cmdstan 0.1.4 → 0.1.8

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Files changed (10) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +16 -0
  3. data/LICENSE.txt +1 -1
  4. data/README.md +6 -6
  5. data/ext/cmdstan/extconf.rb +11 -7
  6. data/lib/cmdstan/mcmc.rb +4 -3
  7. data/lib/cmdstan/model.rb +2 -2
  8. data/lib/cmdstan/utils.rb +12 -2
  9. data/lib/cmdstan/version.rb +1 -1
  10. metadata +6 -48
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data/CHANGELOG.md CHANGED
@@ -1,3 +1,19 @@
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+ ## 0.1.8 (2022-01-16)
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+
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+ - Updated CmdStan to 2.28.1
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+
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+ ## 0.1.7 (2021-08-23)
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+
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+ - Updated CmdStan to 2.27.0
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+
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+ ## 0.1.6 (2021-02-08)
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+
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+ - Updated CmdStan to 2.26.0
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+
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+ ## 0.1.5 (2020-11-21)
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+
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+ - Added `tbb` to path for Linux
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+
1
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  ## 0.1.4 (2020-11-01)
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18
 
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  - Updated CmdStan to 2.25.0
data/LICENSE.txt CHANGED
@@ -1,7 +1,7 @@
1
1
  BSD 3-Clause License
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2
 
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3
  Copyright (c) 2019, Stan Developers and their Assignees
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- Copyright (c) 2020, Andrew Kane
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+ Copyright (c) 2020-2022, Andrew Kane
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  All rights reserved.
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  Redistribution and use in source and binary forms, with or without
data/README.md CHANGED
@@ -2,7 +2,7 @@
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2
 
3
3
  Bayesian inference for Ruby, powered by [CmdStan](https://github.com/stan-dev/cmdstan)
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4
 
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- [![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)
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+ [![Build Status](https://github.com/ankane/cmdstan-ruby/workflows/build/badge.svg?branch=master)](https://github.com/ankane/cmdstan-ruby/actions)
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6
 
7
7
  ## Installation
8
8
 
@@ -64,22 +64,22 @@ This library is modeled after the [CmdStanPy API](https://github.com/stan-dev/cm
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64
 
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  ## History
66
66
 
67
- View the [changelog](https://github.com/ankane/cmdstan/blob/master/CHANGELOG.md)
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+ View the [changelog](https://github.com/ankane/cmdstan-ruby/blob/master/CHANGELOG.md)
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  ## Contributing
70
70
 
71
71
  Everyone is encouraged to help improve this project. Here are a few ways you can help:
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- - [Report bugs](https://github.com/ankane/cmdstan/issues)
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- - Fix bugs and [submit pull requests](https://github.com/ankane/cmdstan/pulls)
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+ - [Report bugs](https://github.com/ankane/cmdstan-ruby/issues)
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+ - Fix bugs and [submit pull requests](https://github.com/ankane/cmdstan-ruby/pulls)
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  - Write, clarify, or fix documentation
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  - Suggest or add new features
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77
 
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  To get started with development:
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79
 
