security update to ruby 3.3 and of all bundles

Author: yannickwurm

.github/workflows/tests.yml

@@ -34,7 +34,7 @@ jobs:
       - name: Set up Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: "3.2"
+          ruby-version: "3.3"
           bundler-cache: true
 
       - name: Install Ruby dependencies

Dockerfile

@@ -3,7 +3,7 @@
 ARG BLAST_VERSION=2.16.0
 
 ## Stage 1: gem dependencies.
-FROM docker.io/library/ruby:3.2-bookworm AS builder
+FROM docker.io/library/ruby:3.3-bookworm AS builder
 
 # Copy over files required for installing gem dependencies.
 WORKDIR /sequenceserver
@@ -22,7 +22,7 @@ RUN bundle install --without=development
 FROM docker.io/ncbi/blast-static:${BLAST_VERSION} AS ncbi-blast
 
 ## Stage 3: Puting it together.
-FROM docker.io/library/ruby:3.2-bookworm AS final
+FROM docker.io/library/ruby:3.3-bookworm AS final
 
 LABEL Description="Intuitive local web frontend for the BLAST bioinformatics tool"
 LABEL MailingList="https://groups.google.com/forum/#!forum/sequenceserver"
@@ -89,7 +89,7 @@ COPY --from=node /usr/src/app/public/sequenceserver-*.min.js public/
 COPY --from=node /usr/src/app/public/css/sequenceserver.min.css public/css/
 
 ## Stage 6 (optional) Pull the example database from the debian package.
-FROM docker.io/library/ruby:3.2-bookworm AS example_db
+FROM docker.io/library/ruby:3.3-bookworm AS example_db
 
 WORKDIR /tmp
 RUN apt-get update && apt-get download ncbi-blast+ && dpkg-deb -xv ncbi-blast+*.deb .

Gemfile

@@ -1,3 +1,3 @@
-source 'http://rubygems.org'
+source 'https://rubygems.org'
 
 gemspec

Gemfile.lock

@@ -13,12 +13,13 @@ PATH
       webrick (~> 1.8, >= 1.8.0)
 
