Merge branch 'develop'

DECIPHER-genomics · Mar 8, 2022 · 0cfe6ce · 0cfe6ce
2 parents 42897bf + dd69e3c
commit 0cfe6ce
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diff --git a/.eslintrc.js b/.eslintrc.js
@@ -9,105 +9,109 @@ const noRestrictedProperies = require('eslint-config-airbnb-base/rules/best-prac
 module.exports = {
   env: {
     browser : true,
-    jquery  : true
+    es6     : true,
+    node    : true,
   },
-  extends : [
+  plugins: [
+    'align-assignments',
+  ],
+  extends: [
     'airbnb-base',
   ],
+  parser        : '@babel/eslint-parser',
+  parserOptions : {
+    requireConfigFile : false,
+    ecmaVersion       : 8,
+    sourceType        : 'module',
+  },
   globals: {
-    Base         : true,
-    Genoverse    : true,
-    RTree        : true,
-    dallianceLib : true,
-    VCFReader    : true,
-    BWReader     : true
+    Genoverse: true,
   },
   ignorePatterns: [
-    '.eslintrc.js',
     'node_modules',
-    'index.js',
+    'dist',
     '**/*.min.js',
-    'js/lib/**/*.js'
+    'src/js/lib/dalliance/*.js',
+    'src/js/lib/jquery-plugins/*.js',
   ],
+  rules: {
+    'align-assignments/align-assignments' : [ 'error', { requiresOnly: false }],
+    'padding-line-between-statements'     : [
+      'error', ...[
+        [ '*', [ 'multiline-block-like', 'return', 'break', 'export', 'throw', 'cjs-export' ]],
+        [ '*', [ 'cjs-import', 'import', 'const', 'let', 'var' ]],
+        [[ 'multiline-block-like', 'return', 'break', 'export', 'throw', 'cjs-export' ], '*' ],
+        [[ 'cjs-import', 'import', 'const', 'let', 'var' ], '*' ],
+        [ 'cjs-import',       'cjs-import', 'any' ],
+        [ 'import',           'import', 'any' ],
+        [ 'singleline-const', 'const', 'any' ],
+        [ 'singleline-let',   'let', 'any' ],
+        [ 'singleline-var',   'var', 'any' ],
+        [ 'expression',       'expression', 'any' ],
+      ].map(
+        ([ prev, next = '*', blankLine = 'always' ]) => ({ prev, next, blankLine })
+      ),
+    ],
+    'max-len'                    : 'off',
+    'no-multi-spaces'            : 'off',
+    'no-multi-assign'            : 'off',
+    'no-nested-ternary'          : 'off',
+    'no-prototype-builtins'      : 'off',
+    'no-plusplus'                : 'off',
+    'operator-linebreak'         : 'off',
+    'prefer-destructuring'       : 'off',
+    'quote-props'                : 'off',
+    'template-curly-spacing'     : 'off',
+    'yoda'                       : 'off',
+    'no-underscore-dangle'       : 'off',
+    'newline-per-chained-call'   : 'off',
+    'default-param-last'         : 'off',
+    'no-promise-executor-return' : 'off',
+    'no-continue'                : 'off',
+    'no-fallthrough'             : 'off',
+    'no-bitwise'                 : 'off',
+    'func-names'                 : 'off',
+    'no-param-reassign'          : 'off',
+
+    'array-bracket-spacing' : [ 'warn', 'always', { objectsInArrays: false, arraysInArrays: false }],
+    'quotes'                : [ 'warn', 'single', { avoidEscape: true }],
+
+    'arrow-parens'                   : [ 'error', 'as-needed', { requireForBlockBody: true }],
+    'function-paren-newline'         : [ 'error', 'consistent' ],
+    'function-call-argument-newline' : [ 'error', 'consistent' ],
+    'linebreak-style'                : [ 'error', 'unix' ],
+    'object-shorthand'               : [ 'error', 'consistent' ],
+
+    'comma-dangle': [ 'error', {
+      arrays    : 'always-multiline',
+      objects   : 'always-multiline',
+      imports   : 'always-multiline',
+      exports   : 'always-multiline',
+      functions : 'never',
+    }],
+    'key-spacing': [ 'error', {
+      singleLine : { beforeColon: false, afterColon: true },
+      multiLine  : { beforeColon: false, afterColon: true },
+      align      : { beforeColon: true,  afterColon: true, on: 'colon' },
+    }],
+    'object-curly-newline': [ 'error', {
+      ObjectExpression : { multiline: true, consistent: true },
+      ObjectPattern    : { multiline: true, consistent: true },
+    }],
+    'import/no-extraneous-dependencies' : [ 'error' ],
+    'import/order'                      : [ 'error', {
+      alphabetize : { order: 'asc' },
+      groups      : [ 'builtin', 'external', 'internal', 'parent', 'sibling' ],
+    }],
+
+    'no-restricted-globals'    : [ 'error', 'event', 'isFinite' ],
+    'no-restricted-properties' : noRestrictedProperies,
+
+    'consistent-return': 'off', // FIXME: async functions and $.events
+  },
   overrides: [
     {
-      files : [ 'js/**/*.js' ],
-      plugins : [ 'es' ],
-      extends : [
-        'airbnb-base',
-        'plugin:es/no-new-in-es2018',
