[merge]

.github/workflows/pip.yaml

@@ -14,8 +14,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [ubuntu-latest]
-        python-version: ["3.7", "3.11"]
+        platform: [ubuntu-22.04]
+        python-version: ["3.10.4", "3.11.0"]
 
     steps:
       - uses: actions/checkout@v4

.github/workflows/publish.yaml

@@ -0,0 +1,34 @@
+name: "Publish to PyPI"
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip
+          pip install build twine
+
+      - name: Build package
+        run: pip install .
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: "__token__"
+          TWINE_PASSWORD: "${{ secrets.PYPI_API_KEY }}"
+        run: |
+          twine upload dist/*

.github/workflows/sphinx.yaml

@@ -9,12 +9,6 @@ on:
     types: [published]
   workflow_dispatch:
 
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -59,16 +53,38 @@ jobs:
         run: mv README_files docs/build/html
 
       # Upload
-      - name: Upload artifacts
+      - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
         with:
           name: github-pages
           path: docs/build/html/
 
+  post-page-artifact:
+    if: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.repo.full_name == github.repository }}
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Post comment preview
+        uses: CDCgov/cfa-actions/post-artifact@v1.0.0
+        with:
+          artifact-name: github-pages
+          gh-token: ${{ secrets.GITHUB_TOKEN}}
+          message: "Thanks for your contribution, ${{ github.actor }}; your `{ artifact-name }` is ready for download [here]({ artifact-url })."
+
   deploy:
     # Deploy to the github-pages environment
     # but not on PRs
     if: ${{ github.event_name != 'pull_request' }}
+    permissions:
+      pages: write
+      id-token: write
+
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}

.gitignore

@@ -1,17 +1,19 @@
 .cache/
 .ipynb_checkpoints/
 .pytest_cache/
+.ropeproject/
+.nocheck/
 _build/
 dist/
 build/
+dist/
 __pycache__/
 *.egg-info/
 .ropeproject/
 
 compile_commands.json
+
 *.html
 *.ipynb
-.nocheck/
-
 *_files
 !README_files

CMakeLists.txt

@@ -13,6 +13,7 @@ include_directories(include/epiworld)
 
 python_add_library(_core MODULE
     src/database.cpp
+    src/entity.cpp
     src/main.cpp
     src/model.cpp
     src/saver.cpp

Vagrantfile

@@ -0,0 +1,34 @@
+Vagrant.configure("2") do |config|
+  config.vm.box = "ubuntu/jammy64"
+
+  config.vm.provider "virtualbox" do |vb|
+    vb.memory = "2048"
+    vb.cpus = 2
+  end
+
+  config.vm.network "private_network", type: "dhcp"
+
+  config.vm.provision "shell", inline: <<-SHELL
+    # Update and install prerequisites
+    sudo apt-get update
+    sudo apt-get install -y python3 python3-pip python3-venv cmake build-essential
+
+    # Create a Python virtual environment
+    python3 -m venv /home/vagrant/epiworldPy-env
+
+    # Activate virtual environment and upgrade pip
+    source /home/vagrant/epiworldPy-env/bin/activate
+    pip install --upgrade pip setuptools wheel
+
+    # Install dependencies from pyproject.toml (if it exists)
+    if [ -f /vagrant/pyproject.toml ]; then
+      pip install .
+    fi
+
+    # Deactivate the virtual environment
+    deactivate
+  SHELL
+
+  # Synchronize the project directory with the VM
+  config.vm.synced_folder ".", "/vagrant"
+end

docs/conf.py

@@ -67,9 +67,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.0.1'
+version = '0.6.0-0'
 # The full version, including alpha/beta/rc tags.
-release = '0.0.1'
+release = '0.6.0-0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

include/epiworld/agent-meat-virus-sampling.hpp

@@ -20,7 +20,7 @@ namespace sampler {
  * @return Virus<TSeq>* of the selected virus. If none selected (or none
  * available,) returns a nullptr;
  */
-template<typename TSeq>
+template<typename TSeq = EPI_DEFAULT_TSEQ>
 inline std::function<void(Agent<TSeq>*,Model<TSeq>*)> make_update_susceptible(
     std::vector< epiworld_fast_uint > exclude = {}
     )
@@ -179,7 +179,7 @@ inline std::function<void(Agent<TSeq>*,Model<TSeq>*)> make_update_susceptible(
  * @return Virus<TSeq>* of the selected virus. If none selected (or none
  * available,) returns a nullptr;
  */
-template<typename TSeq = int>
+template<typename TSeq = EPI_DEFAULT_TSEQ>
 inline std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> make_sample_virus_neighbors(
     std::vector< epiworld_fast_uint > exclude = {}
 )
@@ -347,7 +347,7 @@ inline std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> make_sample_virus_
  * @return Virus<TSeq>* of the selected virus. If none selected (or none
  * available,) returns a nullptr;
  */
-template<typename TSeq = int>
+template<typename TSeq = EPI_DEFAULT_TSEQ>
 inline Virus<TSeq> * sample_virus_single(Agent<TSeq> * p, Model<TSeq> * m)
 {
 

include/epiworld/epiworld.hpp

@@ -18,7 +18,7 @@
 
 /* Versioning */
 #define EPIWORLD_VERSION_MAJOR 0
-#define EPIWORLD_VERSION_MINOR 4
+#define EPIWORLD_VERSION_MINOR 6
 #define EPIWORLD_VERSION_PATCH 0
 
 static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
@@ -88,4 +88,4 @@ namespace epiworld {
 
 }
 
-#endif 
+#endif