Merge branch 'main' into ropensci

.github/workflows/tests.yml

@@ -7,13 +7,13 @@ 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: ['3.0.7', '3.1.6', '3.2.5', '3.3.4']
         failure-allowed: [false]
         include:
         - ruby-version: 'truffleruby'
           failure-allowed: true
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
       with:

.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

.ruby-version

@@ -1 +1 @@
-3.2.1
+3.3.3

Gemfile

@@ -5,8 +5,8 @@ if ENV["CUSTOM_RUBY_VERSION"]
 end
 
 gem 'octokit'
-gem 'sinatra', '3.0.5'
-gem 'sinatra-contrib', '3.0.5'
+gem 'sinatra', '4.0.0'
+gem 'sinatra-contrib', '4.0.0'
 gem 'openssl'
 gem 'puma'
 gem 'sidekiq'

Gemfile.lock

@@ -1,94 +1,107 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    addressable (2.8.4)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     airrecord (1.0.12)
       faraday (>= 1.0, < 3.0)
       faraday-net_http_persistent
       net-http-persistent
-    bibtex-ruby (6.0.0)
+    base64 (0.2.0)
+    bibtex-ruby (6.1.0)
       latex-decode (~> 0.0)
-    cgi (0.3.6)
-    charlock_holmes (0.7.7)
+      racc (~> 1.7)
+    bigdecimal (3.1.8)
+    cgi (0.4.1)
+    charlock_holmes (0.7.9)
     chronic (0.10.2)
-    concurrent-ruby (1.2.2)
-    connection_pool (2.4.0)
-    crack (0.4.5)
+    concurrent-ruby (1.3.4)
+    connection_pool (2.4.1)
+    crack (1.0.0)
+      bigdecimal
       rexml
-    diff-lcs (1.5.0)
-    dotenv (2.8.1)
-    faraday (2.7.4)
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
+    diff-lcs (1.5.1)
+    dotenv (3.1.4)
+    faraday (2.12.0)
+      faraday-net_http (>= 2.0, < 3.4)
+      json
+      logger
     faraday-follow_redirects (0.1.0)
       faraday (>= 2, < 3)
-    faraday-net_http (3.0.2)
+    faraday-net_http (3.3.0)
+      net-http
     faraday-net_http_persistent (2.1.0)
       faraday (~> 2.5)
       net-http-persistent (~> 4.0)
-    faraday-retry (2.1.0)
+    faraday-retry (2.2.1)
       faraday (~> 2.0)
-    github-linguist (7.25.0)
+    github-linguist (8.0.1)
       cgi
       charlock_holmes (~> 0.7.7)
       mini_mime (~> 1.0)
       rugged (~> 1.0)
-    hashdiff (1.0.1)
-    issue (1.0.0)
-      openssl
-      rack
+    hashdiff (1.1.1)
+    issue (1.0.2)
+      openssl (~> 3.2)
+      rack (~> 3.1)
+    json (2.7.2)
     latex-decode (0.4.0)
-    licensee (9.16.0)
-      dotenv (~> 2.0)
-      octokit (>= 4.20, < 7.0)
+    licensee (9.17.1)
+      dotenv (>= 2, < 4)
+      octokit (>= 4.20, < 10.0)
       reverse_markdown (>= 1, < 3)
       rugged (>= 0.24, < 2.0)
       thor (>= 0.19, < 2.0)
-    mini_mime (1.1.2)
-    mini_portile2 (2.8.1)
+    logger (1.6.1)
+    mini_mime (1.1.5)
+    mini_portile2 (2.8.7)
     multi_json (1.15.0)
-    mustermann (3.0.0)
+    mustermann (3.0.3)
       ruby2_keywords (~> 0.0.1)
+    net-http (0.4.1)
+      uri
     net-http-persistent (4.0.2)
