Merge misc. MABE2 support branches into MABE_devel

.github/workflows/CI.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   tidy:
     name: Enforce Tidyness
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with:
@@ -31,7 +31,7 @@ jobs:
       - run: ./ci/test_tidy.sh
   test:
     name: Tests
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
@@ -50,11 +50,14 @@ jobs:
       - uses: actions/checkout@v2
         with:
           submodules: 'recursive'
+      - name: Set up GCC
+        uses: egor-tensin/setup-gcc@v1
+        with:
+          version: 11
       - run: sudo apt-get update -qq
       - run: sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
       - run: sudo apt-get update -qq
-      - run: sudo apt-get install -qq g++-8 cmake build-essential python3-pip python3-virtualenv nodejs tar gzip libpthread-stubs0-dev libc6-dbg gdb
-      - run: sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 90
+      - run: sudo apt-get install -qq cmake build-essential python3-pip python3-virtualenv nodejs tar gzip libpthread-stubs0-dev libc6-dbg gdb
       - run: git fetch origin master:refs/remotes/origin/master
       - run: make install-test-dependencies
       - run: ${CXX} --version
@@ -63,46 +66,39 @@ jobs:
           make ${TEST_SET} CXX=${CXX}
   test-web:
     name: Web Tests
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v2
         with:
           submodules: 'recursive'
+      - name: Set up GCC
+        uses: egor-tensin/setup-gcc@v1
+        with:
+          version: 11
       - run: sudo apt-get update -qq
-      - run: sudo apt-get install -qq g++-8 cmake build-essential python3-pip python3-virtualenv nodejs tar gzip libpthread-stubs0-dev libc6-dbg gdb
-      - run: sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 90
+      - run: sudo apt-get install -qq cmake build-essential python3-pip python3-virtualenv nodejs tar gzip libpthread-stubs0-dev libc6-dbg gdb
       - run: make install-test-dependencies
       - name: Run headless test
         uses: GabrielBB/xvfb-action@v1
         with:
           run: make test-web
   test-coverage:
     name: Measure Test Coverage
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with:
           submodules: 'recursive'
       - run: sudo apt-get update -qq
-      - run: sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
-      - run: wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
-      - run: sudo apt-add-repository "deb https://apt.llvm.org/xenial/ llvm-toolchain-xenial-7 main"
-      - run: sudo apt-get update -qq
-      - run: sudo apt-get install -qq g++-8
-      - run: sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 90
-      - run: sudo apt-get install cmake build-essential python3-virtualenv python3-pip nodejs tar gzip libclang-7-dev llvm llvm-dev libllvm7 llvm-7 llvm-7-dev clang-7 libstdc++-7-dev # might have to happen after we update g++
-      - run: sudo update-alternatives --install /usr/bin/clang++ clang++ /usr/bin/clang++-7 90
-      - run: sudo update-alternatives --install /usr/bin/llvm-config llvm-config /usr/bin/llvm-config-7 90
-      - run: sudo update-alternatives --install /usr/bin/llvm-profdata llvm-profdata /usr/bin/llvm-profdata-7 90
-      - run: sudo update-alternatives --install /usr/bin/llvm-cov llvm-cov /usr/bin/llvm-cov-7 90
+      - run: sudo apt-get install cmake build-essential python3-virtualenv python3-pip nodejs tar gzip clang llvm-dev libclang-dev
       - run: git fetch origin master:refs/remotes/origin/master
       - run: make install-test-dependencies
-      - run: export CXX=clang++-7 && make install-coverage-dependencies
-      - run: export CXX=clang++-7 && make coverage
+      - run: export CXX=clang++ && make install-coverage-dependencies
+      - run: export CXX=clang++ && make coverage
       - run: curl -s https://codecov.io/bash | bash
   test-documentation:
     name: Test Documentation Build
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with:
@@ -119,7 +115,7 @@ jobs:
           dst: stats/doc-coverage.json
   deploy-dockerhub:
     name: Deploy to DockerHub
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     if: github.ref == 'refs/heads/master'
     needs:
       - tidy

