Refactoring Options Handler & Library Cycle Breaking

What to Know As a User:
A number of files have moved. Users that include files in the public API in more refined ways than using #include <cvc4.h> should consult which files have moved. Note though that some files may move again after being cleaned up. A number of small tweaks have been made to the swig interfaces that may cause issues. Please file bug reports for any problems.

The Problem:
The build order of CVC4 used to be [roughly] specified as:
  options < expr < util < libcvc4 < parsers < main
Each of these had their own directories and their own Makefile.am files. With the exception of the util/ directory, each of the subdirectories built exactly one convenience library. The util/ directory additionally built a statistics library. While the order above was partially correct, the build order was more complicated as options/Makefile.am executed building the sources for expr/Makefile.am as part of its BUILT_SOURCES phase. This options/Makefile.am also build the options/h and options.cpp files in other directories. There were cyclical library dependencies between the first four above libraries. All of these aspects combined to make options extremely brittle and hard to develop. Maintaining these between clang versus gcc, and bazel versus autotools has become increasing unpredictable.

The Solution:
To address these cyclic build problems, I am simplifying the build process. Here are the main things that have to happen:
1. util/ will be split into 3 separate directories: base, util, and smt_util. Each will have their own library and Makefile.am file.
2. Dependencies for options/ will be moved into options/. If a type appears as an option, this file will be moved into options.
3. All of the old options_handlers.h files have been refactored.
4. Some files have moved from util into expr/ to resolve cycles. Some of these moves are temporary.
5. I am removing the libstatistics library.

The constraints that the CVC4 build system will eventually satisfy are:
- The include order for both the .h and .cpp files for a directory must respect the order libraries are built. For example, a file in options/ cannot include from the expr/ directory. This includes built source files such as those coming from */kinds files and */options files.
- The types definitions must also respect the build order. Forward type declarations will be allowed in exceptional, justified cases.
- The Makefile.am for a directory cannot generate a file outside of the directory it controls. (Or call another Makefile.am except through subdirectory calls.)
- One library per Makefile.am.
- No extra copies of libraries will be built for the purpose of distinguishing between external and internal visibility in libraries for building parser/ or main/ libraries and binaries. Any function used by parser/ and main/ will be labeled with CVC4_PUBLIC and be in a public API. (AFAICT, libstatistics was being built exactly to skirt this.)

The build order of CVC4 can now be [roughly] specified as
  base < options < util < expr < smt_util < libcvc4 < parsers < main
The distinction between "base < options < util < expr" are currently clean. The relationship between expr and the subsequent directories/libraries are not yet clean.

More details about the directories:

base/
The new directory base/ contains the shared utilities that are absolutely crucial to starting cvc4. The list currently includes just: cvc4_assert.{h,cpp}, output.{h,cpp}, exception.{h,cpp}, and tls.{h, h.in, cpp}. These are things that are required everywhere.

options/
The options/ directory is self contained.
- It contains all of the enums that appear as options. This includes things like theory/bv/bitblast_mode.h .
- There are exactly 4 classes that handled currently using forward declarations currently to this: LogicInfo, LemmaInputChannel, LemmaOutputChannel, and CommandSequence. These will all be removed from options.
- Functionality of the options_handlers.h files has been moved into smt/smt_options_handler.h. The options library itself only uses an interface class defined in options/options_handler_interface.h. We are now using virtual dispatch to avoid using inlined functions as was previously done.
- The */options_handlers.h files have been removed.
- The generated smt/smt_options.cpp file has been be replaced by pushing the functionality that was generated into: options/options_handler_{get,set}_option_template.cpp . The non-generated functionality was moved into smt_engine.cpp.
- All of the options files have been moved from their directories into options/. This means includes like theory/arith/options.h have changed to change to options/arith_options.h .

util/
The util/ directory continues to contain core utility classes that may be used [almost] everywhere. The exception is that these are not used by options/ or base/. This includes things like rational and integer. These may not use anything in expr/ or libcvc4. A number of files have been moved out of this directory as they have cyclic dependencies graph with exprs and types. The build process up to this directory is currently clean.

