From 62048c3d771f87957cb2fad59aaa54f848b8ba9c Mon Sep 17 00:00:00 2001 From: Ray Andrew Date: Mon, 20 Oct 2025 20:16:04 -0500 Subject: [PATCH] update --- darwin/homebrew.nix | 69 +++++++++- flake.lock | 237 ++++++++++++++++++++------------- flake.nix | 2 + home/default.nix | 2 + home/emacs/config/post-init.el | 11 ++ home/shell/default.nix | 2 +- home/ssh/config | 26 ++++ hosts/dango/default.nix | 22 ++- hosts/default.nix | 14 +- overlays/default.nix | 2 +- 10 files changed, 285 insertions(+), 102 deletions(-) diff --git a/darwin/homebrew.nix b/darwin/homebrew.nix index c65896a..f3c5132 100644 --- a/darwin/homebrew.nix +++ b/darwin/homebrew.nix @@ -20,7 +20,9 @@ raycast = mkEnableOption "Enable Raycast"; whatsapp = mkEnableOption "Enable Whatsapp"; vscode = mkEnableOption "Enable VSCode"; + vscode-insiders = mkEnableOption "Enable VSCode Insiders"; firefox = mkEnableOption "Enable Firefox"; + google-chrome = mkEnableOption "Enable Google Chrome"; chromium = mkEnableOption "Enable Chromium"; aldente = mkEnableOption "Enable AlDente"; zotero = mkEnableOption "Enable Zotero"; @@ -50,6 +52,13 @@ pika = mkEnableOption "Enable Pika"; transmission = mkEnableOption "Enable Transmission"; alt-tab = mkEnableOption "Enable Alt-Tab"; + r = mkEnableOption "Enable r"; + rstudio = mkEnableOption "Enable rstudio"; + sratoolkit = mkEnableOption "Enable sratoolkit"; + hisat2 = mkEnableOption "Enable hisat2"; + positron = mkEnableOption "Enable positron"; + claude = mkEnableOption "Enable claude"; + iterm2 = mkEnableOption "Enable iterm2"; }; config = lib.mkMerge [ @@ -58,12 +67,15 @@ inherit user; enable = true; enableRosetta = true; - taps = { - "homebrew/homebrew-core" = inputs.homebrew-core; - "homebrew/homebrew-cask" = inputs.homebrew-cask; - "homebrew/homebrew-createzap" = inputs.homebrew-createzap; - "d12frosted/homebrew-emacs-plus" = inputs.homebrew-emacs-plus; - }; + taps = lib.mkMerge [ + { + "homebrew/homebrew-core" = inputs.homebrew-core; + "homebrew/homebrew-cask" = inputs.homebrew-cask; + "homebrew/homebrew-createzap" = inputs.homebrew-createzap; + "d12frosted/homebrew-emacs-plus" = inputs.homebrew-emacs-plus; + "brewsci/homebrew-bio" = inputs.homebrew-brewsci-bio; + } + ]; mutableTaps = false; }; homebrew = { @@ -145,11 +157,21 @@ "visual-studio-code" ]; }) + (lib.mkIf config.custom.brew.vscode-insiders { + homebrew.casks = [ + "visual-studio-code@insiders" + ]; + }) (lib.mkIf config.custom.brew.firefox { homebrew.casks = [ "firefox" ]; }) + (lib.mkIf config.custom.brew.google-chrome { + homebrew.casks = [ + "google-chrome" + ]; + }) (lib.mkIf config.custom.brew.chromium { homebrew.casks = [ "chromium" @@ -285,5 +307,40 @@ "alt-tab" ]; }) + (lib.mkIf config.custom.brew.r { + homebrew.brews = [ + "r" + ]; + }) + (lib.mkIf config.custom.brew.rstudio { + homebrew.casks = [ + "rstudio" + ]; + }) + (lib.mkIf config.custom.brew.r { + homebrew.brews = [ + "sratoolkit" + ]; + }) + (lib.mkIf config.custom.brew.hisat2 { + homebrew.brews = [ + "hisat2" + ]; + }) + (lib.mkIf config.custom.brew.positron { + homebrew.casks = [ + "positron" + ]; + }) + (lib.mkIf config.custom.brew.claude { + homebrew.casks = [ + "claude" + ]; + }) + (lib.mkIf config.custom.brew.iterm2 { + homebrew.casks = [ + "iterm2" + ]; + }) ]; } diff --git a/flake.lock b/flake.lock index 060ed22..e897791 100644 --- a/flake.lock +++ b/flake.lock @@ -3,16 +3,16 @@ "brew-src": { "flake": false, "locked": { - "lastModified": 1748148946, - "narHash": "sha256-srnyYAqGD27NeBDaEU3hchJdkeOQ2vRe3kWurihFYT8=", + "lastModified": 1758543057, + "narHash": "sha256-lw3V2jOGYphUFHYQ5oARcb6urlbNpUCLJy1qhsGdUmc=", "owner": "Homebrew", "repo": "brew", - "rev": "dc0f9d50fd170492a33fd7234d06de1b94df363c", + "rev": "5b236456eb93133c2bd0d60ef35ed63f1c0712f6", "type": "github" }, "original": { "owner": "Homebrew", - "ref": "4.5.3", + "ref": "4.6.12", "repo": "brew", "type": "github" } @@ -39,11 +39,11 @@ ] }, "locked": { - "lastModified": 1748225455, - "narHash": "sha256-AzlJCKaM4wbEyEpV3I/PUq5mHnib2ryEy32c+qfj6xk=", + "lastModified": 1758287904, + "narHash": "sha256-IGmaEf3Do8o5Cwp1kXBN1wQmZwQN3NLfq5t4nHtVtcU=", "owner": "nix-community", "repo": "disko", - "rev": "a894f2811e1ee8d10c50560551e50d6ab3c392ba", + "rev": "67ff9807dd148e704baadbd4fd783b54282ca627", "type": "github" }, "original": { @@ -71,11 +71,11 @@ "flake-compat_2": { "flake": false, "locked": { - "lastModified": 1696426674, - "narHash": "sha256-kvjfFW7WAETZlt09AgDn1MrtKzP7t90Vf7vypd3OL1U=", + "lastModified": 1747046372, + "narHash": "sha256-CIVLLkVgvHYbgI2UpXvIIBJ12HWgX+fjA8Xf8PUmqCY=", "owner": "edolstra", "repo": "flake-compat", - "rev": "0f9255e01c2351cc7d116c072cb317785dd33b33", + "rev": "9100a0f413b0c601e0533d1d94ffd501ce2e7885", "type": "github" }, "original": { @@ -148,11 +148,11 @@ "zon2nix": "zon2nix" }, "locked": { - "lastModified": 1748372068, - "narHash": "sha256-JeZWDzY1f//amtQSU7TmwAqG8qeyBIdx7JBfgzhEkdY=", + "lastModified": 1760583877, + "narHash": "sha256-zbmESqyuNf6M4jno2+dvpXsorq1QHJNQtnNZ9LP2R3g=", "owner": "ghostty-org", "repo": "ghostty", - "rev": "ad632f10687c087bc45319aad6c8ee272269e5f9", + "rev": "5a9bd0e49ef11499eb0ccb63725cc882b93356e0", "type": "github" }, "original": { @@ -170,11 +170,11 @@ ] }, "locked": { - "lastModified": 1747372754, - "narHash": "sha256-2Y53NGIX2vxfie1rOW0Qb86vjRZ7ngizoo+bnXU9D9k=", + "lastModified": 