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"registry+https://github.com/rust-lang/crates.io-index" +checksum = "c179869f34fc7c01830d3ce7ea2086bc3a07e0d35289b667d0a8bf910258926c" +dependencies = [ + "lzma-sys", +] diff --git a/default.nix b/default.nix new file mode 100644 index 0000000000..89308a3888 --- /dev/null +++ b/default.nix @@ -0,0 +1,10 @@ +(import + ( + fetchTarball { + url = "https://github.com/edolstra/flake-compat/archive/99f1c2157fba4bfe6211a321fd0ee43199025dbf.tar.gz"; + sha256 = "0x2jn3vrawwv9xp15674wjz9pixwjyj3j771izayl962zziivbx2"; + } + ) + { + src = ./.; + }).defaultNix diff --git a/flake.lock b/flake.lock new file mode 100644 index 0000000000..f86273ccb8 --- /dev/null +++ b/flake.lock @@ -0,0 +1,184 @@ +{ + "nodes": { + "flake-utils": { + "locked": { + "lastModified": 1642700792, + "narHash": "sha256-XqHrk7hFb+zBvRg6Ghl+AZDq03ov6OshJLiSWOoX5es=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "846b2ae0fc4cc943637d3d1def4454213e203cba", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, + "mach-nix": { + "inputs": { + "flake-utils": [ + "utils" + ], + "nixpkgs": [ + "nixpkgs" + ], + "pypi-deps-db": [ + "pypi-deps-db" + ] + }, + "locked": { + "lastModified": 1643953409, + "narHash": "sha256-CJDg/RpZdUVyI3QIAXUqIoYDl7VkxFtNE4JWih0ucKc=", + "owner": "DavHau", + "repo": "mach-nix", + "rev": "fe5255e6fd8df57e9507b7af82fc59dda9e9ff2b", + "type": "github" + }, + "original": { + "owner": "DavHau", + "ref": "3.4.0", + "repo": "mach-nix", + "type": "github" + } + }, + "naersk": { + "inputs": { + "nixpkgs": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1639947939, + "narHash": "sha256-pGsM8haJadVP80GFq4xhnSpNitYNQpaXk4cnA796Cso=", + "owner": "nix-community", + "repo": "naersk", + "rev": "2fc8ce9d3c025d59fee349c1f80be9785049d653", + "type": "github" + }, + "original": { + "owner": "nix-community", + "repo": "naersk", + "type": "github" + } + }, + "nixpkgs": { + "locked": { + "lastModified": 1645937171, + "narHash": "sha256-n9f9GZBNMe8UMhcgmmaXNObkH01jjgp7INMrUgBgcy4=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "22dc22f8cedc58fcb11afe1acb08e9999e78be9c", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_2": { + "locked": { + "lastModified": 1643805626, + "narHash": "sha256-AXLDVMG+UaAGsGSpOtQHPIKB+IZ0KSd9WS77aanGzgc=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "554d2d8aa25b6e583575459c297ec23750adb6cb", + "type": "github" + }, + "original": { + "id": "nixpkgs", + "ref": "nixos-unstable", + "type": "indirect" + } + }, + "pypi-deps-db": { + "inputs": { + "flake-utils": "flake-utils", + "nixpkgs": "nixpkgs_2", + "pypi-deps-db": "pypi-deps-db_2" + }, + "locked": { + "lastModified": 1643953409, + "narHash": "sha256-CJDg/RpZdUVyI3QIAXUqIoYDl7VkxFtNE4JWih0ucKc=", + "owner": "DavHau", + "repo": "mach-nix", + "rev": "fe5255e6fd8df57e9507b7af82fc59dda9e9ff2b", + "type": "github" + }, + "original": { + "owner": "DavHau", + "ref": "3.4.0", + "repo": "mach-nix", + "type": "github" + } + }, + "pypi-deps-db_2": { + "flake": false, + "locked": { + "lastModified": 