       connection_pool (~> 2.2)
-    nio4r (2.5.9)
-    nokogiri (1.14.3)
-      mini_portile2 (~> 2.8.0)
+    nio4r (2.7.3)
+    nokogiri (1.16.7)
+      mini_portile2 (~> 2.8.2)
       racc (~> 1.4)
-    octokit (6.1.1)
+    octokit (9.1.0)
       faraday (>= 1, < 3)
       sawyer (~> 0.9)
-    openssl (3.1.0)
-    public_suffix (5.0.1)
-    puma (6.2.1)
+    openssl (3.2.0)
+    public_suffix (6.0.1)
+    puma (6.4.3)
       nio4r (~> 2.0)
-    racc (1.6.2)
-    rack (2.2.6.4)
-    rack-protection (3.0.5)
-      rack
+    racc (1.8.1)
+    rack (3.1.7)
+    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 (0.14.1)
+    redis-client (0.22.2)
       connection_pool
     reverse_markdown (2.1.1)
       nokogiri
-    rexml (3.2.5)
-    rspec (3.12.0)
-      rspec-core (~> 3.12.0)
-      rspec-expectations (~> 3.12.0)
-      rspec-mocks (~> 3.12.0)
-    rspec-core (3.12.1)
-      rspec-support (~> 3.12.0)
-    rspec-expectations (3.12.2)
+    rexml (3.3.7)
+    rspec (3.13.0)
+      rspec-core (~> 3.13.0)
+      rspec-expectations (~> 3.13.0)
+      rspec-mocks (~> 3.13.0)
+    rspec-core (3.13.1)
+      rspec-support (~> 3.13.0)
+    rspec-expectations (3.13.3)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-mocks (3.12.5)
+      rspec-support (~> 3.13.0)
+    rspec-mocks (3.13.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.12.0)
-    rspec-support (3.12.0)
+      rspec-support (~> 3.13.0)
+    rspec-support (3.13.1)
     ruby2_keywords (0.0.5)
-    rugged (1.6.3)
+    rugged (1.7.2)
     sawyer (0.9.2)
       addressable (>= 2.3.5)
       faraday (>= 0.17.3, < 3)
@@ -98,25 +111,28 @@ GEM
       multi_json (~> 1.15)
       rexml (~> 3.2, >= 3.2.5)
       thor (~> 1.2, >= 1.2.1)
-    sidekiq (7.0.8)
+    sidekiq (7.3.2)
       concurrent-ruby (< 2)
       connection_pool (>= 2.3.0)
+      logger
       rack (>= 2.2.4)
-      redis-client (>= 0.11.0)
-    sinatra (3.0.5)
+      redis-client (>= 0.22.2)
+    sinatra (4.0.0)
       mustermann (~> 3.0)
-      rack (~> 2.2, >= 2.2.4)
-      rack-protection (= 3.0.5)
+      rack (>= 3.0.0, < 4)
+      rack-protection (= 4.0.0)
+      rack-session (>= 2.0.0, < 3)
       tilt (~> 2.0)
-    sinatra-contrib (3.0.5)
-      multi_json
+    sinatra-contrib (4.0.0)
+      multi_json (>= 0.0.2)
       mustermann (~> 3.0)
-      rack-protection (= 3.0.5)
-      sinatra (= 3.0.5)
+      rack-protection (= 4.0.0)
+      sinatra (= 4.0.0)
       tilt (~> 2.0)
-    thor (1.2.1)
-    tilt (2.1.0)
-    webmock (3.18.1)
+    thor (1.3.2)
+    tilt (2.4.0)
+    uri (0.13.1)
+    webmock (3.23.1)
       addressable (>= 2.8.0)
       crack (>= 0.3.2)
       hashdiff (>= 0.4.0, < 2.0.0)
@@ -141,9 +157,9 @@ DEPENDENCIES
   rspec
   serrano
   sidekiq
-  sinatra (= 3.0.5)
-  sinatra-contrib (= 3.0.5)
+  sinatra (= 4.0.0)
+  sinatra-contrib (= 4.0.0)
   webmock
 