1760392170, + "narHash": "sha256-WftxJgr2MeDDFK47fQKywzC72L2jRc/PWcyGdjaDzkw=", "owner": "cachix", "repo": "git-hooks.nix", - "rev": "80479b6ec16fefd9c1db3ea13aeb038c60530f46", + "rev": "46d55f0aeb1d567a78223e69729734f3dca25a85", "type": "github" }, "original": { @@ -211,11 +211,11 @@ ] }, "locked": { - "lastModified": 1748391243, - "narHash": "sha256-7sCuihzsTRZemtbTXaFUoGJUfuQErhKEcL9v7HKIo1k=", + "lastModified": 1760500983, + "narHash": "sha256-zfY4F4CpeUjTGgecIJZ+M7vFpwLc0Gm9epM/iMQd4w8=", "owner": "nix-community", "repo": "home-manager", - "rev": "f5b12be834874f7661db4ced969a621ab2d57971", + "rev": "c53e65ec92f38d30e3c14f8d628ab55d462947aa", "type": "github" }, "original": { @@ -232,11 +232,11 @@ ] }, "locked": { - "lastModified": 1743604125, - "narHash": "sha256-ZD61DNbsBt1mQbinAaaEqKaJk2RFo9R/j+eYWeGMx7A=", + "lastModified": 1752603129, + "narHash": "sha256-S+wmHhwNQ5Ru689L2Gu8n1OD6s9eU9n9mD827JNR+kw=", "owner": "nix-community", "repo": "home-manager", - "rev": "180fd43eea296e62ae68e079fcf56aba268b9a1a", + "rev": "e8c19a3cec2814c754f031ab3ae7316b64da085b", "type": "github" }, "original": { @@ -245,14 +245,30 @@ "type": "github" } }, + "homebrew-brewsci-bio": { + "flake": false, + "locked": { + "lastModified": 1760374659, + "narHash": "sha256-j5cjB9AaDtpqiWCcp+VmgudQ274DepjkwGCb5yOG4+8=", + "owner": "brewsci", + "repo": "homebrew-bio", + "rev": "e5964fddfa4894549db328da95132229e0e74936", + "type": "github" + }, + "original": { + "owner": "brewsci", + "repo": "homebrew-bio", + "type": "github" + } + }, "homebrew-cask": { "flake": false, "locked": { - "lastModified": 1748396468, - "narHash": "sha256-/Gj7CaN6FbNclLAH42y7nEz8YR2kfbwK2vgtAqddYs8=", + "lastModified": 1760637639, + "narHash": "sha256-HOAVCudwyIXT6kS2toRsk5xBpcdFeFvJdwusBImi44U=", "owner": "homebrew", "repo": "homebrew-cask", - "rev": "114665418ef815540022339b1b6c5da345b7b2de", + "rev": "ae9776cc5e15c8f1e78286995b5ba4553a779171", "type": "github" }, "original": { @@ -264,11 +280,11 @@ "homebrew-core": { "flake": false, "locked": { - "lastModified": 1748398569, - "narHash": "sha256-krLoQwSftJtLQtoofa03EEYu7uP3xGt12qGA3MIrI0M=", + "lastModified": 1760638362, + "narHash": "sha256-ho+MbgGrQ9SNCb1nRAAJKG7R19UdAswpovh3pILV+74=", "owner": "homebrew", "repo": "homebrew-core", - "rev": "e6a55e76d313f884c2ef8d00df842a1062e4850e", + "rev": "14dbbc218025ca2ea982493fefdd681a504fc3e1", "type": "github" }, "original": { @@ -296,11 +312,11 @@ "homebrew-emacs-plus": { "flake": false, "locked": { - "lastModified": 1743441558, - "narHash": "sha256-Eepinxv05Yl79AoPVJveGDZPKHhlAes7XtUvrssflrU=", + "lastModified": 1759655759, + "narHash": "sha256-YvrVSoT1wGraYPP5OtaULYiboKEjRWWOXqjlQs7iZVE=", "owner": "d12frosted", "repo": "homebrew-emacs-plus", - "rev": "3e95d573d5f13aba7808193b66312b38a7c66851", + "rev": "158df2e4f970e60ab9b3514a4ec64bf9dc985fcf", "type": "github" }, "original": { @@ -314,15 +330,16 @@ "cl-nix-lite": "cl-nix-lite", "flake-compat": "flake-compat_3", "flake-utils": "flake-utils_2", - "nixpkgs": "nixpkgs_2", - "systems": "systems_2" + "nixpkgs": "nixpkgs_3", + "systems": "systems_2", + "treefmt-nix": "treefmt-nix" }, "locked": { - "lastModified": 1742156590, - "narHash": "sha256-aTM/2CrNN5utdVEQGsOA+kl4UozgH7VPLBQL5OXtBrg=", + "lastModified": 1756057867, + "narHash": "sha256-ziR5eQGqRWhW8tf8r0TIplaqNt+HXu1G1X41LUr4IYo=", "owner": "hraban", "repo": "mac-app-util", - "rev": "341ede93f290df7957047682482c298e47291b4d", + "rev": "8414fa1e2cb775b17793104a9095aabeeada63ef", "type": "github" }, "original": { @@ -338,11 +355,11 @@ ] }, "locked": { - "lastModified": 1748352827, - "narHash": "sha256-sNUUP6qxGkK9hXgJ+p362dtWLgnIWwOCmiq72LAWtYo=", + "lastModified": 1760338583, + "narHash": "sha256-IGwy02SH5K2hzIFrKMRsCmyvwOwWxrcquiv4DbKL1S4=", "owner": "nix-darwin", "repo": "nix-darwin", - "rev": "44a7d0e687a87b73facfe94fba78d323a6686a90", + "rev": "9a9ab01072f78823ca627ae5e895e40d493c3ecf", "type": "github" }, "original": { @@ -357,11 +374,11 @@ "brew-src": "brew-src" }, "locked": { - "lastModified": 1748379893, - "narHash": "sha256-7zvNSdEA4KhKA3vosAU3QdzGgSBKxTR2iUEredA8tLc=", + "lastModified": 1758598228, + "narHash": "sha256-qr60maXGbZ4FX5tejPRI3nr0bnRTnZ3AbbbfO6/6jq4=", "owner": "zhaofengli", "repo": "nix-homebrew", - "rev": "77517445732b9ae0b413e4580b1c8e88f804da1c", + "rev": "f36e5db56e117f7df701ab152d0d2036ea85218c", "type": "github" }, "original": { @@ -377,11 +394,11 @@ ] }, "locked": { - "lastModified": 1748145500, - "narHash": "sha256-t9fx0l61WOxtWxXCqlXPWSuG/0XMF9DtE2T7KXgMqJw=", + "lastModified": 1760241904, + "narHash": "sha256-OD7QnaGEVNdukYEbJbUNWPsvnDrpbZOZxVIk6Pt9Jhw=", "owner": "nix-community", "repo": "nix-index-database", - "rev": "a98adbf54d663395df0b9929f6481d4d80fc8927", + "rev": "c9f5ea45f25652ec2f771f9426ccacb21cbbaeaa", "type": "github" }, "original": { @@ -392,11 +409,11 @@ }, "nixos-hardware": { "locked": { - "lastModified": 1747900541, - "narHash": "sha256-dn64Pg9xLETjblwZs9Euu/SsjW80pd6lr5qSiyLY1pg=", + "lastModified": 1760106635, + "narHash": "sha256-2GoxVaKWTHBxRoeUYSjv0AfSOx4qw5CWSFz2b+VolKU=", "owner": "NixOS", "repo": "nixos-hardware", - "rev": "11f2d9ea49c3e964315215d6baa73a8d42672f06", + "rev": "9ed85f8afebf2b7478f25db0a98d0e782c0ed903", "type": "github" }, "original": { @@ -408,27 +425,27 @@ }, "nixpkgs": { "locked": { - "lastModified": 1748189127, - "narHash": "sha256-zRDR+EbbeObu4V2X5QCd2Bk5eltfDlCr5yvhBwUT6pY=", - "rev": "7c43f080a7f28b2774f3b3f43234ca11661bf334", + "lastModified": 