The align_it and align_it_aa methods now belong to the module "Gotoh".

.devcontainer/Dockerfile

@@ -0,0 +1,31 @@
+ARG UBUNTU_VERSION=20.04
+
+FROM ubuntu:${UBUNTU_VERSION} AS base
+
+LABEL org.opencontainers.image.source=https://github.com/cfe-lab/gotoh
+LABEL org.opencontainers.image.description="Gotoh dev container for development and testing"
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+ENV TZ=America/Vancouver \
+    RUBY_VERSION=2.2.2 \
+    BUNDLER_VERSION=1.17.3
+
+RUN apt-get -y update &&\
+    apt-get -y upgrade &&\
+    apt-get install -y curl gpg
+
+RUN echo "deb http://security.ubuntu.com/ubuntu/ bionic-security main" >> /etc/apt/sources.list &&\
+    echo "deb http://security.ubuntu.com/ubuntu/ bionic main" >> /etc/apt/sources.list &&\
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 3B4FE6ACC0B21F32 &&\
+    apt update &&\
+    apt install -y \
+    gawk=1:4.1.4+dfsg-1build1
+
+RUN curl -sSL https://rvm.io/mpapis.asc | gpg --import - && \
+    curl -sSL https://rvm.io/pkuczynski.asc | gpg --import - && \
+    curl -sSL https://get.rvm.io | bash -s stable && \
+    usermod -a -G rvm root
+
+RUN /bin/bash -l -c "source /etc/profile.d/rvm.sh && rvm pkg install openssl"
+RUN /bin/bash -l -c "source /etc/profile.d/rvm.sh && rvm requirements && rvm install ${RUBY_VERSION} --with-openssl-dir=/usr/local/rvm/usr && rvm --default use ${RUBY_VERSION}"

.devcontainer/devcontainer.json

@@ -0,0 +1,15 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
+{
+	"name": "CfE Ubuntu Ruby",
+
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+
+	"updateContentCommand": "cd /workspaces/gotoh/ruby && bundle install",
+
+	"features": {
+    	"ghcr.io/devcontainers/features/git:1": {}
+	}
+}

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: Automated Tests
+
+on: ["push"]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout code from repo
+      uses: actions/checkout@v3
+
+    - name: Log into GitHub Container Registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Build devcontainer and run tests
+      uses: devcontainers/[email protected]
+      with:
+        imageName: ghcr.io/cfe-lab/gotoh_devcontainer
+        cacheFrom: ghcr.io/cfe-lab/gotoh_devcontainer
+        runCmd: cd /workspaces/gotoh/ruby && rake test
+
+    - name: Upload coverage reports to Codecov with GitHub Action
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        root_dir: ${{ github.workspace }}
+        files: ${{ github.workspace }}/ruby/coverage/coverage.xml

.gitignore

@@ -2,3 +2,4 @@
 env/
 __pycache__/
 .pytest_cache/
+.DS_Store

README.md

@@ -56,6 +56,10 @@ to your `requirements.txt` file or similar method.
 
 # Ruby Bindings
 
+The `/ruby` directory contains the directory structure required to build a
+gem containing Gotoh's Ruby bindings.  This gem, named `gotoh`, contains
+a module called `Gotoh` that holds the `align_it` and `align_it_aa` functions.
+
 To build Gotoh's Ruby bindings (which are called "alignment" instead of "gotoh"
 for arbitrary historical reasons), you'll need to have the following installed:
 
@@ -65,8 +69,23 @@ for arbitrary historical reasons), you'll need to have the following installed:
   [RVM](https://rvm.io/) on Linux)
 - A C++ compiler
 
-With these installed, you should be able to build the extension module with
+The "canonical" environment for building this package is the CfE-internal 
+`cfe_ubuntu` Ruby image based on Ubuntu 20.04 (this old version is required 
+to run Ruby 2.2.2).
+
+In your build environment, you should be able to build the extension module
+using the `build_gem.bash` script.  By default this will make a gem with the
+version number `0.1.0.pre`; set the environment variable `GOTOH_VERSION` before
+building to assign a proper version number.
+
+## Manually building the Ruby bindings
+
+If you want to manually build the bindings, e.g. for testing/debugging/development,
+copy `/ruby/ext/gotoh/extconf.rb` to the `/alignment/gotoh/` directory and 
+change the `create_makefile('gotoh/gotoh')` line to `create_makefile('gotoh')`;
+then run
 ```
-    ruby extconf.rb
+    ruby extconf.rb  # generates a Makefile and other supporting files
     make
 ```
+which will build `gotoh.so`, which can be `require`d from Ruby.

