Store messagepack values in database instead of JSON

[hendrikvanantwerpen]

Database access (particularly writing, it seems) is fairly slow. Currently the database is populated with JSON objects, which are pretty verbose. This PR changes that to use messagepack values, which are binary and optimized for small size, if I understand things correctly.

A rough comparison of index times shows a speedup of almost 2x for some files and a database size reduction of almost 3x. The time reduction is more pronounced for smaller files, probably because more of the index work is writing the data, compared to computing it.

[github-actions]

Performance Summary

Comparing base 46d016b with head 024a5e9 on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript index -D base.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
2.375^                                   #                                    
     |                                   #                                    
     |                                   #                                    
     |                                   #                                    
     |                                   #                                    
     |           @                       #                                    
     |           @   :                  :#           :     :                  
     |           @   :                  :#           :     :                  
     |          :@   :              :   :#           :     :                  
     |     :   @:@   :   :  :      ::   :#: @        :    ::    :    :: :     
     |     :   @:@:  :  :: ::@  :  :: : :#: @        ::   ::    :    ::::     
     |    @::  @:@: :: ::: ::@  :  :: :::#: @      ::::  :::   @:  :@:::: @:  
   0 +----------------------------------------------------------------------->Gi
     0                                                                   229.4

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
2.375^                                     #                                  
     |                                     #                                  
     |                                     #                                  
     |                                     #                                  
     |                                     #                                  
     |            @                        #                                  
     |            @                       :#                                  
     |            @       :               :#                                  
     |           :@       :          ::   :#                                  
     |      :    :@  ::   :          ::   :#         @     @            ::    
     |      :   ::@: :  :::  @:     @:: : :#  :  :   @     @        :::::::   
     |    @@:   ::@: :  : :  @::    @:: :::# :: :: : @:    @   :: : :::::::   
   0 +----------------------------------------------------------------------->Gi
     0                                                                   199.0

[github-actions]

Performance Summary

Comparing base 46d016b with head 458db76 on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript index -D base.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
1.308^                                              #                         
     |      @         :                             #     :                   
     |      @         :                             #     :                   
     |      @         :                             #     :                   
     |      @         :                             #     :                   
     |      @         :            :               :#     :             :     
     |      @         :            ::  :           :#     :           : :     
     |      @    :    :     :      ::  :           :#     :          @:::     
     |      @    :    :  :  :      ::  :           :#     :          @:::     
     |      @    :    :  :: :    : :: ::  :   :  : :#     :          @::::    
     |    @@@    : ::::  :: :    : :: ::  :   :  :::#:    :       :  @::::    
     |    @ @    ::: :: ::: :  ::: :: :: ::   :  :::#: :@@:  :: : :::@:::: :@ 
   0 +----------------------------------------------------------------------->Gi
     0                                                                   207.8

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
2.374^                                    ##                                  
     |                                    #                                   
     |                                    #                                   
     |                                    #                                   
     |                                    #                                   
     |                                    #                                   
     |       @    :                       #                                   
     |       @    :                       #                                   
     |       @    :                  :   @#                                   
     |       @   ::   :   :          :   @#          :          :    :  :     
     |       @   :: @ :  ::  :    : ::   @#  :       :          :    : ::     
     |     @:@   :@@@::  ::  :@  :: :: ::@# ::     ::::  ::     : ::@:::: @   
   0 +----------------------------------------------------------------------->Gi
     0                                                                   190.6

[github-actions]

Performance Summary

Comparing base e11f004 with head acb0fab on microsoft/TypeScript@v4.9.5. For details see workflow artifacts. Note that performance is tested on the last commits with changes in stack-graphs, not on every commit.

Before

--------------------------------------------------------------------------------
Command:            base/target/release/tree-sitter-stack-graphs-typescript index -D base.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 base-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
1.545^           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |           #                                                            
     |           #        ::                                                  
     |          @#        :          :                                  ::    
     |          @#        :          :     :                          : :     
     |          @#     ::@:          :     :                          :::     
     |          @#     : @: :::      : :::::          ::              :::     
     |     @@   @#::   : @: ::    :: : : : : ::      ::            ::::::     
     |    :@    @#: :: : @: ::   :: :: : : : :  : :  ::    :  :::: : :::: : : 
   0 +----------------------------------------------------------------------->Gi
     0                                                                   230.3

After

--------------------------------------------------------------------------------
Command:            head/target/release/tree-sitter-stack-graphs-typescript index -D head.sqlite --max-file-time=30 --hide-error-details -- test/src/compiler
Massif arguments:   --massif-out-file=perf.out
ms_print arguments: --x=72 --y=12 head-perf-results/perf.out
--------------------------------------------------------------------------------


    GB
1.055^            #                                                           
     |            #                                                           
     |            #                                                           
     |           @#                  :                                        
     |           @#                  :                                  :     
     |           @#                  :                                : :     
     |           @#       :  :      ::                               @: :     
     |           @#       :  :      ::    :           :              @: :     
     |       @   @#       :  :      :: : ::        @ ::              @: :     
     |      :@   @# :    ::  :      :: ::::        @ ::    :         @:::     
     |     ::@   @#::  @ ::  :  :   :: :::::   ::: @:::  :::     : ::@::: :   
     |     ::@   @#::::@ :::::  :::::: ::::::  ::::@:::: :@: : :@: ::@:::::@: 
   0 +----------------------------------------------------------------------->Gi
     0                                                                   179.8