Merge in latest Avida commits

.github/workflows/ci.yaml

@@ -0,0 +1,54 @@
+name: Continuous Integration
+
+on: [push, pull_request]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y cmake g++ make python3
+    - name: Build Avida
+      run: ./build_avida
+    - name: Run tests
+      run: ./run_tests
+
+  # tests-windows:
+  #   runs-on: windows-latest
+  #   steps:
+  #   - uses: actions/checkout@v2
+  #   - name: Install dependencies
+  #     run: |
+  #       choco install cmake
+  #       choco install git
+  #       choco install python
+  #       refreshenv
+  #   - name: Set up MSVC environment
+  #     run: |
+  #       choco install visualstudio2019buildtools --package-parameters "--add Microsoft.VisualStudio.Component.VC.Tools.x86.x64"
+  #       choco install windows-sdk-10.0 --version 10.0.19041.0
+  #       refreshenv
+  #   - name: Build Avida
+  #     run: |
+  #       bash ./build_avida
+  #   - name: Run tests
+  #     run: |
+  #       bash ./run_tests
+
+  tests-mac:
+    runs-on:  macos-11
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install dependencies
+      run: |
+        brew install cmake
+        brew install python
+    - name: Build Avida
+      run: |
+        ./build_avida
+    - name: Run tests
+      run: |
+        ./run_tests

.gitignore

@@ -7,5 +7,211 @@ cmake_install.cmake
 install_manifest.txt
 .DS_Store
 wbuild
+DerivedData
 
+# Created by https://www.toptal.com/developers/gitignore/api/c++,python
+# Edit at https://www.toptal.com/developers/gitignore?templates=c++,python
 
+### C++ ###
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# End of https://www.toptal.com/developers/gitignore/api/c++,python

.gitmodules

@@ -1,6 +1,9 @@
 [submodule "libs/apto"]
 	path = libs/apto
-	url = git@github.com:dmbryson/apto.git
+	url = https://github.com/dmbryson/apto.git
 [submodule "documentation"]
 	path = documentation
 	url = https://github.com/devosoft/avida.wiki.git
+[submodule "libs/backward-cpp"]
+	path = libs/backward-cpp
+	url = https://github.com/bombela/backward-cpp.git

CMakeLists.txt

@@ -2,6 +2,15 @@ PROJECT(avida-main)
 
 CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
 
+# compile with debugging symbols
+if(NOT WIN32 AND NOT DEFINED ENV{AVIDA_DISABLE_BACKTRACE})
+if(MSVC)
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Zi")
+else()
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
+endif()
+endif()
+
 # Final software is built directly into the work subdirectory.
 SET(EXECUTABLE_OUTPUT_PATH
   "${PROJECT_BINARY_DIR}/bin"
@@ -18,6 +27,9 @@ SET(LIBRARY_OUTPUT_PATH
 INCLUDE_DIRECTORIES(../Empirical/source)
 
 ADD_SUBDIRECTORY(libs/apto)
+if(NOT WIN32 AND NOT DEFINED ENV{AVIDA_DISABLE_BACKTRACE})
+  ADD_SUBDIRECTORY(libs/backward-cpp)
+endif()
 IF(NOT WIN32)
   ADD_SUBDIRECTORY(libs/tcmalloc-1.4)
 ENDIF(NOT WIN32)

avida-core/Avida-Core.xcodeproj/project.pbxproj

@@ -103,8 +103,6 @@
 		7049F3730A66AD7E00640512 /* default-transsmt.org in Create work dir */ = {isa = PBXBuildFile; fileRef = 7049F36F0A66AD7E00640512 /* default-transsmt.org */; };
 		704C6298160CA62F004E9B25 /* cMigrationMatrix.cc in Sources */ = {isa = PBXBuildFile; fileRef = 704C6297160CA62F004E9B25 /* cMigrationMatrix.cc */; };
 		704C629A160CA668004E9B25 /* libapto.a in Frameworks */ = {isa = PBXBuildFile; fileRef = 70FEF6231381B04500A9D082 /* libapto.a */; };
-		704C629E160CA6CC004E9B25 /* libtcmalloc-1.4.a in Frameworks */ = {isa = PBXBuildFile; fileRef = 704C629C160CA6CC004E9B25 /* libtcmalloc-1.4.a */; };
-		704C629F160CA6CC004E9B25 /* libtcmalloc-1.4.a in Frameworks */ = {isa = PBXBuildFile; fileRef = 704C629C160CA6CC004E9B25 /* libtcmalloc-1.4.a */; };
 		704C62A0160CA6D9004E9B25 /* libapto.a in Frameworks */ = {isa = PBXBuildFile; fileRef = 70FEF6231381B04500A9D082 /* libapto.a */; };
 		705B103D1073AEF1002242E6 /* default-heads-sex.org in Create work dir */ = {isa = PBXBuildFile; fileRef = 705B10321073AC1F002242E6 /* default-heads-sex.org */; };
 		705B103E1073AEF1002242E6 /* default-heads.org in Create work dir */ = {isa = PBXBuildFile; fileRef = 705B10331073AC1F002242E6 /* default-heads.org */; };
@@ -734,6 +732,7 @@
 		D7FB16D50ED62684002E939E /* cOrgMessage.cc */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cOrgMessage.cc; sourceTree = "<group>"; };
 		D86E627014F6BA6600AE1489 /* cMigrationMatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cMigrationMatrix.h; sourceTree = "<group>"; };
 		DCC3164D07626CF3008F7A48 /* avida */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = avida; sourceTree = BUILT_PRODUCTS_DIR; };
+		FE754E93200A96010098EA51 /* cCellBox.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = cCellBox.h; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase section */
@@ -752,7 +751,6 @@
 				7038248C14DC3C92003C6901 /* libncurses.5.4.dylib in Frameworks */,
 				7038248B14DC3C8F003C6901 /* libapto.a in Frameworks */,
 				7038248D14DC3C95003C6901 /* (null) in Frameworks */,
-				704C629F160CA6CC004E9B25 /* libtcmalloc-1.4.a in Frameworks */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -769,7 +767,6 @@
 			files = (
 				70FA7AC8138C308000DC70D4 /* libavida-core.a in Frameworks */,
 				70FA7AC9138C308500DC70D4 /* libviewer-core.a in Frameworks */,
-				704C629E160CA6CC004E9B25 /* libtcmalloc-1.4.a in Frameworks */,
 				704C62A0160CA6D9004E9B25 /* libapto.a in Frameworks */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
@@ -1588,6 +1585,7 @@
 				70B08B8C08FB2E5500FC65FE /* tList.h */,
 				70B08B8D08FB2E5500FC65FE /* tMatrix.h */,
 				700E28CF0859FFD700CF158A /* tObjectFactory.h */,
+				FE754E93200A96010098EA51 /* cCellBox.h */,
 			);
 			path = tools;
 			sourceTree = "<group>";