Sync main branch to joss-paper branch

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.0.3
+current_version = 1.0.0
 commit = True
 tag = True
 

.github/workflows/CI.yml

@@ -7,12 +7,13 @@ on:
       - '**'
   schedule:
     - cron: '0 0 * * 0'
+  workflow_dispatch:
 jobs:
   tidy:
     name: Enforce Tidyness
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
       - run: sudo apt-get update -qq
@@ -22,16 +23,24 @@ jobs:
     name: Test Tidy Enforcement on macOS
     runs-on: macos-11
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
+          # sometimes checkout action doesn't result in clean directory?
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.sha || github.ref }}
           submodules: 'recursive'
+      - run: git status --ignored
       - run: brew install coreutils findutils gnu-sed gawk grep rename sphinx-doc
       # adapted from https://stackoverflow.com/a/42878119
       - run: brew link sphinx-doc --force
+      # updates PATH to use Homebrew-installed tools first
+      # see https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#adding-a-system-path
+      - run: echo "/usr/local/bin:$PATH" > $GITHUB_PATH
+      - run: echo $PATH
       - run: ./ci/test_tidy.sh
   test:
     name: Tests
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
       matrix:
@@ -47,14 +56,21 @@ jobs:
       CXX: ${{ matrix.cxx }}
       TEST_SET: ${{ matrix.test-set }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+      - name: Set up GCC
+        uses: egor-tensin/setup-gcc@v1
+        with:
+          version: 11
+      - name: Set up clang
+        uses: egor-tensin/setup-clang@v1
+        with:
+          version: 15
       - 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
@@ -63,60 +79,109 @@ 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
+      - uses: actions/checkout@v3
         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
+      - name: Set up clang
+        uses: egor-tensin/setup-clang@v1
+        with:
+          version: 15
+      - uses: actions/checkout@v3
         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
+  # 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: ${{ steps.meta.outputs.labels }}
   test-documentation:
     name: Test Documentation Build
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
+    needs: build-container
+    container:
+      image: ghcr.io/devosoft/empirical:ACTIONS_BUILD_${{ github.run_number }}
+      # github actions requires root to access mounted volumes
+      options: --user root
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         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: doxygen
+      - run: cd doc && python make_md.py
+      - run: cd doc && make html | ./headtail.sh
+      - run: cd doc && make coverage
+      - run: ls doc/ && ls doc/_build
+      - run: cd doc && python parse_documentation_coverage.py _build/doc-coverage.json >> doc-coverage.json
+      - uses: actions/upload-artifact@v2
+        with:
+          name: doc-coverage
+          path: doc/doc-coverage.json
+  deploy-documentation-coverage:
+    name: Deploy Documentation Coverage
+    runs-on: ubuntu-22.04
+    if: github.ref == 'refs/heads/master'
+    needs: test-documentation
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: doc-coverage
+          path: data
       - uses: sylvanld/action-storage@v1
-        if: github.ref == 'refs/heads/master'
         with:
-          src: doc-coverage.json
-          dst: stats/doc-coverage.json
+          src: data/doc-coverage.json
+          dst: data/doc-coverage.json
   paper:
     runs-on: ubuntu-latest
     name: Paper Draft
@@ -137,9 +202,12 @@ jobs:
           # PDF. Note, this should be the same directory as the input
           # paper.md
           path: paper.pdf
-  deploy-dockerhub:
+  deploy-container:
     name: Deploy to DockerHub
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-22.04
+    permissions:
+      contents: read
+      packages: write
     if: github.ref == 'refs/heads/master'
     needs:
       - tidy

.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/
@@ -48,6 +48,7 @@ demos/Emphatic/Emphatic
 demos/Emphatic/examples/ConceptTest
 demos/Emphatic/examples/ConceptTest.cpp
 demos/MABE/examples/NK
+demos/MAP-Elites-Arm/web/MAP-Elites-Arm.js
 demos/NK.bak/
 demos/NK/NK
 demos/NK/web/NK.js
@@ -76,6 +77,13 @@ demos/NK/web/jquery-1.11.2.min.js
 demos/NK/web/NK.asm.js
 demos/NK/web/NK.html
 demos/NK/web/NK.js.mem
+demos/utils/words/Wordle/Wordle
+demos/utils/words/Wordle/web/
+demos/utils/words/annotate-length
+demos/utils/words/has-only
+demos/utils/words/wordlists/
+demos/utils/words/wordplay-remove
+demos/utils/words/wordplay-shuffle
 
 doc/doxygen/
 examples/*/*
@@ -88,7 +96,6 @@ 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

@@ -0,0 +1,25 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    pre_build:
+      - doxygen
+      - cd doc && python make_md.py
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: doc/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: doc/requirements.txt

CONTRIBUTING.md

@@ -0,0 +1,48 @@
+# Contributing to Empirical
+
+We love your input! We want to make contributing to this project as easy and transparent as possible, whether it's:
+
+- Reporting a bug
+- Proposing new features
+- Submitting new code
+- Writing documentation
+
+## Reporting bugs
+
+To report bugs, please [open an issue on Github](https://github.com/devosoft/Empirical/issues)
+clearly stating the observed (buggy) behavior (screenshots are encouraged), the desired behavior,
+which operating system and compiler you're using (including version), and any additional information that might
+help us fix the bug. If possible, please provide a minimum example that reproduces the bug.
+
+## Requesting features
+
+We welcome suggestions for how to make Empirical better! To give us your ideas, [open an issue on Github](https://github.com/devosoft/Empirical/issues).
+
+## Submitting new code and documentation
+
+Empirical is developed by a group of computational scientists, none of whom can be full-time software developers.
+We try to fix bugs and implement new features as quickly as we can, but we can't make any promises.
+For these reasons, we highly encourage contributors to submit code fixing bugs or implementing new features!
+By working together, we can have a more versatile and robust library than any of us could write individually.
+
+Before writing new code, we reccomend opening an issue or commenting on an existing one to make sure that we're all on the
+same page and agree that your contribution will be consistent with Empirical's goals.
+
+In-depth guides to [getting started with Empirical development](https://empirical.readthedocs.io/en/latest/dev/getting-started.html),
+[coding guidelines for Empirical development](https://empirical.readthedocs.io/en/latest/dev/contribution-guidelines-and-review.html),
+[writing documentation](https://empirical.readthedocs.io/en/latest/dev/adding-documentation.html), and
+[writing tests](https://empirical.readthedocs.io/en/latest/dev/guide-to-testing.html) are available in the documentation.
+
+Once you start working on a feature, we recommend making a pull request and giving it the "Merge: not ready" label. This way it's easy for everyone
+to keep tabs on ongoing Empirical development and the status of new features. Once you're done developing, remove the "Merge: not ready" label and
+add the "Merge: ready" label so that we know your pull request is ready for review.
+
+As part of your pull request, please add yourself to the list of contributors in the [license file](LICENSE.md).
+
+## Code of Conduct
+
+Please note we have a [code of conduct](CODE_OF_CONDUCT.md) and follow it in all your interactions with the project.
+
+## License
+
+By contributing, you agree that your contributions will be released under [Empirical's MIT License](LICENSE.md).