Update documentation toolchain so that it compiles again

.github/workflows/CI.yml

@@ -7,6 +7,7 @@ on:
       - '**'
   schedule:
     - cron: '0 0 * * 0'
+  workflow_dispatch:
 jobs:
   tidy:
     name: Enforce Tidyness
@@ -143,7 +144,7 @@ jobs:
           submodules: 'recursive'
       - run: |
           make -C doc html coverage | ./doc/headtail.sh
-          python doc/parse_documentation_coverage.py doc/_build/doc-coverage.json >> doc-coverage.json
+          python doc/parse_documentation_coverage.py doc/_build/doc-coverage.json >> doc/doc-coverage.json
       - uses: sylvanld/action-storage@v1
         if: github.ref == 'refs/heads/master'
         with:

.gitignore

@@ -1,4 +1,5 @@
 *~
+*.csv
 *.debug
 *.dSYM
 *.gcov
@@ -17,16 +18,15 @@
 *.dat
 *.exe
 *tmp.*
+*-bak.*
+*-bak2.*
 
 */env/*
 */3nv/*
 
 .DS_Store
 a.out
 a.out.js
-fitness.csv
-population.csv
-systematics.csv
 
 incoming/
 tmp/
@@ -88,7 +88,6 @@ examples/*/*
 !examples/*/Makefile
 !examples/timing/BENCHMARKS
 
-tests/*.csv
 tests/StatsConfig.cfg
 tests/web/*.js
 tests/web/package.json

.gitmodules

@@ -10,10 +10,6 @@
   path = third-party/cereal
   url = https://github.com/mmore500/cereal.git
   shallow = true
-[submodule "third-party/span-lite"]
-  path = third-party/span-lite
-  url = https://github.com/martinmoene/span-lite.git
-  shallow = true
 [submodule "third-party/robin-hood-hashing"]
   path = third-party/robin-hood-hashing
   url = https://github.com/martinus/robin-hood-hashing.git

.readthedocs.yaml

@@ -2,22 +2,21 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-#Required
+# Required
 version: 2
 
+# Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.7"
+    python: "3.10"
+
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: doc/conf.py
-
-# Optionally build your docs in additional formats such as PDF
-formats: []
+   configuration: doc/conf.py
 
-# Optionally set the version of Python and requirements required to build your docs
+# Optionally declare the Python requirements required to build your docs
 python:
-  install:
-    - requirements: doc/requirements.txt
+   install:
+   - requirements: doc/requirements.txt

Dockerfile

@@ -1,5 +1,5 @@
 # Pull base image.
-FROM ubuntu:bionic-20210416
+FROM ubuntu:focal-20230412
 
 COPY . /opt/Empirical
 
@@ -8,6 +8,7 @@ SHELL ["/bin/bash", "-c"]
 # Prevent interactive time zone config.
 # adapted from https://askubuntu.com/a/1013396
 ENV DEBIAN_FRONTEND=noninteractive
+ENV SPHINXBUILD="python3.10 -m sphinx"
 
