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Merge misc. MABE2 support branches into MABE_devel #466

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merged 146 commits into from
Jul 19, 2022
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e0a54c2
adding systematics documentation
abbywlsn Jun 4, 2020
1c14505
miniphylotrees makes very simple trees, still needs to incorporate sy…
abbywlsn Jun 16, 2020
2824062
miniphylotrees prints data to csv file now
abbywlsn Jun 18, 2020
d0b9be3
added systematics manager tools, still broken though
abbywlsn Jun 18, 2020
01e3808
new changes to miniphylotrees
abbywlsn Jun 22, 2020
5b47ce7
miniphylotrees works and generates data, concerned about compiler dif…
abbywlsn Jun 25, 2020
10ff45e
new csv with percentile data and miniphylotrees is correctly outputti…
abbywlsn Jun 26, 2020
cf2bbe7
original file with no systematics implementation for example purposes
abbywlsn Jun 26, 2020
7e22970
new miniphylo changes
abbywlsn Jul 1, 2020
c9ad62a
changes made to systematics with percentile functions
abbywlsn Jul 1, 2020
1836ef4
new improvements and updated systematics functions
abbywlsn Jul 23, 2020
14dcc46
cleaned up miniphylotrees
abbywlsn Jul 28, 2020
28294af
updated systematics function, still needs work
abbywlsn Jul 30, 2020
72c442e
cleaning up directories
abbywlsn Jul 31, 2020
516735b
more directory cleaning
abbywlsn Jul 31, 2020
f1c61a3
cleaned up systematics.h
abbywlsn Jul 31, 2020
d0aca02
cleaning up some stuff in GenTrees
abbywlsn Jul 31, 2020
5cf9f74
Fix data file tests
emilydolson Mar 7, 2021
f8824ef
Fix bug when mrca is alive and dies
emilydolson Mar 7, 2021
147c7bd
Merge fixes
emilydolson Mar 7, 2021
75f080c
merge in reorg
emilydolson Mar 7, 2021
3cf3c16
Remove extra files
emilydolson Mar 7, 2021
d0b5037
Merge branch 'fix-systematics' into systematics-normalization
emilydolson Mar 7, 2021
36d675d
Add mrca test
emilydolson Mar 8, 2021
cc286a6
Add mrca test
emilydolson Mar 8, 2021
be947f0
More systematics cleanup, tests, docs
emilydolson Mar 9, 2021
606affa
Add more tests, docs, simplify interface
emilydolson Mar 10, 2021
88b81a7
More docs and tests
emilydolson Mar 10, 2021
5ec6a95
organize systematics.hpp
emilydolson Mar 10, 2021
0e9d158
Clean up documentation
emilydolson Mar 10, 2021
f466fc9
Merge in bits-overhaul
emilydolson Jun 18, 2021
b5d4465
Adjust AnyFunction to obey rule of five
FergusonAJ Sep 28, 2021
9cbf52d
Clean up AnyFunctions fix
FergusonAJ Sep 28, 2021
f9c65ef
Merge in MABE compatability changes
emilydolson Oct 6, 2021
b9cce08
Fix merge conflict
emilydolson Oct 6, 2021
97dccf6
Add version of AddOrg that takes parent position
emilydolson Oct 6, 2021
e16232d
Merge in MABE_devel
emilydolson Oct 6, 2021
849876d
Fix arg names
emilydolson Oct 6, 2021
82bd90d
Add SwapPositions method to systematics
emilydolson Oct 6, 2021
42554c7
Fix parent/child confusion error
emilydolson Oct 6, 2021
8f530e0
Systematics can handle arbitrary number of populations
emilydolson Oct 6, 2021
c6ce913
Use constexpr if to get rid of gross code
emilydolson Oct 6, 2021
9d9148b
Fix template errors
emilydolson Oct 6, 2021
c703f69
Merge branch 'any_function' of github.com:FergusonAJ/Empirical into HEAD
FergusonAJ Oct 8, 2021
f01ddd8
Add VirtualCPU hardware
FergusonAJ Oct 8, 2021
730ffc1
Fix member initialization order
FergusonAJ Oct 8, 2021
8a661a6
Merge in master
emilydolson Oct 11, 2021
5ba6be8
Merge branch 'master' into mabe-systematics
emilydolson Oct 11, 2021
df71c38
Add better tests for systematics DataNodes
emilydolson Oct 11, 2021
31c589c
Fix delete bug in AnyFunction
FergusonAJ Oct 18, 2021
832f90a
Temp. add ids to instruction library
FergusonAJ Oct 18, 2021
dafb92e
Use inst. ids and add QoL to VirtualCPU
FergusonAJ Oct 18, 2021
982b271
Switch VirtualCPU to handle nops on birth/mut.