expr/
The expr/ directory continues to be the home of expressions. The major change is files moving from util/ moving into expr/. The reason for this is that these files form a cycle with files in expr/.
- An example is datatype.h. This includes "expr/expr.h", "expr/type.h" while "expr/command.h" includes datatype.h.
- Another example is predicate.h. This uses expr.h and is also declared in a kinds file and thus appears in kinds.h.
- The rule of thumb is if expr/ pulls it in it needs to be independent of expr/, in which case it is in util/, or it is not, in which case it is pulled into expr/.
- Some files do not have a strong justification currently. Result, ResourceManager and SExpr can be moved back into util/ once the iostream manipulation routines are refactored out of the Node and Expr classes.
- Note the kinds files are expected to remain in the theory/ directories. These are only read in order to build sources.
- This directory is not yet clean. It contains forward references into libcvc4 such as the printer. It also makes some classes used by main/ and parser CVC4_PUBLIC.

smt_util/
The smt_util/ directory contains those utility classes which require exprs, but expr/ does not require them. These are mostly utilities for working with expressions and nodes. Examples include ite_removal.h, LemmaInputChannel and LemmaOutputChannel.

What is up next:
- A number of new #warning "TODO: ..." items have been scattered throughout the code as reminders to myself. Help with these issues is welcomed.
- The expr/ directory needs to be cleaned up in a similar to options/. Before this happens statistics needs to be cleaned up.

19 files changed, 83 insertions, 114 deletions

diff --git a/src/parser/antlr_input.cpp b/src/parser/antlr_input.cpp
index 1d2dbd736..21e48b19e 100644
--- a/src/parser/antlr_input.cpp
+++ b/src/parser/antlr_input.cpp
@@ -18,23 +18,22 @@
 #include <antlr3.h>
 #include <stdint.h>
 
+#include "base/output.h"
+#include "expr/type.h"
 #include "parser/antlr_input.h"
-#include "parser/input.h"
+#include "parser/antlr_line_buffered_input.h"
 #include "parser/bounded_token_buffer.h"
 #include "parser/bounded_token_factory.h"
-#include "parser/antlr_line_buffered_input.h"
+#include "parser/cvc/cvc_input.h"
+#include "parser/input.h"
 #include "parser/memory_mapped_input_buffer.h"
-#include "parser/parser_exception.h"
 #include "parser/parser.h"
-
-#include "expr/command.h"
-#include "expr/type.h"
-#include "parser/cvc/cvc_input.h"
+#include "parser/parser_exception.h"
 #include "parser/smt1/smt1_input.h"
 #include "parser/smt2/smt2_input.h"
 #include "parser/smt2/sygus_input.h"
 #include "parser/tptp/tptp_input.h"
-#include "util/output.h"
+#include "smt_util/command.h"
 
 using namespace std;
 using namespace CVC4;
diff --git a/src/parser/antlr_input.h b/src/parser/antlr_input.h
index 2086db714..baec46e6f 100644
--- a/src/parser/antlr_input.h
+++ b/src/parser/antlr_input.h
@@ -36,14 +36,14 @@
 #include <vector>
 #include <cassert>
 
+#include "base/output.h"
 #include "parser/bounded_token_buffer.h"
-#include "parser/parser_exception.h"
 #include "parser/input.h"
-
+#include "parser/parser_exception.h"
 #include "util/bitvector.h"
 #include "util/integer.h"
 #include "util/rational.h"
-#include "util/output.h"
+
 
 namespace CVC4 {
 
diff --git a/src/parser/antlr_line_buffered_input.cpp b/src/parser/antlr_line_buffered_input.cpp
index 33589110f..cc1d499fb 100644
--- a/src/parser/antlr_line_buffered_input.cpp
+++ b/src/parser/antlr_line_buffered_input.cpp
@@ -29,7 +29,7 @@
 #include <string>
 #include <cassert>
 
-#include "util/output.h"
+#include "base/output.h"
 #include "parser/antlr_line_buffered_input.h"
 
 namespace CVC4 {
diff --git a/src/parser/antlr_tracing.h b/src/parser/antlr_tracing.h
index a94cd4f2f..1709e99a2 100644
--- a/src/parser/antlr_tracing.h
+++ b/src/parser/antlr_tracing.h
@@ -23,7 +23,8 @@
 
