cmdstan 0.1.8 → 0.2.1

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: c0c185c461629fef5231c0378e655dc7f85dc89add5f20c990483a9951a1cb49
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data/CHANGELOG.md

@@ -1,3 +1,21 @@
+## 0.2.1 (2022-07-06)
+
+- Updated CmdStan to 2.30.0
+- Fixed error when `chains` not specified
+
+## 0.2.0 (2022-04-23)
+
+- CmdStan now installs when the first model is compiled rather than on gem installation
+- Added `cmdstan_installed?` and `install_cmdstan` methods
+- Updated CmdStan to 2.29.2
+- Fixed issue with `summary` method
+- Dropped support for Ruby < 2.7
+
+## 0.1.9 (2022-02-07)
+
+- Added support for Linux ARM
+- Updated CmdStan to 2.28.2
+
 ## 0.1.8 (2022-01-16)
 
 - Updated CmdStan to 2.28.1

data/README.md

@@ -9,11 +9,9 @@ Bayesian inference for Ruby, powered by [CmdStan](https://github.com/stan-dev/cm
 Add this line to your application’s Gemfile:
 
 ```ruby
-gem 'cmdstan'
+gem "cmdstan"
 ```
 
-Installation can take a few minutes as CmdStan downloads and builds.
-
 ## Getting Started
 
 Create a Stan file, like `bernoulli.stan`
@@ -32,7 +30,7 @@ model {
 }
 ```
 
-Compile the model
+Compile the model (this can take a few minutes the first time as CmdStan downloads and builds)
 
 ```ruby
 model = CmdStan::Model.new(stan_file: "bernoulli.stan")
@@ -51,6 +49,14 @@ Summarize the results
 fit.summary
 ```
 
+Load a compiled model
+
+```ruby
+model = CmdStan::Model.new(exe_file: "bernoulli")
+```
+
+Check out [Strata](https://github.com/ankane/strata) for shipping models
+
 ## Maximum Likelihood Estimation
 
 ```ruby
@@ -58,6 +64,20 @@ mle = model.optimize(data: data)
 mle.optimized_params
 ```
 
+## Reference
+
+Check if CmdStan is installed
+
+```ruby
+CmdStan.cmdstan_installed?
+```
+
+Install CmdStan manually
+
+```ruby
+CmdStan.install_cmdstan
+```
+
 ## Credits
 
 This library is modeled after the [CmdStanPy API](https://github.com/stan-dev/cmdstanpy).
@@ -81,6 +101,5 @@ To get started with development:
 git clone https://github.com/ankane/cmdstan-ruby.git
 cd cmdstan-ruby
 bundle install
-bundle exec ruby ext/cmdstan/extconf.rb
 bundle exec rake test
 ```