FergusonAJ Oct 19, 2021
334ee44
Fix bug of VirtualCPU instructions with wrong id
FergusonAJ Oct 19, 2021
c732578
Merge in changes to mabe devel
emilydolson Oct 21, 2021
7c2f355
Minor fixes to VirtualCPU instruction ids
FergusonAJ Nov 1, 2021
1a0d6b6
Add linear algebra classes to support path follow
FergusonAJ Nov 1, 2021
74d29cd
Dynamically create VCPU registers to match nops
FergusonAJ Nov 7, 2021
1141f0c
Add expanded nop support, labels, + new searches
FergusonAJ Nov 9, 2021
374a2f4
Add more VirtualCPU helper methods
FergusonAJ Nov 9, 2021
a9efc7d
Quote escape NONE ancestors list
Nov 12, 2021
0d42691
Patch index out of range in VirtualCPU::FindLabel
FergusonAJ Nov 16, 2021
db09a0a
Add missing include in VirtualCPU class
FergusonAJ Nov 22, 2021
f8b0f16
Start refactor of VirtualCPU
FergusonAJ Dec 7, 2021
947e001
Remove old AvidaGP error system from VirtualCPU
FergusonAJ Dec 9, 2021
0c847ca
Refactor and optimize CurateNops in VirtualCPU
FergusonAJ Dec 9, 2021
58457fc
Add checklist of VirtualCPU tests to write
FergusonAJ Dec 9, 2021
6d1baab
Clean CountNops and rename string funcs in VCPU
FergusonAJ Dec 14, 2021
d5f5bab
Refactor nop and label methods in VCPU
FergusonAJ Dec 14, 2021
12a688f
Add docstrings and other cleanups to VirtualCPU
FergusonAJ Dec 14, 2021
d9b5598
Update comments in VirtualCPU
FergusonAJ Dec 14, 2021
68215ab
Switch VirtualCPU to store NOP IDs in a set
FergusonAJ Dec 14, 2021
b9bc6d9
Take pass through first chunk of VirtualCPU tests
FergusonAJ Dec 14, 2021
d251253
Finish first pass of VirtualCPU tests
FergusonAJ Dec 14, 2021
aab8448
Rename method in VirtualCPU
FergusonAJ Jan 10, 2022
9df9742
Change comp. in unordered index map from < to <=
FergusonAJ Jan 10, 2022
9aea202
Merge remote-tracking branch 'charles/MABE_devel' into virtual_cpu_merge
FergusonAJ Jan 20, 2022
75b1605
Merge
emilydolson Jan 20, 2022
0c12188
Temp. fix the AvidaGP vs VCPU instruction issue
FergusonAJ Jan 21, 2022
9866f33
Adding Contributor count shield to readme
anyaevostinar Jan 24, 2022
9f6d1d7
Add minor tweaks to function TypeIDs
FergusonAJ Jan 24, 2022
1fe7f90
Merge pull request #464 from devosoft/anyaevostinar-readme-contributor
mmore500 Jan 25, 2022
a4b58bd
Track instructions executed in VCPU
FergusonAJ Feb 15, 2022
c632767
Add GetSharedAncestor
emilydolson Feb 21, 2022
e5efa81
Fix minor typo
FergusonAJ Mar 24, 2022
86ed514
Remove old linear algebra classes
FergusonAJ Mar 24, 2022
719cb68
Fix compiler warnings
FergusonAJ Mar 25, 2022
c0f4e68
Update VirtualCPU instructions to match MABE
FergusonAJ Mar 25, 2022
56e5c5c
Add stack accessor to VirtualCPU
FergusonAJ May 10, 2022
5ccc125
Clean VirtualCPUOrg_InstLib
FergusonAJ May 10, 2022
bf6411c
Add rough CombinedBinomialDistribution + example
FergusonAJ May 11, 2022
5b4bf98
Add example from last commit to Makefile
FergusonAJ May 11, 2022
a2164b0
Tweak CombinedBinomial to match other dists.
FergusonAJ May 11, 2022
c51ef5a
Add VCPU methods needed in MABE
FergusonAJ May 11, 2022
4198248
Patch bug in InstLib::GetID
FergusonAJ May 11, 2022
4d2e16e
Merge pull request #2 from devosoft/mabe-systematics
FergusonAJ May 11, 2022
7abd59e
Merge remote-tracking branch 'charles/MABE_devel' into virtual_cpu_merge
FergusonAJ May 18, 2022
eef25f1
Patch power of 2 bug in CombinedBinomial
FergusonAJ May 20, 2022
2ae781a
Update data/Datum test
FergusonAJ May 20, 2022
e619a91
Update EventDrivenGP to work with InstLib change
FergusonAJ May 20, 2022
46084f7
Update VirtualCPU tests
FergusonAJ May 20, 2022
e02ad94
Add missing include to Emscripten error trigger
FergusonAJ May 22, 2022
a633423
Reset distributions after Setup in Comb. Binomial
FergusonAJ May 24, 2022
594799f
Merge branch 'MABE_devel' of github.com:Mercere99/Empirical into virt…
FergusonAJ May 24, 2022
d78d135
Fix assert comparison in UnorderedIndexMap
FergusonAJ May 24, 2022
2eb8b55
Fix bound and add zero case to rand exp and geom
FergusonAJ May 24, 2022
1872701
Add docstrings to CombinedBinomialDistribution
FergusonAJ May 24, 2022
1d7957a
Bump to 20.04 and g++11
emilydolson May 24, 2022
37518ee
Fix indentation
emilydolson May 24, 2022
bd93b8d
Update DFA.hpp
emilydolson May 24, 2022
e497d63
Include limits
emilydolson May 24, 2022
c122b28
Try bumping to 22.04
emilydolson May 25, 2022
439f49a
Update other steps to g++ 11
emilydolson May 25, 2022
d975ed1
Update Catch version
emilydolson May 25, 2022
069425d
Update clang
emilydolson May 25, 2022
3b54f10
Restore DFA.hpp
emilydolson May 25, 2022
476ac80
Restore DFA.hpp
emilydolson May 25, 2022
88122d9
Update DFA.hpp
emilydolson May 25, 2022
de7aa3d
Update force-cover
emilydolson May 25, 2022
76d4682
xvfb needs Ubuntu 20.04?