 #include <iostream>
 #include <string>
-#include "util/output.h"
+
+#include "base/output.h"
 
 /* The ANTLR lexer generator, as of v3.2, puts Java trace commands
  * into our beautiful generated C lexer!  How awful!  This is clearly
diff --git a/src/parser/cvc/Cvc.g b/src/parser/cvc/Cvc.g
index 0c356ca57..460b1ee03 100644
--- a/src/parser/cvc/Cvc.g
+++ b/src/parser/cvc/Cvc.g
@@ -476,10 +476,10 @@ Expr addNots(ExprManager* em, size_t n, Expr e) {
 #  define ANTLR3_INLINE_INPUT_8BIT
 #endif /* CVC4_COMPETITION_MODE && !CVC4_SMTCOMP_APPLICATION_TRACK */
 
-#include "parser/antlr_tracing.h"
-#include "util/integer.h"
 #include "parser/antlr_input.h"
+#include "parser/antlr_tracing.h"
 #include "parser/parser.h"
+#include "util/integer.h"
 
 }/* @lexer::includes */
 
@@ -487,10 +487,10 @@ Expr addNots(ExprManager* em, size_t n, Expr e) {
 
 #include <stdint.h>
 #include <cassert>
-#include "expr/command.h"
+#include "parser/antlr_tracing.h"
 #include "parser/parser.h"
+#include "smt_util/command.h"
 #include "util/subrange_bound.h"
-#include "parser/antlr_tracing.h"
 
 namespace CVC4 {
   class Expr;
@@ -541,16 +541,17 @@ namespace CVC4 {
 
 @parser::postinclude {
 
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "base/output.h"
 #include "expr/expr.h"
 #include "expr/kind.h"
 #include "expr/type.h"
 #include "parser/antlr_input.h"
 #include "parser/parser.h"
-#include "util/output.h"
 
-#include <vector>
-#include <string>
-#include <sstream>
 
 #define REPEAT_COMMAND(k, CommandCtor)                      \
   ({                                                        \
diff --git a/src/parser/input.cpp b/src/parser/input.cpp
index 09f71800b..82b6dd32f 100644
--- a/src/parser/input.cpp
+++ b/src/parser/input.cpp
@@ -18,10 +18,11 @@
 #include "parser/parser_exception.h"
 #include "parser/parser.h"
 
-#include "expr/command.h"
+#include "base/output.h"
+#include "smt_util/command.h"
 #include "expr/type.h"
 #include "parser/antlr_input.h"
-#include "util/output.h"
+
 
 using namespace std;
 using namespace CVC4;
diff --git a/src/parser/input.h b/src/parser/input.h
index 312bc92f1..dcb54d256 100644
--- a/src/parser/input.h
+++ b/src/parser/input.h
@@ -20,14 +20,14 @@
 #define __CVC4__PARSER__INPUT_H
 
 #include <iostream>
-#include <string>
 #include <stdio.h>
+#include <string>
 #include <vector>
 
+#include "options/language.h"
 #include "expr/expr.h"
 #include "expr/expr_manager.h"
 #include "parser/parser_exception.h"
-#include "util/language.h"
 
 namespace CVC4 {
 
diff --git a/src/parser/memory_mapped_input_buffer.cpp b/src/parser/memory_mapped_input_buffer.cpp
index 9dcab2085..7be1c9aba 100644
--- a/src/parser/memory_mapped_input_buffer.cpp
+++ b/src/parser/memory_mapped_input_buffer.cpp
@@ -28,8 +28,8 @@
 
 #endif /* _WIN32 */
 
+#include "base/exception.h"
 #include "parser/memory_mapped_input_buffer.h"
-#include "util/exception.h"
 