1643877077, + "narHash": "sha256-jv8pIvRFTP919GybOxXE5TfOkrjTbdo9QiCO1TD3ZaY=", + "owner": "DavHau", + "repo": "pypi-deps-db", + "rev": "da53397f0b782b0b18deb72ef8e0fb5aa7c98aa3", + "type": "github" + }, + "original": { + "owner": "DavHau", + "repo": "pypi-deps-db", + "type": "github" + } + }, + "root": { + "inputs": { + "mach-nix": "mach-nix", + "naersk": "naersk", + "nixpkgs": "nixpkgs", + "pypi-deps-db": "pypi-deps-db", + "rust-overlay": "rust-overlay", + "utils": "utils" + } + }, + "rust-overlay": { + "inputs": { + "flake-utils": [ + "utils" + ], + "nixpkgs": [ + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1645928338, + "narHash": "sha256-pNbkG19Nb4QTNRCIWwxv06JKKJNCUrDzgRrriEd7W1A=", + "owner": "oxalica", + "repo": "rust-overlay", + "rev": "4f6e6588b07427cd8ddc99b664bf0fab02799804", + "type": "github" + }, + "original": { + "owner": "oxalica", + "repo": "rust-overlay", + "type": "github" + } + }, + "utils": { + "locked": { + "lastModified": 1644229661, + "narHash": "sha256-1YdnJAsNy69bpcjuoKdOYQX0YxZBiCYZo4Twxerqv7k=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "3cecb5b042f7f209c56ffd8371b2711a290ec797", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + } + }, + "root": "root", + "version": 7 +} diff --git a/flake.nix b/flake.nix new file mode 100644 index 0000000000..9ec1cd8300 --- /dev/null +++ b/flake.nix @@ -0,0 +1,126 @@ +{ + + inputs = { + nixpkgs.url = "github:NixOS/nixpkgs/nixpkgs-unstable"; + utils.url = "github:numtide/flake-utils"; + + rust-overlay = { + url = "github:oxalica/rust-overlay"; + inputs = { + nixpkgs.follows = "nixpkgs"; + flake-utils.follows = "utils"; + }; + }; + + naersk = { + url = "github:nix-community/naersk"; + inputs = { + nixpkgs.follows = "nixpkgs"; + flake-utils.follows = "utils"; + }; + }; + + mach-nix = { + url = "github:DavHau/mach-nix/3.4.0"; + inputs.nixpkgs.follows = "nixpkgs"; + inputs.flake-utils.follows = "utils"; + inputs.pypi-deps-db.follows = "pypi-deps-db"; + }; + + pypi-deps-db = { + url = "github:DavHau/mach-nix/3.4.0"; + }; + }; + + outputs = { self, nixpkgs, naersk, rust-overlay, mach-nix, pypi-deps-db, utils }: + utils.lib.eachDefaultSystem (system: + let + overlays = [ (import rust-overlay) ]; + pkgs = import nixpkgs { + inherit system overlays; + }; + rustVersion = pkgs.rust-bin.stable.latest.default.override { + #extensions = [ "rust-src" ]; + #targets = [ "x86_64-unknown-linux-musl" ]; + targets = [ "wasm32-wasi" "wasm32-unknown-unknown" "wasm32-unknown-emscripten" ]; + }; + rustPlatform = pkgs.makeRustPlatform { + cargo = rustVersion; + rustc = rustVersion; + }; + naersk-lib = naersk.lib."${system}".override { + cargo = rustPlatform.rust.cargo; + rustc = rustPlatform.rust.rustc; + }; + + python = "python39"; + mach-nix-wrapper = import mach-nix { inherit pkgs python; }; + in + + with pkgs; + { + packages = { + lib = naersk-lib.buildPackage { + pname = "libsourmash"; + root = ./.; + copyLibs = true; + }; + sourmash = mach-nix-wrapper.buildPythonPackage { + src = ./.; + version = "4.3.0"; + requirementsExtra = '' + setuptools >= 48, <60 + milksnake + setuptools_scm[toml] >= 4, <6 + ''; + SETUPTOOLS_SCM_PRETEND_VERSION = "4.3.0"; + DYLD_LIBRARY_PATH = "${self.packages.${system}.lib}/lib"; + NO_BUILD = "1"; + }; + }; + + defaultPackage = self.packages.