README.md

@@ -7,6 +7,8 @@ namespace, so it is simple to incorporate into existing projects.
 [![CI](https://github.com/devosoft/Empirical/workflows/CI/badge.svg)](https://github.com/devosoft/Empirical/actions?query=workflow%3ACI+branch%3Amaster) [![Documentation Status](https://readthedocs.org/projects/empirical/badge/?version=latest)](https://empirical.readthedocs.io/en/latest/?badge=latest) [![DOI](https://zenodo.org/badge/24824563.svg)](https://zenodo.org/badge/latestdoi/24824563) [![codecov](https://codecov.io/gh/devosoft/Empirical/branch/master/graph/badge.svg)](https://codecov.io/gh/devosoft/Empirical)
 [![DockerHub](https://img.shields.io/badge/DockerHub-Hosted-blue)](https://hub.docker.com/r/devosoft/empirical)
 ![Documentation Coverage](https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2Fdevosoft%2FEmpirical%2Fgh-storage%2Fstats%2Fdoc-coverage.json)
+[![GitHub contributors](https://img.shields.io/github/contributors/devosoft/Empirical.svg?style=flat-square)](https://github.com/devosoft/Empirical/graphs/contributors)
+
 
 See our [Built With Empirical Gallery](https://empirical.readthedocs.io/en/latest/BuiltWithEmpiricalGallery) for examples of web tools built with Empirical.
 

doc/blogs/Binomial.md

@@ -40,4 +40,4 @@ before introducing the next bug?
 
 A **Poisson Distribution** is a continuous version of a Binomial Distribution, used for measuring
 the number of independent events that occur in a time period rather than during a specified
-number of events.
+number of events.

doc/library/Evolve/evolve.md

@@ -0,0 +1,30 @@
+# Evolution tools
+
+## World
+
+```{eval-rst}
+.. doxygenfile:: emp/Evolve/World.hpp
+  :project: Empirical
+  :no-link:
+```
+
+## Systematics
+
+```{ref} systematics
+```
+
+## NK
+
+```{eval-rst}
+.. doxygenfile:: emp/Evolve/NK.hpp
+  :project: Empirical
+  :no-link:
+```
+
+## Selection
+
+```{eval-rst}
+.. doxygenfile:: emp/Evolve/World_select.hpp
+  :project: Empirical
+  :no-link:
+```