 RUN \
   echo 'Acquire::http::Timeout "60";' >> "/etc/apt/apt.conf.d/99timeout" \
@@ -31,22 +32,21 @@ RUN \
     && \
   rm -rf /var/lib/apt/lists/* \
     && \
-  find /etc/apt -type f -name '*.list' -exec sed -i 's/\(^deb.*-backports.*\)/#\1/; s/\(^deb.*-updates.*\)/#\1/; s/\(^deb.*-proposed.*\)/#\1/; s/\(^deb.*-security.*\)/#\1/' {} + \
-    && \
   apt-get update -y \
     && \
-  apt-get install -y software-properties-common=0.96.24.32.1 \
+  apt-get install -y software-properties-common \
     && \
   add-apt-repository -y ppa:ubuntu-toolchain-r/test \
     && \
+  add-apt-repository -y ppa:deadsnakes/ppa \
+    && \
   apt-get update -y \
     && \
   apt-get install --no-install-recommends --allow-downgrades -y \
-    dpkg-dev \
-    libc6=2.27-3ubuntu1 \
-    libc6-dev \
-    libc6-dbg \
     build-essential \
+    dpkg-dev \
+    g++-11 \
+    libc6 \
     xvfb \
     x11vnc \
     x11-xkb-utils \
@@ -60,21 +60,14 @@ RUN \
     libnss3 \
     lsb-release \
     xdg-utils \
-    g++-8=8-20180414-1ubuntu2 \
-    gcc-8-base=8-20180414-1ubuntu2 \
-    cpp-8=8-20180414-1ubuntu2 \
-    gcc-8=8-20180414-1ubuntu2 \
-    gcc-8-base=8-20180414-1ubuntu2 \
-    libgcc-8-dev \
-    libstdc++-8-dev \
     cmake \
-    python-virtualenv \
-    python-pip-whl \
-    python-pip \
-    python-setuptools \
+    python3-distutils \
     python3-setuptools \
     python3-virtualenv \
     python3-pip \
+    'python3\.10' \
+    'python3\.10-distutils' \
+    'python3\.10-venv' \
     nodejs \
     npm \
     tar \
@@ -84,7 +77,7 @@ RUN \
     doxygen \
     curl \
     perl \
-    perl-base=5.26.1-6 \
+    perl-base \
     git \
     htop \
     man \
@@ -162,25 +155,47 @@ ENV DISPLAY :99
 RUN echo 'kernel.unprivileged_userns_clone=1' > /etc/sysctl.d/userns.conf
 
 RUN \
-  update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 90 \
+  update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 90 \
   && \
   npm install -g n \
   && \
   n 14.17 \
   && \
+  hash -r \
+  && \
   export python="/usr/bin/python3" \
   && \
   npm install source-map \
   && \
   echo "finalized set up dependency versions"
 
 RUN \
-  pip install wheel==0.30.0 \
+  curl -sS https://bootstrap.pypa.io/get-pip.py | python3 \
+    && \
+  curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10 \
+    && \
+  pip install --upgrade --force-reinstall pip virtualenv \
+    && \
+  pip3 install --upgrade --force-reinstall pip virtualenv \
+    && \
+  python3.10 -m pip install --upgrade --force-reinstall pip virtualenv \
     && \
-  pip3 install wheel==0.30.0 \
+  python3 -m pip install --upgrade --force-reinstall pip virtualenv \
+    && \
+  pip install wheel==0.30.0 six==1.16.0 \
+    && \
+  pip3 install wheel==0.30.0 six==1.16.0 \
+    && \
+  python3.10 -m pip install wheel==0.30.0 six==1.16.0 \
+    && \
+  python3 -m pip install wheel==0.30.0 six==1.16.0 \
     && \
   pip3 install -r /opt/Empirical/doc/requirements.txt \
     && \
+  python3.10 -m pip install -r /opt/Empirical/doc/requirements.txt \
+    && \
+  python3 -m pip install -r /opt/Empirical/doc/requirements.txt \
+    && \
   echo "installed documentation build requirements"
 
 RUN \
@@ -190,13 +205,19 @@ RUN \
     && \
   git submodule init \
     && \
-  git submodule update -f \
+  echo "nameserver 8.8.8.8" > /etc/resolv.conf \
+    && \
+  n=0; until [ $n -ge 3 ]; do git submodule update -f && break || ((n++)); sleep 5; done; if [ $n -eq 3 ]; then echo "Update failed after 3 attempts."; else echo "Update successful!"; fi \
     && \
   echo "initialized submodules"
 
 RUN \
   cd /opt/Empirical \
     && \
+  curl -sS https://bootstrap.pypa.io/get-pip.py | python3 \
+    && \
+  python3 -m pip install virtualenv \
+    && \
   make install-test-dependencies \
     && \
   echo "installed test dependencies"

demos/MAP-Elites-Arm/Makefile

@@ -3,7 +3,7 @@ PROJECT := MAP-Elites-Arm
 EMP_DIR := ../../include
 
 # Flags to use regardless of compiler
-CFLAGS_all := -Wall -Wno-unused-function -std=c++17 -I$(EMP_DIR)/
+CFLAGS_all := -Wall -Wno-unused-function -std=c++20 -I$(EMP_DIR)/
 
