Overlays: Add Smoldyn (Depends on fenix)
Antoine Fauroux
parent
cd960974ff
commit
1b7e4d9a2b
39
flake.lock
39
flake.lock
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@ -1,5 +1,26 @@
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{
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"nodes": {
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"fenix": {
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"inputs": {
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"nixpkgs": [
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"nixpkgs"
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],
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"rust-analyzer-src": "rust-analyzer-src"
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},
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"locked": {
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"lastModified": 1749537578,
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"narHash": "sha256-dYEEiNRw7rClQi4Y7t9jlHjbuUvSbdTdM/jXwXuaDeQ=",
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"owner": "nix-community",
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"repo": "fenix",
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"rev": "5e3ce25aa3048f14f206a6c4fab46af6ad939482",
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"type": "github"
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},
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"original": {
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"owner": "nix-community",
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"repo": "fenix",
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"type": "github"
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}
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},
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"flake-compat": {
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"flake": false,
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"locked": {
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@ -87,12 +108,30 @@
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},
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"root": {
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"inputs": {
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"fenix": "fenix",
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"nix-matlab": "nix-matlab",
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"nixpkgs": "nixpkgs",
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"nixpkgs-unstable": "nixpkgs-unstable",
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"sops-nix": "sops-nix"
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}
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},
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"rust-analyzer-src": {
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"flake": false,
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"locked": {
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"lastModified": 1749493129,
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"narHash": "sha256-nQ+gKRLXkl7gLY836ULyAwR3O0E/+vakZt78OQ+p9Fc=",
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"owner": "rust-lang",
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"repo": "rust-analyzer",
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"rev": "bf6d44581085bb9b6e285902a7fae77325703171",
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"type": "github"
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},
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"original": {
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"owner": "rust-lang",
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"ref": "nightly",
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"repo": "rust-analyzer",
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"type": "github"
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}
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},
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"sops-nix": {
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"inputs": {
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"nixpkgs": [
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@ -16,8 +16,12 @@
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# Follow the system nixpkgs
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inputs.nixpkgs.follows = "nixpkgs";
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};
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fenix = {
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url = "github:nix-community/fenix";
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inputs.nixpkgs.follows = "nixpkgs";
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};
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};
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outputs = { self, nixpkgs, nixpkgs-unstable, sops-nix, nix-matlab }@attrs: let
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outputs = { self, nixpkgs, nixpkgs-unstable, sops-nix, nix-matlab, ... }@attrs: let
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system = "x86_64-linux";
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unfree-overlay = final: prev: {
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unfree = import nixpkgs {
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@ -35,7 +39,7 @@
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config.cudaSupport = true;
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};
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};
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python-overlay = import ./overlays/python.nix;
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python-overlay = import ./overlays/python.nix attrs;
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applyOverlays = overlays: ({...}:{ nixpkgs.overlays = overlays; });
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flakes = {...}: {nix.settings.experimental-features = [ "nix-command" "flakes" ];};
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in {
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@ -45,6 +45,8 @@
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spynnaker
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# fetching neuromorphic data:
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tonic
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# Stochastic simulation
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# smoldyn-py
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# Librairies to deal with mesh
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@ -0,0 +1,56 @@
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{
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lib,
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stdenv,
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fetchFromGitHub,
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cmake,
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pkg-config,
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bzip2,
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libxml2,
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swig,
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python ? null,
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withPython ? false,
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}:
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stdenv.mkDerivation (attrs: {
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pname = "libsbml";
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version = "5.20.4";
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src = fetchFromGitHub {
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owner = "sbmlteam";
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repo = "libsbml";
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rev = "v${attrs.version}";
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hash = "sha256-qWTN033YU4iWzt+mXQaP5W/6IF5nebF4PwNVkyL8wTg=";
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};
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nativeBuildInputs = [
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cmake
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pkg-config
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swig
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] ++ lib.optional withPython python.pkgs.pythonImportsCheckHook;
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buildInputs = [
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bzip2.dev
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libxml2
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] ++ lib.optional withPython python;