doc/library/Evolve/systematics.rst

@@ -0,0 +1,195 @@
+.. SystematicsDocumentation documentation master file, created by
+   sphinx-quickstart on Thu May 28 16:40:07 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+
+Documentation for Systematics
+====================================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+Systematics
+===========
+
+Systematics is a classification of organisms based on evolutionary (phylogenetic) relationships.
+
+***************
+Systematics.h
+***************
+
+This file is part of Empirical and is located in ``Empirical/source/Evolve/Systematics.h``
+
+The systematics manager is used to track genotypes, species, clades, or lineages of organisms in a world.
+
+Systematics allows a user to generate data to form phylogenetic trees.
+
+The program can be run with different levels of abstraction, meaning the data can be generated by position,
+phenotype, or even genotype if you have a lot of RAM.
+
+**Note**: You are responsible for filling in templates! Adding the template just gives you a place to store your data.
+
+Taxon Specifics
+===============
+
+* Taxon - a group of species with similar characteristics
+* Genotypes are the most commonly used Taxon
+
+A user can see the type and number of mutations that ocurred to bring about a taxon.
+
+Some information that can be accessed is:
+
+* taxon ID# ``GetID()``
+* details of organisms in the taxon ``GetInfo()``
+* pointer to the parent group (will return a null pointer if the species was injected)  ``GetParent()``
+* how many organisms currently exist in the group and how many total organisms have ever existed in the group ``GetNumOrgs()``   or ``GetTotOrgs()``
+* how many direct offspring groups exist from this group and how many total extant offspring that exist from this taxa ``GetTotalOffspring()``
+* how deep in the tree the node you are examining is ``GetDepth()``
+* when did this taxon first appear in the population ``GetOriginationTime()``
+* when did the taxon leave the population ``GetDestructionTime()``
+
+New organisms are added to the taxon using ``AddOrg()``.
+New offspring are added to the taxon with ``AddOffspring()`` .
+
+Organisms are removed with ``RemoveOrg()``.
+Offspring are removed with ``RemoveOffspring()`` .
+
+If there are no more remaining organisms or offspring the taxon will deactivate.
+
+
+General Systematics Data
+=========================
+
+Things that systematics can tell you about a phylogeny and how to access them:
+
+* Are we tracking a synchronous population? ``GetTrackSynchronous()``   ``SetTrackSynchronous()``
+* Are we storing all taxa that are still alive in the population? ``GetStoreActive()``   ``SetStoreActive()``
+* Are we storing all taxa that are ancestors of the living organisms in the population? ``GetStoreAncestors()``   ``SetStoreAncestors()``
+* Are we storing all taxa that have died out, as have all of their descendants? ``GetStoreOutside()``   ``SetStoreOutside()``
+* Are we storing any taxa types that have died out? ``GetArchive()``   ``SetArchive()``
+* Are we storing the positions of taxa? ``GetStorePosition()``   ``SetStorePosition()``
+* How many living organisms are currently being tracked? ``GetTotalOrgs()``
+* How many independent trees are being tracked? ``GetNumRoots()``
+* What ID will the next taxon have? ``GetNextID()``
+* What is the average phylogenetic depth of organisms in the population? ``GetAveDepth()``
+* To find the most recent common ancestor (MRCA)  use ``GetMRCA()``  or ``GetMRCADepth()``  to find the distance to the MRCA.
+
+**The systematics class tracks the relationships among all organisms bases on the INFO_TYPE
+provided.  If an offspring has the same value for INFO_TYPE as its parent, it is grouped into
+the same taxon.  Otherwise a new Taxon is created and the old one is used as its parent in
+the phylogeny.  If the provided INFO_TYPE is the organism's genome, a traditional phylogeny
+is formed, with genotypes.  If the organism's behavior/task set is used, then organisms are
+grouped by phenotypes.  If the organism's position is used, the evolutionary path through
+space is tracked.  Any other aspect of organisms can be tracked this way as well.**
+
+
+**Generally, all living organisms' taxa should be tracked and ancestral organisms' taxa should be maintained for lineage.
+However, not all dead taxa should be maintained, it gets too big.**
+
+***************************
+Diversity and Distinction
+***************************
+
+Systematics.h can also be used to find phylogenetic diversity for all extant taxa in the tree,
+assuming all edges from parent to child have a length of one.
+
+When all branch lengths are equal, the phylogenetic diversity is the number of internal nodes plus the number of
+extant taxa minus 1.
+
+You can also find how distinct a specific taxa is from the rest of the population
+based on the amount of unique evolutionary history that it represents.
+
+*****************************
+Synchronous Populations
+*****************************
+
+A synchronous population is a population in which each generation is a discrete time point
+and a completely new set of individual organisms is created for each generation. This means that
+an organism and its parent can never exist at the same time.
+
+An asynchronous population is the opposite, where generations overlap and organisms reproduce
+when they are ready.
+
+In the systematics manager, synchronicity is controlled with
+
+``GetTrackSynchronous()`` which returns true or false and
+``SetTrackSynchronous(input true or false)`` which allows you to use a synchronous or asynchronous population.
+
+
+Using the Systematics Manager
+==============================
+
+The systematics.h file alone will not give you any useful information. You must use a test file in conjunction with the systematics manager
+in order to see output.
+
+To retrieve some results we will use the file Systematics.cc
+which is located in Empirical/tests/Evolve/Systematics.cc.
+
+To compile to code use this command in the tests directory::
+
+ make test-Systematics
+
+
+**********
+Output
+**********
+
+Terminal Output::
+
+   AddOrg 25 (id1, no parent)
+
+   AddOrg -10 (id2; parent id1)
+
+   AddOrg 26 (id3, parent id1)
+
+   AddOrg 27 (id4, parent id2)
+
+The first line of output shows the first organism in the examined phylogeny. This organism is added with AddOrg
+and is assigned an ID of id1. The organism has no parent, as seen in the farthest column of output, meaning that
+organism id1 will be the root of the phylogeny and produce offspring.
+
+If we then look at the first number is parenthesis, we see the second organism with and ID of id2. Id2 is a direct descendant of the id1 organism.
+
+Lastly, if we look at id4, we see that its parent is id2, meaning that we have created another node in the tree
+as the organisms move through generations, producing new offspring.
+
+The terminal output should also include this section::
+
+  Active count:   11 [18|1,0|17] [17|1,2|11] [15|1,0|null] [12|1,1|11] [16|1,0|11] [11|1,3|null] [6|1,0|5] [19|1,0|17] [5|1,1|null] [4|1,0|null] [3|1,0|null]
+
+
+The 11 at the front refers to the number of total taxa in the phylogeny.
+
+If we look at the first set of numbers: ``[18|1, 0|17]``
+
+The first number in brackets, 18 in this case, is the taxon of the organism where
+a mutation occurred. 1, the next number, is the number of mutations that led to this branch.
+0 is the number of offspring from this organism. Lastly, 17 is the id of the parent organism.
+
+As for the second set ``[17|1, 2|11]`` -- this is taxon 17, one mutation occurred,
+id17 had 2 offspring, and its parent is id11.
+
+The last portion of the output has several lines of 3 numbers.
+
+It should look like this: ::
+
+  1 : 0 : -1
+  2 : 0 : -1
+  3 : 0 : 0
+  4 : 0 : 0
+  5 : 0 : 0
+  6 : 0 : 0
+  7 : 0 : 0
+  8 : 0 : 987
+  9 : 0 : 986
+  10 : 0 : 987
+  11 : 0 : 988
+  12 : 0 : 987
+  13 : 0 : 988
+
+The first number is the organism number. The second number is the position of the organism.
+The third number is the fitness of the organism at position 0.