-        'plugin:es/no-new-in-es2017',
-        'plugin:es/no-new-in-es2016',
-        'plugin:es/no-new-in-es2015'
-      ],
-      parserOptions: {
-        parser      : 'espree',
-        ecmaVersion : 5,
-        sourceType  : 'script'
-      },
-      rules: {
-        'linebreak-style'       : [ 'error', 'unix' ],
-        'comma-dangle'          : [ 'error', 'never' ],
-        'quotes'                : [ 'warn', 'single', { avoidEscape: true }], // be more permissive than airbnb - allow 'double quotes containing 'singles''
-        'object-shorthand'      : [ 'error', 'never' ],
-        'array-bracket-spacing' : [ 'warn', 'always', {
-          objectsInArrays : false,
-          arraysInArrays  : false
-        }],
-        'object-curly-newline': [ 'error', {
-          ObjectExpression : { multiline: true, consistent: true },
-          ObjectPattern    : { multiline: true, consistent: true }
-        }],
-        'key-spacing': [ 'error', {
-          singleLine : { beforeColon: false, afterColon: true },
-          multiLine  : { beforeColon: false, afterColon: true },
-          align      : { beforeColon: true,  afterColon: true, on: 'colon' },
-        }],
-        'quote-props'                         : 'off',
-        'no-multi-spaces'                     : 'off',
-        'prefer-destructuring'                : 'off',
-        'no-prototype-builtins'               : 'off',
-        'no-nested-ternary'                   : 'off',
-        'no-plusplus'                         : 'off',
-        'template-curly-spacing'              : 'off',
-        'no-var'                              : 'off',
-        'one-var'                             : 'off',
-        'one-var-declaration-per-line'        : 'off',
-        'vars-on-top'                         : 'off',
-        'func-names'                          : 'off',
-        'prefer-arrow-callback'               : 'off',
-        'prefer-spread'                       : 'off',
-        'prefer-template'                     : 'off',
-        'prefer-rest-params'                  : 'off',
-        'no-param-reassign'                   : 'off',
-        'no-multi-assign'                     : 'off',
-        'no-underscore-dangle'                : 'off',
-        'no-empty'                            : 'off',
-        'switch-colon-spacing'                : 'off',
-        'max-len'                             : 'off',
-        'no-continue'                         : 'off',
-        'consistent-return'                   : 'off',
-        'operator-linebreak'                  : 'off',
-        'guard-for-in'                        : 'off',
-        'no-restricted-syntax'                : 'off',
-        'no-restricted-globals'               : 'off',
-        'function-paren-newline'              : 'off',
-        'no-fallthrough'                      : 'off',
-        'no-bitwise'                          : 'off',
-        'no-cond-assign'                      : 'off',
-        'no-new'                              : 'off',
-        'newline-per-chained-call'            : 'off',
-        'prefer-exponentiation-operator'      : 'off',
-        'no-restricted-properties'            : noRestrictedProperies
-      }
-    },
-    {
-      files : [ '**/*.js' ],
-      excludedFiles: 'js/**/*.js',
-      env   : {
-        es6: true,
-      },
-      plugins : [ 'align-assignments' ],
+      files   : [ 'test/**/*.js' ],
       globals : {
         jest       : true,
         describe   : true,
@@ -119,79 +123,6 @@ module.exports = {
         afterEach  : true,
         beforeEach : true,
       },
-      rules: {
-        'align-assignments/align-assignments' : [ 'error', { requiresOnly: false }],
-        'padding-line-between-statements'     : [
-          'error', ...[
-            [ '*', [ 'multiline-block-like', 'return', 'break', 'export', 'throw', 'cjs-export' ]],
-            [ '*', [ 'cjs-import', 'import', 'const', 'let', 'var' ]],
-            [[ 'multiline-block-like', 'return', 'break', 'export', 'throw', 'cjs-export' ], '*' ],
-            [[ 'cjs-import', 'import', 'const', 'let', 'var' ], '*' ],
-            [ 'cjs-import',       'cjs-import', 'any' ],
-            [ 'import',           'import', 'any' ],
-            [ 'singleline-const', 'const', 'any' ],
-            [ 'singleline-let',   'let', 'any' ],
-            [ 'singleline-var',   'var', 'any' ],
-            [ 'expression',       'expression', 'any' ],
-          ].map(
-            ([ prev, next = '*', blankLine = 'always' ]) => ({ prev, next, blankLine })
-          ),
-        ],
-        'max-len'                    : 'off',