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# libSBML doesn't always make use of pkg-config
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cmakeFlags = [
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"-DLIBXML_INCLUDE_DIR=${lib.getDev libxml2}/include/libxml2"
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"-DLIBXML_LIBRARY=${lib.getLib libxml2}/lib/libxml2${stdenv.hostPlatform.extensions.sharedLibrary}"
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"-DPKG_CONFIG_EXECUTABLE=${lib.getBin pkg-config}/bin/pkg-config"
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"-DSWIG_EXECUTABLE=${lib.getBin swig}/bin/swig"
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] ++ lib.optional withPython "-DWITH_PYTHON=ON";
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postInstall = lib.optional withPython ''
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mv $out/${python.sitePackages}/libsbml/libsbml.py $out/${python.sitePackages}/libsbml/__init__.py
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'';
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pythonImportsCheck = [ "libsbml" ];
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meta = with lib; {
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description = "Library for manipulating Systems Biology Markup Language (SBML)";
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homepage = "https://github.com/sbmlteam/libsbml";
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license = licenses.lgpl21Only;
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maintainers = [ maintainers.kupac ];
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platforms = platforms.all;
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};
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})
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@ -126,4 +126,4 @@ final: final-py: prev-py: {
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pytorch-data
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];
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};
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} // (import ./spynnaker.nix final final-py prev-py)
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} // (import ./spynnaker.nix final final-py prev-py) #// (import ./smoldyn.nix final final-py prev-py)
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@ -1,5 +1,8 @@
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final: prev: {
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inputs: final: prev:
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(inputs.fenix.overlays.default final prev) // {
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pythonPackagesExtensions = prev.pythonPackagesExtensions ++ [(
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(import ./python-packages.nix final)
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)];
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libsbml = final.callPackage ./libsbml.nix { };
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}
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@ -0,0 +1,362 @@
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final: final-py: prev-py: let
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rust-new = p: p.fenix.stable;
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rustPlatform = final.makeRustPlatform {
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inherit (rust-new final) cargo rustc;
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};
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py = final-py;
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pyenv-smoldyn = py.python.withPackages (p: with p; [
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setuptools
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wheel
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pybind11
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pip
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]);
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smoldyn = final.fastStdenv.mkDerivation rec {
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pname = "smoldyn";
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version = "2.74";
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outputs = [ "out" "py" ];
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env.NIX_CFLAGS_COMPILE = "-march=native -mtune=native";
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src = final.fetchzip {
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url = "https://www.smoldyn.org/smoldyn-${version}.zip";
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hash = "sha256-cKUMGgnPrHf2dNyFHmjpERgIMU0OltUZ/uhBfxpU4e4=";
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};
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nativeBuildInputs = with final; [
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cmake
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];
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cmakeFlags = [
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"-DSMOLDYN_VERSION=${version}"
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"-DOPTION_ZLIB=ON"
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];
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buildInputs = with final; [
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libGL
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libGLU
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freeglut
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libtiff
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zlib
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pyenv-smoldyn
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];
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postInstall = ''
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cp -r py $py
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'';
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};
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in {
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libsbml = final.libsbml.override {
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python=py.python;
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withPython=true;
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};
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libcombine = py.buildPythonPackage rec {
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pname = "libcombine";
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version = "0.2.20";
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src = final.fetchFromGitHub {
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owner = "sbmlteam";
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repo = "libcombine";
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rev = "v${version}";
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fetchSubmodules = true;
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hash = "sha256-9MMQr0hQLo1l8B4nlzkk48zohCohdheojRTjKrCE6og=";
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};
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preBuild = ''
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cd ..
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cp src/bindings/python/setup.py .
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'';
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nativeBuildInputs = with final; [
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swig cmake
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];
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buildInputs = with py; [
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libsbml
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final.zlib
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];
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};
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libsedml = py.buildPythonPackage rec {
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pname = "libsedml";
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version = "2.0.28";
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src = final.fetchFromGitHub {
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owner = "fbergmann";
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repo = "libSEDML";
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rev = "v${version}";
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fetchSubmodules = true;
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hash = "sha256-Pxts0kKj3BlfrwhXJjNvL936aSXiTb1cnccsW2lbUaM=";
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};
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preBuild = ''
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cp src/bindings/python/setup.py .
