Merge branch 'joss' into resciencec

ReScience · Feb 15, 2024 · e1c1c20 · e1c1c20
2 parents 548f3b3 + a60ec4e
commit e1c1c20
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -7,7 +7,7 @@ jobs:
     continue-on-error: ${{ matrix.failure-allowed }}
     strategy:
       matrix:
-        ruby-version: ['2.7.8', '3.0.6', '3.1.4', '3.2.2']
+        ruby-version: ['3.0.6', '3.1.4', '3.2.3', '3.3.0']
         failure-allowed: [false]
         include:
         - ruby-version: 'truffleruby'

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,18 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+  - requirements: docs/requirements.txt
diff --git a/.ruby-version b/.ruby-version
@@ -1 +1 @@
-3.2.2
+3.3.0
diff --git a/Gemfile b/Gemfile
@@ -5,8 +5,8 @@ if ENV["CUSTOM_RUBY_VERSION"]
 end
 
 gem 'octokit'
-gem 'sinatra', '3.1.0'
-gem 'sinatra-contrib', '3.1.0'
+gem 'sinatra', '4.0.0'
+gem 'sinatra-contrib', '4.0.0'
 gem 'openssl'
 gem 'puma'
 gem 'sidekiq'

diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,70 +1,78 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.8.5)
+    addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
-    base64 (0.1.1)
-    bibtex-ruby (6.0.0)
+    base64 (0.2.0)
+    bibtex-ruby (6.1.0)
       latex-decode (~> 0.0)
-    cgi (0.3.6)
+      racc (~> 1.7)
+    bigdecimal (3.1.6)
+    cgi (0.4.1)
     charlock_holmes (0.7.7)
     chronic (0.10.2)
-    concurrent-ruby (1.2.2)
+    concurrent-ruby (1.2.3)
     connection_pool (2.4.1)
-    crack (0.4.5)
+    crack (0.4.6)
+      bigdecimal
       rexml
-    diff-lcs (1.5.0)
+    diff-lcs (1.5.1)
     dotenv (2.8.1)
-    faraday (2.7.11)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
+    faraday (2.9.0)
+      faraday-net_http (>= 2.0, < 3.2)
     faraday-follow_redirects (0.1.0)
       faraday (>= 2, < 3)
-    faraday-net_http (3.0.2)
+    faraday-net_http (3.1.0)
+      net-http
     faraday-retry (2.2.0)
       faraday (~> 2.0)
-    github-linguist (7.27.0)
+    github-linguist (7.28.0)
       cgi
       charlock_holmes (~> 0.7.7)
       mini_mime (~> 1.0)
       rugged (~> 1.0)
-    hashdiff (1.0.1)
+    hashdiff (1.1.0)
     issue (1.0.0)
       openssl
       rack
     latex-decode (0.4.0)
-    licensee (9.16.0)
+    licensee (9.16.1)
       dotenv (~> 2.0)
-      octokit (>= 4.20, < 7.0)
+      octokit (>= 4.20, < 9.0)
       reverse_markdown (>= 1, < 3)
       rugged (>= 0.24, < 2.0)
       thor (>= 0.19, < 2.0)
     mini_mime (1.1.5)
-    mini_portile2 (2.8.4)
+    mini_portile2 (2.8.5)
     multi_json (1.15.0)
     mustermann (3.0.0)
       ruby2_keywords (~> 0.0.1)
-    nio4r (2.5.9)
-    nokogiri (1.15.4)
+    net-http (0.4.1)
+      uri
+    nio4r (2.7.0)
+    nokogiri (1.16.0)
       mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
-    octokit (6.1.1)
+    octokit (8.1.0)
+      base64
       faraday (>= 1, < 3)
       sawyer (~> 0.9)
-    ojra (1.1.0)
-      faraday (~> 2.7)
+    ojra (1.1.1)
+      faraday (~> 2.9)
     openssl (3.2.0)
-    public_suffix (5.0.3)
-    puma (6.4.0)
+    public_suffix (5.0.4)
+    puma (6.4.2)
       nio4r (~> 2.0)
-    racc (1.7.1)
-    rack (2.2.8)
-    rack-protection (3.1.0)
-      rack (~> 2.2, >= 2.2.4)
+    racc (1.7.3)
+    rack (3.0.9)
+    rack-protection (4.0.0)
+      base64 (>= 0.1.0)
+      rack (>= 3.0.0, < 4)
+    rack-session (2.0.0)
+      rack (>= 3.0.0)
     rack-test (2.1.0)
       rack (>= 1.3)
-    redis-client (0.17.0)
+    redis-client (0.19.1)
       connection_pool
     reverse_markdown (2.1.1)
       nokogiri
@@ -93,24 +101,26 @@ GEM
       multi_json (~> 1.15)
       rexml (~> 3.2, >= 3.2.5)
       thor (~> 1.2, >= 1.2.1)
-    sidekiq (7.1.4)
+    sidekiq (7.2.1)
       concurrent-ruby (< 2)
       connection_pool (>= 2.3.0)
       rack (>= 2.2.4)
-      redis-client (>= 0.14.0)
-    sinatra (3.1.0)
+      redis-client (>= 0.19.0)
+    sinatra (4.0.0)
       mustermann (~> 3.0)
-      rack (~> 2.2, >= 2.2.4)
-      rack-protection (= 3.1.0)
+      rack (>= 3.0.0, < 4)
+      rack-protection (= 4.0.0)
+      rack-session (>= 2.0.0, < 3)
       tilt (~> 2.0)
-    sinatra-contrib (3.1.0)
-      multi_json
+    sinatra-contrib (4.0.0)
+      multi_json (>= 0.0.2)
       mustermann (~> 3.0)
-      rack-protection (= 3.1.0)
-      sinatra (= 3.1.0)
+      rack-protection (= 4.0.0)
+      sinatra (= 4.0.0)
       tilt (~> 2.0)
-    thor (1.2.2)
+    thor (1.3.0)
     tilt (2.3.0)
+    uri (0.13.0)
     webmock (3.19.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
@@ -136,9 +146,9 @@ DEPENDENCIES
   rspec
   serrano
   sidekiq
-  sinatra (= 3.1.0)
-  sinatra-contrib (= 3.1.0)
+  sinatra (= 4.0.0)
+  sinatra-contrib (= 4.0.0)
   webmock
 
