automatic update by http://atom.io/packages/sync-settings

init.coffee

# Your init script
#
# Atom will evaluate this file each time a new window is opened. It is run
# after packages are loaded/activated and after the previous editor state
# has been restored.
#
# An example hack to log to the console when each text editor is saved.
#
# atom.workspace.observeTextEditors (editor) ->
#   editor.onDidSave ->
#     console.log "Saved! #{editor.getPath()}"

document.body.classList.add('an-old-hope-modify-ui')

keymap.cson

# Your keymap
#
# Atom keymaps work similarly to style sheets. Just as style sheets use
# selectors to apply styles to elements, Atom keymaps use selectors to associate
# keystrokes with events in specific contexts.
#
# You can create a new keybinding in this file by typing "key" and then hitting
# tab.
#
# Here's an example taken from Atom's built-in keymap:
#
# 'atom-text-editor':
#   'enter': 'editor:newline'
#
# 'atom-workspace':
#   'ctrl-shift-p': 'core:move-up'
#   'ctrl-p': 'core:move-down'
#
# You can find more information about keymaps in these guides:
# * https://atom.io/docs/latest/using-atom-basic-customization#customizing-key-bindings
# * https://atom.io/docs/latest/behind-atom-keymaps-in-depth
#
# This file uses CoffeeScript Object Notation (CSON).
# If you are unfamiliar with CSON, you can read more about it here:
# https://github.com/bevry/cson#what-is-cson

'body':
  'shift-cmd-T': 'pane:reopen-closed-item'

'.platform-darwin atom-workspace':
  'ctrl-shift-cmd-T': 'terminal-plus:new'

'.atom-text-editor:not(.mini)':
  'cmd-l': 'go-to-line:toggle'

