diff --git a/flake.lock b/flake.lock index 049dcba..f317a24 100644 --- a/flake.lock +++ b/flake.lock @@ -3,19 +3,20 @@ "biobricks-R": { "inputs": { "flake-utils": [ + "dev-shell", "flake-utils" ], "nixpkgs": [ + "dev-shell", "nixpkgs" - ], - "poetry2nix": "poetry2nix" + ] }, "locked": { - "lastModified": 1695748200, - "narHash": "sha256-mxVCkoeLZBSInR6TgSs3L3BBQCzUx+ZXXt5vbPHFX38=", + "lastModified": 1695748726, + "narHash": "sha256-+PyXIuejK2ck4HlZzoJQQ/Ucu/7HonEfB4wuhcsBjKU=", "owner": "biobricks-ai", "repo": "biobricks-R", - "rev": "5aedfac7af4edbddb2922129af5ffe366038f8e0", + "rev": "c22e6b225d11a4cbd472b70fdc5b6c6f4acf5a53", "type": "github" }, "original": { @@ -24,27 +25,31 @@ "type": "github" } }, - "flake-utils": { + "dev-shell": { "inputs": { - "systems": "systems" + "biobricks-R": "biobricks-R", + "flake-utils": "flake-utils", + "hdt-cpp": "hdt-cpp", + "morph-kgc": "morph-kgc", + "nixpkgs": "nixpkgs" }, "locked": { - "lastModified": 1689068808, - "narHash": "sha256-6ixXo3wt24N/melDWjq70UuHQLxGV8jZvooRanIHXw0=", - "owner": "numtide", - "repo": "flake-utils", - "rev": "919d646de7be200f3bf08cb76ae1f09402b6f9b4", + "lastModified": 1695998847, + "narHash": "sha256-PDjTcvy6XIZZK/pwFNGcA3hNLawFG2RYszLxmH0Gtv4=", + "owner": "biobricks-ai", + "repo": "dev-shell", + "rev": "fee3a34c610dae3919196c25ca03acec9b65d75b", "type": "github" }, "original": { - "owner": "numtide", - "repo": "flake-utils", + "owner": "biobricks-ai", + "repo": "dev-shell", "type": "github" } }, - "flake-utils_2": { + "flake-utils": { "inputs": { - "systems": "systems_2" + "systems": "systems" }, "locked": { "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=", @@ -61,9 +66,11 @@ "hdt-cpp": { "inputs": { "flake-utils": [ + "dev-shell", "flake-utils" ], "nixpkgs": [ + "dev-shell", "nixpkgs" ] }, @@ -81,51 +88,39 @@ "type": "github" } }, - "nix-github-actions": { + "morph-kgc": { "inputs": { + "flake-utils": [ + "dev-shell", + "flake-utils" + ], "nixpkgs": [ - "biobricks-R", - "poetry2nix", + "dev-shell", "nixpkgs" - ] + ], + "poetry2nix": "poetry2nix" }, "locked": { - "lastModified": 1688870561, - "narHash": "sha256-4UYkifnPEw1nAzqqPOTL2MvWtm3sNGw1UTYTalkTcGY=", - "owner": "nix-community", - "repo": "nix-github-actions", - "rev": "165b1650b753316aa7f1787f3005a8d2da0f5301", + "lastModified": 1695678755, + "narHash": "sha256-x8Vw79qjOVtK5FPUe3q0vBUpbuPBPVZ/FEupiMN+6R4=", + "owner": "insilica", + "repo": "nix-morph-kgc", + "rev": "884a9570682288dbd770523f031fa38bdd38e4f9", "type": "github" }, "original": { - "owner": "nix-community", - "repo": "nix-github-actions", + "owner": "insilica", + "repo": "nix-morph-kgc", "type": "github" } }, "nixpkgs": { "locked": { - "lastModified": 1689192006, - "narHash": "sha256-QM0f0d8oPphOTYJebsHioR9+FzJcy1QNIzREyubB91U=", - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "2de8efefb6ce7f5e4e75bdf57376a96555986841", - "type": "github" - }, - "original": { - "owner": "NixOS", - "ref": "nixos-unstable", - "repo": "nixpkgs", - "type": "github" - } - }, - "nixpkgs_2": { - "locked": { - "narHash": "sha256-kXZ1pUoImD9OEbPCwpTz4tHsNTr4CIyIfXb3ocuR8sI=", - "rev": "261abe8a44a7e8392598d038d2e01f7b33cf26d0", - "revCount": 491123, + "narHash": "sha256-4Ne11kNRnQsmSJCRSSNkFRSnHC4Y5gPDBIQGjjPfJiU=", + "rev": "5cfafa12d57374f48bcc36fda3274ada276cf69e", + "revCount": 