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'';
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buildInputs = [
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final.cmake
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];
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};
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pyomexmeta = py.buildPythonPackage rec {
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pname = "pyomexmeta";
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version = "1.2.14";
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src = final.fetchFromGitHub {
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owner = "sys-bio";
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repo = "libOmexMeta";
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rev = "v${version}";
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hash = "sha256-OMCq8uR3kC5cZpFyy28A02OSiVO4b49lFyWmbCeaw6c=";
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};
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};
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# https://github.com/simularium/simulariumio/blob/main/pyproject.toml
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simulariumio = py.buildPythonPackage rec {
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pname = "simulariumio";
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version = "1.12.0";
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src = final.fetchFromGitHub {
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owner = "simularium";
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repo = "simulariumio";
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rev = "v${version}";
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hash = "sha256-Jl7KXEXeheYJRpgVcHyK6YUzyQMafQnABlrZM9d7c9g=";
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leaveDotGit = true;
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};
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format = "pyproject";
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nativeBuildInputs = with py; [
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setuptools
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setuptools_scm
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wheel
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];
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SETUPTOOLS_SCM_PRETEND_VERSION=version;
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propagatedBuildInputs = with py; [
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numpy
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pandas
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pint
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];
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};
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# https://github.com/biosimulators/Biosimulators_simularium
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biosimulator_simularium = py.buildPythonPackage rec {
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pname = "biosimulator";
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version = "0.6.3";
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src = final.fetchFromGitHub {
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owner = "biosimulators";
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repo = "biosimulators_simularium";
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rev = "v${version}";
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hash = "sha256-t0YM5Ika6Glvw3wvV71w7IHo6AovXz+7012rueEkoFw=";
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};
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format = "pyproject";
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nativeBuildInputs = with py; [
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poetry-core
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];
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};
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biosimulator_util = py.buildPythonPackage rec {
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pname = "biosimulator";
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version = "0.2.3";
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src = final.fetchFromGitHub {
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owner = "biosimulators";
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repo = "biosimulators_utils";
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rev = "${version}";
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hash = "sha256-/4HxruGpyJ6Guk4or/i+XI1JnHh2y7tWmw0AgdP5bkU=";
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};
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nativeBuildInputs = with py; [
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pip
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];
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propagatedBuildInputs = with py; [
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capturer
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pkg_utils
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jsonschema
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flaky
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bezier
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rdflib
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kisao
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appdirs
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matplotlib
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docker
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cement
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regex
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biopython
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lxml
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natsort
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simplejson
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libcombine
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libsedml
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pyomexmeta
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pyyaml
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evalidate
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];
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doCheck = false;
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};
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# https://github.com/yaroslaff/evalidate
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evalidate = py.buildPythonPackage rec {
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pname = "evalidate";
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version = "2.0.3";
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format = "pyproject";
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src = final.fetchFromGitHub {
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owner = "yaroslaff";
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repo = "evalidate";
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rev = "v${version}";
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hash = "sha256-0SdGjsddX/iYeXpB9AdD7hnBH8raGHvSZ7D30a3sRXE=";
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};
