Merge pull request #2 from emilydolson/submodule-emp

Submodularize Empirical

.github/workflows/ci.yaml

@@ -56,7 +56,6 @@ jobs:
   docker-build:
     name: Docker Image Build
     runs-on: ubuntu-22.04
-    needs: tests
     if: github.event_name == 'push' && github.ref == 'refs/heads/master'
     steps:
       - uses: actions/checkout@v2

.gitmodules

@@ -7,3 +7,6 @@
 [submodule "libs/backward-cpp"]
 	path = libs/backward-cpp
 	url = https://github.com/bombela/backward-cpp.git
+[submodule "libs/Empirical"]
+	path = libs/Empirical
+	url = https://github.com/devosoft/Empirical.git

.vscode/c_cpp_properties.json

@@ -5,7 +5,7 @@
             "defines": [],
             "cStandard": "c11",
             "browse": {
-                "path": [ "${workspaceFolder}", "${workspaceFolder}/avida-core/include/public", "${workspaceFolder}/avida-core/include/private", "${workspaceFolder}/../Empirical/source", "${workspaceFolder}/avida-core/include/public/avida/core/*" ],
+                "path": [ "${workspaceFolder}", "${workspaceFolder}/avida-core/include/public", "${workspaceFolder}/avida-core/include/private", "${workspaceFolder}/libs/Empirical/include/emp", "${workspaceFolder}/avida-core/include/public/avida/core/*" ],
                 "limitSymbolsToIncludedHeaders": true
             },
             "includePath": [
@@ -19,7 +19,7 @@
                 "${workspaceFolder}/avida-core/source/core",
                 "${workspaceFolder}/avida-core/source/actions",
                 "${workspaceFolder}/avida-core/source/script",
-                "${workspaceFolder}/../Empirical/source"
+                "${workspaceFolder}/libs/Empirical/include/emp"
             ]
         }
     ],

CMakeLists.txt

@@ -24,7 +24,7 @@ SET(LIBRARY_OUTPUT_PATH
   "Built libraries are placed here before installation."
 )
 
-INCLUDE_DIRECTORIES(../Empirical/include/emp)
+INCLUDE_DIRECTORIES(libs/Empirical/include/emp)
 
 ADD_SUBDIRECTORY(libs/apto)
 if(NOT WIN32 AND NOT DEFINED ENV{AVIDA_DISABLE_BACKTRACE})
@@ -34,7 +34,7 @@ IF(NOT WIN32)
   ADD_SUBDIRECTORY(libs/tcmalloc-1.4)
 ENDIF(NOT WIN32)
 ADD_SUBDIRECTORY(avida-core)
-# ADD_SUBDIRECTORY(../Empirical/include/emp .)
+# ADD_SUBDIRECTORY(libs/Empirical/include/emp .)
 
 # Default location for installed software/configs/ docs is the build directory.
 SET(CMAKE_INSTALL_PREFIX

README.md

@@ -1,7 +1,5 @@
 This is a version of Avida with the systematics tracker and open-ended evolution metrics from [Empirical](https://github.com/devosoft/Empirical).
-Specifically, it has been tested and is known to be compatible with [this release](https://github.com/emilydolson/Empirical/tree/OEE_metrics_paper_submission)
-of Empirical. The build file expects the directory containing that version of Empirical to be in the same directory as this
-repository (i.e. `ls` should show `Empirical` and `avida-empirical`).
+Empirical is managed as a submodule in this repository, pinned to a known-compatible commit.
 
 Other than that, this is the same as normal Avida. The README for normal Avida follows.
 

avida-core/source/main/cOrgMessagePredicate.h

@@ -86,8 +86,13 @@ struct cOrgMessagePred_CountDemeMessages : public cOrgMessagePredicate {
 	}
 
   virtual void Print(int update, std::ostream& out) {
-		// out << update << " COUNT " << 
-		// std::accumulate(m_msg_counts.begin(), m_msg_counts.end(), 0, apply2nd<MessageCounts::iterator, plus<int> >()) << " ";
+		out << update << " COUNT " << 
+		std::accumulate(
+			std::begin(m_msg_counts),
+			std::end(m_msg_counts),
+			int{},
+			[](auto first, auto second) { return first + second.second; }
+		) << " ";
 		for(MessageCounts::iterator i=m_msg_counts.begin(); i!=m_msg_counts.end(); ++i) {
 			out << " " << i->second;
 		}

build_avida

@@ -2,8 +2,7 @@
 
 set -e
 
-git submodule init
-git submodule update
+git submodule update --init --recursive
 
 do_build() {
   (