315532800, + "narHash": "sha256-sV6pJNzFkiPc6j9Bi9JuHBnWdVhtKB/mHgVmMPvDFlk=", + "rev": "82c2e0d6dde50b17ae366d2aa36f224dc19af469", "type": "tarball", - "url": "https://releases.nixos.org/nixos/25.05/nixos-25.05.802491.7c43f080a7f2/nixexprs.tar.xz" + "url": "https://releases.nixos.org/nixpkgs/nixpkgs-25.11pre877938.82c2e0d6dde5/nixexprs.tar.xz" }, "original": { "type": "tarball", - "url": "https://channels.nixos.org/nixos-25.05/nixexprs.tar.xz" + "url": "https://channels.nixos.org/nixpkgs-unstable/nixexprs.tar.xz" } }, "nixpkgs-firefox-darwin": { "inputs": { - "nixpkgs": "nixpkgs_4" + "nixpkgs": "nixpkgs_6" }, "locked": { - "lastModified": 1748394362, - "narHash": "sha256-XDEHo8SjRuGSzGqvGG4iRShLDa8yL65iRM2+hi1bZeQ=", + "lastModified": 1760576526, + "narHash": "sha256-PdxUxGacfkSC8e+FBTuYEWHnkmWyVWdUWgzwh/LG6+M=", "owner": "bandithedoge", "repo": "nixpkgs-firefox-darwin", - "rev": "7d37224d9b7b8e315d37095772ca732df7ea40b6", + "rev": "b6dbc82afbb2475690b5e98a277eca13adae6fd2", "type": "github" }, "original": { @@ -438,6 +455,19 @@ } }, "nixpkgs_2": { + "locked": { + "lastModified": 1758360447, + "narHash": "sha256-XDY3A83bclygHDtesRoaRTafUd80Q30D/Daf9KSG6bs=", + "rev": "8eaee110344796db060382e15d3af0a9fc396e0e", + "type": "tarball", + "url": "https://releases.nixos.org/nixos/unstable/nixos-25.11pre864002.8eaee1103447/nixexprs.tar.xz" + }, + "original": { + "type": "tarball", + "url": "https://channels.nixos.org/nixos-unstable/nixexprs.tar.xz" + } + }, + "nixpkgs_3": { "locked": { "lastModified": 1732617236, "narHash": "sha256-PYkz6U0bSEaEB1al7O1XsqVNeSNS+s3NVclJw7YC43w=", @@ -453,13 +483,29 @@ "type": "github" } }, - "nixpkgs_3": { + "nixpkgs_4": { "locked": { - "lastModified": 1748190013, - "narHash": "sha256-R5HJFflOfsP5FBtk+zE8FpL8uqE7n62jqOsADvVshhE=", + "lastModified": 1754340878, + "narHash": "sha256-lgmUyVQL9tSnvvIvBp7x1euhkkCho7n3TMzgjdvgPoU=", "owner": "nixos", "repo": "nixpkgs", - "rev": "62b852f6c6742134ade1abdd2a21685fd617a291", + "rev": "cab778239e705082fe97bb4990e0d24c50924c04", + "type": "github" + }, + "original": { + "owner": "nixos", + "ref": "nixpkgs-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "nixpkgs_5": { + "locked": { + "lastModified": 1760524057, + "narHash": "sha256-EVAqOteLBFmd7pKkb0+FIUyzTF61VKi7YmvP1tw4nEw=", + "owner": "nixos", + "repo": "nixpkgs", + "rev": "544961dfcce86422ba200ed9a0b00dd4b1486ec5", "type": "github" }, "original": { @@ -469,7 +515,7 @@ "type": "github" } }, - "nixpkgs_4": { + "nixpkgs_6": { "locked": { "lastModified": 1746683680, "narHash": "sha256-+5zk+UbG0+GQlKt+gIKm+OhlYvHmkAHFXvf7hl1HDeM=", @@ -491,6 +537,7 @@ "ghostty": "ghostty", "git-hooks": "git-hooks", "home-manager": "home-manager", + "homebrew-brewsci-bio": "homebrew-brewsci-bio", "homebrew-cask": "homebrew-cask", "homebrew-core": "homebrew-core", "homebrew-createzap": "homebrew-createzap", @@ -500,10 +547,10 @@ "nix-homebrew": "nix-homebrew", "nix-index-database": "nix-index-database", "nixos-hardware": "nixos-hardware", - "nixpkgs": "nixpkgs_3", + "nixpkgs": "nixpkgs_5", "nixpkgs-firefox-darwin": "nixpkgs-firefox-darwin", "sops-nix": "sops-nix", - "treefmt-nix": "treefmt-nix", + "treefmt-nix": "treefmt-nix_2", "zen-browser": "zen-browser" } }, @@ -514,11 +561,11 @@ ] }, "locked": { - "lastModified": 1747603214, - "narHash": "sha256-lAblXm0VwifYCJ/ILPXJwlz0qNY07DDYdLD+9H+Wc8o=", + "lastModified": 1760393368, + "narHash": "sha256-8mN3kqyqa2PKY0wwZ2UmMEYMcxvNTwLaOrrDsw6Qi4E=", "owner": "Mic92", "repo": "sops-nix", - "rev": "8d215e1c981be3aa37e47aeabd4e61bb069548fd", + "rev": "ab8d56e85b8be14cff9d93735951e30c3e86a437", "type": "github" }, "original": { @@ -558,17 +605,35 @@ } }, "treefmt-nix": { + "inputs": { + "nixpkgs": "nixpkgs_4" + }, + "locked": { + "lastModified": 1755934250, + "narHash": "sha256-CsDojnMgYsfshQw3t4zjRUkmMmUdZGthl16bXVWgRYU=", + "owner": "numtide", + "repo": "treefmt-nix", + "rev": "74e1a52d5bd9430312f8d1b8b0354c92c17453e5", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "treefmt-nix", + "type": "github" + } + }, + "treefmt-nix_2": { "inputs": { "nixpkgs": [ "nixpkgs" ] }, "locked": { - "lastModified": 1748243702, - "narHash": "sha256-9YzfeN8CB6SzNPyPm2XjRRqSixDopTapaRsnTpXUEY8=", + "lastModified": 1760120816, + "narHash": "sha256-gq9rdocpmRZCwLS5vsHozwB6b5nrOBDNc2kkEaTXHfg=", "owner": "numtide", "repo": "treefmt-nix", - "rev": "1f3f7b784643d488ba4bf315638b2b0a4c5fb007", + "rev": "761ae7aff00907b607125b2f57338b74177697ed", "type": "github" }, "original": { @@ -585,11 +650,11 @@ ] }, "locked": { - "lastModified": 1748387888, - "narHash": "sha256-f3O26vbN1r8ylC7KtEwjzAmKRRFu+jK+vVuQF2ynTsQ=", + "lastModified": 1760588585, + "narHash": "sha256-NufqXao2i6d7N1HFKp8hM8XAD8Q6s/zU2wNd065Ybus=", "owner": "0xc000022070", "repo": "zen-browser-flake", - "rev": "a5bf612551ffd48cbae957c386203d1175dba3cf", + "rev": "5a651a6a3bb5c9bd694adbd2c34f55b4abff9a2c", "type": "github" }, "original": { @@ -601,7 +666,8 @@ "zig": { "inputs": { "flake-compat": [ - "ghostty" + "ghostty", + "flake-compat" ], "flake-utils": [ "ghostty", @@ -613,11 +679,11 @@ ] }, "locked": { - "lastModified": 1748261582, - "narHash": "sha256-3i0IL3s18hdDlbsf0/E+5kyPRkZwGPbSFngq5eToiAA=", + "lastModified": 1760401936, + "narHash": "sha256-/zj5GYO5PKhBWGzbHbqT+ehY8EghuABdQ2WGfCwZpCQ=", "owner": "mitchellh", "repo": "zig-overlay", - "rev": "aafb1b093fb838f7a02613b719e85ec912914221", + "rev": "365085b6652259753b598d43b723858184980bbe", "type": "github" }, "original": { @@ -628,27 +694,20 @@ }, "zon2nix": { "inputs": { - "flake-utils": [ - "ghostty", - "flake-utils" - ], - "nixpkgs": [ - "ghostty", - "nixpkgs" - ] + "nixpkgs": "nixpkgs_2" }, "locked": { - "lastModified": 1742104771, - "narHash": "sha256-LhidlyEA9MP8jGe1rEnyjGFCzLLgCdDpYeWggibayr0=", + "lastModified": 1758405547, + "narHash": "sha256-WgaDgvIZMPvlZcZrpPMjkaalTBnGF2lTG+62znXctWM=", "owner": "jcollie", "repo": "zon2nix", - "rev": "56c159be489cc6c0e73c3930bd908ddc6fe89613", + "rev": "bf983aa90ff169372b9fa8c02e57ea75e0b42245", "type": "github" }, "original": { "owner": "jcollie", - "ref": "56c159be489cc6c0e73c3930bd908ddc6fe89613", "repo": "zon2nix", + "rev": "bf983aa90ff169372b9fa8c02e57ea75e0b42245", "type": "github" } } diff --git a/flake.nix b/flake.nix index 8d2a25e..9696e5b 100644 --- a/flake.nix +++ b/flake.nix @@ -36,6 +36,8 @@ homebrew-createzap.flake = false; homebrew-emacs-plus.url = "github:d12frosted/homebrew-emacs-plus"; homebrew-emacs-plus.flake = false; + homebrew-brewsci-bio.url = "github:brewsci/homebrew-bio"; + homebrew-brewsci-bio.flake = false; }; outputs = diff --git a/home/default.nix b/home/default.nix index 13cc09b..d755b41 100644 --- a/home/default.nix +++ b/home/default.nix @@ -42,9 +42,11 @@ fontconfig pandoc duckdb + hyperfine (pkgs.python311.withPackages (ppkgs: [ ppkgs.numpy ])) + aider-chat ] ++ lib.optionals pkgs.stdenv.isDarwin [ coreutils ] ++ (lib.attrValues config.custom.shell.packages); diff --git a/home/emacs/config/post-init.el b/home/emacs/config/post-init.el index 68123e1..c655ef0 100644 --- a/home/emacs/config/post-init.el +++ b/home/emacs/config/post-init.el @@ -38,6 +38,8 @@ (global-auto-revert-mode t) ;; Automatically reload file and show changes if the file has changed (indent-tabs-mode nil) + (editorconfig-mode t) + ;;(dired-kill-when-opening-new-dired-buffer t) ;; Dired don't create new buffer (recentf-mode t) ;; Enable recent file mode (recentf-max-saved-items 50) @@ -650,3 +652,12 @@ frame if FRAME is nil, and to 1 if AMT is nil." (todo))) ("w" "Work" agenda "" ((org-agenda-files '("work.org"))))))) + +;; (use-package editorconfig +;; :init +;; (setq editorconfig-lisp-use-default-indent t) ; restores alignment for elisp +;; :demand +;; :custom +;; (editorconfig-trim-whitespaces-mode 'ws-butler-mode) +;; :config +;; (editorconfig-mode 1)) diff --git a/home/shell/default.nix b/home/shell/default.nix index 1904667..cfb5aea 100644 --- a/home/shell/default.nix +++ b/home/shell/default.nix @@ -52,7 +52,7 @@ ''; }; programs.zsh = { - initExtra = lib.mkAfter '' + initContent = lib.mkAfter '' export PATH="${dots}/home/shell/bin:$PATH" ''; }; diff --git a/home/ssh/config b/home/ssh/config index 2662370..df248f0 100644 --- a/home/ssh/config +++ b/home/ssh/config @@ -90,6 +90,32 @@ Host corona ControlMaster auto ControlPersist yes LogLevel FATAL + # ProxyJump