Merge pull request #493 from devosoft/update-MABE_devel

Sync master into MABE_devel
devosoft · Dec 7, 2023 · 60ce0e8 · 60ce0e8
2 parents 705ed80 + 51415be
commit 60ce0e8
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -104,25 +104,61 @@ jobs:
       - run: export CXX=clang++ && make install-coverage-dependencies
       - run: export CXX=clang++ && make coverage
       - run: curl -s https://codecov.io/bash | bash
+  # adapted from https://docs.github.com/en/packages/managing-github-packages-using-github-actions-workflows/publishing-and-installing-a-package-with-github-actions#publishing-a-package-using-an-action
+  build-container:
+    name: Build Docker Image
+    runs-on: ubuntu-22.04
+    env:
+      REGISTRY: ghcr.io
+      IMAGE_NAME: ${{ github.repository }}
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: 'recursive'
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: type=raw,value=ACTIONS_BUILD_${{ github.run_number }}
+      - name: Push to GHCR
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
   test-documentation:
     name: Test Documentation Build
     runs-on: ubuntu-22.04
+    needs: build-container
+    container:
+      image: ghcr.io/devosoft/empirical:ACTIONS_BUILD_${{ github.run_number }}
+      # github actions requires root to access mounted volumes
+      options: --user root
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v1
         with:
           submodules: 'recursive'
-      - uses: mmore500/actions-setup-docker@94429ebc8d9edb4e8c8afb2667bce1e89435f74f
-      - run: docker build -t devosoft/empirical .
-      - run: docker ps -a
-      - run: sudo docker run --name empirical devosoft/empirical /bin/bash -c "set -o pipefail && cd /opt/Empirical/doc && make html coverage | ./headtail.sh && python /opt/Empirical/doc/parse_documentation_coverage.py /opt/Empirical/doc/_build/doc-coverage.json >> /opt/Empirical/doc-coverage.json"
-      - run: sudo docker cp empirical:/opt/Empirical/doc-coverage.json .
+      - run: |
+          make -C doc html coverage | ./doc/headtail.sh
+          python doc/parse_documentation_coverage.py doc/_build/doc-coverage.json >> doc-coverage.json
       - uses: sylvanld/action-storage@v1
         if: github.ref == 'refs/heads/master'
         with:
           src: doc-coverage.json
           dst: stats/doc-coverage.json
-  deploy-dockerhub:
-    name: Deploy to DockerHub
+  deploy-container:
+    name: Deploy to DockerHub and ghcr.io
     runs-on: ubuntu-22.04
     if: github.ref == 'refs/heads/master'
     needs:
@@ -144,3 +180,12 @@ jobs:
           password: ${{ secrets.DOCKER_PASSWORD }}
           repository: devosoft/empirical
           tag_with_ref: true
+      - name: Push to GHCR
+        uses: docker/build-push-action@v1
+        with:
+          context: .
+          push: true
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          repository: devosoft/empirical
+          tag_with_ref: true
diff --git a/.readthedocs.yml → .readthedocs.yaml b/.readthedocs.yml → .readthedocs.yaml
@@ -1,10 +1,15 @@
-# .readthedocs.yml
+# .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 #Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.7"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: doc/conf.py
@@ -14,6 +19,5 @@ formats: []
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: doc/requirements.txt
diff --git a/doc/requirements.in b/doc/requirements.in
@@ -2,7 +2,7 @@ sphinx==3.2.1
 exhale==0.2.3
 sphinx-rtd-theme==0.5.0
 coverxygen==1.5.0
-breathe==4.22.1
+breathe==4.26.1
 myst-parser==0.12.9
 # @mmore500 2021-10
 # docutils 0.18.0 crashes docs build due to exception

diff --git a/doc/requirements.txt b/doc/requirements.txt
@@ -12,7 +12,7 @@ babel==2.9.1
     # via sphinx
 beautifulsoup4==4.10.0
     # via bs4
-breathe==4.22.1
+breathe==4.26.1
     # via
     #   -r requirements.in
     #   exhale

diff --git a/include/emp/Evolve/NK-const.hpp b/include/emp/Evolve/NK-const.hpp
@@ -14,6 +14,7 @@
 #define EMP_EVOLVE_NK_CONST_HPP_INCLUDE
 
 #include <array>
+#include <stddef.h>
 
 #include "../base/assert.hpp"
 #include "../bits/BitSet.hpp"

diff --git a/include/emp/Evolve/NK.hpp b/include/emp/Evolve/NK.hpp
@@ -19,6 +19,7 @@
 #define EMP_EVOLVE_NK_HPP_INCLUDE
 
 #include <array>
+#include <stddef.h>
 
 #include "../base/vector.hpp"
 #include "../bits/BitVector.hpp"

diff --git a/include/emp/Evolve/OEE.hpp b/include/emp/Evolve/OEE.hpp
@@ -11,6 +11,7 @@
 #define EMP_EVOLVE_OEE_HPP_INCLUDE
 