data/lib/cmdstan/install.rb

@@ -0,0 +1,100 @@
+module CmdStan
+  module Install
+    def cmdstan_version
+      "2.30.0"
+    end
+
+    def cmdstan_installed?
+      Dir.exist?(CmdStan.path)
+    end
+
+    def install_cmdstan
+      version = cmdstan_version
+      dir = CmdStan.path
+
+      # no stanc3 binary for Mac ARM
+      if RbConfig::CONFIG["host_os"] !~ /darwin/i && RbConfig::CONFIG["host_cpu"] =~ /arm|aarch64/i
+        checksum = "8ab1eaa83af100336e31fed1bcb854f30e7f775feb1274552fc706ed177969ef"
+        url = "https://github.com/stan-dev/cmdstan/releases/download/v#{version}/cmdstan-#{version}-linux-arm64.tar.gz"
+      else
+        checksum = "009c2ea0043aa4a91c03ac78932e64f3cff4faa3e73413a2e0269d5be2d8de6c"
+        url = "https://github.com/stan-dev/cmdstan/releases/download/v#{version}/cmdstan-#{version}.tar.gz"
+      end
+
+      puts "Installing CmdStan version: #{version}"
+      puts "Install directory: #{dir}"
+
+      # only needed if default path
+      FileUtils.mkdir_p(File.expand_path("../../tmp", __dir__)) unless ENV["CMDSTAN"]
+
+      if Dir.exist?(dir)
+        puts "Already installed"
+        return true
+      end
+
+      Dir.mktmpdir do |tmpdir|
+        puts "Downloading..."
+        download_path = File.join(tmpdir, "cmdstan-#{version}.tar.gz")
+        download_file(url, download_path, checksum)
+
+        puts "Unpacking..."
+        path = File.join(tmpdir, "cmdstan-#{version}")
+        FileUtils.mkdir_p(path)
+        tar_args = Gem.win_platform? ? ["--force-local"] : []
+        system "tar", "xzf", download_path, "-C", path, "--strip-components=1", *tar_args
+
+        puts "Building..."
+        make_command = Gem.win_platform? ? "mingw32-make" : "make"
+        Dir.chdir(path) do
+          # disable precompiled header to save space
+          output, status = Open3.capture2e(make_command, "build", "PRECOMPILED_HEADERS=false")
+          if status.exitstatus != 0
+            puts output
+            raise Error, "Build failed"
+          end
+        end
+
+        FileUtils.mv(path, dir)
+      end
+
+      puts "Installed"
+
+      true
+    end
+
+    private
+
+    def download_file(url, download_path, checksum, redirects = 0)
+      raise Error, "Too many redirects" if redirects > 10
+
+      uri = URI(url)
+      location = nil
+
+      Net::HTTP.start(uri.host, uri.port, use_ssl: true) do |http|
+        request = Net::HTTP::Get.new(uri)
+        http.request(request) do |response|
+          case response
+          when Net::HTTPRedirection
+            location = response["location"]
+          when Net::HTTPSuccess
+            digest = Digest::SHA2.new
+
+            File.open(download_path, "wb") do |f|
+              response.read_body do |chunk|
+                f.write(chunk)
+                digest.update(chunk)
+              end
+            end
+
+            raise Error, "Bad checksum: #{digest.hexdigest}" if digest.hexdigest != checksum
+          else
+            raise Error, "Bad response"
+          end
+        end
+      end
+
+      # outside of Net::HTTP block to close previous connection
+      download_file(location, download_path, checksum, redirects + 1) if location
+    end
+  end
+end

data/lib/cmdstan/mcmc.rb

@@ -30,7 +30,7 @@ module CmdStan
       run_command "#{CmdStan.path}/bin/stansummary#{extension}", "--csv_filename=#{path}", *@output_files.map(&:path)
 
       result = {}
-      CSV.foreach(path, headers: true, converters: :numeric) do |row|
+      CSV.foreach(path, skip_lines: /^#/, headers: true, converters: :numeric) do |row|
         value = row.to_h
         name = value.delete("name")
         result[name] = value if name == "lp__" || !name.end_with?("__")

data/lib/cmdstan/model.rb

@@ -18,8 +18,12 @@ module CmdStan
     end
 
     def compile
+      unless ENV["CMDSTAN"] || CmdStan.cmdstan_installed?
+        CmdStan.install_cmdstan
+      end
+
       Dir.chdir(CmdStan.path) do
-        run_command make_command, @exe_file
+        run_command make_command, @exe_file, "PRECOMPILED_HEADERS=false"
       end
     end
 
@@ -32,7 +36,7 @@ module CmdStan
       data_file.write(data.to_json)
       data_file.close
 
-      chain ||= 4
+      chains ||= 4
 
       output_files = []
       chains.times do |chain|

data/lib/cmdstan/version.rb

@@ -1,3 +1,3 @@
 module CmdStan
-  VERSION = "0.1.8"
+  VERSION = "0.2.1"
 end

data/lib/cmdstan.rb

@@ -1,10 +1,14 @@
 # stdlib
+require "digest"
 require "csv"
+require "fileutils"
 require "json"
+require "net/http"
 require "open3"
 require "tempfile"
 