${system}.sourmash; + + devShell = mkShell { + nativeBuildInputs = [ + clang_13 + ]; + + buildInputs = [ + rustPlatform.rust.cargo + openssl + pkgconfig + + git + stdenv.cc.cc.lib + (python310.withPackages (ps: with ps; [ virtualenv tox setuptools ])) + (python39.withPackages (ps: with ps; [ virtualenv setuptools ])) + (python38.withPackages (ps: with ps; [ virtualenv setuptools ])) + + rust-cbindgen + + wasmtime + wasm-pack + nodejs-16_x + + py-spy + heaptrack + cargo-watch + cargo-limit + cargo-outdated + cargo-udeps + nixpkgs-fmt + + llvmPackages_13.libclang + llvmPackages_13.libcxxClang + ]; + + BINDGEN_EXTRA_CLANG_ARGS = "-isystem ${llvmPackages_13.libclang.lib}/lib/clang/${lib.getVersion clang}/include"; + LIBCLANG_PATH = "${llvmPackages_13.libclang.lib}/lib"; + LD_LIBRARY_PATH = "${stdenv.cc.cc.lib}/lib64:$LD_LIBRARY_PATH"; + + # workaround for https://github.com/NixOS/nixpkgs/blob/48dfc9fa97d762bce28cc8372a2dd3805d14c633/doc/languages-frameworks/python.section.md#python-setuppy-bdist_wheel-cannot-create-whl + SOURCE_DATE_EPOCH = 315532800; # 1980 + }; + }); +} diff --git a/nix/rust.nix b/nix/rust.nix deleted file mode 100644 index 0938a178a2..0000000000 --- a/nix/rust.nix +++ /dev/null @@ -1,15 +0,0 @@ -# nix/rust.nix -{ sources ? import ./sources.nix }: -let - pkgs = - import sources.nixpkgs { overlays = [ (import sources.rust-overlay) ]; }; - rustVersion = pkgs.rust-bin.stable.latest.default.override { - #extensions = [ "rust-src" ]; - #targets = [ "x86_64-unknown-linux-musl" ]; - targets = [ "wasm32-wasi" "wasm32-unknown-unknown" ]; - }; -in -pkgs.makeRustPlatform { - cargo = rustVersion; - rustc = rustVersion; -} diff --git a/nix/sources.json b/nix/sources.json deleted file mode 100644 index dd5dac1531..0000000000 --- a/nix/sources.json +++ /dev/null @@ -1,38 +0,0 @@ -{ - "niv": { - "branch": "master", - "description": "Easy dependency management for Nix projects", - "homepage": "https://github.com/nmattia/niv", - "owner": "nmattia", - "repo": "niv", - "rev": "9cb7ef336bb71fd1ca84fc7f2dff15ef4b033f2a", - "sha256": "1ajyqr8zka1zlb25jx1v4xys3zqmdy3prbm1vxlid6ah27a8qnzh", - "type": "tarball", - "url": "https://github.com/nmattia/niv/archive/9cb7ef336bb71fd1ca84fc7f2dff15ef4b033f2a.tar.gz", - "url_template": "https://github.com///archive/.tar.gz" - }, - "nixpkgs": { - "branch": "nixpkgs-unstable", - "description": "Nix Packages collection", - "homepage": "", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "1882c6b7368fd284ad01b0a5b5601ef136321292", - "sha256": "0zg7ak2mcmwzi2kg29g4v9fvbvs0viykjsg2pwaphm1fi13s7s0i", - "type": "tarball", - "url": "https://github.com/NixOS/nixpkgs/archive/1882c6b7368fd284ad01b0a5b5601ef136321292.tar.gz", - "url_template": "https://github.com///archive/.tar.gz" - }, - "rust-overlay": { - "branch": "master", - "description": null, - "homepage": null, - "owner": "oxalica", - "repo": "rust-overlay", - "rev": "14c48021a9a5fe6ea8ae6b21c15caa106afa9d19", - "sha256": "009nlf6if5nrkk9sl25n3ahh8l9bfmfbs3d1l8n4rb92hq2sdvjd", - "type": "tarball", - "url": "https://github.com/oxalica/rust-overlay/archive/14c48021a9a5fe6ea8ae6b21c15caa106afa9d19.tar.gz", - "url_template": "https://github.com///archive/.tar.gz" - } -} diff --git a/nix/sources.nix b/nix/sources.nix deleted file mode 100644 index 