packages.json

[
	{
		"name": "Zen",
		"version": "0.18.0"
	},
	{
		"name": "about",
		"version": "1.8.1"
	},
	{
		"name": "archive-view",
		"version": "0.64.3"
	},
	{
		"name": "ariake-dark-syntax",
		"version": "0.1.3",
		"theme": "syntax"
	},
	{
		"name": "atom-beautify",
		"version": "0.32.5"
	},
	{
		"name": "atom-clock",
		"version": "0.1.16"
	},
	{
		"name": "atom-dark-syntax",
		"version": "0.29.0",
		"theme": "syntax"
	},
	{
		"name": "atom-dark-ui",
		"version": "0.53.2",
		"theme": "ui"
	},
	{
		"name": "atom-html-preview",
		"version": "0.2.5"
	},
	{
		"name": "atom-image-resize",
		"version": "0.3.0"
	},
	{
		"name": "atom-light-syntax",
		"version": "0.29.0",
		"theme": "syntax"
	},
	{
		"name": "atom-light-ui",
		"version": "0.46.2",
		"theme": "ui"
	},
	{
		"name": "atom-material-syntax",
		"version": "1.0.8",
		"theme": "syntax"
	},
	{
		"name": "atom-material-ui",
		"version": "2.1.3",
		"theme": "ui"
	},
	{
		"name": "atom-spotify2",
		"version": "2.1.2"
	},
	{
		"name": "autocomplete-atom-api",
		"version": "0.10.7"
	},
	{
		"name": "autocomplete-css",
		"version": "0.17.5"
	},
	{
		"name": "autocomplete-html",
		"version": "0.8.4"
	},
	{
		"name": "autocomplete-plus",
		"version": "2.40.6"
	},
	{
		"name": "autocomplete-python",
		"version": "1.10.5"
	},
	{
		"name": "autocomplete-snippets",
		"version": "1.12.0"
	},
	{
		"name": "autoflow",
		"version": "0.29.3"
	},
	{
		"name": "autosave",
		"version": "0.24.6"
	},
	{
		"name": "background-tips",
		"version": "0.28.0"
	},
	{
		"name": "base16-syntax",
		"version": "1.8.1",
		"theme": "syntax"
	},
	{
		"name": "base16-tomorrow-dark-theme",
		"version": "1.5.0",
		"theme": "syntax"
	},
	{
		"name": "base16-tomorrow-light-theme",
		"version": "1.5.0",
		"theme": "syntax"
	},
	{
		"name": "batman-syntax",
		"version": "1.1.0",
		"theme": "syntax"
	},
	{
		"name": "bookmarks",
		"version": "0.45.1"
	},
	{
		"name": "bracket-matcher",
		"version": "0.89.2"
	},
	{
		"name": "browser-plus",
		"version": "0.0.98"
	},
	{
		"name": "busy-signal",
		"version": "1.4.3"
	},
	{
		"name": "color-picker",
		"version": "2.3.0"
	},
	{
		"name": "colorful-json",
		"version": "1.1.0"
	},
	{
		"name": "command-palette",
		"version": "0.43.5"
	},
	{
		"name": "dalek",
		"version": "0.2.2"
	},
	{
		"name": "deprecation-cop",
		"version": "0.56.9"
	},
	{
		"name": "dev-live-reload",
		"version": "0.48.1"
	},
	{
		"name": "encoding-selector",
		"version": "0.23.8"
	},
	{
		"name": "exception-reporting",
		"version": "0.43.1"
	},
	{
		"name": "file-header",
		"version": "1.13.9"
	},
	{
		"name": "file-icons",
		"version": "2.1.21"
	},
	{
		"name": "find-and-replace",
		"version": "0.215.9"
	},
	{
		"name": "fuzzy-finder",
		"version": "1.8.1"
	},
	{
		"name": "git-diff",
		"version": "1.3.9"
	},
	{
		"name": "git-plus",
		"version": "7.10.2"
	},
	{
		"name": "github",
		"version": "0.14.5"
	},
	{
		"name": "github-atom-dark-syntax",
		"version": "0.5.0",
		"theme": "syntax"
	},
	{
		"name": "github-atom-light-syntax",
		"version": "0.5.0",
		"theme": "syntax"
	},
	{
		"name": "go-to-line",
		"version": "0.33.0"
	},
	{
		"name": "grammar-selector",
		"version": "0.50.1"
	},
	{
		"name": "haskell-grammar",
		"version": "0.4.0"
	},
	{
		"name": "highlight-selected",
		"version": "0.13.1"
	},
	{
		"name": "image-view",
		"version": "0.62.4"
	},
	{
		"name": "incompatible-packages",
		"version": "0.27.3"
	},
	{
		"name": "intentions",
		"version": "1.1.5"
	},
	{
		"name": "keybinding-resolver",
		"version": "0.38.1"
	},
	{
		"name": "language-babel",
		"version": "2.85.0"
	},
	{
		"name": "language-c",
		"version": "0.59.3"
	},
	{
		"name": "language-clojure",
		"version": "0.22.7"
	},
	{
		"name": "language-coffee-script",
		"version": "0.49.3"
	},
	{
		"name": "language-csharp",
		"version": "1.0.1"
	},
	{
		"name": "language-css",
		"version": "0.42.10"
	},
	{
		"name": "language-gfm",
		"version": "0.90.3"
	},
	{
		"name": "language-git",
		"version": "0.19.1"
	},
	{
		"name": "language-go",
		"version": "0.45.3"
	},
	{
		"name": "language-graphql",
		"version": "0.10.1"
	},
	{
		"name": "language-html",
		"version": "0.49.0"
	},
	{
		"name": "language-hyperlink",
		"version": "0.16.3"
	},
	{
		"name": "language-ini",
		"version": "1.20.0"
	},
	{
		"name": "language-java",
		"version": "0.29.0"
	},
	{
		"name": "language-javascript",
		"version": "0.128.5"