 # Native compiler information
 CXX_nat := g++
@@ -12,7 +12,7 @@ CFLAGS_nat_debug := -g -DEMP_TRACK_MEM -Wnon-virtual-dtor -Wcast-align -Woverloa
 
 # Emscripten compiler information
 CXX_web := emcc
-OFLAGS_web_all := -s "EXTRA_EXPORTED_RUNTIME_METHODS=['ccall', 'cwrap']" -s TOTAL_MEMORY=67108864 --js-library $(EMP_DIR)/emp/web/library_emp.js -s EXPORTED_FUNCTIONS="['_main', '_empCppCallback']" -s DISABLE_EXCEPTION_CATCHING=1 -s NO_EXIT_RUNTIME=1 #--embed-file configs
+OFLAGS_web_all := -s "EXPORTED_RUNTIME_METHODS=['ccall', 'cwrap']" -s TOTAL_MEMORY=67108864 --js-library $(EMP_DIR)/emp/web/library_emp.js -s EXPORTED_FUNCTIONS="['_main', '_empCppCallback']" -s DISABLE_EXCEPTION_CATCHING=1 -s NO_EXIT_RUNTIME=1 #--embed-file configs
 OFLAGS_web := -Oz -DNDEBUG
 # OFLAGS_web_debug := -g4 -Oz -pedantic -Wno-dollar-in-identifier-extension -s ASSERTIONS=2
 OFLAGS_web_debug := -g4 -pedantic -Wno-dollar-in-identifier-extension -s ASSERTIONS=2

demos/NK/Makefile

@@ -3,7 +3,7 @@ PROJECT := NK
 EMP_DIR := ../../include
 
 # Flags to use regardless of compiler
-CFLAGS_all := -Wall -Wno-unused-function -std=c++17 -I$(EMP_DIR)/
+CFLAGS_all := -Wall -Wno-unused-function -std=c++20 -I$(EMP_DIR)/
 
 # Native compiler information
 CXX_nat := g++

demos/SelectionAnalyze/Makefile

@@ -1,6 +1,6 @@
 # Flags to use regardless of compiler
 CFLAGS_all := -Wall -Wno-unused-function -I../../include/
-CFLAGS_version := -std=c++17
+CFLAGS_version := -std=c++20
 
 # Emscripten compiler information
 CXX_web := emcc

demos/SpatialCoop2017/Makefile

@@ -3,7 +3,7 @@ PROJECT := SimplePDWorld
 EMP_DIR := ../../include
 
 # Flags to use regardless of compiler
-CFLAGS_all := -Wall -Wno-unused-function -std=c++17 -I$(EMP_DIR)/
+CFLAGS_all := -Wall -Wno-unused-function -std=c++20 -I$(EMP_DIR)/
 
 # Native compiler information
 CXX_nat := g++

demos/Sudoku/Makefile

@@ -1,5 +1,5 @@
 # Flags to use regardless of compiler
-CFLAGS_all := -std=c++17 -Wall -Wno-unused-function -I../../include/
+CFLAGS_all := -std=c++20 -Wall -Wno-unused-function -I../../include/
 
 # Emscripten compiler information
 CXX_web := emcc

demos/utils/graphs/web/Makefile

@@ -1,7 +1,7 @@
 CXX_web := emcc
 # OFLAGS_web := -g4 -Wall
 OFLAGS_web := -oz -DNDEBUG
-CFLAGS_web := -std=c++17 $(OFLAGS_web) -s EXPORTED_FUNCTIONS="['_empLoadString']" -I../../../../include/
+CFLAGS_web := -std=c++20 $(OFLAGS_web) -s EXPORTED_FUNCTIONS="['_empLoadString']" -I../../../../include/
 
 default: web