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nativeBuildInputs = with py; [
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hatchling
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];
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propagatedBuildInputs = with py; [
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uritools
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];
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};
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pkg_utils = py.buildPythonPackage rec {
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pname = "pkg_utils";
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version = "0.0.5";
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src = final.fetchFromGitHub {
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owner = "KarrLab";
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repo = "pkg_utils";
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rev = "${version}";
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hash = "sha256-u6t4z1MoEkgoPkZtJuTYUbL5HyrkYthSPu9bhm8IZwo=";
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};
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nativeBuildInputs = with py; [
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pip
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];
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propagatedBuildInputs = with py; [
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glob2
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requirements-parser
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configparser
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];
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};
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pronto = py.buildPythonPackage rec {
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pname = "pronto";
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version = "2.7.0";
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src = final.fetchFromGitHub {
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owner = "althonos";
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repo = "pronto";
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rev = "v${version}";
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hash = "sha256-e+Nf+0kOH8d8KU2U9imxfeP1AjY2g/oZwZmQG394cts=";
|
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};
|
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|
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nativeBuildInputs = with py; [
|
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setuptools
|
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];
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buildInputs = with py; [
|
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python-dateutil
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];
|
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format = "pyproject";
|
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};
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kisao = py.buildPythonPackage rec {
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pname = "kisao";
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version = "2.34";
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src = final.fetchFromGitHub {
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owner = "SED-ML";
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repo = "Kisao";
|
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rev = "${version}";
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hash = "sha256-ozL1G9ylRhQL+lUCLwb2LSjooF5P8AgiWRMOWrBrDl8=";
|
||||
};
|
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|
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prePatch = ''
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cd libkisao/python
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'';
|
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|
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nativeBuildInputs = with py; [
|
||||
pip
|
||||
];
|
||||
|
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propagatedBuildInputs = with py; [
|
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pkg_utils
|
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termcolor
|
||||
pronto
|
||||
python-dateutil
|
||||
networkx
|
||||
fastobo
|
||||
chardet
|
||||
];
|
||||
};
|
||||
|
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fastobo = py.buildPythonPackage rec {
|
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pname = "fastobo";
|
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version = "0.13.0";
|
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|
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src = final.fetchFromGitHub {
|
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owner = "fastobo";
|
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repo = "fastobo-py";
|
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rev = "v${version}";
|
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hash = "sha256-8v9KjYX6Fy/ALFlYfSXpW40p0z54F5tpr10TAWenizk=";
|
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};
|
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|
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cargoDeps = rustPlatform.fetchCargoTarball {
|
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inherit src;
|
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name = "${pname}-${version}";
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hash = "sha256-USh7WK18I8A4VdGsUAnbrSiJuBYyq4539MlyS5ANSGo=";
|
||||
};
|
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|
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format = "pyproject";
|
||||
|
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nativeBuildInputs = [
|
||||
rustPlatform.cargoSetupHook
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(rustPlatform.maturinBuildHook.override {
|
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pkgsHostTarget = {
|
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inherit (rust-new final.pkgsHostTarget) cargo rustc;
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inherit (final.pkgsHostTarget) maturin;
|
||||
};
|
||||
})
|
||||
];
|
||||
};
|
||||
|
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bezier = py.buildPythonPackage rec {
|
||||
pname = "bezier";
|
||||
version = "2020.2.3";
|
||||
|
||||
src = final.fetchFromGitHub {
|
||||
owner = "dhermes";
|
||||
repo = "bezier";
|
||||
rev = "${version}";
|
||||
hash = "sha256-yuq2+Yy9XO2KwLlsB0IxjseG/axNBa5KuxBZ2J22ruE=";
|
||||
};
|
||||
BEZIER_NO_EXTENSION="1";
|
||||
nativeBuildInputs = with py; [
|
||||
pip
|
||||
];
|
||||
buildInputs = with py; [
|
||||
pytest
|
||||
matplotlib
|
||||
seaborn
|
||||
scipy
|
||||
];
|
||||
propagatedBuildInputs = with py; [
|
||||
numpy
|
||||
sympy
|
||||
];
|
||||
};
|
||||
|
||||
smoldyn-py = py.buildPythonPackage {
|
||||
pname = "smoldyn";
|
||||
version = smoldyn.version;
|
||||
|
||||
src = smoldyn.py;
|
||||
|
||||
postPatch = ''
|
||||
sed -e '37,38d' -i setup.py
|
||||
'';
|
||||
|
||||
propagatedBuildInputs = with py; [
|
||||
biosimulator_util
|
||||
biosimulator_simularium
|
||||
simulariumio
|
||||
numpy
|
||||
pandas
|
||||
h5py
|
||||
openpyxl
|
||||
pyvista
|
||||
];
|
||||
};
|
||||
}
|
||||
Loading…
Reference in New Issue