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.

7 files changed, 24 insertions, 54 deletions

diff --git a/src/theory/arrays/array_info.h b/src/theory/arrays/array_info.h
index f3c6385e5..d9f77d50f 100644
--- a/src/theory/arrays/array_info.h
+++ b/src/theory/arrays/array_info.h
@@ -18,17 +18,18 @@
 #ifndef __CVC4__THEORY__ARRAYS__ARRAY_INFO_H
 #define __CVC4__THEORY__ARRAYS__ARRAY_INFO_H
 
-#include "util/backtrackable.h"
-#include "context/cdlist.h"
-#include "context/cdhashmap.h"
-#include "expr/node.h"
-#include "util/statistics_registry.h"
-#include "util/ntuple.h"
 #include <ext/hash_set>
 #include <ext/hash_map>
 #include <iostream>
 #include <map>
 
+#include "context/backtrackable.h"
+#include "context/cdlist.h"
+#include "context/cdhashmap.h"
+#include "expr/node.h"
+#include "expr/statistics_registry.h"
+#include "util/ntuple.h"
+
 namespace CVC4 {
 namespace theory {
 namespace arrays {
diff --git a/src/theory/arrays/kinds b/src/theory/arrays/kinds
index c18492a58..d5f313ca1 100644
--- a/src/theory/arrays/kinds
+++ b/src/theory/arrays/kinds
@@ -35,7 +35,7 @@ operator STORE 3 "array store; first parameter is an array term, second is the s
 constant STORE_ALL \
     ::CVC4::ArrayStoreAll \
     ::CVC4::ArrayStoreAllHashFunction \
-    "util/array_store_all.h" \
+    "expr/array_store_all.h" \
     "array store-all; payload is an instance of the CVC4::ArrayStoreAll class (this is not supported by arrays decision procedure yet, but it is used for returned array models)"
 
 # used internally by array theory
diff --git a/src/theory/arrays/options b/src/theory/arrays/options
deleted file mode 100644
index 8ed80c1f1..000000000
--- a/src/theory/arrays/options
+++ /dev/null
@@ -1,32 +0,0 @@
-#
-# Option specification file for CVC4
-# See src/options/base_options for a description of this file format
-#
-
-module ARRAYS "theory/arrays/options.h" Arrays theory
-
-option arraysOptimizeLinear --arrays-optimize-linear bool :default true :read-write
- turn on optimization for linear array terms (see de Moura FMCAD 09 arrays paper)
-
-option arraysLazyRIntro1 --arrays-lazy-rintro1 bool :default true :read-write
- turn on optimization to only perform RIntro1 rule lazily (see Jovanovic/Barrett 2012: Being Careful with Theory Combination)
-
-option arraysModelBased --arrays-model-based bool :default false :read-write
- turn on model-based array solver
-
-option arraysEagerIndexSplitting --arrays-eager-index bool :default true :read-write
- turn on eager index splitting for generated array lemmas
-
-option arraysEagerLemmas --arrays-eager-lemmas bool :default false :read-write
- turn on eager lemma generation for arrays
-
-option arraysConfig --arrays-config int :default 0 :read-write
- set different array option configurations - for developers only
-
-option arraysReduceSharing --arrays-reduce-sharing bool :default false :read-write
- use model information to reduce size of care graph for arrays
-
-option arraysPropagate --arrays-prop int :default 2 :read-write
- propagation effort for arrays: 0 is none, 1 is some, 2 is full
-
-endmodule
diff --git a/src/theory/arrays/static_fact_manager.cpp b/src/theory/arrays/static_fact_manager.cpp
index 1743e3b30..0d04ce097 100644
--- a/src/theory/arrays/static_fact_manager.cpp
+++ b/src/theory/arrays/static_fact_manager.cpp
@@ -18,9 +18,9 @@
 
 #include <iostream>
 
-#include "theory/arrays/static_fact_manager.h"
-#include "util/cvc4_assert.h"
+#include "base/cvc4_assert.h"
 #include "expr/node.h"
+#include "theory/arrays/static_fact_manager.h"
 
 using namespace std;
 
diff --git a/src/theory/arrays/theory_arrays.cpp b/src/theory/arrays/theory_arrays.cpp
index d872ab42c..5af7f02db 100644
--- a/src/theory/arrays/theory_arrays.cpp
+++ b/src/theory/arrays/theory_arrays.cpp
@@ -14,17 +14,18 @@
  ** Implementation of the theory of arrays.
  **/
 
-
 #include "theory/arrays/theory_arrays.h"
-#include "theory/valuation.h"
-#include "expr/kind.h"
+
 #include <map>
+
+#include "expr/kind.h"
+#include "options/arrays_options.h"
+#include "options/smt_options.h"
+#include "smt/logic_exception.h"
+#include "smt_util/command.h"
 #include "theory/rewriter.h"
-#include "expr/command.h"
 #include "theory/theory_model.h"
-#include "theory/arrays/options.h"
-#include "smt/options.h"
-#include "smt/logic_exception.h"
+#include "theory/valuation.h"
 
 
 using namespace std;
diff --git a/src/theory/arrays/theory_arrays.h b/src/theory/arrays/theory_arrays.h
index b2e039912..717c654d2 100644
--- a/src/theory/arrays/theory_arrays.h
+++ b/src/theory/arrays/theory_arrays.h
@@ -19,13 +19,13 @@
 #ifndef __CVC4__THEORY__ARRAYS__THEORY_ARRAYS_H
 #define __CVC4__THEORY__ARRAYS__THEORY_ARRAYS_H
 
-#include "theory/theory.h"
-#include "theory/arrays/array_info.h"
-#include "util/statistics_registry.h"
-#include "theory/uf/equality_engine.h"
 #include "context/cdhashmap.h"
 #include "context/cdhashset.h"
 #include "context/cdqueue.h"
+#include "expr/statistics_registry.h"
+#include "theory/arrays/array_info.h"
+#include "theory/theory.h"
+#include "theory/uf/equality_engine.h"
 
 namespace CVC4 {
 namespace theory {
diff --git a/src/theory/arrays/union_find.cpp b/src/theory/arrays/union_find.cpp
index 9e6978c92..3f71b350e 100644
--- a/src/theory/arrays/union_find.cpp
+++ b/src/theory/arrays/union_find.cpp
@@ -18,9 +18,9 @@
 
 #include <iostream>
 
-#include "theory/arrays/union_find.h"
-#include "util/cvc4_assert.h"
+#include "base/cvc4_assert.h"
 #include "expr/node.h"
+#include "theory/arrays/union_find.h"
 
 using namespace std;