 #include <deque>
+#include <stddef.h>
 
 #include "../base/Ptr.hpp"
 #include "../base/vector.hpp"

diff --git a/include/emp/Evolve/Resource.hpp b/include/emp/Evolve/Resource.hpp
@@ -15,6 +15,7 @@
 #ifndef EMP_EVOLVE_RESOURCE_HPP_INCLUDE
 #define EMP_EVOLVE_RESOURCE_HPP_INCLUDE
 
+#include <stddef.h>
 
 #include "World.hpp"
 

diff --git a/include/emp/Evolve/StateGrid.hpp b/include/emp/Evolve/StateGrid.hpp
@@ -21,6 +21,7 @@
 
 
 #include <map>
+#include <stddef.h>
 #include <string>
 
 #include "../base/assert.hpp"

diff --git a/include/emp/Evolve/Systematics.hpp b/include/emp/Evolve/Systematics.hpp
@@ -28,6 +28,7 @@
 #include <ostream>
 #include <set>
 #include <sstream>
+#include <stddef.h>
 #include <string>
 #include <unordered_set>
 

diff --git a/include/emp/Evolve/World.hpp b/include/emp/Evolve/World.hpp
@@ -26,6 +26,7 @@
 
 #include <functional>
 #include <map>
+#include <stddef.h>
 #include <unordered_map>
 
 #include "../base/Ptr.hpp"

diff --git a/include/emp/Evolve/World_iterator.hpp b/include/emp/Evolve/World_iterator.hpp
@@ -15,6 +15,8 @@
 #ifndef EMP_EVOLVE_WORLD_ITERATOR_HPP_INCLUDE
 #define EMP_EVOLVE_WORLD_ITERATOR_HPP_INCLUDE
 
+#include <stddef.h>
+
 #include "../base/Ptr.hpp"
 
 namespace emp {

diff --git a/include/emp/Evolve/World_output.hpp b/include/emp/Evolve/World_output.hpp
@@ -12,6 +12,8 @@
 #ifndef EMP_EVOLVE_WORLD_OUTPUT_HPP_INCLUDE
 #define EMP_EVOLVE_WORLD_OUTPUT_HPP_INCLUDE
 
+#include <stddef.h>
+
 #include "../base/vector.hpp"
 #include "../data/DataFile.hpp"   // Helper to determine when specific events should occur.
 #include "../tools/string_utils.hpp"

diff --git a/include/emp/Evolve/World_select.hpp b/include/emp/Evolve/World_select.hpp
@@ -12,6 +12,7 @@
 
 #include <functional>
 #include <map>
+#include <stddef.h>
 
 #include "../base/array.hpp"
 #include "../base/assert.hpp"

diff --git a/include/emp/Evolve/World_structure.hpp b/include/emp/Evolve/World_structure.hpp
@@ -10,7 +10,9 @@
 #ifndef EMP_EVOLVE_WORLD_STRUCTURE_HPP_INCLUDE
 #define EMP_EVOLVE_WORLD_STRUCTURE_HPP_INCLUDE
 
+#include <cstdint>
 #include <set>
+#include <stddef.h>
 
 #include "../base/array.hpp"
 #include "../base/assert.hpp"

diff --git a/include/emp/base/Ptr.hpp b/include/emp/base/Ptr.hpp
@@ -31,6 +31,7 @@
 #define EMP_BASE_PTR_HPP_INCLUDE
 
 #include <cstring>
+#include <stddef.h>
 #include <unordered_map>
 
 #include "assert.hpp"

diff --git a/include/emp/base/_emscripten_assert_trigger.hpp b/include/emp/base/_emscripten_assert_trigger.hpp
@@ -13,6 +13,7 @@
 
 #include <iostream>
 #include <sstream>
+#include <stddef.h>
 #include <string>
 
 #include <emscripten.h>

diff --git a/include/emp/base/_emscripten_error_trigger.hpp b/include/emp/base/_emscripten_error_trigger.hpp
@@ -13,6 +13,7 @@
 #define EMP_BASE__EMSCRIPTEN_ERROR_TRIGGER_HPP_INCLUDE
 
 #include <iostream>
+#include <stddef.h>
 #include <string>
 
 namespace emp {

diff --git a/include/emp/base/_native_assert_trigger.hpp b/include/emp/base/_native_assert_trigger.hpp
@@ -13,6 +13,7 @@
 
 #include <iostream>
 #include <sstream>
+#include <stddef.h>
 #include <string>
 
 #include "_is_streamable.hpp"

diff --git a/include/emp/base/_native_error_trigger.hpp b/include/emp/base/_native_error_trigger.hpp
@@ -12,6 +12,7 @@
 #define EMP_BASE__NATIVE_ERROR_TRIGGER_HPP_INCLUDE
 
 
+#include <stddef.h>
 #include <string>
 
 namespace emp {

diff --git a/include/emp/base/_tdebug_assert_trigger.hpp b/include/emp/base/_tdebug_assert_trigger.hpp
@@ -11,6 +11,7 @@
 #ifndef EMP_BASE__TDEBUG_ASSERT_TRIGGER_HPP_INCLUDE
 #define EMP_BASE__TDEBUG_ASSERT_TRIGGER_HPP_INCLUDE
 
