cmdstan 0.1.1 → 0.1.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,3 +1,24 @@
+## 0.1.6 (2021-02-08)
+
+- Updated CmdStan to 2.26.0
+
+## 0.1.5 (2020-11-21)
+
+- Added `tbb` to path for Linux
+
+## 0.1.4 (2020-11-01)
+
+- Updated CmdStan to 2.25.0
+
+## 0.1.3 (2020-05-29)
+
+- Added `tempfile` dependency
+- Use a single job for installation
+
+## 0.1.2 (2020-04-10)
+
+- Added `tbb` to path for Windows
+
 ## 0.1.1 (2020-04-09)
 
 - Added support for Windows

data/LICENSE.txt

@@ -1,6 +1,7 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Andrew Kane
+Copyright (c) 2019, Stan Developers and their Assignees
+Copyright (c) 2020-2021, Andrew Kane
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

data/README.md

@@ -2,7 +2,7 @@
 
 Bayesian inference for Ruby, powered by [CmdStan](https://github.com/stan-dev/cmdstan)
 
-[![Build Status](https://travis-ci.org/ankane/cmdstan.svg?branch=master)](https://travis-ci.org/ankane/cmdstan) [![Build status](https://ci.appveyor.com/api/projects/status/n9sp7b34m6du5ltw/branch/master?svg=true)](https://ci.appveyor.com/project/ankane/cmdstan/branch/master)
+[![Build Status](https://github.com/ankane/cmdstan/workflows/build/badge.svg?branch=master)](https://github.com/ankane/cmdstan/actions)
 
 ## Installation
 

data/ext/cmdstan/extconf.rb

@@ -3,8 +3,8 @@ require "fileutils"
 require "net/http"
 require "tmpdir"
 
-version = "2.22.1"
-checksum = "d12e46bda4bd3db9e8abe0554712b56e41f8e7843900338446d9a3b1acc2d0ce"
+version = "2.26.0"
+checksum = "0bc5529a4818e70ef8181191a515ea5e1a6fce326dda41a040f99deb89bcb663"
 url = "https://github.com/stan-dev/cmdstan/releases/download/v#{version}/cmdstan-#{version}.tar.gz"
 
 $stdout.sync = true
@@ -61,4 +61,4 @@ system "tar", "zxf", download_path, "-C", path, "--strip-components=1", *tar_arg
 
 # build
 make_command = Gem.win_platform? ? "mingw32-make" : "make"
-system make_command, "build", "-j"
+system make_command, "build"

data/lib/cmdstan.rb

@@ -2,6 +2,7 @@
 require "csv"
 require "json"
 require "open3"
+require "tempfile"
 
 # modules
 require "cmdstan/utils"

data/lib/cmdstan/mcmc.rb

@@ -25,11 +25,12 @@ module CmdStan
     end
 
     def summary
-      csv_file = Tempfile.new
-      run_command "#{CmdStan.path}/bin/stansummary#{extension}", "--csv_file=#{csv_file.path}", *@output_files.map(&:path)
+      # add suffix since path can't already exist
+      path = "#{Tempfile.new.path}.csv"
+      run_command "#{CmdStan.path}/bin/stansummary#{extension}", "--csv_filename=#{path}", *@output_files.map(&:path)
 
       result = {}
-      CSV.foreach(csv_file.path, headers: true, converters: :numeric) do |row|
+      CSV.foreach(path, 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/mle.rb

@@ -12,6 +12,7 @@ module CmdStan
       CSV.foreach(@output_file.path, skip_lines: /^#/, headers: true, converters: :numeric) do |row|
         return row.to_h
       end
+      raise "Bug detected"
     end
 
     def column_names

data/lib/cmdstan/model.rb

@@ -61,7 +61,7 @@ module CmdStan
         args << "num_samples=#{sampling_iters.to_i}" if sampling_iters
         args += ["algorithm=hmc", "adapt", "engaged=1"]
 
-        run_command *args
+        run_command(*args)
 
         output_files << output_file
       end
@@ -99,7 +99,7 @@ module CmdStan
       args << "algorithm=#{algorithm.to_s.downcase}" if algorithm
       args << "iter=#{iter.to_i}" if iter
 
-      run_command *args
+      run_command(*args)
 
       MLE.new(output_file)
     end

data/lib/cmdstan/utils.rb

@@ -3,9 +3,22 @@ module CmdStan
     private
 
     def run_command(*args)
+      env = {}
+      # add tbb to path
+      tbblib = ENV["STAN_TBB"] || File.join(CmdStan.path, "stan", "lib", "stan_math", "lib", "tbb")
+      if windows?
+        # uses ; for separator
+        raise "Invalid TBB path" if tbblib.include?(";")
+        env["PATH"] = "#{tbblib};#{ENV["PATH"]}"
+      elsif !mac?
+        # uses : for separator
+        raise "Invalid TBB path" if tbblib.include?(":")
+        env["LD_LIBRARY_PATH"] = "#{tbblib}:#{ENV["LD_LIBRARY_PATH"]}"
+      end
+
       # use an open3 method since it does escaping (like system)
       # use capture2e so we don't need to worry about deadlocks
-      output, status = Open3.capture2e(*args)
+      output, status = Open3.capture2e(env, *args)
       if status.exitstatus != 0
         $stderr.puts output
         raise Error, "Command failed"
@@ -20,6 +33,10 @@ module CmdStan
       windows? ? ".exe" : ""
     end
 
+    def mac?
+      RbConfig::CONFIG["host_os"] =~ /darwin/i
+    end
+
     def windows?
       Gem.win_platform?
     end

data/lib/cmdstan/version.rb

@@ -1,3 +1,3 @@
 module CmdStan
-  VERSION = "0.1.1"
+  VERSION = "0.1.6"
 end

metadata

@@ -1,59 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: cmdstan
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.6
 platform: ruby
 authors:
 - Andrew Kane
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-04-10 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: minitest
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '5'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '5'
-description: 
-email: andrew@chartkick.com
+date: 2021-02-08 00:00:00.000000000 Z
+dependencies: []
+description:
+email: andrew@ankane.org
 executables: []
 extensions:
 - ext/cmdstan/extconf.rb
@@ -74,7 +32,7 @@ homepage: https://github.com/ankane/cmdstan
 licenses:
 - BSD-3-Clause
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -89,8 +47,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
-signing_key: 
+rubygems_version: 3.2.3
+signing_key:
 specification_version: 4
 summary: Bayesian inference for Ruby, powered by CmdStan
 test_files: []