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80
  ```sh
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- git clone https://github.com/ankane/cmdstan.git
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- cd cmdstan
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+ git clone https://github.com/ankane/cmdstan-ruby.git
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+ cd cmdstan-ruby
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83
  bundle install
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84
  bundle exec ruby ext/cmdstan/extconf.rb
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  bundle exec rake test
data/ext/cmdstan/extconf.rb CHANGED
@@ -3,13 +3,19 @@ require "fileutils"
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3
  require "net/http"
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  require "tmpdir"
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5
 
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- version = "2.25.0"
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- checksum = "6bd90c6513d386f22007750f136c3f8db0132aa3e80c7298095516c68ab95a4a"
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+ version = "2.28.1"
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+ checksum = "eacadb4a1ca6997c9858e301780e729e53a9b5207b19ae2616abc882677e7637"
8
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  url = "https://github.com/stan-dev/cmdstan/releases/download/v#{version}/cmdstan-#{version}.tar.gz"
9
9
 
10
+ path = ENV["CMDSTAN"] || File.expand_path("../../tmp/cmdstan", __dir__)
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+ FileUtils.mkdir_p(path)
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+ raise "Directory not empty. Run: rake clean" unless Dir.empty?(path)
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+
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  $stdout.sync = true
11
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- def download_file(url, download_path, checksum)
16
+ def download_file(url, download_path, checksum, redirects = 0)
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+ raise "Too many redirects" if redirects > 10
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+
13
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  uri = URI(url)
14
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  location = nil
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@@ -35,7 +41,7 @@ def download_file(url, download_path, checksum)
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  end
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  puts # newline
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- abort "Bad checksum" if digest.hexdigest != checksum
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+ abort "Bad checksum: #{digest.hexdigest}" if digest.hexdigest != checksum
39
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  else
40
46
  abort "Bad response"
41
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  end
@@ -43,7 +49,7 @@ def download_file(url, download_path, checksum)
43
49
  end
44
50
 
45
51
  # outside of Net::HTTP block to close previous connection
46
- download_file(location, download_path, checksum) if location
52
+ download_file(location, download_path, checksum, redirects + 1) if location
47
53
  end
48
54
 
49
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  # download
@@ -52,8 +58,6 @@ download_path = "#{Dir.tmpdir}/cmdstan-#{version}.tar.gz"
52
58
  download_file(url, download_path, checksum)
53
59
 
54
60
  # extract
55
- path = ENV["CMDSTAN"] || File.expand_path("../../tmp/cmdstan", __dir__)
56
- FileUtils.mkdir_p(path)
57
61
  Dir.chdir(path)
58
62
  # TODO use Gem::Package::TarReader from Rubygems
59
63
  tar_args = Gem.win_platform? ? ["--force-local"] : []
data/lib/cmdstan/mcmc.rb CHANGED
@@ -25,11 +25,12 @@ module CmdStan
25
25
  end
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26
 
27
27
  def summary
28
- csv_file = Tempfile.new
29
- run_command "#{CmdStan.path}/bin/stansummary#{extension}", "--csv_file=#{csv_file.path}", *@output_files.map(&:path)
28
+ # add suffix since path can't already exist
29
+ path = "#{Tempfile.new.path}.csv"
30
+ run_command "#{CmdStan.path}/bin/stansummary#{extension}", "--csv_filename=#{path}", *@output_files.map(&:path)
30
31
 
31
32
  result = {}
32
- CSV.foreach(csv_file.path, headers: true, converters: :numeric) do |row|
33
+ CSV.foreach(path, headers: true, converters: :numeric) do |row|
33
34
  value = row.to_h
34
35
  name = value.delete("name")
35
36
  result[name] = value if name == "lp__" || !name.end_with?("__")
data/lib/cmdstan/model.rb CHANGED
@@ -61,7 +61,7 @@ module CmdStan
61
61
  args << "num_samples=#{sampling_iters.to_i}" if sampling_iters
62
62
  args += ["algorithm=hmc", "adapt", "engaged=1"]
63
63
 
64
- run_command *args
64
+ run_command(*args)
65
65
 
66
66
  output_files << output_file
67
67
  end
@@ -99,7 +99,7 @@ module CmdStan
99
99
  args << "algorithm=#{algorithm.to_s.downcase}" if algorithm
100
100
  args << "iter=#{iter.to_i}" if iter
101
101
 
102
- run_command *args
102
+ run_command(*args)
103
103
 
104
104
  MLE.new(output_file)
105
105
  end
