Merge branch 'master' into feature/incomplete-probability-calls

Author: adamhaber

Dockerfile

@@ -658,6 +658,7 @@ pipeline {
 
                 // Checkout gh-pages as a test so we build docs from this branch
                 runShell("""
+                    git remote set-branches --add origin gh-pages
                     git checkout --track  origin/gh-pages
                     git checkout master
                 """)
@@ -702,4 +703,4 @@ pipeline {
           script {utils.mailBuildResults()}
         }
     }
-}
+}

Jenkinsfile

@@ -55,8 +55,8 @@ pipeline {
     stages {
         stage("Build") {
             agent {
-                dockerfile {
-                    filename 'docker/debian/Dockerfile'
+                docker {
+                    image 'stanorg/stanc3:debian'
                     args "-u root --entrypoint=\'\'"
                     label 'linux-ec2'
                 }
@@ -108,8 +108,8 @@ pipeline {
                 }
                 stage("Build stanc.js") {
                     agent {
-                        dockerfile {
-                            filename 'docker/debian/Dockerfile'
+                        docker {
+                            image 'stanorg/stanc3:debian'
                             //Forces image to ignore entrypoint
                             args "-u root --entrypoint=\'\'"
                             label 'linux-ec2'
@@ -134,8 +134,8 @@ pipeline {
                 }
                 stage("Build & test a static Linux binary") {
                     agent {
-                        dockerfile {
-                            filename 'docker/static/Dockerfile'
+                        docker {
+                            image 'stanorg/stanc3:static'
                             //Forces image to ignore entrypoint
                             args "-u 1000 --entrypoint=\'\'"
                             label 'linux-ec2'
@@ -167,8 +167,8 @@ pipeline {
                 // Cross compiling for windows on debian
                 stage("Build & test static Windows binary") {
                     agent {
-                        dockerfile {
-                            filename 'docker/debian-windows/Dockerfile'
+                        docker {
+                            image 'stanorg/stanc3:debian-windows'
                             label 'linux-ec2'
                             //Forces image to ignore entrypoint
                             args "-u 1000 --entrypoint=\'\'"
@@ -178,7 +178,7 @@ pipeline {
 
                         script {
                             checkoutRepository("sh")
-                        }                        
+                        }
                         runShell("""
                             eval \$(opam env)
                             dune subst

Jenkinsfile-test-binaries

@@ -28,12 +28,44 @@ The entrypoint for the compiler is in `src/stanc/stanc.ml` which sequences the v
 ### Distinct stanc Phases
 
 The phases of stanc are summarized in the following information flowchart and list.
-
+<!---
+digraph G {
+    rankdir=TB;
+    ranksep=.25;
+    bgcolor=white;
+    size=5;
+    node [shape="box"];
+
+    origin[style=invis];
+    stanc[label="stanc/stanc.ml"];
+    lexer[label="frontend/lexer.mll"];
+    parser[label="frontend/parser.mly"];
+    type[label="frontend/Typechecker.ml"];
+    lower[label="frontend/Ast_to_Mir.ml"];
+    transform[label="*_backend/Transform_Mir.ml"];
+    optimize[label="analysis_and_optimization/Optimize.ml"];
+    codegen[label="*_backend/*_code_gen.ml"];
+    output[shape="oval" label=".hpp file"]
+
+
+    origin -> stanc[label=" .stan file path"];
+    stanc -> lexer[label=" string"];
+    lexer -> parser[label=" tokens"];
+    parser -> type[label=" untyped AST"];
+    type -> lower[label=" typed AST"];
+    lower -> transform[label=" MIR"];
+    transform -> optimize[label=" transformed MIR"];
+    transform -> codegen[label="                                  "];
+    optimize -> codegen[headlabel="optimized MIR      "];
+    codegen -> output[label=" C++ code"];
+
+}
+--->
 ![stanc3 information flow](docs/img/information-flow.png)
 
 1. [Lex](src/frontend/lexer.mll) the Stan language into tokens.
 1. [Parse](src/frontend/parser.mly) Stan language into AST that represents the syntax quite closely and aides in development of pretty-printers and linters. `stanc --debug-ast` to print this out.
-1. Typecheck & add type information [Semantic_check.ml](src/frontend/Semantic_check.ml).  `stanc --debug-decorated-ast`
+1. Typecheck & add type information [Typechecker.ml](src/frontend/Typechecker.ml).  `stanc --debug-decorated-ast`
 1. [Lower](src/frontend/Ast_to_Mir.ml) into [Middle Intermediate Representation](src/middle/Mir.ml) (AST -> MIR) `stanc --debug-mir` (or `--debug-mir-pretty`)
 1. Analyze & optimize (MIR -> MIR)
 1. Backend MIR transform (MIR -> MIR) [Transform_Mir.ml](src/stan_math_backend/Transform_Mir.ml)  `stanc --debug-transformed-mir`