Merge pull request #2634 from kbase/develop

Merging up for 5.0.0 release

.flake8

@@ -1,8 +1,10 @@
 [flake8]
 # https://ljvmiranda921.github.io/notebook/2018/06/21/precommits-using-black-and-flake8/
 ignore = E203, E266, E501, W503, F403, F401, E402, C901
-# max-line-length = 79
-# max-complexity = 15
 select = B,C,E,F,W,T4,B9
 exclude =
- ./test/selenium_scripts/
+.git,
+.github,
+deployment,
+docs,
+node_modules

.github/codecov.yml

@@ -0,0 +1,23 @@
+codecov:
+  require_ci_to_pass: yes
+
+coverage:
+  precision: 2
+  round: down
+  range: "70...100"
+
+parsers:
+  gcov:
+    branch_detection:
+      conditional: yes
+      loop: yes
+      method: no
+      macro: no
+
+comment:
+  layout: "reach,diff,flags,files,footer"
+  behavior: default
+  require_changes: no
+
+github_checks:
+    annotations: false

.github/pull_request_template.md

@@ -5,7 +5,8 @@
 * List any dependencies that are required for this change.
 
 # Jira Ticket / Issue #
-e.g. https://kbase-jira.atlassian.net/browse/DATAUP-X
+
+Related Jira ticket: https://kbase-jira.atlassian.net/browse/DATAUP-X
 - [ ] Added the Jira Ticket to the title of the PR (e.g. `DATAUP-69 Adds a PR template`)
 
 # Testing Instructions
@@ -22,9 +23,9 @@ e.g. https://kbase-jira.atlassian.net/browse/DATAUP-X
 - [ ] My changes generate no new warnings
 - [ ] I have added tests that prove my fix is effective or that my feature works
 - [ ] New and existing unit tests pass locally with my changes
-- [ ] Any dependent changes have been merged and published in downstream modules
 - [ ] (JavaScript) I have run Prettier and ESLint on changed code manually or with a git precommit hook
 - [ ] (Python) I have run Black and Flake8 on changed Python code manually or with a git precommit hook
+- [ ] Any dependent changes have been merged and published in downstream modules
 
 # Updating Version and Release Notes (if applicable)
 

.github/workflows/integration_test.yml

@@ -17,16 +17,15 @@ jobs:
         auto-update-conda: true
         condarc-file: test/condarc.yml
 
-    - name: Use Node JS 14.x
+    - name: Use Node JS 16.x
       uses: actions/setup-node@v1
       with:
-        node-version: 14.x
+        node-version: 16.x
 
     - name: Install JS dependencies
       run: |
         npm ci
-        npm install bower
-        ./node_modules/bower/bin/bower install
+        npm run install-npm
 
     - name: Install Narrative Application
       shell: bash -l {0}

.github/workflows/unit_test.yml

@@ -17,16 +17,15 @@ jobs:
         auto-update-conda: true
         condarc-file: test/condarc.yml
 
-    - name: Use Node JS 14.x
-      uses: actions/setup-node@v1
+    - name: Use Node JS 16.x
+      uses: actions/setup-node@v2.1.2
       with:
-        node-version: 14.x
+        node-version: 16.x
 
     - name: Install JS dependencies
       run: |
         npm ci
-        npm install bower
-        ./node_modules/bower/bin/bower install
+        npm run install-npm
 
     - name: Install Narrative Application
       shell: bash -l {0}
@@ -37,25 +36,36 @@ jobs:
           sed -i 's/{{ if ne .Env.CONFIG_ENV "prod" }} true {{- else }} false {{- end }}/true/' src/config.json
           jupyter notebook --version
 
+    - name: Set up environment vars
+      run: |
+        echo "KBASE_TEST_TOKEN=${{ secrets.NARRATIVE_TEST_TOKEN }}" >> $GITHUB_ENV
+
     - name: Run Narrative Backend Tests
+      id: test_backend
       shell: bash -l {0}
       run: make test-backend
+      continue-on-error: true
 