data/lib/cmdstan/utils.rb CHANGED
@@ -4,10 +4,16 @@ module CmdStan
4
4
 
5
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  def run_command(*args)
6
6
  env = {}
7
+ # add tbb to path
8
+ tbblib = ENV["STAN_TBB"] || File.join(CmdStan.path, "stan", "lib", "stan_math", "lib", "tbb")
7
9
  if windows?
8
- # add tbb to path
9
- tbblib = ENV["STAN_TBB"] || File.join(CmdStan.path, "stan", "lib", "stan_math", "lib", "tbb")
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+ # uses ; for separator
11
+ raise "Invalid TBB path" if tbblib.include?(";")
10
12
  env["PATH"] = "#{tbblib};#{ENV["PATH"]}"
13
+ elsif !mac?
14
+ # uses : for separator
15
+ raise "Invalid TBB path" if tbblib.include?(":")
16
+ env["LD_LIBRARY_PATH"] = "#{tbblib}:#{ENV["LD_LIBRARY_PATH"]}"
11
17
  end
12
18
 
13
19
  # use an open3 method since it does escaping (like system)
@@ -27,6 +33,10 @@ module CmdStan
27
33
  windows? ? ".exe" : ""
28
34
  end
29
35
 
36
+ def mac?
37
+ RbConfig::CONFIG["host_os"] =~ /darwin/i
38
+ end
39
+
30
40
  def windows?
31
41
  Gem.win_platform?
32
42
  end
data/lib/cmdstan/version.rb CHANGED
@@ -1,3 +1,3 @@
1
1
  module CmdStan
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- VERSION = "0.1.4"
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+ VERSION = "0.1.8"
3
3
  end
metadata CHANGED
@@ -1,59 +1,17 @@
1
1
  --- !ruby/object:Gem::Specification
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2
  name: cmdstan
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3
  version: !ruby/object:Gem::Version
4
- version: 0.1.4
4
+ version: 0.1.8
5
5
  platform: ruby
6
6
  authors:
7
7
  - Andrew Kane
8
8
  autorequire:
9
9
  bindir: bin
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10
  cert_chain: []
11
- date: 2020-11-01 00:00:00.000000000 Z
12
- dependencies:
13
- - !ruby/object:Gem::Dependency
14
- name: bundler
15
- requirement: !ruby/object:Gem::Requirement
16
- requirements:
17
- - - ">="
18
- - !ruby/object:Gem::Version
19
- version: '0'
20
- type: :development
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- prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
24
- - - ">="
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- - !ruby/object:Gem::Version
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- version: '0'
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- - !ruby/object:Gem::Dependency
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- name: rake
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- requirement: !ruby/object:Gem::Requirement
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- requirements:
31
- - - ">="
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- - !ruby/object:Gem::Version
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- version: '0'
34
- type: :development
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- prerelease: false
36
- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
38
- - - ">="
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- - !ruby/object:Gem::Version
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- version: '0'
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- - !ruby/object:Gem::Dependency
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- name: minitest
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- requirement: !ruby/object:Gem::Requirement
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- requirements:
45
- - - ">="
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- - !ruby/object:Gem::Version
47
- version: '5'
48
- type: :development
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- prerelease: false
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- version_requirements: !ruby/object:Gem::Requirement
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- requirements:
52
- - - ">="
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- - !ruby/object:Gem::Version
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- version: '5'
11
+ date: 2022-01-17 00:00:00.000000000 Z
12
+ dependencies: []
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13
  description:
56
- email: andrew@chartkick.com
14
+ email: andrew@ankane.org
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15
  executables: []
58
16
  extensions:
59
17
  - ext/cmdstan/extconf.rb
@@ -70,7 +28,7 @@ files:
70
28
  - lib/cmdstan/model.rb
71
29
  - lib/cmdstan/utils.rb
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30
  - lib/cmdstan/version.rb
73
- homepage: https://github.com/ankane/cmdstan
31
+ homepage: https://github.com/ankane/cmdstan-ruby
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32
  licenses:
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33
  - BSD-3-Clause
76
34
  metadata: {}
@@ -89,7 +47,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
89
47
  - !ruby/object:Gem::Version
90
48
  version: '0'
91
49
  requirements: []
92
- rubygems_version: 3.1.4
50
+ rubygems_version: 3.3.3
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51
  signing_key:
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52
  specification_version: 4
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53
  summary: Bayesian inference for Ruby, powered by CmdStan