doc/library/index.md

@@ -11,6 +11,7 @@ compiler/compiler
 data/data
 datastructs/datastructs
 debug/debug
+Evolve/evolve
 functional/functional
 io/io
 math/math

examples/math/CombinedBinomialDistribution.cpp

@@ -0,0 +1,35 @@
+/**
+ *  @note This file is part of Empirical, https://github.com/devosoft/Empirical
+ *  @copyright Copyright (C) Michigan State University, MIT Software license; see doc/LICENSE.md
+ *  @date 2022-2022
+ *
+ *  @file CombinedBinomialDistribution.cpp
+ *  @brief Some examples code for using emp::CombinedBinomialDistribution
+ */
+
+
+#include "emp/math/CombinedBinomialDistribution.hpp"
+#include "emp/math/Random.hpp"
+
+int main(int argc, char* argv[])
+{
+  if(argc != 4){
+    std::cout << "Error! Expecting exactly three command line arguments: "
+              << "p n num_trials" << std::endl;
+    emp_assert(false);
+  }
+  double p = std::stod(argv[1]);
+  size_t n = std::stoi(argv[2]);
+  size_t num_trials = std::stoi(argv[3]);
+
+  emp::Random random;
+  emp::CombinedBinomialDistribution distribution(p, 1);
+
+  double mean = 0;
+
+  for(size_t i = 0; i < num_trials; i++){
+    mean += (double)distribution.PickRandom(n, random) / num_trials;
+  }
+  std::cout << "Mean after " << num_trials << " trials: " << mean << std::endl;
+  return 0;
+}

examples/math/Makefile

@@ -19,7 +19,7 @@ CFLAGS_web_debug := $(CFLAGS_all) $(OFLAGS_web_debug) --js-library ../../include
 CFLAGS_web_opt := $(CFLAGS_all) $(OFLAGS_web_opt) --js-library ../../include/emp/web/library_emp.js -s EXPORTED_FUNCTIONS="['_main', '_empCppCallback']" -s NO_EXIT_RUNTIME=1
 #CFLAGS_web := $(CFLAGS_all) $(OFLAGS_web) --js-library ../../include/emp/web/library_emp.js -s EXPORTED_FUNCTIONS="['_main', '_empCppCallback']" -s DISABLE_EXCEPTION_CATCHING=1 -s NO_EXIT_RUNTIME=1
 
-TARGETS := combos constants Distribution info_theory math Random Range stats
+TARGETS := combos constants Distribution info_theory math Random Range stats CombinedBinomialDistribution
 
 default: native