 namespace CVC4 {
 namespace parser {
diff --git a/src/parser/options b/src/parser/options
deleted file mode 100644
index 66e95889f..000000000
--- a/src/parser/options
+++ /dev/null
@@ -1,34 +0,0 @@
-#
-# Option specification file for CVC4
-# See src/options/base_options for a description of this file format
-#
-
-module PARSER "parser/options.h" Parser
-
-common-option strictParsing --strict-parsing bool
- be less tolerant of non-conforming inputs
-
-option memoryMap --mmap bool
- memory map file input
-
-option semanticChecks /--no-checking bool :default DO_SEMANTIC_CHECKS_BY_DEFAULT :link /--no-type-checking
- disable ALL semantic checks, including type checks
-
-option globalDeclarations global-declarations bool :default false
- force all declarations and definitions to be global
-
-# this is to support security in the online version, and in other similar contexts
-# (--no-include-file disables filesystem access in TPTP and SMT2 parsers)
-# the name --no-include-file is legacy: it also now limits any filesystem access
-# (read or write) for example by using --dump-to (or the equivalent set-option) or
-# set-option :regular-output-channel/:diagnostic-output-channel.  However, the main
-# driver is still permitted to read the input file given on the command-line if any.
-# creation/use of temp files are still permitted (but the paths aren't given by the
-# user).  Also note this is only safe for the version invoked through the main driver,
-# there are ways via the API to get the CVC4 library to open a file for reading or
-# writing and thus leak information from an existing file, or overwrite an existing
-# file with malicious content.
-undocumented-option filesystemAccess /--no-filesystem-access bool :default true
-undocumented-alias --no-include-file = --no-filesystem-access
-
-endmodule
diff --git a/src/parser/parser.cpp b/src/parser/parser.cpp
index d17d5d141..0e8a9e241 100644
--- a/src/parser/parser.cpp
+++ b/src/parser/parser.cpp
@@ -14,24 +14,26 @@
  ** Parser state implementation.
  **/
 
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <iterator>
+#include "parser/parser.h"
+
 #include <stdint.h>
+
 #include <cassert>
+#include <fstream>
+#include <iostream>
+#include <iterator>
+#include <sstream>
 
-#include "parser/input.h"
-#include "parser/parser.h"
-#include "parser/parser_exception.h"
-#include "expr/command.h"
+#include "base/output.h"
 #include "expr/expr.h"
 #include "expr/kind.h"
+#include "expr/resource_manager.h"
 #include "expr/type.h"
-#include "util/output.h"
-#include "util/resource_manager.h"
 #include "options/options.h"
-#include "smt/options.h"
+#include "options/smt_options.h"
+#include "parser/input.h"
+#include "parser/parser_exception.h"
+#include "smt_util/command.h"
 
 using namespace std;
 using namespace CVC4::kind;
diff --git a/src/parser/parser_builder.cpp b/src/parser/parser_builder.cpp
index a2faec704..08e0232aa 100644
--- a/src/parser/parser_builder.cpp
+++ b/src/parser/parser_builder.cpp
@@ -13,20 +13,19 @@
  **
  ** A builder for parsers.
  **/
+#include "parser/parser_builder.h"
 
 #include <string>
 
-#include "parser/parser_builder.h"
+#include "expr/expr_manager.h"
+#include "options/parser_options.h"
+#include "options/smt_options.h"
 #include "parser/input.h"
 #include "parser/parser.h"
 #include "smt1/smt1.h"
 #include "smt2/smt2.h"
 #include "tptp/tptp.h"
 
-#include "expr/expr_manager.h"
-#include "parser/options.h"
-#include "smt/options.h"
-
 namespace CVC4 {
 namespace parser {
 
@@ -168,7 +167,7 @@ ParserBuilder& ParserBuilder::withOptions(const Options& options) {
       .withParseOnly(options[options::parseOnly])
       .withIncludeFile(options[options::filesystemAccess]);
   if(options.wasSetByUser(options::forceLogic)) {
-    retval = retval.withForcedLogic(options[options::forceLogic].getLogicString());
+    retval = retval.withForcedLogic(options[options::forceLogic]->getLogicString());
   }
   return retval;
 }
diff --git a/src/parser/parser_builder.h b/src/parser/parser_builder.h
index 71810bf7c..fe652286b 100644
--- a/src/parser/parser_builder.h
+++ b/src/parser/parser_builder.h
@@ -21,10 +21,9 @@
 
 #include <string>
 
+#include "options/language.h"
 #include "parser/input.h"
 