 BUNDLED WITH
-   2.3.4
+   2.5.14

README.md

@@ -1,8 +1,8 @@
 # Buffy
 
-A service to provide a bot helping scientific journals manage submission reviews.
+A service to provide a bot helping scientific journals and communities manage submission reviews.
 
-Buffy automates common editorial tasks like those needed by [The Journal of Open Source Software](https://joss.theoj.org/) or [rOpenSci](https://ropensci.org/).
+Buffy automates common editorial tasks like those needed by [The Journal of Open Source Software](https://joss.theoj.org/), [rOpenSci](https://ropensci.org/), [JuliaCon](https://proceedings.juliacon.org/) or [pyOpenSci](https://www.pyopensci.org/).
 
 [![Build Status](https://github.com/openjournals/buffy/actions/workflows/tests.yml/badge.svg)](https://github.com/openjournals/buffy/actions/workflows/tests.yml)
 [![Documentation Status](https://readthedocs.org/projects/buffy/badge/?version=latest)](https://buffy.readthedocs.io/en/latest/?badge=latest)

app/lib/doi_checker.rb

@@ -9,30 +9,52 @@ def initialize(entries=[])
   end
 
   def check_dois
-    doi_summary = {ok: [], missing: [], invalid: []}
+    doi_summary = {ok: [], skip: [], missing: [], invalid: []}
 
     if @entries.any?
       @entries.each do |entry|
-        if entry.has_field?('doi') && !entry.doi.empty?
+        # handle special cases first
+        if special_case = handle_special_case(entry)
+          doi_validity = special_case
+        elsif entry.has_field?('doi') && !entry.doi.empty?
+          # Validate entries with DOIs
           doi_validity = validate_doi(entry.doi.value)
-          doi_summary[doi_validity[:validity]].push(doi_validity[:msg])
-        # If there's no DOI present, check Crossref to see if we can find a candidate DOI for this entry.
         elsif entry.has_field?('title')
-            candidate_doi = crossref_lookup(entry.title.value)
-            if candidate_doi == "CROSSREF-ERROR"
-              truncated_title = entry.title.to_s[0,50]
-              truncated_title += "..." if truncated_title.length < entry.title.to_s.length
-              doi_summary[:missing].push("Errored finding suggestions for \"#{truncated_title}\", please try later")
-            elsif candidate_doi
-              doi_summary[:missing].push("#{candidate_doi} may be a valid DOI for title: #{entry.title}")
-            end
+          # Try and find candidate entries if doi absent, but title present
+          doi_validity = handle_missing_doi(entry)
+        else
+          doi_validity = {validity: :missing, msg: "Entry without DOI or title found"}
         end
+
+        doi_summary[doi_validity[:validity]].push(doi_validity[:msg])
       end
     end
 
     doi_summary
   end
 
+  # any special case should return false if not applicable, and an object like
+  # {:validity => :ok, :msg => "whatever"} otherwise.
+  # Add additional special cases as private methods and chain in a tidy sequence plz <3
+  def handle_special_case(entry)
+    acm_105555_prefix(entry) || false
+  end
+
+
+  # If there's no DOI present, check Crossref to see if we can find a candidate DOI for this entry.
+  def handle_missing_doi(entry)
+    candidate_doi = crossref_lookup(entry.title.value)
+    truncated_title = entry.title.to_s[0,50]
+    truncated_title += "..." if truncated_title.length < entry.title.to_s.length
+    if candidate_doi == "CROSSREF-ERROR"
+      { validity: :missing, msg: "Errored finding suggestions for \"#{truncated_title}\", please try later" }
+    elsif candidate_doi
+      { validity: :missing, msg: "#{candidate_doi} may be a valid DOI for title: #{truncated_title}" }
+    else
+      { validity: :skip, msg: "No DOI given, and none found for title: #{truncated_title}" }
+    end
+  end
+
   def validate_doi(doi_string)
     return { validity: :invalid, msg: "Empty DOI string" } if doi_string.nil? || doi_string.empty?
 
@@ -108,4 +130,16 @@ def levenshtein_distance(s, t)
   def similar?(string_1, string_2)
     levenshtein_distance(string_1, string_2) < 3
   end
+
+  private
+
+  def acm_105555_prefix(entry)
+    if entry.has_field?('doi') && entry.doi.include?("10.5555/")
+      { validity: :invalid, msg: "#{entry.doi} is INVALID - 10.5555 is a known broken prefix, replace with https://dl.acm.org/doi/{doi} in the {url} field" }
+    elsif entry.has_field?('url') && entry.url.include?("https://dl.acm.org/doi/10.5555")
+      { validity: :skip, msg: "#{entry.url} - non-DOI with 10.5555 correctly placed in the url field, editor should ensure this resolves" }
+    else
+      false
+    end
+  end
 end

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

app/lib/responder.rb

@@ -181,6 +181,7 @@ def locals
     from_context = Sinatra::IndifferentHash[
                      issue_id: context.issue_id,
                      issue_author: context.issue_author,
+                     issue_title: context.issue_title,
                      repo: context.repo,
                      sender: context.sender,
                      bot_name: bot_name ]

app/lib/responder_registry.rb

@@ -93,7 +93,7 @@ def self.available_responders
         responder_class = Object.const_get(name)
         available_responders[responder_class.key] = responder_class
       rescue NameError => err
-        logger.warn("There is a mismatch in a Responder class name/module: #{err.message}")
+        Logger.new(STDOUT).warn("There is a mismatch in a Responder class name/module: #{err.message}")
       end
     end
 

app/lib/utilities.rb

@@ -23,9 +23,4 @@ def run_cloc(local_path)
     status.success? ? result : nil
   end
 
-  def run_gitinspector(local_path)
-    result, stderr, status = Open3.capture3("PYTHONIOENCODING=utf-8 gitinspector -f** #{local_path}")
-    status.success? ? result : nil
-  end
-
 end