1938409ddd..0000000000 --- a/nix/sources.nix +++ /dev/null @@ -1,174 +0,0 @@ -# This file has been generated by Niv. - -let - - # - # The fetchers. fetch_ fetches specs of type . - # - - fetch_file = pkgs: name: spec: - let - name' = sanitizeName name + "-src"; - in - if spec.builtin or true then - builtins_fetchurl { inherit (spec) url sha256; name = name'; } - else - pkgs.fetchurl { inherit (spec) url sha256; name = name'; }; - - fetch_tarball = pkgs: name: spec: - let - name' = sanitizeName name + "-src"; - in - if spec.builtin or true then - builtins_fetchTarball { name = name'; inherit (spec) url sha256; } - else - pkgs.fetchzip { name = name'; inherit (spec) url sha256; }; - - fetch_git = name: spec: - let - ref = - if spec ? ref then spec.ref else - if spec ? branch then "refs/heads/${spec.branch}" else - if spec ? tag then "refs/tags/${spec.tag}" else - abort "In git source '${name}': Please specify `ref`, `tag` or `branch`!"; - in - builtins.fetchGit { url = spec.repo; inherit (spec) rev; inherit ref; }; - - fetch_local = spec: spec.path; - - fetch_builtin-tarball = name: throw - ''[${name}] The niv type "builtin-tarball" is deprecated. You should instead use `builtin = true`. - $ niv modify ${name} -a type=tarball -a builtin=true''; - - fetch_builtin-url = name: throw - ''[${name}] The niv type "builtin-url" will soon be deprecated. You should instead use `builtin = true`. - $ niv modify ${name} -a type=file -a builtin=true''; - - # - # Various helpers - # - - # https://github.com/NixOS/nixpkgs/pull/83241/files#diff-c6f540a4f3bfa4b0e8b6bafd4cd54e8bR695 - sanitizeName = name: - ( - concatMapStrings (s: if builtins.isList s then "-" else s) - ( - builtins.split "[^[:alnum:]+._?=-]+" - ((x: builtins.elemAt (builtins.match "\\.*(.*)" x) 0) name) - ) - ); - - # The set of packages used when specs are fetched using non-builtins. - mkPkgs = sources: system: - let - sourcesNixpkgs = - import (builtins_fetchTarball { inherit (sources.nixpkgs) url sha256; }) { inherit system; }; - hasNixpkgsPath = builtins.any (x: x.prefix == "nixpkgs") builtins.nixPath; - hasThisAsNixpkgsPath = == ./.; - in - if builtins.hasAttr "nixpkgs" sources - then sourcesNixpkgs - else if hasNixpkgsPath && ! hasThisAsNixpkgsPath then - import {} - else - abort - '' - Please specify either (through -I or NIX_PATH=nixpkgs=...) or - add a package called "nixpkgs" to your sources.json. - ''; - - # The actual fetching function. - fetch = pkgs: name: spec: - - if ! builtins.hasAttr "type" spec then - abort "ERROR: niv spec ${name} does not have a 'type' attribute" - else if spec.type == "file" then fetch_file pkgs name spec - else if spec.type == "tarball" then fetch_tarball pkgs name spec - else if spec.type == "git" then fetch_git name spec - else if spec.type == "local" then fetch_local spec - else if spec.type == "builtin-tarball" then fetch_builtin-tarball name - else if spec.type == "builtin-url" then fetch_builtin-url name - else - abort "ERROR: niv spec ${name} has unknown type ${builtins.toJSON spec.type}"; - - # If the environment variable NIV_OVERRIDE_${name} is set, then use - # the path directly as opposed to the fetched source. - replace = name: drv: - let - saneName = stringAsChars (c: if isNull (builtins.match "[a-zA-Z0-9]" c) then "_" else c) name; - ersatz = builtins.getEnv "NIV_OVERRIDE_${saneName}"; - in - if ersatz == "" then drv else - # this turns the string into an actual Nix path (for both absolute and - # relative paths) - if builtins.substring 0 1 ersatz == "/" then /. + ersatz else /. + builtins.getEnv "PWD" + "/${ersatz}"; - - # Ports of functions for older nix versions - - # a Nix version of mapAttrs if the built-in doesn't exist - mapAttrs = builtins.mapAttrs or ( - f: set: with builtins; - listToAttrs (map (attr: { name = attr; value = f attr set.${attr}; }) (attrNames set)) - ); - - # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/lists.nix#L295 - range = first: last: if first > last then [] else builtins.genList (n: first + n) (last - first + 1); - - # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L257 - stringToCharacters = s: map (p: builtins.substring p 1 s) (range 0 (builtins.stringLength s - 1)); - - # https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L269 - stringAsChars = f: s: concatStrings (map f (stringToCharacters s)); - concatMapStrings = f: list: concatStrings (map f list); - concatStrings = builtins.concatStringsSep ""; - - # https://github.com/NixOS/nixpkgs/blob/8a9f58a375c401b96da862d969f66429def1d118/lib/attrsets.nix#L331 - optionalAttrs = cond: as: if cond then as else {}; - - # fetchTarball version that is compatible between all the versions of Nix - builtins_fetchTarball = { url, name ? null, sha256 }@attrs: - let - inherit (builtins) lessThan nixVersion fetchTarball; - in - if lessThan nixVersion "1.12" then - fetchTarball ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; })) - else - fetchTarball attrs; - - # fetchurl version that is compatible between all the versions of Nix - builtins_fetchurl = { url, name ? null, sha256 }@attrs: - let - inherit (builtins) lessThan nixVersion fetchurl; - in - if lessThan nixVersion "1.12" then - fetchurl ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; })) - else - fetchurl attrs; - - # Create the final "sources" from the config - mkSources = config: - mapAttrs ( - name: spec: - if builtins.hasAttr "outPath" spec - then abort - "The values in sources.json should not have an 'outPath' attribute" - else - spec // { outPath = replace name (fetch config.pkgs name spec); } - ) config.sources; - - # The "config" used by the fetchers - mkConfig = - { sourcesFile ? if builtins.pathExists ./sources.json then ./sources.json else null - , sources ? if isNull sourcesFile then {} else builtins.fromJSON (builtins.readFile sourcesFile) - , system ? builtins.currentSystem - , pkgs ? mkPkgs sources system - }: rec { - # The sources, i.e. the attribute set of spec name to spec - inherit sources; - - # The "pkgs" (evaluated nixpkgs) to use for e.g. non-builtin fetchers - inherit pkgs; - }; - -in -mkSources (mkConfig {}) // { __functor = _: settings: mkSources (mkConfig settings); } diff --git a/setup.py b/setup.py index 08d7dbc8f8..9384aba4b4 100644 --- a/setup.py +++ b/setup.py @@ -5,6 +5,24 @@ DEBUG_BUILD = os.environ.get("SOURMASH_DEBUG") == "1" +NO_BUILD = os.environ.get("NO_BUILD") == "1" + + +def find_dylib(name, paths): + to_find = None + if sys.platform == 'darwin': + to_find = f'lib{name}.dylib' + elif sys.platform == 'win32': + to_find = f'{name}.dll' + else: + to_find = f'lib{name}.so' + + for path in paths.split(":"): + for filename in os.listdir(path): + if filename == to_find: + return os.path.join(path, filename) + + raise LookupError('dylib %r not found' % name) def build_native(spec): @@ -18,15 +36,21 @@ def build_native(spec): cmd.append("--release") target = "release" - build = spec.add_external_build(cmd=cmd, path=".") + if NO_BUILD: + dylib = lambda: find_dylib("sourmash", os.environ["DYLD_LIBRARY_PATH"]) + header_filename = lambda: "include/sourmash.h" + else: + build = spec.add_external_build(cmd=cmd, path=".") + dylib=lambda: build.find_dylib("sourmash", in_path="target/%s" % target) + header_filename=lambda: build.find_header("sourmash.h", in_path="include") rtld_flags = ["NOW"] if sys.platform == "darwin": rtld_flags.append("NODELETE") spec.add_cffi_module( module_path="sourmash._lowlevel", - dylib=lambda: build.find_dylib("sourmash", in_path="target/%s" % target), - header_filename=lambda: build.find_header("sourmash.h", in_path="include"), + dylib=dylib, + header_filename=header_filename, rtld_flags=rtld_flags, ) diff --git a/shell.nix b/shell.nix index f3c250cada..47458ad8c0 100644 --- a/shell.nix +++ b/shell.nix @@ -1,46 +1,10 @@ -let - sources = import ./nix/sources.nix; - rustPlatform = import ./nix/rust.nix { inherit sources; }; - pkgs = import sources.nixpkgs { overlays = [ (import sources.rust-overlay) ]; }; -in - with pkgs; - - pkgs.mkShell { - nativeBuildInputs = [ - clang_13 - ]; - - buildInputs = [ - rustPlatform.rust.cargo - openssl - pkg-config - - git - stdenv.cc.cc.lib - (python310.withPackages(ps: with ps; [ virtualenv tox setuptools ])) - (python39.withPackages(ps: with ps; [ virtualenv setuptools ])) - (python38.withPackages(ps: with ps; [ virtualenv setuptools ])) - - rust-cbindgen - - wasmtime - wasm-pack - nodejs-16_x - - py-spy - heaptrack - cargo-watch - cargo-limit - cargo-udeps - - llvmPackages_13.libclang - llvmPackages_13.libcxxClang - ]; - - BINDGEN_EXTRA_CLANG_ARGS = "-isystem ${llvmPackages_13.libclang.lib}/lib/clang/${lib.getVersion clang}/include"; - LIBCLANG_PATH = "${llvmPackages_13.libclang.lib}/lib"; - LD_LIBRARY_PATH = "${stdenv.cc.cc.lib}/lib64:$LD_LIBRARY_PATH"; - - # workaround for https://github.com/NixOS/nixpkgs/blob/48dfc9fa97d762bce28cc8372a2dd3805d14c633/doc/languages-frameworks/python.section.md#python-setuppy-bdist_wheel-cannot-create-whl - SOURCE_DATE_EPOCH = 315532800; # 1980 - } +(import + ( + fetchTarball { + url = "https://github.com/edolstra/flake-compat/archive/99f1c2157fba4bfe6211a321fd0ee43199025dbf.tar.gz"; + sha256 = "0x2jn3vrawwv9xp15674wjz9pixwjyj3j771izayl962zziivbx2"; + } + ) + { + src = ./.; + }).shellNix diff --git a/src/core/Cargo.toml b/src/core/Cargo.toml index 0efe6dc1c2..736e506c20 100644 --- a/src/core/Cargo.toml +++ b/src/core/Cargo.toml @@ -42,7 +42,7 @@ serde = { version = "1.0.110", features = ["derive"] } serde_json = "1.0.53" primal-check = "0.3.1" thiserror = "1.0" -typed-builder = "0.9.0" +typed-builder = "0.10.0" twox-hash = "1.6.0" vec-collections = "0.3.4" piz = "0.4.0"