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v2.0.0-alpha.1 (#47)
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New design and basic functionality
* Simplify user interface and code (electron renderer/main interface, client state etc), 
* RAxML command and partition file generated reactively
* Build scripts tested for Mac OS and Windows
* Support phylip format (both strict and relaxed)

Fixes #9, fixes #46
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danieledler authored Sep 29, 2019
1 parent 5fed4a4 commit 1cf1393
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Showing 67 changed files with 11,738 additions and 3,836 deletions.
15 changes: 15 additions & 0 deletions .babelrc
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{
"presets": [
[
"@babel/preset-env", {
"targets": {
"node": "current"
}
}
]
],
"plugins": [
["@babel/plugin-proposal-decorators", { "legacy": true }],
["@babel/plugin-proposal-class-properties", { "loose": true }]
]
}
16 changes: 16 additions & 0 deletions .editorconfig
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# EditorConfig is awesome: http://EditorConfig.org

# top-most EditorConfig file
root = true

[*]
end_of_line = lf
indent_style = space
indent_size = 2
max_line_length = 120
charset = utf-8
trim_trailing_whitespace = true
insert_final_newline = true

[*.md]
trim_trailing_whitespace = false
8 changes: 7 additions & 1 deletion .gitignore
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Expand Up @@ -9,6 +9,7 @@
# production
/build
/dist
/release