alignment/gotoh/.gitignore

@@ -0,0 +1,5 @@
+Makefile
+*.so
+*.o
+extconf.h
+build/*

alignment/gotoh/gotoh.cpp

@@ -852,11 +852,11 @@ void widen_gaps(string* seq)
        return ret;
     }
 
-
-    extern "C" void Init_alignment()
+    extern "C" void Init_cfe_gotoh()
     {
-       rb_define_global_function("align_it", (VALUE(*)(...))align_it, 4);
-       rb_define_global_function("align_it_aa", (VALUE(*)(...))align_it_aa, 4);
+        VALUE gotoh = rb_define_module("CfeGotoh"); 
+        rb_define_module_function(gotoh, "align_it", (VALUE(*)(...))align_it, 4);
+        rb_define_module_function(gotoh, "align_it_aa", (VALUE(*)(...))align_it_aa, 4);
     }
 
 #endif

ruby/.gitignore

@@ -0,0 +1,3 @@
+*.gem
+coverage/*
+.DS_Store

ruby/Gemfile

@@ -0,0 +1,9 @@
+source 'https://rubygems.org'
+ruby '2.2.2'
+
+# To install all these gems, run "gem install bundler", then "bundle install".
+
+gem 'minitest', '5.15.0'
+gem 'minitest-reporters', '1.7.1'
+gem 'simplecov', '0.17.1'
+gem 'simplecov-cobertura', '1.4.2'

ruby/Gemfile.lock

@@ -0,0 +1,36 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    ansi (1.5.0)
+    builder (3.3.0)
+    docile (1.3.5)
+    json (2.5.1)
+    minitest (5.15.0)
+    minitest-reporters (1.7.1)
+      ansi
+      builder
+      minitest (>= 5.0)
+      ruby-progressbar
+    ruby-progressbar (1.13.0)
+    simplecov (0.17.1)
+      docile (~> 1.1)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-cobertura (1.4.2)
+      simplecov (~> 0.8)
+    simplecov-html (0.10.2)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  minitest (= 5.15.0)
+  minitest-reporters (= 1.7.1)
+  simplecov (= 0.17.1)
+  simplecov-cobertura (= 1.4.2)
+
+RUBY VERSION
+   ruby 2.2.2p95
+
+BUNDLED WITH
+   1.17.3

ruby/build_gem.bash

@@ -0,0 +1,5 @@
+#! /usr/bin/env bash
+
+cp ../alignment/gotoh/gotoh.cpp ext/cfe_gotoh/cfe_gotoh.cpp
+gem build cfe_gotoh.gemspec
+rm ext/cfe_gotoh/cfe_gotoh.cpp

ruby/cfe_gotoh.gemspec

@@ -0,0 +1,18 @@
+Gem::Specification.new do |s|
+  s.name = "cfe_gotoh"
+  s.version = ENV['CFE_GOTOH_VERSION'] || '0.1.0.pre'
+  s.summary = "CfE implementation of the Gotoh sequence alignment algorithm"
+  s.files = [
+    'lib/cfe_gotoh.rb',
+    'ext/cfe_gotoh/cfe_gotoh.cpp'
+  ]
+  s.extensions = [
+    'ext/cfe_gotoh/extconf.rb',
+  ]
+  s.authors = [
+    "Conan Woods",
+    "Jamie Kai",
+    "David Rickett",
+    "Richard Liang"
+  ]
+end

ruby/ext/.gitignore

@@ -0,0 +1 @@
+.DS_Store

ruby/ext/cfe_gotoh/.gitignore

@@ -0,0 +1,6 @@
+cfe_gotoh.cpp
+cfe_gotoh.o
+cfe_gotoh.so
+extconf.h
+Makefile
+mkmf.log