     - name: Run Narrative Frontend Unit Tests
+      id: test_frontend
       shell: bash -l {0}
       run: make test-frontend-unit
-
-    - name: make test output available as artifact in case of failure
-      if: ${{ failure() }}
-      uses: actions/upload-artifact@v2
-      with:
-        name: karma-result.json
-        path: karma-result.json
+      continue-on-error: true
 
     - name: Send to Codecov
+      id: send_to_codecov
       uses: codecov/[email protected]
+      continue-on-error: true
       with:
         file: |
           ./python-coverage/coverage.xml
           ./js-coverage/lcov/lcov.info
         fail_ci_if_error: true
+
+    - name: outcome
+      if: steps.test_backend.outcome != 'success' || steps.test_frontend.outcome != 'success' || steps.send_to_codecov.outcome != 'success'
+      run: |
+        echo "backend tests: ${{ steps.test_backend.outcome }}"
+        echo "frontend tests: ${{ steps.test_frontend.outcome }}"
+        echo "upload coverage: ${{ steps.send_to_codecov.outcome }}"
+        exit 1

.gitignore

@@ -24,6 +24,7 @@ my_narrative_venv/
 narrative_venv/
 new_narrative_env_2/
 js-coverage
+python-coverage/
 cover
 _attic
 
@@ -104,4 +105,4 @@ target/
 .idea
 
 # For yarn users
-yarn.lock
+yarn.lock

.husky/pre-commit

@@ -0,0 +1,4 @@
+#!/bin/sh
+. "$(dirname "$0")/_/husky.sh"
+
+npm run husky_msg && npx lint-staged && npm run compile_css

.husky/pre-push

@@ -1,5 +1,4 @@
 #!/bin/sh
 . "$(dirname "$0")/_/husky.sh"
 
-#npm run husky_msg && npm run prettier_check
-npx lint-staged
+npm run update_browserslist

.prettierignore

@@ -9,4 +9,4 @@ kbase-extension/static/ext_modules
 kbase-extension/static/kbase/js/patched-components
 node_modules
 cover
-venv
+venv

.stylelintrc.css.json

@@ -0,0 +1,41 @@
+{
+    "extends": "stylelint-config-standard",
+    "plugins": [
+      "stylelint-no-indistinguishable-colors",
+      "stylelint-color-format"
+    ],
+    "rules": {
+      "color-named": "never",
+      "color-no-hex": true,
+      "color-format/format": {
+        "format": "rgb"
+      },
+      "color-function-notation": "modern",
+      "declaration-block-no-redundant-longhand-properties": true,
+      "font-family-name-quotes": "always-where-recommended",
+      "font-family-no-missing-generic-family-keyword": [
+        true,
+        {
+          "ignoreFontFamilies": ["FontAwesome", "Glyphicons Halflings", "kbase-icons"]
+        }
+      ],
+      "length-zero-no-unit": true,
+      "no-descending-specificity": null,
+      "plugin/stylelint-no-indistinguishable-colors": false,
+      "selector-max-compound-selectors": 5,
+      "selector-max-class": 5,
+      "selector-no-qualifying-type": [
+        true,
+        {
+          "ignore": ["attribute", "class"]
+        }
+      ],
+      "shorthand-property-no-redundant-values": true
+    },
+    "ignoreFiles": [
+      "kbase-extension/static/ext_components/**/*.css",
+      "kbase-extension/static/ext_packages/**/*.css",
+      "kbase-extension/static/kbase/js/patched-components/**/*.css",
+      "docs/**/*.css"
+    ]
+}