-        'no-multi-spaces'            : 'off',
-        'no-multi-assign'            : 'off',
-        'no-nested-ternary'          : 'off',
-        'no-prototype-builtins'      : 'off',
-        'no-plusplus'                : 'off',
-        'operator-linebreak'         : 'off',
-        'prefer-destructuring'       : 'off',
-        'quote-props'                : 'off',
-        'template-curly-spacing'     : 'off',
-        'yoda'                       : 'off',
-        'no-underscore-dangle'       : 'off',
-        'newline-per-chained-call'   : 'off',
-        'default-param-last'         : 'off',
-        'no-promise-executor-return' : 'off',
-        'no-continue'                : 'off',
-        'no-fallthrough'             : 'off',
-        'no-bitwise'                 : 'off',
-        'func-names'                 : 'off',
-        'no-param-reassign'          : 'off',
-
-        'array-bracket-spacing' : [ 'warn', 'always', { objectsInArrays: false, arraysInArrays: false }],
-        'quotes'                : [ 'warn', 'single', { avoidEscape: true }],
-
-        'arrow-parens'                   : [ 'error', 'as-needed', { requireForBlockBody: true }],
-        'function-paren-newline'         : [ 'error', 'consistent' ],
-        'function-call-argument-newline' : [ 'error', 'consistent' ],
-        'linebreak-style'                : [ 'error', 'unix' ],
-        'object-shorthand'               : [ 'error', 'consistent' ],
-
-        'comma-dangle': [ 'error', {
-          arrays    : 'always-multiline',
-          objects   : 'always-multiline',
-          imports   : 'always-multiline',
-          exports   : 'always-multiline',
-          functions : 'never',
-        }],
-        'key-spacing': [ 'error', {
-          singleLine : { beforeColon: false, afterColon: true },
-          multiLine  : { beforeColon: false, afterColon: true },
-          align      : { beforeColon: true,  afterColon: true, on: 'colon' },
-        }],
-        'object-curly-newline': [ 'error', {
-          ObjectExpression : { multiline: true, consistent: true },
-          ObjectPattern    : { multiline: true, consistent: true },
-        }],
-        'import/no-extraneous-dependencies' : [ 'error' ],
-        'import/order'                      : [ 'error', {
-          alphabetize : { order: 'asc' },
-          groups      : [ 'builtin', 'external', 'internal', 'parent', 'sibling' ],
-        }],
-
-        'no-restricted-globals'    : [ 'error', 'event', 'isFinite' ],
-        'no-restricted-properties' : noRestrictedProperies,
-      }
     },
-  ]
+  ],
 };
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -3,22 +3,21 @@ name: test
 on:
   push:
     branches:
-      - gh-pages
       - master
+      - develop
 jobs:
   test:
-
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        node-version: [14.x]
+        node-version: [16.x]
 
     steps:
-    - uses: actions/checkout@v2
-    - name: npm install and test
-      uses: actions/setup-node@v1
-      with:
-        node-version: ${{ matrix.node-version }}
-    - run: npm install
-    - run: npm test
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v1
+        with:
+          node-version: ${{ matrix.node-version }}
+      - run: yarn install
+      - run: yarn lint
+      - run: yarn test
diff --git a/.github/workflows/update-gh-pages.yml b/.github/workflows/update-gh-pages.yml
@@ -0,0 +1,33 @@
+name: update gh-pages
+
+on:
+  push:
+    branches:
+      - master
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        node-version: [16.x]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-node@v1
+        with:
+          node-version: ${{ matrix.node-version }}
+      - run: yarn install
+      - run: yarn build --env public-path=/Genoverse/dist/
+      - name: Commit and push files
+        run: |
+          echo $GITHUB_ACTOR
+          git config --local user.email "[email protected]"
+          git config --local user.name $GITHUB_ACTOR
+          git fetch --all
+          git checkout gh-pages
+          git pull
+          git reset --hard origin/master
+          git add -f dist
+          git commit -m "Added dist folder"
+          git push --force origin gh-pages
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
 /data*
 *.DS_Store
-node_modules/*
+node_modules
+dist
diff --git a/.npmignore b/.npmignore
@@ -0,0 +1 @@
+/data*
diff --git a/LICENSE.TXT b/LICENSE.TXT
@@ -1,5 +1,5 @@
 Copyright (c) 2011 Genome Research Ltd.
-Author: Evgeny Bragin
+Author: Simon Brent, Evgeny Bragin
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:
@@ -21,4 +21,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.