+#include <stddef.h>
 #include <string>
 
 namespace emp {

diff --git a/include/emp/base/_tdebug_error_trigger.hpp b/include/emp/base/_tdebug_error_trigger.hpp
@@ -12,6 +12,7 @@
 #define EMP_BASE__TDEBUG_ERROR_TRIGGER_HPP_INCLUDE
 
 
+#include <stddef.h>
 #include <string>
 
 namespace emp {

diff --git a/include/emp/base/array.hpp b/include/emp/base/array.hpp
@@ -21,6 +21,8 @@
 #include <array>
 #include <initializer_list>
 #include <iterator>
+#include <stddef.h>
+#include <vector>
 
 #include "../../../third-party/cereal/include/cereal/cereal.hpp"
 

diff --git a/include/emp/base/errors.hpp b/include/emp/base/errors.hpp
@@ -42,6 +42,7 @@
 #include <iostream>
 #include <map>
 #include <sstream>
+#include <stddef.h>
 #include <string>
 
 /// If we are in emscripten, make sure to include the header.

diff --git a/include/emp/base/map.hpp b/include/emp/base/map.hpp
@@ -19,6 +19,7 @@
 
 #include <initializer_list>
 #include <map>
+#include <stddef.h>
 
 #include "assert.hpp"
 #include "MapProxy.hpp"

diff --git a/include/emp/base/optional.hpp b/include/emp/base/optional.hpp
@@ -15,6 +15,7 @@
 #define EMP_BASE_OPTIONAL_HPP_INCLUDE
 
 #include <optional>
+#include <stddef.h>
 #include <type_traits>
 #include <utility>
 

diff --git a/include/emp/base/unordered_map.hpp b/include/emp/base/unordered_map.hpp
@@ -12,6 +12,7 @@
 #define EMP_BASE_UNORDERED_MAP_HPP_INCLUDE
 
 #include <initializer_list>
+#include <stddef.h>
 #include <unordered_map>
 
 #include "assert.hpp"

diff --git a/include/emp/base/vector.hpp b/include/emp/base/vector.hpp
@@ -22,6 +22,7 @@
 
 #include <initializer_list>
 #include <iterator>
+#include <stddef.h>
 #include <utility>
 #include <vector>
 

diff --git a/include/emp/bits/BitArray.hpp b/include/emp/bits/BitArray.hpp
@@ -17,10 +17,12 @@
 
 
 #include <bitset>
+#include <cstdint>
 #include <cstring>
 #include <initializer_list>
 #include <iostream>
 #include <span>
+#include <stddef.h>
 
 #include "../base/assert.hpp"
 #include "../base/Ptr.hpp"

diff --git a/include/emp/bits/BitMatrix.hpp b/include/emp/bits/BitMatrix.hpp
@@ -12,6 +12,7 @@
 #define EMP_BITS_BITMATRIX_HPP_INCLUDE
 
 #include <iostream>
+#include <stddef.h>
 #include <typeinfo>
 
 

diff --git a/include/emp/bits/BitSet.hpp b/include/emp/bits/BitSet.hpp
@@ -12,6 +12,7 @@
 #ifndef EMP_BITS_BITSET_HPP_INCLUDE
 #define EMP_BITS_BITSET_HPP_INCLUDE
 
+#include <stddef.h>
 
 #include "BitArray.hpp"
 

diff --git a/include/emp/bits/BitVector.hpp b/include/emp/bits/BitVector.hpp
@@ -30,10 +30,12 @@
 
 
 #include <bitset>
+#include <cstdint>
 #include <cstring>
 #include <initializer_list>
 #include <iostream>
 #include <span>
+#include <stddef.h>
 
 #include "../base/assert.hpp"
 #include "../base/Ptr.hpp"

diff --git a/include/emp/bits/_bitset_helpers.hpp b/include/emp/bits/_bitset_helpers.hpp
@@ -10,6 +10,7 @@
 #ifndef EMP_BITS__BITSET_HELPERS_HPP_INCLUDE
 #define EMP_BITS__BITSET_HELPERS_HPP_INCLUDE
 
+#include <stddef.h>
 
 namespace emp {
 

diff --git a/include/emp/bits/bitset_utils.hpp b/include/emp/bits/bitset_utils.hpp
@@ -14,6 +14,7 @@
 #include <algorithm>
 #include <cstdint>       // uint8_t, uint16_t, etc.
 #include <sstream>
+#include <stddef.h>
 #include <string>
 
 #include "../base/Ptr.hpp"

diff --git a/include/emp/compiler/DFA.hpp b/include/emp/compiler/DFA.hpp
@@ -11,7 +11,9 @@
 #ifndef EMP_COMPILER_DFA_HPP_INCLUDE
 #define EMP_COMPILER_DFA_HPP_INCLUDE
 
+#include <cstdint>
 #include <limits>
+#include <stddef.h>
 #include <string>
 
 #include "../base/array.hpp"