491245, "type": "tarball", - "url": "https://api.flakehub.com/f/pinned/NixOS/nixpkgs/0.2305.491123+rev-261abe8a44a7e8392598d038d2e01f7b33cf26d0/018acd67-263f-7f69-b7a8-1dc50d54a19a/source.tar.gz" + "url": "https://api.flakehub.com/f/pinned/NixOS/nixpkgs/0.2305.491245+rev-5cfafa12d57374f48bcc36fda3274ada276cf69e/018adbc4-3796-7d17-a794-61091c15d9d2/source.tar.gz" }, "original": { "type": "tarball", @@ -134,29 +129,34 @@ }, "poetry2nix": { "inputs": { - "flake-utils": "flake-utils", - "nix-github-actions": "nix-github-actions", - "nixpkgs": "nixpkgs" + "flake-utils": [ + "dev-shell", + "morph-kgc", + "flake-utils" + ], + "nixpkgs": [ + "dev-shell", + "morph-kgc", + "nixpkgs" + ] }, "locked": { - "lastModified": 1695386222, - "narHash": "sha256-5lgnhCCGW0NH5+m5iTED8u6NSSM/dbH9LBPvX0x0XXg=", + "lastModified": 1674537260, + "narHash": "sha256-DTki81bWzHHRka0ZLayYS5La3t+npRVZvfDH8mx/Las=", "owner": "nix-community", "repo": "poetry2nix", - "rev": "093383b3d7fdd36846a7d84e128ca11865800538", + "rev": "a20e27e0555621d35de171270cd041631fc7cb23", "type": "github" }, "original": { - "id": "poetry2nix", - "type": "indirect" + "owner": "nix-community", + "repo": "poetry2nix", + "type": "github" } }, "root": { "inputs": { - "biobricks-R": "biobricks-R", - "flake-utils": "flake-utils_2", - "hdt-cpp": "hdt-cpp", - "nixpkgs": "nixpkgs_2" + "dev-shell": "dev-shell" } }, "systems": { @@ -173,21 +173,6 @@ "repo": "default", "type": "github" } - }, - "systems_2": { - "locked": { - "lastModified": 1681028828, - "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", - "owner": "nix-systems", - "repo": "default", - "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", - "type": "github" - }, - "original": { - "owner": "nix-systems", - "repo": "default", - "type": "github" - } } }, "root": "root", diff --git a/flake.nix b/flake.nix index ece468e..0f4fe60 100644 --- a/flake.nix +++ b/flake.nix @@ -1,46 +1,7 @@ { description = "Tox21 biobrick"; - inputs = { - nixpkgs.url = "https://flakehub.com/f/NixOS/nixpkgs/*.tar.gz"; - flake-utils.url = "https://flakehub.com/f/numtide/flake-utils/*.tar.gz"; - biobricks-R = { - url = "github:biobricks-ai/biobricks-R"; - inputs.flake-utils.follows = "flake-utils"; - inputs.nixpkgs.follows = "nixpkgs"; - }; - hdt-cpp = { - url = "github:insilica/nix-hdt"; - inputs.flake-utils.follows = "flake-utils"; - inputs.nixpkgs.follows = "nixpkgs"; - }; - }; + inputs = { dev-shell.url = "github:biobricks-ai/dev-shell"; }; - outputs = { self, nixpkgs, flake-utils, biobricks-R, hdt-cpp }: - flake-utils.lib.eachDefaultSystem (system: - with import nixpkgs { inherit system; }; - let - # tmducken requires duckdb 0.8.1 or later, and nixos-23.05 only had 0.7 - duckdb-version = "0.8.1"; - duckdb = (pkgs.duckdb.overrideAttrs (oldAttrs: rec { - version = duckdb-version; - src = fetchFromGitHub { - owner = "duckdb"; - repo = "duckdb"; - rev = "v${duckdb-version}"; - sha256 = "sha256-LEv9yURkYvONObTbIA4CS+umwCRMH8gRQaDtzbCzID4="; - }; - })); - in { - devShells.default = mkShell { - buildInputs = [ - biobricks-R.packages.${system}.rEnv - clojure - hdt-cpp.packages.${system}.default - duckdb - jdk - ]; - env = { DUCKDB_HOME = "${duckdb}/lib"; }; - }; - }); + outputs = { self, dev-shell }: { devShells = dev-shell.devShells; }; }