	},
	{
		"name": "language-json",
		"version": "0.19.1"
	},
	{
		"name": "language-latex",
		"version": "1.1.1"
	},
	{
		"name": "language-less",
		"version": "0.34.2"
	},
	{
		"name": "language-lisp",
		"version": "0.2.0"
	},
	{
		"name": "language-lua",
		"version": "0.9.11"
	},
	{
		"name": "language-make",
		"version": "0.22.3"
	},
	{
		"name": "language-mustache",
		"version": "0.14.5"
	},
	{
		"name": "language-objective-c",
		"version": "0.15.1"
	},
	{
		"name": "language-ocaml",
		"version": "1.9.5"
	},
	{
		"name": "language-perl",
		"version": "0.38.1"
	},
	{
		"name": "language-php",
		"version": "0.43.2"
	},
	{
		"name": "language-property-list",
		"version": "0.9.1"
	},
	{
		"name": "language-python",
		"version": "0.49.5"
	},
	{
		"name": "language-ruby",
		"version": "0.71.4"
	},
	{
		"name": "language-ruby-on-rails",
		"version": "0.25.3"
	},
	{
		"name": "language-rust",
		"version": "0.4.12"
	},
	{
		"name": "language-sass",
		"version": "0.61.4"
	},
	{
		"name": "language-shellscript",
		"version": "0.26.3"
	},
	{
		"name": "language-source",
		"version": "0.9.0"
	},
	{
		"name": "language-sql",
		"version": "0.25.10"
	},
	{
		"name": "language-swift",
		"version": "0.5.0"
	},
	{
		"name": "language-text",
		"version": "0.7.4"
	},
	{
		"name": "language-thrift",
		"version": "1.0.2"
	},
	{
		"name": "language-todo",
		"version": "0.29.4"
	},
	{
		"name": "language-toml",
		"version": "0.18.2"
	},
	{
		"name": "language-typescript",
		"version": "0.3.3"
	},
	{
		"name": "language-xml",
		"version": "0.35.2"
	},
	{
		"name": "language-yaml",
		"version": "0.32.0"
	},
	{
		"name": "latex",
		"version": "0.50.0"
	},
	{
		"name": "latex-plus",
		"version": "0.9.1"
	},
	{
		"name": "line-ending-selector",
		"version": "0.7.6"
	},
	{
		"name": "link",
		"version": "0.31.4"
	},
	{
		"name": "linter",
		"version": "2.2.0"
	},
	{
		"name": "linter-flake8",
		"version": "2.3.0"
	},
	{
		"name": "linter-ui-default",
		"version": "1.7.1"
	},
	{
		"name": "markdown-preview",
		"version": "0.159.20"
	},
	{
		"name": "markdown-preview-plus",
		"version": "3.3.0"
	},
	{
		"name": "markdown-scroll-sync",
		"version": "2.1.2"
	},
	{
		"name": "markdown-toc",
		"version": "0.4.2"
	},
	{
		"name": "markdown-writer",
		"version": "2.7.3"
	},
	{
		"name": "merge-conflicts",
		"version": "1.4.5"
	},
	{
		"name": "metrics",
		"version": "1.2.6"
	},
	{
		"name": "minimap",
		"version": "4.29.8"
	},
	{
		"name": "notifications",
		"version": "0.70.5"
	},
	{
		"name": "one-dark-syntax",
		"version": "1.8.2",
		"theme": "syntax"
	},
	{
		"name": "one-dark-ui",
		"version": "1.12.1",
		"theme": "ui"
	},
	{
		"name": "one-light-syntax",
		"version": "1.8.2",
		"theme": "syntax"
	},
	{
		"name": "one-light-ui",
		"version": "1.12.1",
		"theme": "ui"
	},
	{
		"name": "open-on-github",
		"version": "1.3.1"
	},
	{
		"name": "package-generator",
		"version": "1.3.0"
	},
	{
		"name": "pandoc",
		"version": "0.2.2"
	},
	{
		"name": "pdf-view",
		"version": "0.70.0"
	},
	{
		"name": "pretty-json",
		"version": "2.0.1"
	},
	{
		"name": "pure-syntax",
		"version": "0.3.0",
		"theme": "syntax"
	},
	{
		"name": "python-indent",
		"version": "1.1.5"
	},
	{
		"name": "remote-ftp",
		"version": "2.2.0"
	},
	{
		"name": "set-syntax",
		"version": "0.4.0"
	},
	{
		"name": "settings-view",
		"version": "0.254.2"
	},
	{
		"name": "snippets",
		"version": "1.3.3"
	},
	{
		"name": "solarized-dark-syntax",
		"version": "1.1.4",
		"theme": "syntax"
	},
	{
		"name": "solarized-light-syntax",
		"version": "1.1.4",
		"theme": "syntax"
	},
	{
		"name": "sort-lines",
		"version": "0.18.0"
	},
	{
		"name": "spell-check",
		"version": "0.73.4"
	},
	{
		"name": "status-bar",
		"version": "1.8.15"
	},
	{
		"name": "styleguide",
		"version": "0.49.11"
	},
	{
		"name": "symbols-tree-view",
		"version": "0.14.0"
	},
	{
		"name": "symbols-view",
		"version": "0.118.2"
	},
	{
		"name": "sync-settings",
		"version": "0.8.6"
	},
	{
		"name": "tabs",
		"version": "0.109.1"
	},
	{
		"name": "timecop",
		"version": "0.36.2"
	},
	{
		"name": "tool-bar",
		"version": "1.1.7"
	},
	{
		"name": "tree-view",
		"version": "0.222.0"
	},
	{
		"name": "update-package-dependencies",
		"version": "0.13.1"
	},
	{
		"name": "welcome",
		"version": "0.36.6"
	},
	{
		"name": "whitespace",
		"version": "0.37.5"
	},
	{
		"name": "wrap-guide",
		"version": "0.40.3"
	}
]

