Merge pull request #158 from TuringLang/dev

Merge changes in dev branch into master

Author: yebai

.github/workflows/CompatHelper.yml

@@ -3,7 +3,7 @@ name: CompatHelper
 on:
   schedule:
     - cron: '00 00 * * *'
-
+  workflow_dispatch:
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
@@ -14,4 +14,4 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
-        run: julia -e 'using CompatHelper; CompatHelper.main(; master_branch = "dev")'
+        run: julia -e 'using CompatHelper; CompatHelper.main(; master_branch = "dev", subdirs = ["", "test"])'

.github/workflows/DynamicPPL-CI.yml

@@ -3,14 +3,12 @@ name: DynamicPPL-CI
 on:
   push:
     branches:
-      - master
-      - dev
       # This is where pull requests from "bors r+" are built.
       - staging
       # This is where pull requests from "bors try" are built.
       - trying
-  # Enable building pull requests.
-  pull_request:
+      # Build the master branch.
+      - master
 
 jobs:
   test:
@@ -19,9 +17,9 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.0'
+          - '1.3'
           - '1'
-          - 'nightly'
+          # - 'nightly'
         os:
           - ubuntu-latest
           - macOS-latest
@@ -30,6 +28,8 @@ jobs:
           - x86
           - x64
         exclude:
+          - os: windows-latest
+            arch: x86
           - os: macOS-latest
             arch: x86
     steps:

.github/workflows/TagBot.yml

@@ -2,6 +2,7 @@ name: TagBot
 on:
   schedule:
     - cron: 0 0 * * *
+  workflow_dispatch:
 jobs:
   TagBot:
     runs-on: ubuntu-latest

.gitignore

@@ -3,4 +3,6 @@
 *.jl.mem
 .DS_Store
 /Manifest.toml
+/test/Manifest.toml
 /dev/
+/test/gdemo_default.jls

.travis.yml

@@ -2,19 +2,18 @@
 language: julia
 branches:
   only:
-    # Enable building pull requests to master and dev.
-    - master
-    - dev
     # This is where pull requests from "bors r+" are built.
     - staging
     # This is where pull requests from "bors try" are built.
     - trying
+    # Build the master branch.
+    - master
 os:
   - linux
   - osx
 matrix:
   include:
-    - julia: 1.0
+    - julia: 1.3
     - julia: 1
       env: JULIA_NUM_THREADS=1
     - julia: 1
@@ -32,4 +31,5 @@ notifications:
 after_success:
   - if [[ $TRAVIS_JULIA_VERSION = 1 ]] && [[ $JULIA_NUM_THREADS = 1 ]] && [[ $TRAVIS_OS_NAME = linux ]]; then
       julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(process_folder())';
+      julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(process_folder())';
     fi

Project.toml

@@ -1,51 +1,21 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-authors = ["mohamed82008 <mohamed82008@gmail.com>"]
-version = "0.8.2"
+version = "0.9.0"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
+NaturalSort = "c020b1a1-e9b0-503a-9c33-f039bfc54a85"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
 [compat]
 AbstractMCMC = "1"
 Bijectors = "0.5.2, 0.6, 0.7, 0.8"
-Distributions = "0.22, 0.23"
+Distributions = "0.23.8"
 MacroTools = "0.5.1"
+NaturalSort = "1"
 ZygoteRules = "0.2"
-julia = "1"
-
-[extras]
-AdvancedHMC = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170"
-BinaryProvider = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c"
-DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-EllipticalSliceSampling = "cad2338a-1db2-11e9-3401-43bc07c9ede2"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
-Libtask = "6f1fad26-d15e-5dc8-ae53-837a1d7b8c9f"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
-LogDensityProblems = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c"
-Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
-MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d"
-Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
-PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
-ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
-SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-StatsFuns = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
-UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
-Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-
-[targets]
-test = ["AdvancedHMC", "AdvancedMH", "DistributionsAD", "DocStringExtensions", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "Logging", "MCMCChains", "Markdown", "PDMats", "ProgressLogging", "Random", "Reexport", "Requires", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test", "Tracker", "UUIDs", "Zygote"]
+julia = "1.3"

bors.toml

@@ -6,14 +6,14 @@ status = [
   "test (1, ubuntu-latest, x64)",
   "test (1.%, macOS-latest, x64)",
   "test (1, macOS-latest, x64)",
-  "test (1.%, windows-latest, x86)",
-  "test (1, windows-latest, x86)",
   "test (1.%, windows-latest, x64)",
   "test (1, windows-latest, x64)"
 ]
 delete_merged_branches = true
-# Uncomment this to require at least on approval of a project member.
-#required_approvals = 1
+# Require at least on approval of a project member.
+required_approvals = 1
+# Squash commits before merging.
+use_squash_merge = true
 # Uncomment this to use a two hour timeout.
 # The default is one hour.
 #timeout_sec = 7200

src/DynamicPPL.jl

@@ -3,9 +3,10 @@ module DynamicPPL
 using AbstractMCMC: AbstractSampler, AbstractChains, AbstractModel
 using Distributions
 using Bijectors
-using MacroTools
 
 import AbstractMCMC
+import NaturalSort
+import MacroTools
 import ZygoteRules
 
 import Random
@@ -51,25 +52,20 @@ export  AbstractVarInfo,
         inspace,
         subsumes,
 # Compiler
-        ModelGen,
         @model,
         @varname,
 # Utilities
         vectorize,
         reconstruct,
         reconstruct!,
         Sample,
-        Chain,
         init,
         vectorize,
         set_resume!,
 # Model
-        ModelGen,
         Model,
         getmissings,
         getargnames,
-        getdefaults,
-        getgenerator,
 # Samplers
         Sampler,
         SampleFromPrior,
@@ -93,14 +89,14 @@ export  AbstractVarInfo,
         @logprob_str,
 # Convenience functions
         logprior,
-        logjoint
+        logjoint,
+# Convenience macros
+        @addlogprob!
 
 # Reexport
 using Distributions: loglikelihood
 export loglikelihood
 
-const DEBUG = Bool(parse(Int, get(ENV, "DEBUG_DYNAMICPPL", "0")))
-
 # Used here and overloaded in Turing
 function getspace end