic/leo2/default.nix +++ b/pkgs/applications/science/logic/leo2/default.nix @@ -45,6 +45,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A high-performance typed higher order prover"; + mainProgram = "leo"; maintainers = [ maintainers.raskin ]; platforms = platforms.unix; license = licenses.bsd3; diff --git a/pkgs/applications/science/logic/leo3/binary.nix b/pkgs/applications/science/logic/leo3/binary.nix index 332b28db5fb6..0cdf8a4dc210 100644 --- a/pkgs/applications/science/logic/leo3/binary.nix +++ b/pkgs/applications/science/logic/leo3/binary.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An automated theorem prover for classical higher-order logic with choice"; + mainProgram = "leo3"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.bsd3; maintainers = [maintainers.raskin]; diff --git a/pkgs/applications/science/logic/logisim-evolution/default.nix b/pkgs/applications/science/logic/logisim-evolution/default.nix index affbfc170b90..3d86c8cafdbc 100644 --- a/pkgs/applications/science/logic/logisim-evolution/default.nix +++ b/pkgs/applications/science/logic/logisim-evolution/default.nix @@ -1,25 +1,45 @@ -{ lib, stdenv, fetchurl, jre, makeWrapper, copyDesktopItems, makeDesktopItem, unzip }: +{ lib +, stdenv +, fetchurl +, jre +, makeBinaryWrapper +, copyDesktopItems +, makeDesktopItem +, desktopToDarwinBundle +, unzip +}: -stdenv.mkDerivation rec { +let + icon = fetchurl { + url = "https://github.com/logisim-evolution/logisim-evolution/raw/9e0afa3cd6a8bfa75dab61830822cde83c70bb4b/artwork/logisim-evolution-icon.svg"; + hash = "sha256-DNRimhNFt6jLdjqv7o2cNz38K6XnevxD0rGymym3xBs="; + }; +in +stdenv.mkDerivation (finalAttrs: { pname = "logisim-evolution"; version = "3.8.0"; src = fetchurl { - url = "https://github.com/logisim-evolution/logisim-evolution/releases/download/v${version}/logisim-evolution-${version}-all.jar"; - sha256 = "sha256-TFm+fa3CMp0OMhnKBc6cLIWGQbIG/OpOOCG7ea7wbCw="; + url = "https://github.com/logisim-evolution/logisim-evolution/releases/download/v${finalAttrs.version}/logisim-evolution-${finalAttrs.version}-all.jar"; + hash = "sha256-TFm+fa3CMp0OMhnKBc6cLIWGQbIG/OpOOCG7ea7wbCw="; }; - dontUnpack = true; - nativeBuildInputs = [ makeWrapper copyDesktopItems unzip ]; + nativeBuildInputs = [ + makeBinaryWrapper + copyDesktopItems + unzip + ] ++ lib.optionals stdenv.isDarwin [ + desktopToDarwinBundle + ]; desktopItems = [ (makeDesktopItem { - name = pname; + name = "logisim-evolution"; desktopName = "Logisim-evolution"; exec = "logisim-evolution"; icon = "logisim-evolution"; - comment = meta.description; + comment = finalAttrs.meta.description; categories = [ "Education" ]; }) ]; @@ -29,22 +49,19 @@ stdenv.mkDerivation rec { mkdir -p $out/bin makeWrapper ${jre}/bin/java $out/bin/logisim-evolution --add-flags "-jar $src" - - # Create icons - unzip $src "resources/logisim/img/*" - for size in 16 32 48 128 256; do - install -D "./resources/logisim/img/logisim-icon-$size.png" "$out/share/icons/hicolor/''${size}x''${size}/apps/logisim-evolution.png" - done + install -Dm444 ${icon} $out/share/icons/hicolor/scalable/apps/logisim-evolution.svg runHook postInstall ''; - meta = with lib; { + meta = { + changelog = "https://github.com/logisim-evolution/logisim-evolution/releases/tag/v${finalAttrs.version}"; homepage = "https://github.com/logisim-evolution/logisim-evolution"; description = "Digital logic designer and simulator"; - maintainers = with maintainers; [ emilytrau ]; - sourceProvenance = with sourceTypes; [ binaryBytecode ]; - license = licenses.gpl2Plus; - platforms = platforms.unix; + mainProgram = "logisim-evolution"; + maintainers = with lib.maintainers; [ emilytrau ]; + sourceProvenance = with lib.sourceTypes; [ binaryBytecode ]; + license = lib.licenses.gpl3Only; + platforms = lib.platforms.unix; }; -} +}) diff --git a/pkgs/applications/science/logic/logisim/default.nix b/pkgs/applications/science/logic/logisim/default.nix index ea8a1416a77a..d278f1e78468 100644 --- a/pkgs/applications/science/logic/logisim/default.nix +++ b/pkgs/applications/science/logic/logisim/default.nix @@ -1,25 +1,39 @@ -{ lib, stdenv, fetchurl, jre, makeWrapper, copyDesktopItems, makeDesktopItem, unzip }: +{ lib +, stdenv +, fetchurl +, jre +, makeBinaryWrapper +, copyDesktopItems +, makeDesktopItem +, desktopToDarwinBundle +, unzip +}: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "logisim"; version = "2.7.1"; src = fetchurl { - url = "mirror://sourceforge/project/circuit/${lib.versions.majorMinor version}.x/${version}/logisim-generic-${version}.jar"; - sha256 = "1hkvc9zc7qmvjbl9579p84hw3n8wl3275246xlzj136i5b0phain"; + url = "mirror://sourceforge/project/circuit/${lib.versions.majorMinor finalAttrs.version}.x/${finalAttrs.version}/logisim-generic-${finalAttrs.version}.jar"; + hash = "sha256-Nip4wSrRjCA/7YaIcsSgHNnBIUE3nZLokrviw35ie8I="; }; - dontUnpack = true; - nativeBuildInputs = [ makeWrapper copyDesktopItems unzip ]; + nativeBuildInputs = [ + makeBinaryWrapper + copyDesktopItems + unzip + ] ++ lib.optionals stdenv.isDarwin [ + desktopToDarwinBundle + ]; desktopItems = [ (makeDesktopItem { - name = pname; + name = "logisim"; desktopName = "Logisim"; exec = "logisim"; icon = "logisim"; - comment = meta.description; + comment = finalAttrs.meta.description; categories = [ "Education" ]; }) ]; @@ -34,18 +48,19 @@ stdenv.mkDerivation rec { unzip $src "resources/logisim/img/*" for size in 16 20 24 48 64 128 do - install -D "./resources/logisim/img/logisim-icon-$size.png" "$out/share/icons/hicolor/''${size}x''${size}/apps/logisim.png" + install -Dm444 "./resources/logisim/img/logisim-icon-$size.png" "$out/share/icons/hicolor/''${size}x''${size}/apps/logisim.png" done runHook postInstall ''; - meta = with lib; { + meta = { homepage = "http://www.cburch.com/logisim/"; description = "Educational tool for designing and simulating digital logic circuits"; - maintainers = with maintainers; [ emilytrau ]; - sourceProvenance = with sourceTypes; [ binaryBytecode ]; - license = licenses.gpl2Plus; - platforms = platforms.unix; + mainProgram = "logisim"; + maintainers = with lib.maintainers; [ emilytrau ]; + sourceProvenance = with lib.sourceTypes; [ binaryBytecode ]; + license = lib.licenses.gpl2Only; + platforms = lib.platforms.unix; }; -} +}) diff --git a/pkgs/applications/science/logic/ltl2ba/default.nix b/pkgs/applications/science/logic/ltl2ba/default.nix index 30c13c6036f9..19ade58fbfaa 100644 --- a/pkgs/applications/science/logic/ltl2ba/default.nix +++ b/pkgs/applications/science/logic/ltl2ba/default.nix @@ -23,6 +23,7 @@ stdenv.mkDerivation rec { meta = { description = "Fast translation from LTL formulae to Buchi automata"; + mainProgram = "ltl2ba"; homepage = "http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"; license = lib.licenses.gpl2Plus; platforms = lib.platforms.darwin ++ lib.platforms.linux; diff --git a/pkgs/applications/science/logic/metis-prover/default.nix b/pkgs/applications/science/logic/metis-prover/default.nix index 5b17403dc7f4..bd6f71860bdb 100644 --- a/pkgs/applications/science/logic/metis-prover/default.nix +++ b/pkgs/applications/science/logic/metis-prover/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation { meta = with lib; { description = "Automatic theorem prover for first-order logic with equality"; + mainProgram = "metis"; homepage = "https://www.gilith.com/research/metis/"; license = licenses.mit; maintainers = with maintainers; [ gebner ]; diff --git a/pkgs/applications/science/logic/monosat/default.nix b/pkgs/applications/science/logic/monosat/default.nix index 5b894d2c9376..067ba8ceb1b3 100644 --- a/pkgs/applications/science/logic/monosat/default.nix +++ b/pkgs/applications/science/logic/monosat/default.nix @@ -61,6 +61,7 @@ let meta = { description = "SMT solver for Monotonic Theories"; + mainProgram = "monosat"; platforms = platforms.unix; license = if includeGplCode then licenses.gpl2 else licenses.mit; homepage = "https://github.com/sambayless/monosat"; diff --git a/pkgs/applications/science/logic/msat/default.nix b/pkgs/applications/science/logic/msat/default.nix index dc2b1a221199..299fe95224eb 100644 --- a/pkgs/applications/science/logic/msat/default.nix +++ b/pkgs/applications/science/logic/msat/default.nix @@ -9,5 +9,6 @@ with ocamlPackages; buildDunePackage { meta = msat.meta // { description = "SAT solver binary based on the msat library"; + mainProgram = "msat"; }; } diff --git a/pkgs/applications/science/logic/naproche/default.nix b/pkgs/applications/science/logic/naproche/default.nix index f6743745a7b6..d2070ba8240f 100644 --- a/pkgs/applications/science/logic/naproche/default.nix +++ b/pkgs/applications/science/logic/naproche/default.nix @@ -2,13 +2,13 @@ with haskellPackages; mkDerivation { pname = "Naproche-SAD"; - version = "unstable-2023-07-11"; + version = "unstable-2024-01-18"; src = fetchFromGitHub { owner = "naproche"; repo = "naproche"; - rev = "4c399d49a86987369bec6e1ac5ae3739cd6db0a8"; - sha256 = "sha256-Ji6yxbDEcwuYAzIZwK5sHNltK1WBFBfpyoEtoID/U4k="; + rev = "bb3dbcbd2173e3334bc5bdcd04c07c6836a11387"; + hash = "sha256-DWcowUjy8/VBuhqvDYlVINHssF4KhuzT0L+m1YwUxoE="; }; isExecutable = true; @@ -20,11 +20,7 @@ with haskellPackages; mkDerivation { ]; prePatch = "hpack"; - - checkPhase = '' - export NAPROCHE_EPROVER=${eprover}/bin/eprover - dist/build/Naproche-SAD/Naproche-SAD examples/cantor.ftl.tex -t 60 --tex=on - ''; + doCheck = false; # Tests are broken in upstream postInstall = '' wrapProgram $out/bin/Naproche-SAD \ @@ -35,4 +31,5 @@ with haskellPackages; mkDerivation { description = "Write formal proofs in natural language and LaTeX"; maintainers = with lib.maintainers; [ jvanbruegge ]; license = lib.licenses.gpl3Only; + mainProgram = "Naproche-SAD"; } diff --git a/pkgs/applications/science/logic/open-wbo/default.nix b/pkgs/applications/science/logic/open-wbo/default.nix index 3677eb39de6a..2290ff29224b 100644 --- a/pkgs/applications/science/logic/open-wbo/default.nix +++ b/pkgs/applications/science/logic/open-wbo/default.nix @@ -21,6 +21,7 @@ stdenv.mkDerivation { meta = with lib; { broken = (stdenv.isLinux && stdenv.isAarch64); description = "State-of-the-art MaxSAT and Pseudo-Boolean solver"; + mainProgram = "open-wbo"; maintainers = with maintainers; [ gebner ]; platforms = platforms.unix; license = licenses.mit; diff --git a/pkgs/applications/science/logic/opensmt/default.nix b/pkgs/applications/science/logic/opensmt/default.nix index 6d073400209d..4a5f453f3547 100644 --- a/pkgs/applications/science/logic/opensmt/default.nix +++ b/pkgs/applications/science/logic/opensmt/default.nix @@ -31,6 +31,7 @@ stdenv.mkDerivation rec { meta = with lib; { broken = (stdenv.isLinux && stdenv.isAarch64); description = "A satisfiability modulo theory (SMT) solver"; + mainProgram = "opensmt"; maintainers = [ maintainers.raskin ]; platforms = platforms.linux; license = if enableReadline then licenses.gpl2Plus else licenses.mit; diff --git a/pkgs/applications/science/logic/ott/default.nix b/pkgs/applications/science/logic/ott/default.nix index a00c565fb4e0..b8197aaa4123 100644 --- a/pkgs/applications/science/logic/ott/default.nix +++ b/pkgs/applications/science/logic/ott/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation rec { meta = { description = "A tool for the working semanticist"; + mainProgram = "ott"; longDescription = '' Ott is a tool for writing definitions of programming languages and calculi. It takes as input a definition of a language syntax and diff --git a/pkgs/applications/science/logic/potassco/clingcon.nix b/pkgs/applications/science/logic/potassco/clingcon.nix index 4966bf608bc9..957ebfd3ec43 100644 --- a/pkgs/applications/science/logic/potassco/clingcon.nix +++ b/pkgs/applications/science/logic/potassco/clingcon.nix @@ -32,6 +32,7 @@ stdenv.mkDerivation rec { meta = { description = "Extension of clingo to handle constraints over integers"; + mainProgram = "clingcon"; license = lib.licenses.mit; platforms = lib.platforms.unix; homepage = "https://potassco.org/"; diff --git a/pkgs/applications/science/logic/prooftree/default.nix b/pkgs/applications/science/logic/prooftree/default.nix index 4e65c018d1a2..adb64f02c14f 100644 --- a/pkgs/applications/science/logic/prooftree/default.nix +++ b/pkgs/applications/science/logic/prooftree/default.nix @@ -19,6 +19,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A program for proof-tree visualization"; + mainProgram = "prooftree"; longDescription = '' Prooftree is a program for proof-tree visualization during interactive proof development in a theorem prover. It is currently being developed diff --git a/pkgs/applications/science/logic/redprl/default.nix b/pkgs/applications/science/logic/redprl/default.nix index 656f3f1b653e..2749730f9d66 100644 --- a/pkgs/applications/science/logic/redprl/default.nix +++ b/pkgs/applications/science/logic/redprl/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation { meta = with lib; { description = "A proof assistant for Nominal Computational Type Theory"; + mainProgram = "redprl"; homepage = "http://www.redprl.org/"; license = licenses.mit; maintainers = with maintainers; [ acowley ]; diff --git a/pkgs/applications/science/logic/satallax/default.nix b/pkgs/applications/science/logic/satallax/default.nix index af11cd0d6d8f..bd3e9d3e8351 100644 --- a/pkgs/applications/science/logic/satallax/default.nix +++ b/pkgs/applications/science/logic/satallax/default.nix @@ -80,6 +80,7 @@ stdenv.mkDerivation rec { meta = { description = "Automated theorem prover for higher-order logic"; + mainProgram = "satallax"; license = lib.licenses.mit; maintainers = [ lib.maintainers.raskin ]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix index 86c3db9942a1..288ddc06806a 100644 --- a/pkgs/applications/science/logic/tlaplus/toolbox.nix +++ b/pkgs/applications/science/logic/tlaplus/toolbox.nix @@ -90,6 +90,7 @@ stdenv.mkDerivation rec { meta = { homepage = "http://research.microsoft.com/en-us/um/people/lamport/tla/toolbox.html"; description = "IDE for the TLA+ tools"; + mainProgram = "tla-toolbox"; longDescription = '' Integrated development environment for the TLA+ tools, based on Eclipse. You can use it to create and edit your specs, run the PlusCal translator, view the pretty-printed diff --git a/pkgs/applications/science/logic/vampire/default.nix b/pkgs/applications/science/logic/vampire/default.nix index a3c1aa3f131d..62427e2ee455 100644 --- a/pkgs/applications/science/logic/vampire/default.nix +++ b/pkgs/applications/science/logic/vampire/default.nix @@ -47,6 +47,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://vprover.github.io/"; description = "The Vampire Theorem Prover"; + mainProgram = "vampire"; platforms = platforms.unix; license = licenses.bsd3; maintainers = with maintainers; [ gebner ]; diff --git a/pkgs/applications/science/logic/workcraft/default.nix b/pkgs/applications/science/logic/workcraft/default.nix index 89f6e23c79d3..cc512acad793 100644 --- a/pkgs/applications/science/logic/workcraft/default.nix +++ b/pkgs/applications/science/logic/workcraft/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = { homepage = "https://workcraft.org/"; description = "Framework for interpreted graph modeling, verification and synthesis"; + mainProgram = "workcraft"; platforms = lib.platforms.linux; license = lib.licenses.mit; maintainers = with lib.maintainers; [ timor ]; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index b247599a0813..f35da4a732b0 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -79,6 +79,7 @@ let common = { version, sha256, patches ? [ ], tag ? "z3" }: meta = with lib; { description = "A high-performance theorem prover and SMT solver"; + mainProgram = "z3"; homepage = "https://github.com/Z3Prover/z3"; changelog = "https://github.com/Z3Prover/z3/releases/tag/z3-${version}"; license = licenses.mit; diff --git a/pkgs/applications/science/logic/zchaff/default.nix b/pkgs/applications/science/logic/zchaff/default.nix index 57f673042dc8..5e22ff448ed3 100644 --- a/pkgs/applications/science/logic/zchaff/default.nix +++ b/pkgs/applications/science/logic/zchaff/default.nix @@ -24,6 +24,7 @@ clangStdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.princeton.edu/~chaff/zchaf"; description = "Accelerated SAT Solver from Princeton"; + mainProgram = "zchaff"; license = licenses.mit; maintainers = with maintainers; [ siraben ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/machine-learning/fasttext/default.nix b/pkgs/applications/science/machine-learning/fasttext/default.nix index 301308f90136..b0a36bedc536 100644 --- a/pkgs/applications/science/machine-learning/fasttext/default.nix +++ b/pkgs/applications/science/machine-learning/fasttext/default.nix @@ -15,6 +15,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Library for text classification and representation learning"; + mainProgram = "fasttext"; homepage = "https://fasttext.cc/"; license = licenses.mit; platforms = platforms.unix; diff --git a/pkgs/applications/science/machine-learning/finalfrontier/default.nix b/pkgs/applications/science/machine-learning/finalfrontier/default.nix index 6b76eea33cef..1a6e9351d3a7 100644 --- a/pkgs/applications/science/machine-learning/finalfrontier/default.nix +++ b/pkgs/applications/science/machine-learning/finalfrontier/default.nix @@ -44,6 +44,7 @@ rustPlatform.buildRustPackage rec { meta = with lib; { description = "Utility for training word and subword embeddings"; + mainProgram = "finalfrontier"; homepage = "https://github.com/finalfusion/finalfrontier/"; license = licenses.asl20; maintainers = with maintainers; [ ]; diff --git a/pkgs/applications/science/machine-learning/labelimg/default.nix b/pkgs/applications/science/machine-learning/labelimg/default.nix index 23703ed09952..244eaa05d695 100644 --- a/pkgs/applications/science/machine-learning/labelimg/default.nix +++ b/pkgs/applications/science/machine-learning/labelimg/default.nix @@ -29,6 +29,7 @@ ''; meta = with lib; { description = "A graphical image annotation tool and label object bounding boxes in images"; + mainProgram = "labelImg"; homepage = "https://github.com/tzutalin/labelImg"; license = licenses.mit; platforms = platforms.linux; diff --git a/pkgs/applications/science/machine-learning/uarmsolver/default.nix b/pkgs/applications/science/machine-learning/uarmsolver/default.nix index 811f1bd23c80..12bca5531364 100644 --- a/pkgs/applications/science/machine-learning/uarmsolver/default.nix +++ b/pkgs/applications/science/machine-learning/uarmsolver/default.nix @@ -23,6 +23,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "universal Association Rule Mining Solver"; + mainProgram = "uARMSolver"; homepage = "https://github.com/firefly-cpp/uARMSolver"; license = licenses.mit; platforms = platforms.linux; diff --git a/pkgs/applications/science/math/LiE/default.nix b/pkgs/applications/science/math/LiE/default.nix index d05cc90ca44c..7eb9edbb3b19 100644 --- a/pkgs/applications/science/math/LiE/default.nix +++ b/pkgs/applications/science/math/LiE/default.nix @@ -9,6 +9,7 @@ stdenv.mkDerivation { meta = { description = "A Computer algebra package for Lie group computations"; + mainProgram = "lie"; homepage = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/"; license = lib.licenses.lgpl3; # see the website diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index f4cc1f1fbfea..acfc38686ea4 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -15,13 +15,13 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation (finalAttrs: { pname = "R"; - version = "4.3.2"; + version = "4.3.3"; src = let inherit (finalAttrs) pname version; in fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-s/V2CsLu6AJqPw7vyyW0dyPZeAOO7o6ER2IJTIYMRSo="; + sha256 = "sha256-gIUSMTk7hb84d+6eObKC51Dthkxexgy9aObhOfBSAzA="; }; outputs = [ "out" "tex" ]; diff --git a/pkgs/applications/science/math/almonds/default.nix b/pkgs/applications/science/math/almonds/default.nix index ec3891667c58..2b05b552253d 100644 --- a/pkgs/applications/science/math/almonds/default.nix +++ b/pkgs/applications/science/math/almonds/default.nix @@ -19,6 +19,7 @@ with python3.pkgs; buildPythonApplication rec { meta = with lib; { description = "Terminal Mandelbrot fractal viewer"; + mainProgram = "almonds"; homepage = "https://github.com/Tenchi2xh/Almonds"; license = licenses.mit; maintainers = with maintainers; [ infinisil ]; diff --git a/pkgs/applications/science/math/bcal/default.nix b/pkgs/applications/science/math/bcal/default.nix index fdf07a2a3299..9ba028d1cb65 100644 --- a/pkgs/applications/science/math/bcal/default.nix +++ b/pkgs/applications/science/math/bcal/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Storage conversion and expression calculator"; + mainProgram = "bcal"; homepage = "https://github.com/jarun/bcal"; license = licenses.gpl3Only; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/bliss/default.nix b/pkgs/applications/science/math/bliss/default.nix index 4fccc3a46403..33969c705d05 100644 --- a/pkgs/applications/science/math/bliss/default.nix +++ b/pkgs/applications/science/math/bliss/default.nix @@ -30,6 +30,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An open source tool for computing automorphism groups and canonical forms of graphs. It has both a command line user interface as well as C++ and C programming language APIs"; + mainProgram = "bliss"; homepage = "http://www.tcs.hut.fi/Software/bliss/"; license = licenses.lgpl3; platforms = [ "i686-linux" "x86_64-linux" "aarch64-linux" ]; diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix index 0f8982eac5b9..699f3d25caf7 100644 --- a/pkgs/applications/science/math/calc/default.nix +++ b/pkgs/applications/science/math/calc/default.nix @@ -56,6 +56,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { homepage = "http://www.isthe.com/chongo/tech/comp/calc/"; description = "C-style arbitrary precision calculator"; + mainProgram = "calc"; changelog = "https://github.com/lcn2/calc/blob/v${finalAttrs.version}/CHANGES"; # The licensing situation depends on readline (see section 3 of the LGPL) # If linked against readline then GPLv2 otherwise LGPLv2.1 diff --git a/pkgs/applications/science/math/calculix/default.nix b/pkgs/applications/science/math/calculix/default.nix index 7a89fdd73c84..8af2ea9f4bce 100644 --- a/pkgs/applications/science/math/calculix/default.nix +++ b/pkgs/applications/science/math/calculix/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "http://www.calculix.de/"; description = "Three-dimensional structural finite element program"; + mainProgram = "ccx"; license = licenses.gpl2Plus; maintainers = with maintainers; [ gebner ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/cemu-ti/default.nix b/pkgs/applications/science/math/cemu-ti/default.nix index 2f2440eacfed..c8d5bea6f602 100644 --- a/pkgs/applications/science/math/cemu-ti/default.nix +++ b/pkgs/applications/science/math/cemu-ti/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Third-party TI-84 Plus CE / TI-83 Premium CE emulator, focused on developer features"; + mainProgram = "CEmu"; homepage = "https://ce-programming.github.io/CEmu"; license = licenses.gpl3Plus; maintainers = with maintainers; [ luc65r ]; diff --git a/pkgs/applications/science/math/clp/default.nix b/pkgs/applications/science/math/clp/default.nix index 4cfff4702e69..06032b4a3182 100644 --- a/pkgs/applications/science/math/clp/default.nix +++ b/pkgs/applications/science/math/clp/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { license = licenses.epl20; homepage = "https://github.com/coin-or/Clp"; description = "An open-source linear programming solver written in C++"; + mainProgram = "clp"; platforms = platforms.darwin ++ platforms.linux; maintainers = [ maintainers.vbgl ]; }; diff --git a/pkgs/applications/science/math/ecm/default.nix b/pkgs/applications/science/math/ecm/default.nix index c59b1a8729a2..222db0e98e6a 100644 --- a/pkgs/applications/science/math/ecm/default.nix +++ b/pkgs/applications/science/math/ecm/default.nix @@ -23,6 +23,7 @@ stdenv.mkDerivation { meta = { description = "Elliptic Curve Method for Integer Factorization"; + mainProgram = "ecm"; license = lib.licenses.gpl2Plus; homepage = "http://ecm.gforge.inria.fr/"; maintainers = [ lib.maintainers.roconnor ]; diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index 674a5ea0d973..358e491b2f4a 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "unstable-2024-03-11"; + version = "unstable-2024-03-20"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "dfa24af6c747e1c90d79a462c2a5a0716b3a1dc0"; - hash = "sha256-kgC+E/ecgl27Hs+qCyqg8CjbEyB91AgN397DST/dPMI="; + rev = "262a6525225be7bcef52c3072b1061db3c238055"; + hash = "sha256-QH8mLlcCOuq77vLer8RsSnD9VeJu9kAVv2qWAH3ky6I="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib;{ description = "Computer algebra system written in C"; + mainProgram = "eigenmath"; homepage = "https://georgeweigt.github.io"; license = licenses.bsd2; maintainers = with maintainers; [ nickcao ]; diff --git a/pkgs/applications/science/math/engauge-digitizer/default.nix b/pkgs/applications/science/math/engauge-digitizer/default.nix index 4c26dc2887c8..95306a0820fa 100644 --- a/pkgs/applications/science/math/engauge-digitizer/default.nix +++ b/pkgs/applications/science/math/engauge-digitizer/default.nix @@ -52,6 +52,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Engauge Digitizer is a tool for recovering graph data from an image file"; + mainProgram = "engauge"; homepage = "https://markummitchell.github.io/engauge-digitizer"; license = with licenses; [ gpl2Only ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/math/getdp/default.nix b/pkgs/applications/science/math/getdp/default.nix index b5f4263c793d..d28f59e4be2f 100644 --- a/pkgs/applications/science/math/getdp/default.nix +++ b/pkgs/applications/science/math/getdp/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "getdp"; - version = "3.5.0"; + version = "3.6.0"; src = fetchurl { url = "http://getdp.info/src/getdp-${version}-source.tgz"; - sha256 = "sha256-C/dsSe+puIQBpFfBL3qr2XWXrUnvYy0/uTCKqOpDe9w="; + sha256 = "sha256-N1cb72W77Dr+TzeHpLgv5FuFb+SJqyGcfn+kOfEvZgA="; }; inherit (petsc) mpiSupport; @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A General Environment for the Treatment of Discrete Problems"; + mainProgram = "getdp"; longDescription = '' GetDP is a free finite element solver using mixed elements to discretize de Rham-type complexes in one, two and three dimensions. The main diff --git a/pkgs/applications/science/math/glsurf/default.nix b/pkgs/applications/science/math/glsurf/default.nix index b4e8c6fb23db..d2ebba75638b 100644 --- a/pkgs/applications/science/math/glsurf/default.nix +++ b/pkgs/applications/science/math/glsurf/default.nix @@ -66,6 +66,7 @@ stdenv.mkDerivation rec { meta = { homepage = "https://raffalli.eu/~christophe/glsurf/"; description = "A program to draw implicit surfaces and curves"; + mainProgram = "glsurf"; license = lib.licenses.gpl2Plus; platforms = lib.platforms.all; }; diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix index 62a0c3c405df..669d3a3ab8f1 100644 --- a/pkgs/applications/science/math/gmsh/default.nix +++ b/pkgs/applications/science/math/gmsh/default.nix @@ -64,6 +64,7 @@ stdenv.mkDerivation rec { meta = { description = "A three-dimensional finite element mesh generator"; + mainProgram = "gmsh"; homepage = "https://gmsh.info/"; license = lib.licenses.gpl2Plus; }; diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix index 087807013694..50d7df24417a 100644 --- a/pkgs/applications/science/math/jags/default.nix +++ b/pkgs/applications/science/math/jags/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Just Another Gibbs Sampler"; + mainProgram = "jags"; license = licenses.gpl2; homepage = "http://mcmc-jags.sourceforge.net"; maintainers = [ maintainers.andres ]; diff --git a/pkgs/applications/science/math/lp_solve/default.nix b/pkgs/applications/science/math/lp_solve/default.nix index ee54def6eb97..fdabc8896a58 100644 --- a/pkgs/applications/science/math/lp_solve/default.nix +++ b/pkgs/applications/science/math/lp_solve/default.nix @@ -59,6 +59,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A Mixed Integer Linear Programming (MILP) solver"; + mainProgram = "lp_solve"; homepage = "https://lpsolve.sourceforge.net"; license = licenses.gpl2Plus; maintainers = with maintainers; [ smironov ]; diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix index 6456608e7dbc..1de6d416a0e6 100644 --- a/pkgs/applications/science/math/msieve/default.nix +++ b/pkgs/applications/science/math/msieve/default.nix @@ -1,12 +1,13 @@ -{ lib, stdenv, fetchurl, zlib, gmp, ecm }: +{ lib, stdenv, fetchsvn, zlib, gmp, ecm }: stdenv.mkDerivation rec { pname = "msieve"; - version = "1.53"; + version = "r1050"; - src = fetchurl { - url = "mirror://sourceforge/msieve/msieve/Msieve%20v${version}/msieve${lib.replaceStrings ["."] [""] version}_src.tar.gz"; - sha256 = "1d1vv7j4rh3nnxsmvafi73qy7lw7n3akjlm5pjl3m936yapvmz65"; + src = fetchsvn { + url = "svn://svn.code.sf.net/p/msieve/code/trunk"; + rev = "1050"; + hash = "sha256-cn6OhE4zhrpB7BFrRdOnucjATbfo5mLkK7O0Usx1quE="; }; buildInputs = [ zlib gmp ecm ]; @@ -23,6 +24,7 @@ stdenv.mkDerivation rec { meta = { description = "A C library implementing a suite of algorithms to factor large integers"; + mainProgram = "msieve"; license = lib.licenses.publicDomain; homepage = "http://msieve.sourceforge.net/"; maintainers = [ lib.maintainers.roconnor ]; diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index ef8c041039b1..c1feeffdcb6d 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -4,11 +4,11 @@ }: stdenv.mkDerivation rec { pname = "nauty"; - version = "2.7r4"; + version = "2.8.8"; src = fetchurl { - url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] [""] version}.tar.gz"; - sha256 = "sha256-uBDIWm/imfO0yfJKr5KcrH+VRsLzXCDh3Qrbx0CISKY="; + url = "https://pallini.di.uniroma1.it/nauty${builtins.replaceStrings ["."] ["_"] version}.tar.gz"; + sha256 = "sha256-FZ0hVoEKa7JAQQzWHrZBrdhQiNnxXIiM2qN7hoH5Kc4="; }; outputs = [ "out" "dev" ]; @@ -44,7 +44,7 @@ stdenv.mkDerivation rec { # I'm not sure if the filename will remain the same for future changelog or # if it will track changes to minor releases. Lets see. Better than nothing # in any case. - changelog = "https://pallini.di.uniroma1.it/changes24-27.txt"; + changelog = "https://pallini.di.uniroma1.it/changes24-28.txt"; homepage = "https://pallini.di.uniroma1.it/"; }; } diff --git a/pkgs/applications/science/math/nota/default.nix b/pkgs/applications/science/math/nota/default.nix index 897785ef6e8b..810d7d6d72bc 100644 --- a/pkgs/applications/science/math/nota/default.nix +++ b/pkgs/applications/science/math/nota/default.nix @@ -37,4 +37,5 @@ mkDerivation rec { homepage = "https://kary.us/nota"; license = lib.licenses.mpl20; maintainers = with lib.maintainers; [ dtzWill ]; + mainProgram = "nota"; } diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix index ffe17bc3dec2..2fe77aa14a65 100644 --- a/pkgs/applications/science/math/palp/default.nix +++ b/pkgs/applications/science/math/palp/default.nix @@ -10,11 +10,11 @@ let in stdenv.mkDerivation rec { pname = "palp"; - version = "2.20"; + version = "2.21"; src = fetchurl { url = "http://hep.itp.tuwien.ac.at/~kreuzer/CY/palp/${pname}-${version}.tar.gz"; - sha256 = "1q1cl3vpdir16szy0jcadysydcrjp48hqxyx42kr8g9digkqjgkj"; + sha256 = "sha256-fkp78hmZioRMC8zgoXbknQdDy0tQWg4ZUym/LsGW3dc="; }; hardeningDisable = [ diff --git a/pkgs/applications/science/math/pcalc/default.nix b/pkgs/applications/science/math/pcalc/default.nix index 97888b712eb1..64ab5acebed2 100644 --- a/pkgs/applications/science/math/pcalc/default.nix +++ b/pkgs/applications/science/math/pcalc/default.nix @@ -19,6 +19,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://vapier.github.io/pcalc/"; description = "Programmer's calculator"; + mainProgram = "pcalc"; license = licenses.gpl2Plus; maintainers = with maintainers; [ ftrvxmtrx ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index bbfc8aed4428..9a37eeac66da 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation { meta = { description = "The Persistent Homology Software"; + mainProgram = "perseus"; longDescription = '' Persistent homology - or simply, persistence - is an algebraic topological invariant of a filtered cell complex. Perseus diff --git a/pkgs/applications/science/math/programmer-calculator/default.nix b/pkgs/applications/science/math/programmer-calculator/default.nix index ee48a1d0f1a3..9cb220ceca6a 100644 --- a/pkgs/applications/science/math/programmer-calculator/default.nix +++ b/pkgs/applications/science/math/programmer-calculator/default.nix @@ -21,6 +21,7 @@ gccStdenv.mkDerivation rec { meta = with lib; { description = "A terminal calculator for programmers"; + mainProgram = "pcalc"; longDescription = '' Terminal calculator made for programmers working with multiple number representations, sizes, and overall close to the bits diff --git a/pkgs/applications/science/math/ratpoints/default.nix b/pkgs/applications/science/math/ratpoints/default.nix index 42e6b7d00a5e..69b972fe9790 100644 --- a/pkgs/applications/science/math/ratpoints/default.nix +++ b/pkgs/applications/science/math/ratpoints/default.nix @@ -27,6 +27,7 @@ stdenv.mkDerivation rec { meta = { description = "A program to find rational points on hyperelliptic curves"; + mainProgram = "ratpoints"; license = lib.licenses.gpl2Plus; maintainers = [lib.maintainers.raskin]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/math/ries/default.nix b/pkgs/applications/science/math/ries/default.nix index eb759723256d..5c0626913e3c 100644 --- a/pkgs/applications/science/math/ries/default.nix +++ b/pkgs/applications/science/math/ries/default.nix @@ -14,6 +14,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://mrob.com/pub/ries/"; description = "Tool to produce a list of equations that approximately solve to a given number"; + mainProgram = "ries"; platforms = platforms.all; maintainers = with maintainers; [ symphorien ]; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/math/ripser/default.nix b/pkgs/applications/science/math/ripser/default.nix index 50ccee58f503..83cf6bc51aa4 100644 --- a/pkgs/applications/science/math/ripser/default.nix +++ b/pkgs/applications/science/math/ripser/default.nix @@ -50,6 +50,7 @@ stdenv.mkDerivation { meta = { description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes"; + mainProgram = "ripser"; homepage = "https://github.com/Ripser/ripser"; license = lib.licenses.lgpl3; maintainers = with lib.maintainers; [erikryb]; diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 765c691c9555..6624dcc36528 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -15,7 +15,7 @@ let pkgs = pkgs.python3.pkgs.overrideScope (self: super: { # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies sagelib = self.callPackage ./sagelib.nix { - inherit flint arb; + inherit flint3; inherit sage-src env-locations singular; inherit (maxima) lisp-compiler; linbox = pkgs.linbox.override { withSage = true; }; @@ -73,7 +73,7 @@ let sagelib = python3.pkgs.sagelib; sage-docbuild = python3.pkgs.sage-docbuild; inherit env-locations; - inherit python3 singular palp flint pythonEnv maxima; + inherit python3 singular palp flint3 pythonEnv maxima; pkg-config = pkgs.pkg-config; # not to confuse with pythonPackages.pkg-config }; @@ -125,9 +125,7 @@ let ignoreCollisions = true; } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible - arb = pkgs.arb.override { inherit flint; }; - - singular = pkgs.singular.override { inherit flint; }; + singular = pkgs.singular.override { inherit flint3; }; maxima = pkgs.maxima-ecl.override { lisp-compiler = pkgs.ecl.override { @@ -149,7 +147,7 @@ let # openblas instead of openblasCompat. Apparently other packages somehow use flints # blas when it is available. Alternative would be to override flint to use # openblasCompat. - flint = pkgs.flint.override { withBlas = false; }; + flint3 = pkgs.flint3.override { withBlas = false; }; # Multiple palp dimensions need to be available and sage expects them all to be # in the same folder. diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix index 39d358a1f9a8..1ca0f471a7ee 100644 --- a/pkgs/applications/science/math/sage/env-locations.nix +++ b/pkgs/applications/science/math/sage/env-locations.nix @@ -3,7 +3,6 @@ , pari , singular , maxima -, conway_polynomials , graphs , elliptic_curves , polytopes_db @@ -27,16 +26,13 @@ writeTextFile rec { export GPDOCDIR="${pari}/share/pari/doc" export SINGULARPATH='${singular}/share/singular' export SINGULAR_SO='${singular}/lib/libSingular.so' - export GAP_SO='${gap}/lib/libgap.so' export SINGULAR_EXECUTABLE='${singular}/bin/Singular' export MAXIMA_FAS='${maxima}/lib/maxima/${maxima.version}/binary-ecl/maxima.fas' export MAXIMA_PREFIX="${maxima}" - export CONWAY_POLYNOMIALS_DATA_DIR='${conway_polynomials}/share/conway_polynomials' export GRAPHS_DATA_DIR='${graphs}/share/graphs' export ELLCURVE_DATA_DIR='${elliptic_curves}/share/ellcurves' export POLYTOPE_DATA_DIR='${polytopes_db}/share/reflexive_polytopes' - export GAP_LIB_DIR='${gap}/lib/gap' - export GAP_SHARE_DIR='${gap}/share/gap' + export GAP_ROOT_PATHS='${gap}/lib/gap;${gap}/share/gap' export ECLDIR='${maxima.lisp-compiler}/lib/${maxima.lisp-compiler.pname}-${maxima.lisp-compiler.version}/' export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs" export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona" diff --git a/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix index fb8c3ec8a204..b45998bbcb86 100644 --- a/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix +++ b/pkgs/applications/science/math/sage/python-modules/sage-docbuild.nix @@ -4,6 +4,7 @@ , jupyter-sphinx , sphinx , sphinx-copybutton +, sphinx-inline-tabs }: buildPythonPackage rec { @@ -15,6 +16,7 @@ buildPythonPackage rec { jupyter-sphinx sphinx sphinx-copybutton + sphinx-inline-tabs ]; preBuild = '' diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix index 4c22470de910..4f179ea3a42b 100644 --- a/pkgs/applications/science/math/sage/sage-env.nix +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -42,7 +42,7 @@ , flintqs , blas , lapack -, flint +, flint3 , gmp , mpfr , zlib @@ -155,7 +155,7 @@ writeTextFile rec { # cython needs to find these libraries, otherwise will fail with `ld: cannot find -lflint` or similar export LDFLAGS='${ lib.concatStringsSep " " (map (pkg: "-L${pkg}/lib") [ - flint + flint3 gap glpk gmp @@ -174,7 +174,7 @@ writeTextFile rec { singular gmp.dev glpk - flint + flint3 gap mpfr.dev ]) diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index a77565e4072a..11bcc9ee3d5a 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -10,14 +10,14 @@ # all get the same sources with the same patches applied. stdenv.mkDerivation rec { - version = "10.2"; + version = "10.3"; pname = "sage-src"; src = fetchFromGitHub { owner = "sagemath"; repo = "sage"; rev = version; - sha256 = "sha256-VXnPdJhtw5Y/anecrVpevJDCyBVfnjksyuuZslNipm4="; + hash = "sha256-OHtMv8t0RrP6R8XIREU+C1vpazeQLWa75wx9Mv6BN1U="; }; # contains essential files (e.g., setup.cfg) generated by the bootstrap script. @@ -25,8 +25,8 @@ stdenv.mkDerivation rec { configure-src = fetchurl { # the hash below is the tagged commit's _parent_. it can also be found by looking for # the "configure" asset at https://github.com/sagemath/sage/releases/tag/${version} - url = "mirror://sageupstream/configure/configure-b2813506039143e6f0abe859ab67a343abf72c2e.tar.gz"; - sha256 = "sha256-a1v0XyoKI+zO6Sjm8DzEwItRHbIgRDbpj4UfwVH+/hw="; + url = "mirror://sageupstream/configure/configure-ab1a517b64b02bf15bbcb8d7c2d4d643bd5eff9b.tar.gz"; + hash = "sha256-pe9AxTM+gFSR4/eVfUzay+4bwjoubbYeDPc+avKjlaw="; }; # Patches needed because of particularities of nix or the way this is packaged. @@ -62,11 +62,11 @@ stdenv.mkDerivation rec { # should come from or be proposed to upstream. This list will probably never # be empty since dependencies update all the time. packageUpgradePatches = [ - # https://github.com/sagemath/sage/pull/37123, to land in 10.3.beta7 + # https://github.com/sagemath/sage/pull/37492 (fetchpatch { - name = "scipy-1.12-upgrade.patch"; - url = "https://github.com/sagemath/sage/commit/54eec464e9fdf18b411d9148aecb918178e95909.diff"; - sha256 = "sha256-9wyNrcSfF6mYFTIV4ev2OdD7igb0AeyZZYWSc/+JrIU="; + name = "singular-4.3.2p14-upgrade.patch"; + url = "https://github.com/sagemath/sage/commit/a0c56816b051e97da44ac0a4e4d4f6915cf7fa0f.diff"; + sha256 = "sha256-WGMmPeBoj2LUC+2qxWuaJL89QUuGt6axGvxWkpM9LYg="; }) ]; diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix index 227e4bbdbfdb..81b55e841d24 100644 --- a/pkgs/applications/science/math/sage/sage.nix +++ b/pkgs/applications/science/math/sage/sage.nix @@ -56,6 +56,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"; + mainProgram = "sage"; homepage = "https://www.sagemath.org"; license = licenses.gpl2Plus; maintainers = teams.sage.members; diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index 5a1f4ee473c9..b67b74e3a0f2 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -10,7 +10,6 @@ , iml , libpng , readline -, arb , blas , boost , brial @@ -18,7 +17,7 @@ , eclib , ecm , fflas-ffpack -, flint +, flint3 , gap , giac , givaro @@ -45,6 +44,7 @@ , singular , sqlite , symmetrica +, conway-polynomials , cvxopt , cypari2 , cysignals @@ -92,6 +92,7 @@ buildPythonPackage rec { version = src.version; pname = "sagelib"; src = sage-src; + pyproject = true; nativeBuildInputs = [ iml @@ -112,7 +113,6 @@ buildPythonPackage rec { propagatedBuildInputs = [ # native dependencies (TODO: determine which ones need to be propagated) - arb blas boost brial @@ -120,7 +120,7 @@ buildPythonPackage rec { eclib ecm fflas-ffpack - flint + flint3 gap giac givaro @@ -149,6 +149,7 @@ buildPythonPackage rec { symmetrica # from src/sage/setup.cfg and requirements.txt + conway-polynomials cvxopt cypari2 cysignals @@ -202,11 +203,7 @@ buildPythonPackage rec { mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython" mkdir -p "var/lib/sage/installed" - # version lower bounds are useful, but upper bounds are a hassle because - # Sage tests already catch any relevant API breakage. - # according to the discussion at https://trac.sagemath.org/ticket/33520, - # upper bounds will be less noisy starting from Sage 9.6. - sed -i 's/, <[^, ]*//' build/pkgs/*/install-requires.txt + sed -i "/sage-conf/d" src/{setup.cfg,pyproject.toml,requirements.txt} cd build/pkgs/sagelib/src ''; diff --git a/pkgs/applications/science/math/scalp/default.nix b/pkgs/applications/science/math/scalp/default.nix index 4145407d7aaa..fc230a11966f 100644 --- a/pkgs/applications/science/math/scalp/default.nix +++ b/pkgs/applications/science/math/scalp/default.nix @@ -50,6 +50,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Scalable Linear Programming Library"; + mainProgram = "scalp"; homepage = "https://digidev.digi.e-technik.uni-kassel.de/scalp/"; license = licenses.lgpl3; platforms = platforms.unix; diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index f77bd5a92243..a6c64066d88e 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -5,7 +5,7 @@ , sharutils , file , getconf -, flint +, flint3 , ntl , cddlib , gfan @@ -18,13 +18,13 @@ # want it to match the upstream format because sage depends on it. , texinfo4 , texliveSmall -, enableDocs ? !stdenv.isDarwin +, enableDocs ? true , enableGfanlib ? true }: stdenv.mkDerivation rec { pname = "singular"; - version = "4.3.2p2"; + version = "4.3.2p16"; # since the tarball does not contain tests, we fetch from GitHub. src = fetchFromGitHub { @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { # if a release is tagged (which sometimes does not happen), it will # be in the format below. rev = "Release-${lib.replaceStrings ["."] ["-"] version}"; - sha256 = "sha256-dtZmN8xUCZ9eSgmtBxqfJeWsM4W5Baq7xWXuNAxNLjA="; + sha256 = "sha256-5JZgI5lnfX4JlBSEAL7Wv6uao/57GBaMqwgslJt9Bjk="; # the repository's .gitattributes file contains the lines "/Tst/ # export-ignore" and "/doc/ export-ignore" so some directories are @@ -68,7 +68,7 @@ stdenv.mkDerivation rec { ncurses readline ntl - flint + flint3 lrcalc gfan ] ++ lib.optionals enableGfanlib [ diff --git a/pkgs/applications/science/math/speedcrunch/default.nix b/pkgs/applications/science/math/speedcrunch/default.nix index 98bc6b031f19..a77474b86ffa 100644 --- a/pkgs/applications/science/math/speedcrunch/default.nix +++ b/pkgs/applications/science/math/speedcrunch/default.nix @@ -23,6 +23,7 @@ mkDerivation rec { homepage = "http://speedcrunch.org"; license = licenses.gpl2Plus; description = "A fast power user calculator"; + mainProgram = "speedcrunch"; longDescription = '' SpeedCrunch is a fast, high precision and powerful desktop calculator. Among its distinctive features are a scrollable display, up to 50 decimal diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/applications/science/math/weka/default.nix index 004060f832c2..6f907ba9c0c3 100644 --- a/pkgs/applications/science/math/weka/default.nix +++ b/pkgs/applications/science/math/weka/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.cs.waikato.ac.nz/ml/weka/"; description = "Collection of machine learning algorithms for data mining tasks"; + mainProgram = "weka"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl2Plus; maintainers = [ maintainers.mimame ]; diff --git a/pkgs/applications/science/math/wxmaxima/default.nix b/pkgs/applications/science/math/wxmaxima/default.nix index 057a11fa3cdd..4d2815d12997 100644 --- a/pkgs/applications/science/math/wxmaxima/default.nix +++ b/pkgs/applications/science/math/wxmaxima/default.nix @@ -46,6 +46,7 @@ stdenv.mkDerivation (finalAttrs:{ meta = with lib; { description = "Cross platform GUI for the computer algebra system Maxima"; + mainProgram = "wxmaxima"; license = licenses.gpl2; homepage = "https://wxmaxima-developers.github.io/wxmaxima/"; maintainers = with maintainers; [ doronbehar ]; diff --git a/pkgs/applications/science/math/zegrapher/default.nix b/pkgs/applications/science/math/zegrapher/default.nix index 32633eb8015d..2beaf5757a55 100644 --- a/pkgs/applications/science/math/zegrapher/default.nix +++ b/pkgs/applications/science/math/zegrapher/default.nix @@ -26,6 +26,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://zegrapher.com/"; description = "An open source math plotter"; + mainProgram = "ZeGrapher"; longDescription = '' An open source, free and easy to use math plotter. It can plot functions, sequences, parametric equations and data on the plane. diff --git a/pkgs/applications/science/misc/bada-bib/default.nix b/pkgs/applications/science/misc/bada-bib/default.nix index 0eafebd9628c..189531532574 100644 --- a/pkgs/applications/science/misc/bada-bib/default.nix +++ b/pkgs/applications/science/misc/bada-bib/default.nix @@ -75,6 +75,7 @@ python3Packages.buildPythonApplication rec { meta = with lib; { homepage = "https://github.com/RogerCrocker/BadaBib"; description = "A simple BibTeX Viewer and Editor"; + mainProgram = "badabib"; maintainers = [ maintainers.Cogitri ]; license = licenses.gpl3Plus; }; diff --git a/pkgs/applications/science/misc/colmap/default.nix b/pkgs/applications/science/misc/colmap/default.nix index a029f5440b25..64a7952be4cc 100644 --- a/pkgs/applications/science/misc/colmap/default.nix +++ b/pkgs/applications/science/misc/colmap/default.nix @@ -37,7 +37,7 @@ mkDerivation rec { nativeBuildInputs = [ cmake ] ++ lib.optionals cudaSupport [ - cudaPackages.autoAddOpenGLRunpathHook + cudaPackages.autoAddDriverRunpath ]; meta = with lib; { diff --git a/pkgs/applications/science/misc/convertall/default.nix b/pkgs/applications/science/misc/convertall/default.nix index 9a7ac2a8b13c..534562b028d8 100644 --- a/pkgs/applications/science/misc/convertall/default.nix +++ b/pkgs/applications/science/misc/convertall/default.nix @@ -30,6 +30,7 @@ in stdenv.mkDerivation rec { meta = with lib; { homepage = "https://convertall.bellz.org/"; description = "Graphical unit converter"; + mainProgram = "convertall"; license = licenses.gpl2Plus; maintainers = with maintainers; [ orivej ]; platforms = pyqt5.meta.platforms; diff --git a/pkgs/applications/science/misc/cwltool/default.nix b/pkgs/applications/science/misc/cwltool/default.nix index fb3b26a12edf..9b4c711aba8f 100644 --- a/pkgs/applications/science/misc/cwltool/default.nix +++ b/pkgs/applications/science/misc/cwltool/default.nix @@ -84,6 +84,7 @@ python3.pkgs.buildPythonApplication rec { meta = with lib; { description = "Common Workflow Language reference implementation"; + mainProgram = "cwltool"; homepage = "https://www.commonwl.org"; changelog = "https://github.com/common-workflow-language/cwltool/releases/tag/${version}"; license = with licenses; [ asl20 ]; diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index bd5b698988d4..f4aaac1a3823 100644 --- a/pkgs/applications/science/misc/cytoscape/default.nix +++ b/pkgs/applications/science/misc/cytoscape/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation rec { meta = { homepage = "http://www.cytoscape.org"; description = "A general platform for complex network analysis and visualization"; + mainProgram = "cytoscape"; license = lib.licenses.lgpl21; maintainers = [lib.maintainers.mimame]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/misc/foldingathome/client.nix b/pkgs/applications/science/misc/foldingathome/client.nix index 108dcc284ea9..6ff159cc54cb 100644 --- a/pkgs/applications/science/misc/foldingathome/client.nix +++ b/pkgs/applications/science/misc/foldingathome/client.nix @@ -3,18 +3,23 @@ , fetchFromGitHub , ocl-icd , openssl +, re2 +, libevent +, git +, zlib +, expat , scons , stdenv , extraPkgs ? [ ] }: let - version = "8.3.1"; + version = "8.3.7"; cbangSrc = fetchFromGitHub { owner = "cauldrondevelopmentllc"; repo = "cbang"; rev = "bastet-v${version}"; - hash = "sha256-cuyfJG5aDJ6e2SllxwKTViG0j8FWHvjcTaaBBtkgEdU="; + sha256 = "sha256-acAImItdkgo6PBFL6Vu/caIdcnvp/3VEW2lgVDgKy9g="; }; fah-client = stdenv.mkDerivation { @@ -25,10 +30,10 @@ let owner = "FoldingAtHome"; repo = "fah-client-bastet"; rev = "v${version}"; - hash = "sha256-Ztc2im4Xmk8f6GotGRgA5zDkcyQFnodUvroJVl+ApT4="; + sha256 = "sha256-d+LY/R4TAko+2e2W76KEBQ8fXj0hzzmBOm+c4tksXMA="; }; - nativeBuildInputs = [ scons ]; + nativeBuildInputs = [ scons re2 libevent git ]; buildInputs = [ openssl ]; @@ -63,7 +68,7 @@ in buildFHSEnv { name = fah-client.name; - targetPkgs = _: [ fah-client ocl-icd ] ++ extraPkgs; + targetPkgs = _: [ fah-client ocl-icd zlib expat ] ++ extraPkgs; runScript = "/bin/fah-client"; diff --git a/pkgs/applications/science/misc/gephi/default.nix b/pkgs/applications/science/misc/gephi/default.nix index 22c453dbab30..ab8134daf3ae 100644 --- a/pkgs/applications/science/misc/gephi/default.nix +++ b/pkgs/applications/science/misc/gephi/default.nix @@ -37,6 +37,7 @@ mavenJdk11.buildMavenPackage rec { meta = with lib; { description = "A platform for visualizing and manipulating large graphs"; + mainProgram = "gephi"; homepage = "https://gephi.org"; sourceProvenance = with sourceTypes; [ fromSource diff --git a/pkgs/applications/science/misc/gplates/default.nix b/pkgs/applications/science/misc/gplates/default.nix index 4ab17c22934e..74dd61a2228c 100644 --- a/pkgs/applications/science/misc/gplates/default.nix +++ b/pkgs/applications/science/misc/gplates/default.nix @@ -67,6 +67,7 @@ in stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Desktop software for the interactive visualisation of plate-tectonics"; + mainProgram = "gplates"; homepage = "https://www.gplates.org"; license = licenses.gpl2Only; platforms = platforms.all; diff --git a/pkgs/applications/science/misc/netlogo/default.nix b/pkgs/applications/science/misc/netlogo/default.nix index db8f0a717aa1..13c3c36f90ae 100644 --- a/pkgs/applications/science/misc/netlogo/default.nix +++ b/pkgs/applications/science/misc/netlogo/default.nix @@ -46,6 +46,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A multi-agent programmable modeling environment"; + mainProgram = "netlogo"; longDescription = '' NetLogo is a multi-agent programmable modeling environment. It is used by many tens of thousands of students, teachers and researchers worldwide. diff --git a/pkgs/applications/science/misc/nextinspace/default.nix b/pkgs/applications/science/misc/nextinspace/default.nix index 78e21dcd8788..742b4cb622c2 100644 --- a/pkgs/applications/science/misc/nextinspace/default.nix +++ b/pkgs/applications/science/misc/nextinspace/default.nix @@ -37,6 +37,7 @@ python3.pkgs.buildPythonApplication rec { meta = with lib; { description = "Print upcoming space-related events in your terminal"; + mainProgram = "nextinspace"; homepage = "https://github.com/The-Kid-Gid/nextinspace"; license = licenses.gpl3Only; maintainers = with maintainers; [ penguwin ]; diff --git a/pkgs/applications/science/misc/reason-shell/default.nix b/pkgs/applications/science/misc/reason-shell/default.nix index aa1544669ed8..848f31abe4c6 100644 --- a/pkgs/applications/science/misc/reason-shell/default.nix +++ b/pkgs/applications/science/misc/reason-shell/default.nix @@ -32,6 +32,7 @@ rustPlatform.buildRustPackage rec { meta = with lib; { description = "A shell for research papers"; + mainProgram = "reason"; homepage = "https://github.com/jaywonchung/reason"; changelog = "https://github.com/jaywonchung/reason/releases/tag/${src.rev}"; license = licenses.mit; diff --git a/pkgs/applications/science/misc/rink/default.nix b/pkgs/applications/science/misc/rink/default.nix index b7e523f67474..1e88047eba72 100644 --- a/pkgs/applications/science/misc/rink/default.nix +++ b/pkgs/applications/science/misc/rink/default.nix @@ -23,6 +23,7 @@ rustPlatform.buildRustPackage rec { meta = with lib; { description = "Unit-aware calculator"; + mainProgram = "rink"; homepage = "https://rinkcalc.app"; license = with licenses; [ mpl20 gpl3Plus ]; maintainers = with maintainers; [ sb0 Br1ght0ne ]; diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 5081b471fc95..628b40cd1300 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -89,6 +89,7 @@ python3.pkgs.buildPythonApplication rec { homepage = "https://snakemake.github.io"; license = licenses.mit; description = "Python-based execution environment for make-like workflows"; + mainProgram = "snakemake"; longDescription = '' Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, diff --git a/pkgs/applications/science/misc/vite/default.nix b/pkgs/applications/science/misc/vite/default.nix index c748b6d1bd3f..f1c9329c94df 100644 --- a/pkgs/applications/science/misc/vite/default.nix +++ b/pkgs/applications/science/misc/vite/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = { description = "Visual Trace Explorer (ViTE), a tool to visualize execution traces"; + mainProgram = "vite"; longDescription = '' ViTE is a trace explorer. It is a tool to visualize execution diff --git a/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix index a13a071584fd..75ab576212d7 100644 --- a/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix +++ b/pkgs/applications/science/molecular-dynamics/dl-poly-classic/default.nix @@ -35,6 +35,7 @@ stdenv.mkDerivation { meta = with lib; { homepage = "https://www.ccp5.ac.uk/DL_POLY_C"; description = "DL_POLY Classic is a general purpose molecular dynamics simulation package"; + mainProgram = "DLPOLY.X"; license = licenses.bsdOriginal; platforms = platforms.unix; maintainers = [ maintainers.costrouc ]; diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index db27bb188cf5..4c2a80c2f1b7 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -63,7 +63,7 @@ stdenv.mkDerivation (finalAttrs: { pkg-config # Although not always needed, it is needed if cmakeFlags include # GPU_API=cuda, and it doesn't users that don't enable the GPU package. - cudaPackages.autoAddOpenGLRunpathHook + cudaPackages.autoAddDriverRunpath ]; passthru = { diff --git a/pkgs/applications/science/physics/nnpdf/default.nix b/pkgs/applications/science/physics/nnpdf/default.nix index 26e8247f85e3..d0104095f39a 100644 --- a/pkgs/applications/science/physics/nnpdf/default.nix +++ b/pkgs/applications/science/physics/nnpdf/default.nix @@ -55,6 +55,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "An open-source machine learning framework for global analyses of parton distributions"; + mainProgram = "evolven3fit"; homepage = "https://docs.nnpdf.science/"; license = licenses.gpl3Only; maintainers = [ maintainers.veprbl ]; diff --git a/pkgs/applications/science/physics/quantomatic/default.nix b/pkgs/applications/science/physics/quantomatic/default.nix index 4baa65201e0b..caff65f1d71b 100644 --- a/pkgs/applications/science/physics/quantomatic/default.nix +++ b/pkgs/applications/science/physics/quantomatic/default.nix @@ -23,6 +23,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A piece of software for reasoning about monoidal theories; in particular, quantum information processing"; + mainProgram = "quantomatic"; license = licenses.gpl3; homepage = "https://quantomatic.github.io/"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; diff --git a/pkgs/applications/science/physics/sacrifice/default.nix b/pkgs/applications/science/physics/sacrifice/default.nix index ec0620d3d8ed..352b65dc700c 100644 --- a/pkgs/applications/science/physics/sacrifice/default.nix +++ b/pkgs/applications/science/physics/sacrifice/default.nix @@ -40,6 +40,7 @@ stdenv.mkDerivation { meta = { description = "A standalone contribution to AGILe for steering Pythia 8"; + mainProgram = "run-pythia"; license = lib.licenses.gpl2; homepage = "https://agile.hepforge.org/trac/wiki/Sacrifice"; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/physics/xflr5/default.nix b/pkgs/applications/science/physics/xflr5/default.nix index eb60c12e9f0c..497be8fcbaa9 100644 --- a/pkgs/applications/science/physics/xflr5/default.nix +++ b/pkgs/applications/science/physics/xflr5/default.nix @@ -15,6 +15,7 @@ mkDerivation rec { meta = with lib; { description = "An analysis tool for airfoils, wings and planes"; + mainProgram = "xflr5"; homepage = "https://sourceforge.net/projects/xflr5/"; license = licenses.gpl3; maintainers = [ maintainers.esclear ]; diff --git a/pkgs/applications/science/physics/xnec2c/default.nix b/pkgs/applications/science/physics/xnec2c/default.nix index 87daa8cac853..26ec1518fed5 100644 --- a/pkgs/applications/science/physics/xnec2c/default.nix +++ b/pkgs/applications/science/physics/xnec2c/default.nix @@ -32,6 +32,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.xnec2c.org/"; description = "Graphical antenna simulation"; + mainProgram = "xnec2c"; license = licenses.gpl3; maintainers = with maintainers; [ mvs ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/programming/plm/default.nix b/pkgs/applications/science/programming/plm/default.nix index e4213fe7a8ff..a0a16515e228 100644 --- a/pkgs/applications/science/programming/plm/default.nix +++ b/pkgs/applications/science/programming/plm/default.nix @@ -31,6 +31,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Free cross-platform programming exerciser"; + mainProgram = "plm"; homepage = "http://people.irisa.fr/Martin.Quinson/Teaching/PLM/"; license = licenses.gpl3; sourceProvenance = with sourceTypes; [ binaryBytecode ]; diff --git a/pkgs/applications/science/robotics/betaflight-configurator/default.nix b/pkgs/applications/science/robotics/betaflight-configurator/default.nix index e8e5fbba4e49..252eadc1c39c 100644 --- a/pkgs/applications/science/robotics/betaflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/betaflight-configurator/default.nix @@ -43,6 +43,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "The Betaflight flight control system configuration tool"; + mainProgram = "betaflight-configurator"; longDescription = '' A crossplatform configuration tool for the Betaflight flight control system. Various types of aircraft are supported by the tool and by Betaflight, e.g. diff --git a/pkgs/applications/science/robotics/emuflight-configurator/default.nix b/pkgs/applications/science/robotics/emuflight-configurator/default.nix index 0a733261ea2b..2c51355eb54f 100644 --- a/pkgs/applications/science/robotics/emuflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/emuflight-configurator/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "The Emuflight flight control system configuration tool"; + mainProgram = "emuflight-configurator"; longDescription = '' A crossplatform configuration tool for the Emuflight flight control system. Various types of aircraft are supported by the tool and by Emuflight, e.g. diff --git a/pkgs/applications/science/robotics/inav-configurator/default.nix b/pkgs/applications/science/robotics/inav-configurator/default.nix index 9efb9163e5e0..f5216eaf6c92 100644 --- a/pkgs/applications/science/robotics/inav-configurator/default.nix +++ b/pkgs/applications/science/robotics/inav-configurator/default.nix @@ -44,6 +44,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "The iNav flight control system configuration tool"; + mainProgram = "inav-configurator"; longDescription = '' A crossplatform configuration tool for the iNav flight control system. Various types of aircraft are supported by the tool and by iNav, e.g. diff --git a/pkgs/applications/science/robotics/mission-planner/default.nix b/pkgs/applications/science/robotics/mission-planner/default.nix index 856fdfec8235..f6e7e5f114fa 100644 --- a/pkgs/applications/science/robotics/mission-planner/default.nix +++ b/pkgs/applications/science/robotics/mission-planner/default.nix @@ -46,6 +46,7 @@ in stdenv.mkDerivation rec { meta = with lib; { description = "An ArduPilot ground station"; + mainProgram = "mission-planner"; longDescription = '' Full-featured ground station application for the ArduPilot open source autopilot project. Lets you both flash, configure and control ArduPilot diff --git a/pkgs/applications/science/robotics/sumorobot-manager/default.nix b/pkgs/applications/science/robotics/sumorobot-manager/default.nix index 343f9fad105b..eb9322f0fb22 100644 --- a/pkgs/applications/science/robotics/sumorobot-manager/default.nix +++ b/pkgs/applications/science/robotics/sumorobot-manager/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Desktop App for managing SumoRobots"; + mainProgram = "sumorobot-manager"; homepage = "https://www.robokoding.com/kits/sumorobot/sumomanager/"; license = licenses.mit; maintainers = with maintainers; [ abbradar ]; |