settings.json

{
	"Zen": {
		"minimap": true,
		"tabs": "multiple",
		"width": 150
	},
	"atom-package-deps": {
		"ignored": []
	},
	"autocomplete-python": {
		"pythonPaths": "/usr/local/bin/python3",
		"useKite": false
	},
	"core": {
		"automaticallyUpdate": false,
		"customFileTypes": {
			"source.ini": [
				".buckconfig",
				".hgrc",
				".flowconfig"
			],
			"source.json": [
				"BUCK.autodeps"
			],
			"source.python": [
				"BUCK"
			]
		},
		"disabledPackages": [
			"atom-image-resize",
			"file-header",
			"linter",
			"linter-flake8",
			"linter-ui-default",
			"markdown-preview"
		],
		"telemetryConsent": "no",
		"themes": [
			"one-dark-ui",
			"pure-syntax"
		]
	},
	"editor": {
		"fontFamily": "Fira Mono",
		"fontSize": 13,
		"scrollPastEnd": true
	},
	"exception-reporting": {
		"userId": "ebc51bd8-c84e-4308-af36-1871c58bdca7"
	},
	"file-header": {
		"username": "Krishnan"
	},
	"github": {},
	"linter": {
		"lintOnChangeInterval": 200
	},
	"linter-flake8": {
		"flakeErrors": true,
		"maxLineLength": 80,
		"pycodestyleErrorsToWarnings": true
	},
	"linter-pycodestyle": {
		"executablePath": "/usr/local/bin/pycodestyle",
		"maxLineLength": 120
	},
	"linter-ui-default": {
		"panelHeight": 69,
		"showPanel": true
	},
	"minimap": {
		"disablePythonDocLinks": true
	},
	"nuclide": {
		"nuclide-distraction-free-mode": {
			"hideToolBar": true
		},
		"nuclide-flow": {
			"enableTypeHints": false,
			"flowAutocompleteResultsFirst": false,
			"functionSnippetShouldIncludeArguments": false,
			"stopFlowOnExit": false,
			"warnOnNotInstalled": false
		},
		"nuclide-home": {
			"showHome": false
		},
		"nuclide-objc": {
			"enableAutomaticSquareBracketInsertion": false
		},
		"nuclide-ocaml": {
			"enableDiagnostics": false
		},
		"nuclide-python": {
			"includeOptionalArguments": true,
			"lintOnFly": true,
			"pathToPython": "python3"
		},
		"nuclide-remote-projects": {
			"connectionProfiles": [
				{
					"deletable": true,
					"displayTitle": "Orkney",
					"params": {
						"authMethod": "PRIVATE_KEY",
						"cwd": "/old/home/krishnan/projects",
						"displayTitle": "Orkney",
						"pathToPrivateKey": "/Users/Krishnan/.ssh/id_rsa",
						"remoteServerCommand": "/home/krishnan/.npm_packages/bin/nuclide-start-server -k",
						"server": "172.23.213.49",
						"sshPort": "22",
						"username": "krishnan"
					},
					"saveable": true
				}
			]
		},
		"nuclide-working-sets": {
			"workingSets": [
				{
					"active": true,
					"name": "ae",
					"uris": [
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/.git",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/.gitignore",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/__init__.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/data",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/out",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/10x megacell autoencoder.ipynb",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/__init__.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/emt data autoencoder.ipynb",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/load_rnaseq.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/logs",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/visualizing_1M_neurons.ipynb",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/rnaseq/weights",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/__init__.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/ae experiments.ipynb",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/ae.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/combine.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/experiments",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/flu_weights",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/main.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/marrow_weights",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/notebooks",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/svm",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/train_marrow.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/tsne.py",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/utils",
						"nuclide://localhost/old/home/krishnan/projects/Nnetbio/visualization/zika_weights",
						"nuclide://localhost/old/home/krishnan/projects/bio-autoencoder",
						"nuclide://localhost/old/home/krishnan/projects/bioautoencoder"
					]
				}
			]
		}
	},
	"sync-settings": {},
	"tool-bar": {
		"visible": false
	},
	"welcome": {
		"showOnStartup": false
	}
}