-#include "util/language.h"
-
 namespace CVC4 {
 
 class ExprManager;
diff --git a/src/parser/parser_exception.h b/src/parser/parser_exception.h
index 3b211371c..de47767c9 100644
--- a/src/parser/parser_exception.h
+++ b/src/parser/parser_exception.h
@@ -23,7 +23,7 @@
 #include <string>
 #include <sstream>
 
-#include "util/exception.h"
+#include "base/exception.h"
 
 namespace CVC4 {
 namespace parser {
diff --git a/src/parser/smt1/Smt1.g b/src/parser/smt1/Smt1.g
index a885fe990..98825f1c3 100644
--- a/src/parser/smt1/Smt1.g
+++ b/src/parser/smt1/Smt1.g
@@ -63,7 +63,7 @@ options {
 
 #include <stdint.h>
 
-#include "expr/command.h"
+#include "smt_util/command.h"
 #include "parser/parser.h"
 #include "parser/antlr_tracing.h"
 
@@ -101,6 +101,9 @@ namespace CVC4 {
 
 @parser::postinclude {
 
+#include <vector>
+
+#include "base/output.h"
 #include "expr/expr.h"
 #include "expr/kind.h"
 #include "expr/type.h"
@@ -108,9 +111,7 @@ namespace CVC4 {
 #include "parser/parser.h"
 #include "parser/smt1/smt1.h"
 #include "util/integer.h"
-#include "util/output.h"
 #include "util/rational.h"
-#include <vector>
 
 using namespace CVC4;
 using namespace CVC4::parser;
@@ -573,7 +574,7 @@ annotation[CVC4::Command*& smt_command]
     annotatedFormulas[pats,pat] '}'
   | attribute[key]
     ( userValue[value]
-      { smt_command = new SetInfoCommand(key.c_str() + 1, value); }
+      { smt_command = new SetInfoCommand(key.c_str() + 1, SExpr(value)); }
     | { smt_command = new EmptyCommand(std::string("annotation: ") + key); }
     )
   ;
diff --git a/src/parser/smt1/smt1.cpp b/src/parser/smt1/smt1.cpp
index 8d827b17e..01bc8901e 100644
--- a/src/parser/smt1/smt1.cpp
+++ b/src/parser/smt1/smt1.cpp
@@ -18,7 +18,7 @@ namespace std {
 }
 
 #include "expr/type.h"
-#include "expr/command.h"
+#include "smt_util/command.h"
 #include "parser/parser.h"
 #include "parser/smt1/smt1.h"
 
diff --git a/src/parser/smt2/Smt2.g b/src/parser/smt2/Smt2.g
index d2409ba15..8ac1fa34c 100644
--- a/src/parser/smt2/Smt2.g
+++ b/src/parser/smt2/Smt2.g
@@ -75,9 +75,9 @@ using namespace CVC4::parser;
 }/* @lexer::postinclude */
 
 @parser::includes {
-#include "expr/command.h"
 #include "parser/parser.h"
 #include "parser/antlr_tracing.h"
+#include "smt_util/command.h"
 
 namespace CVC4 {
   class Expr;
@@ -102,21 +102,22 @@ namespace CVC4 {
 
 @parser::postinclude {
 
+#include <set>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "base/output.h"
 #include "expr/expr.h"
 #include "expr/kind.h"
 #include "expr/type.h"
 #include "parser/antlr_input.h"
 #include "parser/parser.h"
 #include "parser/smt2/smt2.h"
+#include "util/floatingpoint.h"
+#include "util/hash.h"
 #include "util/integer.h"
-#include "util/output.h"
 #include "util/rational.h"
-#include "util/hash.h"
-#include "util/floatingpoint.h"
-#include <vector>
-#include <set>
-#include <string>
-#include <sstream>
 // \todo Review the need for this header
 #include "math.h"
 
@@ -995,10 +996,7 @@ smt25Command[CVC4::Command*& cmd]
     /* echo */
   | ECHO_TOK
     ( simpleSymbolicExpr[sexpr]
-      { std::stringstream ss;
-        ss << sexpr;
-        cmd = new EchoCommand(ss.str());
-      }
+      { cmd = new EchoCommand(sexpr.toString()); }
     | { cmd = new EchoCommand(); }
     )
 