 BUNDLED WITH
-   2.3.4
+   2.5.4
diff --git a/app/lib/paper_file.rb b/app/lib/paper_file.rb
@@ -64,7 +64,7 @@ def self.find(search_path)
 
     if Dir.exist? search_path
       Find.find(search_path).each do |path|
-        if path =~ /paper\.tex$|paper\.md$/
+        if path =~ /\/paper\.tex$|\/paper\.md$/
           paper_path = path
           break
         end

diff --git a/app/workers/repo_checks_worker.rb b/app/workers/repo_checks_worker.rb
@@ -52,8 +52,8 @@ def repo_summary
   def detect_languages
     repo = Rugged::Repository.new(path)
     project = Linguist::Repository.new(repo, repo.head.target_id)
-
-    top_3 = project.languages.keys.take(3)
+    ordered_languages = project.languages.sort_by { |_, size| size }.reverse
+    top_3 = ordered_languages.first(3).map {|l,s| l}
     label_issue(top_3) unless top_3.empty?
   end
 

diff --git a/docs/conf.py b/docs/conf.py
@@ -31,6 +31,7 @@
 extensions = [
     'sphinx.ext.mathjax',
     'recommonmark',
+    'sphinx_rtd_theme',
 ]
 
 # Add any paths that contain templates here, relative to this directory.

diff --git a/spec/paper_file_spec.rb b/spec/paper_file_spec.rb
@@ -144,7 +144,7 @@
 
     it "should return a nil PaperFile if no paper file found" do
       expect(Dir).to receive(:exist?).with("/repo/path/").and_return(true)
-      allow(Find).to receive(:find).with("/repo/path/").and_return(["lib/papers.pdf", "./docs", "app"])
+      allow(Find).to receive(:find).with("/repo/path/").and_return(["lib/papers.pdf", "lib/other_paper.md", "./docs", "app"])
 
       paper_file = PaperFile.find("/repo/path/")
 

diff --git a/spec/workers/repo_checks_worker_spec.rb b/spec/workers/repo_checks_worker_spec.rb
@@ -72,7 +72,7 @@
   describe "#detect_languages" do
     before do
       repo = OpenStruct.new(head: OpenStruct.new(target_id: 33))
-      expected_languages = OpenStruct.new(languages: {"Ruby"=>176110, "HTML"=>664, "TeX"=>475, "Go"=>21})
+      expected_languages = OpenStruct.new(languages: {"Go"=>21, "HTML"=>664, "Ruby"=>176110, "TeX"=>475, "XML" => 100})
       allow(Rugged::Repository).to receive(:new).and_return(repo)
       allow(Linguist::Repository).to receive(:new).with(repo, 33).and_return(expected_languages)
     end