snippets.cson

# Your snippets
#
# Atom snippets allow you to enter a simple prefix in the editor and hit tab to
# expand the prefix into a larger code block with templated values.
#
# You can create a new snippet in this file by typing "snip" and then hitting
# tab.
#
# An example CoffeeScript snippet to expand log to console.log:
#
# '.source.coffee':
#   'Console log':
#     'prefix': 'log'
#     'body': 'console.log $1'
#
# This file uses CoffeeScript Object Notation (CSON).
# If you are unfamiliar with CSON, you can read more about it here:
# https://github.com/bevry/cson#what-is-cson

styles.less

/*
 * Your Stylesheet
 *
 * This stylesheet is loaded when Atom starts up and is reloaded automatically
 * when it is changed and saved.
 *
 * Add your own CSS or Less to fully customize Atom.
 * If you are unfamiliar with Less, you can read more about it here:
 * http://lesscss.org
 */
/*
 * Examples
 * (To see them, uncomment and save)
 */
/*
  * Your Stylesheet
  *
  * This stylesheet is loaded when Atom starts up and is reloaded automatically
  * when it is changed.
  *
  * If you are unfamiliar with LESS, you can read more about it here:
  * http://www.lesscss.org
  */

.atom-text-editor {
    @font-family: 'Monoid Regular Loose'
}

/* more subtle invisibles */
.atom-text-editor::shadow {
    .invisible-character {
        color: #504949;
        opacity: 0.5;
    }
    .indent-guide {
        opacity: 0.5;
    }
}

/* thicker cursor */
.atom-text-editor .cursor {
    border-left-width: 2px;
}
.atom-text-editor.is-focused .line-number.cursor-line-no-selection,
.atom-text-editor.is-focused .line.cursor-line {
    background-color: rgba(53, 57, 60, 0);
}
.atom-text-editor.is-focused .selection .region {
    background-color: RGBA(100, 110, 100, 0.6);
    color: #fff !important;
    text-shadow: none;
}

/* green comments */
.comment.block.documentation .punctuation.definition.comment, .comment.block.documentation  {
    color: green;
    font-weight:normal;
}