 # modules
+require "cmdstan/install"
 require "cmdstan/utils"
 require "cmdstan/mcmc"
 require "cmdstan/mle"
@@ -14,6 +18,8 @@ require "cmdstan/version"
 module CmdStan
   class Error < StandardError; end
 
+  extend Install
+
   class << self
     attr_accessor :path
   end

metadata

@@ -1,28 +1,26 @@
 --- !ruby/object:Gem::Specification
 name: cmdstan
 version: !ruby/object:Gem::Version
-  version: 0.1.8
+  version: 0.2.1
 platform: ruby
 authors:
 - Andrew Kane
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2022-01-17 00:00:00.000000000 Z
+date: 2022-07-06 00:00:00.000000000 Z
 dependencies: []
 description:
 email: andrew@ankane.org
 executables: []
-extensions:
-- ext/cmdstan/extconf.rb
+extensions: []
 extra_rdoc_files: []
 files:
 - CHANGELOG.md
 - LICENSE.txt
 - README.md
-- ext/cmdstan/Makefile
-- ext/cmdstan/extconf.rb
 - lib/cmdstan.rb
+- lib/cmdstan/install.rb
 - lib/cmdstan/mcmc.rb
 - lib/cmdstan/mle.rb
 - lib/cmdstan/model.rb
@@ -40,14 +38,14 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: '2.4'
+      version: '2.7'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.3.3
+rubygems_version: 3.3.7
 signing_key:
 specification_version: 4
 summary: Bayesian inference for Ruby, powered by CmdStan

data/ext/cmdstan/Makefile

@@ -1,5 +0,0 @@
-install:
-	@echo "Nothing to do"
-
-clean:
-	@echo "Nothing to do"

data/ext/cmdstan/extconf.rb

@@ -1,68 +0,0 @@
-require "digest"
-require "fileutils"
-require "net/http"
-require "tmpdir"
-
-version = "2.28.1"
-checksum = "eacadb4a1ca6997c9858e301780e729e53a9b5207b19ae2616abc882677e7637"
-url = "https://github.com/stan-dev/cmdstan/releases/download/v#{version}/cmdstan-#{version}.tar.gz"
-
-path = ENV["CMDSTAN"] || File.expand_path("../../tmp/cmdstan", __dir__)
-FileUtils.mkdir_p(path)
-raise "Directory not empty. Run: rake clean" unless Dir.empty?(path)
-
-$stdout.sync = true
-
-def download_file(url, download_path, checksum, redirects = 0)
-  raise "Too many redirects" if redirects > 10
-
-  uri = URI(url)
-  location = nil
-
-  Net::HTTP.start(uri.host, uri.port, use_ssl: true) do |http|
-    request = Net::HTTP::Get.new(uri)
-    http.request(request) do |response|
-      case response
-      when Net::HTTPRedirection
-        location = response["location"]
-      when Net::HTTPSuccess
-        digest = Digest::SHA2.new
-
-        i = 0
-        File.open(download_path, "wb") do |f|
-          response.read_body do |chunk|
-            f.write(chunk)
-            digest.update(chunk)
-
-            # print progress
-            putc "." if i % 50 == 0
-            i += 1
-          end
-        end
-        puts # newline
-
-        abort "Bad checksum: #{digest.hexdigest}" if digest.hexdigest != checksum
-      else
-        abort "Bad response"
-      end
-    end
-  end
-
-  # outside of Net::HTTP block to close previous connection
-  download_file(location, download_path, checksum, redirects + 1) if location
-end
-
-# download
-puts "Downloading #{url}..."
-download_path = "#{Dir.tmpdir}/cmdstan-#{version}.tar.gz"
-download_file(url, download_path, checksum)
-
-# extract
-Dir.chdir(path)
-# TODO use Gem::Package::TarReader from Rubygems
-tar_args = Gem.win_platform? ? ["--force-local"] : []
-system "tar", "zxf", download_path, "-C", path, "--strip-components=1", *tar_args
-
-# build
-make_command = Gem.win_platform? ? "mingw32-make" : "make"
-system make_command, "build"