.stylelintrc.yaml

@@ -0,0 +1,60 @@
+extends:
+- stylelint-config-standard
+- stylelint-config-sass-guidelines
+
+plugins:
+- stylelint-color-format
+- stylelint-scss
+# - stylelint-no-indistinguishable-colors
+
+ignoreFiles:
+- kbase-extension/static/**/*.{less,scss,css}
+
+rules:
+  color-named: never
+  color-no-hex: true
+  color-format/format:
+    format: rgb
+  color-function-notation: modern
+  declaration-block-no-redundant-longhand-properties: true
+  declaration-block-no-shorthand-property-overrides: true
+  font-family-no-missing-generic-family-keyword:
+    - true
+    - ignoreFontFamilies:
+        - FontAwesome
+        - "Glyphicons Halflings"
+        - kbase-icons
+  function-url-quotes: never
+  length-zero-no-unit: true
+  max-nesting-depth: 10
+  no-descending-specificity: null
+  # set to true to enable
+  # plugin/stylelint-no-indistinguishable-colors: false
+  selector-class-pattern: null
+  selector-max-compound-selectors: 5
+  selector-max-class: 5
+  selector-max-id: 1
+  selector-no-qualifying-type:
+  - true
+  - ignore:
+    - attribute
+    - class
+  shorthand-property-no-redundant-values: true
+  unit-allowed-list:
+    - [em, px, rem, "%"]
+    - ignoreProperties:
+        x:
+          - background-image
+        s:
+          - transition
+        deg:
+          - background
+  value-keyword-case:
+    - lower
+    - ignoreKeywords: [
+        /^\$/
+      ]
+    - ignoreProperties: [
+        "/^font.*/",
+        url
+      ]

Dockerfile

@@ -22,11 +22,22 @@ ARG SKIP_MINIFY
 
 EXPOSE 8888
 
+# install NodeJS 16.x (latest LTS until ~October 2022, https://nodejs.org/en/about/releases/)
+RUN \
+    curl -fsSL https://deb.nodesource.com/setup_16.x | sudo -E bash - && \
+    sudo apt-get install -y nodejs
+
 # install pyopenssl cryptography idna and requests is the same as installing
 # requests[security]
 RUN source activate base && \
-    conda install -c conda-forge ndg-httpsclient==0.5.1 pyasn1==0.4.5 pyopenssl==19.0.0 cryptography==2.7 idna==2.8 requests==2.21.0 \
-          beautifulsoup4==4.8.1 html5lib==1.0.1
+    conda install -c conda-forge ndg-httpsclient==0.5.1 \
+          pyasn1==0.4.5 \
+          pyopenssl==19.0.0 \
+          cryptography==2.7 \
+          idna==2.8 \
+          requests==2.21.0 \
+          beautifulsoup4==4.8.1 \
+          html5lib==1.0.1
 
 # Copy in the narrative repo
 ADD ./ /kb/dev_container/narrative
@@ -40,8 +51,7 @@ RUN \
     ./src/scripts/kb-update-config -f src/config.json.templ -o /kb/deployment/ui-common/narrative_version && \
     # install JS deps
     npm install -g grunt-cli && \
-    npm install && \
-    ./node_modules/.bin/bower install --allow-root --config.interactive=false && \
+    npm install && npm run install-npm && \
     # Compile Javascript down into an itty-bitty ball unless SKIP_MINIFY is non-empty
     echo Skip=$SKIP_MINIFY && \
     [ -n "$SKIP_MINIFY" ] || npm run minify && \

Gruntfile.js

@@ -2,7 +2,7 @@ const crypto = require('crypto');
 
 module.exports = function (grunt) {
     'use strict';
-    grunt.loadNpmTasks('grunt-regex-replace');
+    require('load-grunt-tasks')(grunt);
 
     grunt.initConfig({
         // This inserts the reference to the compiled, minified JS file into page.html at
@@ -23,5 +23,43 @@ module.exports = function (grunt) {
                 ],
             },
         },
+
+        // Run CSS / SCSS-related tasks
+        // these files are modified in place
+        postcss: {
+            // autoprefix and minify the concatenated css files
+            concat: {
+                options: {
+                    processors: [
+                        // add vendor prefixes
+                        require('autoprefixer')(),
+                        // minify
+                        require('cssnano')([
+                            'default',
+                            {
+                                normalizeWhitespace: {
+                                    exclude: true,
+                                },
+                            },
+                        ]),
+                    ],
+                },
+                src: ['kbase-extension/static/kbase/css/all_concat.css'],
+            },
+        },
+
+        // runs the npm command to compile scss -> css and run autoprefixer on it
+        shell: {
+            compile_css: {
+                command: 'npm run compile_css',
+            },
+        },
+
+        // watch scss files for any changes
+        // when they change, regenerate the compiled css files
+        watch: {
+            files: 'kbase-extension/scss/**/*.scss',
+            tasks: ['shell:compile_css'],
+        },
     });
 };