Merge pull request #732 from tadast/tt/ci

Improve CI setup

Author: yannickwurm

.github/workflows/tests.yml

@@ -1,29 +1,16 @@
-# Run the old Travis tests within GitHub Actions, and upload the CodeClimate Report
-#
 # If nektos/act is installed as a GitHub CLI extension...
 # https://github.com/nektos/act#installation-as-github-cli-extension
 # ...then run this locally with:
 # gh act -j test
 # Appending to $PATH: https://www.scivision.dev/github-actions-path-append/
-# Conditionals predicated on status-codes:
-# https://github.com/orgs/community/discussions/25809
-#
-# One can *try* action-validator, but there are false-negatives:
-# (https://github.com/mpalmer/action-validator
-#
-# State does *not* persist between jobs...
-# https://github.com/actions/checkout/issues/19
-# ...so all this needs to happen in a single job.
-#
+
   name: Tests
   on:
     push:
       branches:
-       - 1.0.x
        - master
     pull_request:
       branches:
-       - 1.0.x
        - master
   env:
     CC_TEST_REPORTER_ID: ec48bb03c72db6b43ce71fd488110b4707abfde4386c144d886d711378d8db64
@@ -32,31 +19,44 @@
       runs-on: ubuntu-latest
       steps:
         - uses: actions/checkout@v3
+
         - name: Get BLAST
           working-directory: /opt
-          run: wget -c "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.14.1/ncbi-blast-2.14.1+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
+          run: wget -c "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.15.0/ncbi-blast-2.15.0+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
+
         - name: BLAST PATH
-          run: mkdir /opt/bin && echo "/opt/bin:/opt/ncbi-blast-2.14.1+/bin" >> $GITHUB_PATH
-        - uses: browser-actions/setup-chrome@latest
-        - run: chrome --version
+          run: mkdir /opt/bin && echo "/opt/bin:/opt/ncbi-blast-2.15.0+/bin" >> $GITHUB_PATH
+
         - name: Get CodeClimate
           working-directory: /opt
           run: wget -c "https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64" -O bin/cc-test-reporter && chmod +x bin/cc-test-reporter
+
+        - uses: browser-actions/setup-chrome@latest
+        - run: chrome --version
+
         - name: Set up Ruby
           uses: ruby/setup-ruby@v1
           with:
             ruby-version: '3.2'
             bundler-cache: true
+
         - name: Install Ruby dependencies
           run: bundle install
+
         - name: Setup Node.js
           uses: actions/setup-node@v3
           with:
             node-version: '16'
+
         - name: Install NPM Dependencies
           run: npm install
+
+        - name: Instal Jest
+          run: npm install --save-dev jest
+
         - name: Build JS and CSS assets
           run: npm run build
+
         - name: Check assets were compiled and checked-in
           continue-on-error: true
           run: |
@@ -66,23 +66,47 @@
               echo "Changes detected in 'public' directory. Please compile assets locally and commit the changes."
               exit 1
             fi
+
         - name: Create SequenceServer config file
           run: bundle exec bin/sequenceserver -s -d spec/database/v5/sample
+
         - name: CodeClimate before-build hook
           run: cc-test-reporter before-build
+
         - name: Run main specs and import spec for BLAST 2.9.0+
-          id: rspec
-          continue-on-error: true
+          id: rspec_tests
           run: bundle exec rspec spec/*_spec.rb spec/blast_versions/blast_2.9.0/*
-        - name: CodeClimate after-build (success)
-          if: steps.rspec.outcome == 'success'
-          run: cc-test-reporter after-build --exit-code 0
-        - name: CodeClimate after-build (failure)
-          if: steps.rspec.outcome != 'success'
-          run: cc-test-reporter after-build --exit-code 1
-        - name: upload code coverage results
+          continue-on-error: true
+
+        - name: upload rspec coverage report
           uses: actions/upload-artifact@v3
-          if: success() || failure()
           with:
-            name: code-coverage-report
+            name: rspec-code-coverage-report
             path: coverage
+
+        - name: format-coverage (Rspec)
+          run: cc-test-reporter format-coverage --output coverage/codeclimate_rspec.json
+
+        - name: Jest tests
+          id: jest_tests
+          run: npm test -- --coverage
+          continue-on-error: true
+
+        - name: upload Jest coverage report
+          uses: actions/upload-artifact@v3
+          with:
+            name: jest-code-coverage-report
+            path: coverage/lcov-report/
+
+        - name: format-coverage (Jest)
+          run: cc-test-reporter format-coverage coverage/lcov.info --input-type lcov --output coverage/codeclimate_jest.json
+
+        - name: sum-coverage
+          run: cc-test-reporter sum-coverage --parts 2 coverage/codeclimate_*.json
+
+        - name: upload coverage to code-CodeClimate
+          run: cc-test-reporter upload-coverage
+
+        - name: Assert both test suites passed in full
+          if: steps.rspec_tests.outcome != 'success' || steps.jest_tests.outcome != 'success'
+          run: exit 1