@@ -1446,12 +1444,12 @@ simpleSymbolicExprNoKeyword[CVC4::SExpr& sexpr]
   | HEX_LITERAL
     { assert( AntlrInput::tokenText($HEX_LITERAL).find("#x") == 0 );
       std::string hexString = AntlrInput::tokenTextSubstr($HEX_LITERAL, 2);
-      sexpr = Integer(hexString, 16);
+      sexpr = SExpr(Integer(hexString, 16));
     }
   | BINARY_LITERAL
     { assert( AntlrInput::tokenText($BINARY_LITERAL).find("#b") == 0 );
       std::string binString = AntlrInput::tokenTextSubstr($BINARY_LITERAL, 2);
-      sexpr = Integer(binString, 2);
+      sexpr = SExpr(Integer(binString, 2));
     }
   | str[s,false]
     { sexpr = SExpr(s); }
diff --git a/src/parser/smt2/smt2.cpp b/src/parser/smt2/smt2.cpp
index d3af9143a..355b58067 100644
--- a/src/parser/smt2/smt2.cpp
+++ b/src/parser/smt2/smt2.cpp
@@ -13,14 +13,14 @@
  **
  ** Definitions of SMT2 constants.
  **/
+#include "parser/smt2/smt2.h"
+
 
 #include "expr/type.h"
-#include "expr/command.h"
+#include "parser/antlr_input.h"
 #include "parser/parser.h"
 #include "parser/smt1/smt1.h"
-#include "parser/smt2/smt2.h"
-#include "parser/antlr_input.h"
-
+#include "smt_util/command.h"
 #include "util/bitvector.h"
 
 // ANTLR defines these, which is really bad!
diff --git a/src/parser/tptp/Tptp.g b/src/parser/tptp/Tptp.g
index 62dcc70f5..a2bad4988 100644
--- a/src/parser/tptp/Tptp.g
+++ b/src/parser/tptp/Tptp.g
@@ -83,7 +83,7 @@ using namespace CVC4::parser;
 }/* @lexer::postinclude */
 
 @parser::includes {
-#include "expr/command.h"
+#include "smt_util/command.h"
 #include "parser/parser.h"
 #include "parser/tptp/tptp.h"
 #include "parser/antlr_tracing.h"
@@ -92,6 +92,11 @@ using namespace CVC4::parser;
 
 @parser::postinclude {
 
+#include <algorithm>
+#include <iterator>
+#include <vector>
+
+#include "base/output.h"
 #include "expr/expr.h"
 #include "expr/kind.h"
 #include "expr/type.h"
@@ -99,11 +104,7 @@ using namespace CVC4::parser;
 #include "parser/parser.h"
 #include "parser/tptp/tptp.h"
 #include "util/integer.h"
-#include "util/output.h"
 #include "util/rational.h"
-#include <vector>
-#include <iterator>
-#include <algorithm>
 
 using namespace CVC4;
 using namespace CVC4::parser;
@@ -203,7 +204,7 @@ parseCommand returns [CVC4::Command* cmd = NULL]
         filename = filename.substr(0, filename.length() - 2);
       }
       CommandSequence* seq = new CommandSequence();
-      seq->addCommand(new SetInfoCommand("name", filename));
+      seq->addCommand(new SetInfoCommand("name", SExpr(filename)));
       if(PARSER_STATE->hasConjecture()) {
         seq->addCommand(new QueryCommand(MK_CONST(bool(false))));
       } else {
diff --git a/src/parser/tptp/tptp.h b/src/parser/tptp/tptp.h
index 2cd8f4339..4fdbc236d 100644
--- a/src/parser/tptp/tptp.h
+++ b/src/parser/tptp/tptp.h
@@ -19,13 +19,14 @@
 #ifndef __CVC4__PARSER__TPTP_H
 #define __CVC4__PARSER__TPTP_H
 
-#include "parser/parser.h"
-#include "expr/command.h"
-#include "util/hash.h"
-#include <ext/hash_set>
 #include <cassert>
-#include "parser/options.h"
+#include <ext/hash_set>
+
+#include "options/parser_options.h"
 #include "parser/antlr_input.h"
+#include "parser/parser.h"
+#include "smt_util/command.h"
+#include "util/hash.h"
 
 namespace CVC4 {