 GEM
-  remote: http://rubygems.org/
+  remote: https://rubygems.org/
   specs:
-    addressable (2.8.5)
-      public_suffix (>= 2.0.2, < 6.0)
-    ast (2.4.2)
-    base64 (0.2.0)
+    addressable (2.9.0)
+      public_suffix (>= 2.0.2, < 8.0)
+    ast (2.4.3)
+    base64 (0.3.0)
+    bigdecimal (4.1.2)
     capybara (3.40.0)
       addressable
       matrix
@@ -28,92 +29,107 @@ GEM
       rack-test (>= 0.6.3)
       regexp_parser (>= 1.5, < 3.0)
       xpath (~> 3.2)
-    capybara-screenshot (1.0.26)
+    capybara-screenshot (1.0.27)
       capybara (>= 1.0, < 4)
       launchy
+    childprocess (5.1.0)
+      logger (~> 1.5)
     coderay (1.1.3)
-    diff-lcs (1.5.1)
-    docile (1.4.0)
-    domain_name (0.5.20190701)
-      unf (>= 0.0.5, < 1.0.0)
+    diff-lcs (1.6.2)
+    docile (1.4.1)
+    domain_name (0.6.20240107)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.1.6)
       domain_name (~> 0.5)
-    json (2.3.0)
-    json_pure (2.6.3)
-    launchy (2.5.2)
+    io-console (0.8.2)
+    json (2.19.5)
+    json_pure (2.8.1)
+    language_server-protocol (3.17.0.5)
+    launchy (3.1.1)
       addressable (~> 2.8)
-    matrix (0.4.2)
-    method_source (1.0.0)
-    mime-types (3.4.1)
-      mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.0218.1)
+      childprocess (~> 5.0)
+      logger (~> 1.6)
+    lint_roller (1.1.0)
+    logger (1.7.0)
+    matrix (0.4.3)
+    method_source (1.1.0)
+    mime-types (3.7.0)
+      logger
+      mime-types-data (~> 3.2025, >= 3.2025.0507)
+    mime-types-data (3.2026.0414)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.7)
-    mustermann (3.0.0)
-      ruby2_keywords (~> 0.0.1)
+    mini_portile2 (2.8.9)
+    mustermann (3.1.1)
     netrc (0.11.0)
-    nokogiri (1.16.6)
+    nokogiri (1.19.3)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
-    ox (2.14.16)
-    parallel (1.23.0)
-    parser (3.2.2.0)
+    ox (2.14.26)
+      bigdecimal (>= 3.0)
+    parallel (2.1.0)
+    parser (3.3.11.1)
       ast (~> 2.4.1)
-    pry (0.14.2)
+      racc
+    prism (1.9.0)
+    pry (0.16.0)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.3)
-    racc (1.8.0)
-    rack (3.1.7)
-    rack-protection (4.0.0)
+      reline (>= 0.6.0)
+    public_suffix (7.0.5)
+    racc (1.8.1)
+    rack (3.2.6)
+    rack-protection (4.2.1)
       base64 (>= 0.1.0)
+      logger (>= 1.6.0)
       rack (>= 3.0.0, < 4)
-    rack-session (2.0.0)
+    rack-session (2.1.2)
+      base64 (>= 0.1.0)
       rack (>= 3.0.0)
-    rack-test (2.1.0)
+    rack-test (2.2.0)
       rack (>= 1.3)
     rack_csrf (2.7.0)
       rack (>= 1.1.0)
-    rackup (2.1.0)
+    rackup (2.3.1)
       rack (>= 3)
-      webrick (~> 1.8)
     rainbow (3.1.1)
-    regexp_parser (2.8.2)
+    regexp_parser (2.12.0)
+    reline (0.6.3)
+      io-console (~> 0.5)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.7)
-    rspec (3.13.0)
+    rexml (3.4.4)
+    rspec (3.13.2)
       rspec-core (~> 3.13.0)
       rspec-expectations (~> 3.13.0)
       rspec-mocks (~> 3.13.0)
-    rspec-core (3.13.0)
+    rspec-core (3.13.6)
       rspec-support (~> 3.13.0)
-    rspec-expectations (3.13.0)
+    rspec-expectations (3.13.5)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-mocks (3.13.0)
+    rspec-mocks (3.13.8)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-support (3.13.1)
-    rubocop (1.50.2)
+    rspec-support (3.13.7)
+    rubocop (1.86.1)
       json (~> 2.3)
-      parallel (~> 1.10)
-      parser (>= 3.2.0.0)
+      language_server-protocol (~> 3.17.0.2)
+      lint_roller (~> 1.1.0)
+      parallel (>= 1.10)
+      parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.8, < 3.0)
-      rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.28.0, < 2.0)
+      regexp_parser (>= 2.9.3, < 3.0)
+      rubocop-ast (>= 1.49.0, < 2.0)
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.28.0)
-      parser (>= 3.2.1.0)
+      unicode-display_width (>= 2.4.0, < 4.0)
+    rubocop-ast (1.49.1)
+      parser (>= 3.3.7.2)
+      prism (~> 1.7)
     ruby-progressbar (1.13.0)
-    ruby2_keywords (0.0.5)
-    rubyzip (2.3.2)
+    rubyzip (2.4.1)
     selenium-webdriver (4.18.1)
       base64 (~> 0.2)
       rexml (~> 3.2, >= 3.2.5)
@@ -123,22 +139,22 @@ GEM
       docile (~> 1.1)
       simplecov-html (~> 0.11)
       simplecov_json_formatter (~> 0.1)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.2)
     simplecov_json_formatter (0.1.4)
-    sinatra (4.0.0)
+    sinatra (4.2.1)
+      logger (>= 1.6.0)
       mustermann (~> 3.0)
       rack (>= 3.0.0, < 4)
-      rack-protection (= 4.0.0)
+      rack-protection (= 4.2.1)
       rack-session (>= 2.0.0, < 3)
       tilt (~> 2.0)
     slop (3.6.0)
-    tilt (2.2.0)
-    unf (0.1.4)
-      unf_ext
-    unf_ext (0.0.8.2)
-    unicode-display_width (2.4.2)
-    webrick (1.8.1)
-    websocket (1.2.10)
+    tilt (2.7.0)
+    unicode-display_width (3.2.0)
+      unicode-emoji (~> 4.1)
+    unicode-emoji (4.2.0)
+    webrick (1.9.2)
+    websocket (1.2.11)
     xpath (3.2.0)
       nokogiri (~> 1.8)