.travis.yml

@@ -18,11 +18,11 @@ GEM
       public_suffix (>= 2.0.2, < 6.0)
     ast (2.4.2)
     base64 (0.2.0)
-    capybara (3.39.2)
+    capybara (3.40.0)
       addressable
       matrix
       mini_mime (>= 0.1.3)
-      nokogiri (~> 1.8)
+      nokogiri (~> 1.11)
       rack (>= 1.6.0)
       rack-test (>= 0.6.3)
       regexp_parser (>= 1.5, < 3.0)
@@ -31,8 +31,8 @@ GEM
       capybara (>= 1.0, < 4)
       launchy
     coderay (1.1.3)
-    diff-lcs (1.5.0)
-    docile (1.3.2)
+    diff-lcs (1.5.1)
+    docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
     http-accept (1.7.0)
@@ -52,7 +52,7 @@ GEM
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
     netrc (0.11.0)
-    nokogiri (1.15.4)
+    nokogiri (1.16.2)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
     ox (2.14.16)
@@ -83,19 +83,19 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     rexml (3.2.6)
-    rspec (3.12.0)
-      rspec-core (~> 3.12.0)
-      rspec-expectations (~> 3.12.0)
-      rspec-mocks (~> 3.12.0)
-    rspec-core (3.12.2)
-      rspec-support (~> 3.12.0)
-    rspec-expectations (3.12.3)
+    rspec (3.13.0)
+      rspec-core (~> 3.13.0)
+      rspec-expectations (~> 3.13.0)
+      rspec-mocks (~> 3.13.0)
+    rspec-core (3.13.0)
+      rspec-support (~> 3.13.0)
+    rspec-expectations (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-mocks (3.12.6)
+      rspec-support (~> 3.13.0)
+    rspec-mocks (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-support (3.12.1)
+      rspec-support (~> 3.13.0)
+    rspec-support (3.13.1)
     rubocop (1.50.2)
       json (~> 2.3)
       parallel (~> 1.10)
@@ -111,15 +111,17 @@ GEM
     ruby-progressbar (1.13.0)
     ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
-    selenium-webdriver (4.15.0)
+    selenium-webdriver (4.18.1)
+      base64 (~> 0.2)
       rexml (~> 3.2, >= 3.2.5)
       rubyzip (>= 1.2.2, < 3.0)
       websocket (~> 1.0)
-    simplecov (0.17.1)
+    simplecov (0.22.0)
       docile (~> 1.1)
-      json (>= 1.8, < 3)
-      simplecov-html (~> 0.10.0)
-    simplecov-html (0.10.2)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.4)
     sinatra (4.0.0)
       mustermann (~> 3.0)
       rack (>= 3.0.0, < 4)
@@ -141,15 +143,15 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  capybara (~> 3.15, >= 3.15.1)
+  capybara (~> 3.40, >= 3.40.0)
   capybara-screenshot (~> 1.0, >= 1.0.23)
   pry
   rack-test (~> 2.1)
-  rspec (~> 3.7, >= 3.7.0)
+  rspec (~> 3.13, >= 3.13.0)
   rubocop (~> 1.50, >= 1.50.1)
-  selenium-webdriver (~> 4.15.0, >= 4.15.0)
+  selenium-webdriver (~> 4.18.0, >= 4.18.1)
   sequenceserver!
-  simplecov (~> 0.17.0, >= 0.17.0)
+  simplecov (~> 0.22.0, >= 0.22.0)
 
 BUNDLED WITH
    2.4.16

Gemfile.lock

@@ -3,10 +3,6 @@ module.exports = {
     roots: [
         '<rootDir>/public/js'
     ],
-    collectCoverageFrom: [
-        '<rootDir>/public/js/**/*.{js,jsx,ts,tsx}',
-        '!<rootDir>/public/js/**/*.d.ts'
-    ],
     setupFiles: [
         'react-app-polyfill/jsdom'
     ],
@@ -45,6 +41,7 @@ module.exports = {
         'download_links': '<rootDir>/public/js/null_plugins/download_links.js',
         'hit_buttons': '<rootDir>/public/js/null_plugins/hit_buttons.js',
         'search_header_plugin': '<rootDir>/public/js/null_plugins/search_header_plugin.js',
+        'circos$': '<rootDir>/public/js/tests/mocks/circos.js',
     },
     watchPlugins: [
         'jest-watch-typeahead/filename',