oslic + +Host tuolumne + ForwardX11Trusted yes + User sinurat1 + HostName tuolumne.llnl.gov + ControlMaster auto + ControlPersist yes + LogLevel FATAL + # ProxyJump oslic + +Host matrix + ForwardX11Trusted yes + User sinurat1 + HostName matrix.llnl.gov + ControlMaster auto + ControlPersist yes + LogLevel FATAL + +Host oslic + ForwardX11Trusted yes + User sinurat1 + HostName oslic.llnl.gov + ControlMaster auto + ControlPersist yes + LogLevel FATAL Host czgitlab HostName czgitlab.llnl.gov diff --git a/hosts/dango/default.nix b/hosts/dango/default.nix index 2885fc0..1e8bc8b 100644 --- a/hosts/dango/default.nix +++ b/hosts/dango/default.nix @@ -47,16 +47,36 @@ chatgpt = true; antinote = true; swish = true; - rectangle = false; + rectangle = true; emacs = true; drawio = true; soulver = true; pika = true; transmission = true; alt-tab = true; + r = true; + rstudio = true; + sratoolkit = true; + hisat2 = true; + google-chrome = true; + vscode-insiders = true; + positron = true; + claude = true; + iterm2 = true; }; }; + hm.home.packages = with pkgs; [ + # bowtie2 + samtools + python311Packages.htseq + wget + igv + claude-code + nodejs_24 + ghidra-bin + ]; + hm.custom = { emacs.enable = true; neovim.enable = true; diff --git a/hosts/default.nix b/hosts/default.nix index 676de36..98fac02 100644 --- a/hosts/default.nix +++ b/hosts/default.nix @@ -15,7 +15,7 @@ let overlays = [ (import ../overlays { inherit inputs; - inherit (pkgs) system; + inherit system; }) ]; }; @@ -57,7 +57,7 @@ let users.${user} = { imports = [ - inputs.nix-index-database.hmModules.nix-index + inputs.nix-index-database.homeModules.nix-index inputs.sops-nix.homeManagerModules.sops ../home ] ++ lib.optional (builtins.pathExists ./${host}/home.nix) ./${host}/home.nix; @@ -88,7 +88,7 @@ let overlays = [ (import ../overlays { inherit inputs; - inherit (pkgs) system; + inherit system; }) inputs.nixpkgs-firefox-darwin.overlay ]; @@ -129,7 +129,7 @@ let users.${user} = { imports = [ - inputs.nix-index-database.hmModules.nix-index + inputs.nix-index-database.homeModules.nix-index inputs.sops-nix.homeManagerModules.sops inputs.mac-app-util.homeManagerModules.default ../home @@ -150,6 +150,12 @@ let inputs.home-manager.darwinModules.home-manager inputs.mac-app-util.darwinModules.default inputs.nix-homebrew.darwinModules.nix-homebrew + ( + { config, ... }: + { + homebrew.taps = builtins.attrNames config.nix-homebrew.taps; + } + ) ]; }; in diff --git a/overlays/default.nix b/overlays/default.nix index 7204461..429998f 100644 --- a/overlays/default.nix +++ b/overlays/default.nix @@ -18,5 +18,5 @@ _: prev: { }); # use nixfmt-rfc-style as the default - nixfmt = prev.nixfmt-rfc-style; + nixfmt = prev.nixfmt or prev.nixfmt-rfc-style; }