# misc
.DS_Store
Expand All @@ -22,4 +23,9 @@ yarn-debug.log*
yarn-error.log*

# external dependencies
/bin/raxml
/static/bin

# output
RAxML_*
*.reduced
*_concat.*
17 changes: 17 additions & 0 deletions .prettierrc
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{
"overrides": [
{
"files": [".prettierrc", ".babelrc", ".eslintrc", ".stylelintrc"],
"options": {
"parser": "json"
}
}
],
"singleQuote": true,
"printWidth": 80,
"tabWidth": 2,
"useTabs": false,
"semi": true,
"bracketSpacing": true,
"jsxBracketSameLine": false
}
11 changes: 11 additions & 0 deletions TODO.md
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Todo:
- Github page for downloading the latest release
- Choose light or dark theme
- Option for empirical frequencies?
- In the Output section, add collapsable list of output files with descriptions
- Option to remove existing files (shell.moveItemToTrash(fullPath))
- Spinning wheel while running to distinguishing it from getting stuck
- Fix parsing a relaxed phylip as strict
- Don't make multithreaded binaries available if num cpus is one.
- Implement auto-updating/checking mechanism.
- Create publish script
13 changes: 13 additions & 0 deletions craco.config.js
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module.exports = {
babel: {
plugins: [
["@babel/plugin-proposal-decorators", { legacy: true }],
["@babel/plugin-proposal-class-properties", { loose: true }]
]
},
webpack: {
configure: {
target: 'electron-renderer'
}
}
};
10 changes: 10 additions & 0 deletions jsconfig.json
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{
"compilerOptions": {
"target": "esnext"
},
"exclude": [
"node_modules",
"build",
"dist"
]
}
161 changes: 117 additions & 44 deletions package.json
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@@ -1,90 +1,163 @@
{
"name": "raxmlgui2",
"version": "0.2.0",
"name": "raxmlGUI2",
"productName": "raxmlGUI2",
"version": "2.0.0-beta.1",
"private": true,
"author": "Captain Electron",
"author": "AntonelliLab",
"license": "ISC",
"description": "raxmlGUI2 - A new graphical front-end for RAxML",
"homepage": "./",
"main": "public/electron.js",
"repository": {
"type": "git",
"url": "git+https://github.com/AntonelliLab/raxmlGUI.git"
},
"bugs": {
"url": "https://github.com/AntonelliLab/raxmlGUI2/issues"
},
"keywords": [
"Electron",
"RAxML",
"GUI",
"Phylogenetics"
],
"main": "build/electron.js",
"scripts": {
"start": "cross-env ELECTRON_START_URL=http://localhost:3000/ run-p react-start electron-dev",
"react-start": "cross-env BROWSER=none react-scripts start",
"react-build": "react-scripts build",
"react-test": "react-scripts test --env=jsdom",
"react-start": "cross-env BROWSER=none craco start",
"react-build": "craco build",
"react-test": "craco test --env=jsdom",
"react-eject": "react-scripts eject",
"wait-dev": "wait-on $ELECTRON_START_URL",
"electron-start": "nodemon --watch src/electron src/electron.js .",
"electron-dev": "cross-env DEV=true run-s wait-dev electron-start",
"electron-dev": "electron-webpack dev",
"electron-start": "cross-env DEV=true run-s wait-dev electron-dev",
"electron-build": "electron-builder",
"electron-pack": "electron-builder --dir",
"release": "yarn react-build && electron-builder --publish=always",
"build": "yarn react-build && yarn electron-build"
"electron-build-win": "electron-builder -w",
"electron-build-linux": "electron-builder -l",
"electron-build-all": "electron-builder -mwl",
"electron-pack": "electron-builder --dir -c.compression=store -c.mac.identity=null",
"electron-pack-win": "electron-builder -w --dir -c.compression=store",
"electron-compile": "electron-webpack",
"electron-copy": "shx cp dist/main/main.js build/electron.js",
"compile": "run-s electron-compile electron-copy",
"build": "run-s react-build compile electron-build",
"build-win": "run-s react-build compile electron-build-win",
"build-all": "run-s react-build compile electron-build-all",
"dist-pack": "run-s react-build compile electron-pack",
"dist-pack-win": "run-s react-build compile electron-pack-win",
"postinstall": "electron-builder install-app-deps"
},
"dependencies": {
"@material-ui/core": "^3.9.2",
"@material-ui/icons": "^3.0.2",
"classnames": "^2.2.5",
"@babel/plugin-proposal-decorators": "^7.4.4",
"@craco/craco": "^5.3.0",
"@material-ui/core": "^4.3.2",
"@material-ui/icons": "^4.2.1",
"@material-ui/styles": "^4.3.0",
"bionode-fasta": "^0.5.6",
"bionode-seq": "^0.1.1",
"classnames": "^2.2.6",
"clean-stack": "^2.2.0",
"clsx": "^1.0.4",
"computed-async-mobx": "^4.2.0",
"cpus": "^1.0.2",
"crypto-random-string": "^1.0.0",
"d3-array": "^2.0.3",
"d3-array": "^2.2.0",
"d3-format": "^1.3.2",
"electron-is-dev": "^1.0.1",
"mobx": "^5.9.0",
"mobx-react": "^5.4.3",
"electron-better-ipc": "^0.4.0",
"electron-is-dev": "^1.1.0",
"electron-unhandled": "^3.0.0",
"electron-util": "^0.12.1",
"filenamify": "^4.1.0",
"lodash": "^4.17.15",
"mobx": "^5.13.0",
"mobx-react": "^6.1.3",
"mobx-utils": "^5.4.1",
"parse-filepath": "^1.0.2",
"prop-types": "^15.6.0",
"react": "^16.2.0",
"react-dom": "^16.2.0",
"react-dropzone": "^10.0.4",
"react-scripts": "2.1.8"
"prop-types": "^15.7.2",
"react": "^16.9.0",
"react-dom": "^16.9.0",
"react-dropzone": "^10.1.7",
"react-msa-viewer": "^1.0.1",
"react-scripts": "3.1.1",
"react-split-pane": "^0.1.87",
"serialize-error": "^4.1.0",
"source-map-support": "^0.5.13"
},
"devDependencies": {
"cross-env": "^5.1.3",
"electron": "^4.1.0",
"electron-builder": "^20.39.0",
"@babel/core": "^7.5.5",
"@babel/plugin-proposal-class-properties": "^7.5.5",
"@babel/preset-env": "^7.5.5",
"cross-env": "^5.2.0",
"devtron": "^1.4.0",
"electron": "^6.0.2",
"electron-builder": "^21.2.0",
"electron-devtools-installer": "^2.2.4",
"nodemon": "^1.14.11",
"npm-run-all": "^4.1.2",
"typescript": "^3.3.3333",
"wait-on": "^3.2.0"
"electron-webpack": "^2.7.4",
"nodemon": "^1.19.1",
"npm-run-all": "^4.1.5",
"prettier": "^1.18.2",
"shx": "^0.3.2",
"typescript": "^3.5.3",
"wait-on": "^3.3.0"
},
"browserslist": [
">0.2%",
"not dead",
"not ie <= 11",
"not op_mini all"
],
"electronWebpack": {
"commonSourceDirectory": "src/common",
"staticSourceDirectory": "static",
"main": {
"sourceDirectory": "src/main"
},
"renderer": {
"sourceDirectory": null
}
},
"build": {
"appId": "org.jtklein.raxmlGUI2",
"productName": "raxmlGUI2",
"directories": {
"buildResources": "build",
"output": "dist"
},
"files": [
"src/electron/*"
"src/main/*"
],
"extraResources": [
"assets/"
],
"mac": {
"category": "public.app-category.education",
"extraFiles": [
"extraResources": [
{
"from": "bin/raxml",
"to": "bin",
"from": "static/bin",
"to": "static/bin",
"filter": [
"**/*-Mac"
]
},
{
"from": "static/example-files/fasta",
"to": "static/example-files",
"filter": [
"*.txt"
]
}
]
},
"win": {
"target": [
"nsis",
"msi"
"msi",
"portable"
],
"extraFiles": [
"extraResources": [
{
"from": "bin/raxml",
"to": "bin",
"from": "static/bin",
"to": "static/bin",
"filter": [
"**/*-Windows.exe"
"**/*.exe"
]
}
]
Expand All @@ -97,10 +170,10 @@
"AppImage"
],
"category": "Education",
"extraFiles": [
"extraResources": [
{
"from": "bin/raxml",
"to": "bin",
"from": "static/bin",
"to": "static/bin",
"filter": [
"**/*-Linux"
]
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