emilydolson May 25, 2022
279a03d
Remove trailing whitespace
emilydolson May 25, 2022
efd4878
Update force cover for llvm 14
emilydolson May 25, 2022
bcdf742
Merge remote-tracking branch 'upstream/update-g++' into virtual_cpu_m…
FergusonAJ May 25, 2022
931c4a2
Update submodules per Emily's update-g++ branch
FergusonAJ May 25, 2022
300203c
Switch to Catch v2.13.9
FergusonAJ May 25, 2022
a73f0da
Update force-cover to newest version
FergusonAJ May 25, 2022
806a047
Conduct first pass on alphabetizing includes
FergusonAJ May 25, 2022
545f124
Match boilerplate to appease tidy checks
FergusonAJ May 25, 2022
e94617a
Fix newlines at end of files
FergusonAJ May 25, 2022
e2431e9
Add missing license notices
FergusonAJ May 25, 2022
1b3b79e
Remove tabs and fix whitespace
FergusonAJ May 25, 2022
5f49154
Remove trailing whitespace
FergusonAJ May 25, 2022
ec9cd09
Clean up comments in VirtualCPU.Load
FergusonAJ May 25, 2022
069d895
Remove trailing whitespace from VirtualCPU
FergusonAJ May 25, 2022
b3f6744
Ensure nops work in VCPU regardless of inst order
FergusonAJ May 25, 2022
d1619ac
Add constant for VCPU maximum nop insts. in lib.
FergusonAJ May 25, 2022
fd23917
Fix missing flag reset in VirtualCPU
FergusonAJ Jun 20, 2022
a943b5b
Rework reset methods in VirtualCPU
FergusonAJ Jun 28, 2022
7e1a308
Remove trailing whitespace
FergusonAJ Jun 28, 2022
d227523
Fix spacing in VirtualCPU
FergusonAJ Jun 28, 2022
b0279e4
Remove virtual from VirtualCPU::ResetHardware
FergusonAJ Jun 29, 2022
c255c9d
Make more VirtualCPU methods const
FergusonAJ Jun 30, 2022
6cdc08d
Add GetNumInstsCopied method to VirtualCPU
FergusonAJ Jun 30, 2022
78306cf
Switch VCPU inst methods from using index to ID
FergusonAJ Jul 4, 2022
399535c
Track insts. copied and executed in VirtualCPU
FergusonAJ Jul 6, 2022
b4b2024
Check if file exists while loading VCPU genome
FergusonAJ Jul 7, 2022
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Switch VCPU inst methods from using index to ID
FergusonAJ committed Jul 4, 2022
commit 78306cfce58ac111b8e5868de93982e8e95bd4e3
10 changes: 6 additions & 4 deletions include/emp/hardware/VirtualCPU.hpp
Original file line number Diff line number Diff line change
@@ -230,17 +230,19 @@ namespace emp{
}
/// Return the first instruction in the instruction library
inst_t GetDefaultInst() const{
return inst_t(0, GetInstLib()->GetID(0));
return inst_t(GetInstLib()->GetIndex(0), 0);
}
/// Add one or more default instructions to the end of the genome
void PushDefaultInst(size_t count=1) {
PushInst( inst_t(0, GetInstLib()->GetID(0)), count );
PushInst( inst_t(GetInstLib()->GetIndex(0), 0), count );
nops_need_curated = true;
}
/// Return a random instruction from the instruction library
inst_t GetRandomInst(Random & rand) {
size_t idx = rand.GetUInt(GetInstLib()->GetSize());
size_t id = GetInstLib()->GetID(idx);
size_t id = rand.GetUInt(GetInstLib()->GetSize());
size_t idx = GetInstLib()->GetIndex(id);
//size_t idx = rand.GetUInt(GetInstLib()->GetSize());
//size_t id = GetInstLib()->GetID(idx);
return inst_t(idx, id);
}
/// Overwrite the instruction at the given genome index with passed instruction