🚧 metapop WIP II

.devcontainer/devcontainer.json

@@ -0,0 +1,25 @@
+{
+    "image": "mcr.microsoft.com/devcontainers/python:3.9",
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": [
+                "ms-python.python",
+                "ms-python.debugpy",
+                "ms-toolsai.jupyter",
+                "ms-toolsai.jupyter-renderers",
+                "charliermarsh.ruff",
+                "github.codespace",
+                "github.copilot",
+                "github.copilot-chat",
+                "mechatroner.raincsv",
+                "vscode-icons-team.vscode-icons"
+            ]
+        }
+    },
+    "postCreateCommand": {
+        "uv": "pip install uv",
+        "tox": "uv tool install tox --with tox-uv"
+      }
+}

.readthedocs.yml

@@ -6,7 +6,7 @@ formats: all
 build:
   os: ubuntu-22.04
   tools:
-    python: "3"
+    python: "3.9"
 python:
   install:
     - requirements: docs/requirements.txt

MANIFEST.in

@@ -20,4 +20,8 @@ include LICENSE
 include README.rst
 include README.MD
 
+exclude .gitmodules
+recursive-exclude .devcontainer *
+recursive-exclude mosaic-data *
+recursive-exclude mosaic-pkg *
 global-exclude *.py[cod] __pycache__/* *.so *.dylib

README.rst

@@ -27,19 +27,19 @@ Overview
 
 .. |version| image:: https://img.shields.io/pypi/v/laser-cholera.svg
     :alt: PyPI Package latest release
-    :target: https://test.pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera/
 
 .. |wheel| image:: https://img.shields.io/pypi/wheel/laser-cholera.svg
     :alt: PyPI Wheel
-    :target: https://test.pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera/
 
 .. |supported-versions| image:: https://img.shields.io/pypi/pyversions/laser-cholera.svg
     :alt: Supported versions
-    :target: https://test.pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera/
 
 .. |supported-implementations| image:: https://img.shields.io/pypi/implementation/laser-cholera.svg
     :alt: Supported implementations
-    :target: https://test.pypi.org/project/laser-cholera
+    :target: https://test.pypi.org/project/laser-cholera/
 
 .. |commits-since| image:: https://img.shields.io/github/commits-since/InstituteforDiseaseModeling/laser-cholera/v0.0.0.svg
     :alt: Commits since latest release

docs/reference/index.rst

@@ -1,7 +1,7 @@
-Reference
-=========
+laser_cholera
+=============
 
 .. toctree::
-    :glob:
+   :maxdepth: 4
 
-    laser_cholera*
+   laser_cholera

docs/reference/laser_cholera.metapop.rst

@@ -0,0 +1,50 @@
+laser\_cholera.metapop package
+==============================
+
+.. automodule:: laser_cholera.metapop
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+laser\_cholera.metapop.births module
+------------------------------------
+
+.. automodule:: laser_cholera.metapop.births
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.metapop.model module
+-----------------------------------
+
+.. automodule:: laser_cholera.metapop.model
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.metapop.params module
+------------------------------------
+
+.. automodule:: laser_cholera.metapop.params
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.metapop.scenario module
+--------------------------------------
+
+.. automodule:: laser_cholera.metapop.scenario
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.metapop.transmission module
+------------------------------------------
+
+.. automodule:: laser_cholera.metapop.transmission
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/reference/laser_cholera.rst

@@ -1,11 +1,58 @@
-laser_cholera
-=============
+laser\_cholera package
+======================
 
-.. testsetup::
+.. automodule:: laser_cholera
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
-    from laser_cholera import *
+Subpackages
+-----------
 
-.. automodule:: laser_cholera
-    :members:
-    :undoc-members:
-    :special-members: __init__, __len__
+.. toctree::
+   :maxdepth: 4
+
+   laser_cholera.metapop
+
+Submodules
+----------
+
+laser\_cholera.cli module
+-------------------------
+
+.. automodule:: laser_cholera.cli
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.core module
+--------------------------
+
+.. automodule:: laser_cholera.core
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.iso\_codes module
+--------------------------------
+
+.. automodule:: laser_cholera.iso_codes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.proppop module
+-----------------------------
+
+.. automodule:: laser_cholera.proppop
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+laser\_cholera.utils module
+---------------------------
+
+.. automodule:: laser_cholera.utils
+   :members:
+   :undoc-members:
+   :show-inheritance:

pyproject.toml

@@ -44,6 +44,10 @@ dependencies = [
     "matplotlib",
 ]
 
+[project.optional-dependencies]
+"dev" = ["uv", "tox"]
+# "docs" = ["sphinx", "sphinx-rtd-theme"]
+
 [project.urls]
 Homepage = "https://example.com"
 Documentation = "https://laser-cholera.readthedocs.io/en/latest/"
@@ -53,7 +57,7 @@ Changelog = "https://github.com/InstituteforDiseaseModeling/laser-cholera/blob/m
 
 [project.scripts]
 cli = "laser_cholera.cli:run"
-cholera = "laser_measles.cholera.model:run"
+cholera = "laser_cholera.cholera.model:run"
 
 [tool.ruff]
 extend-exclude = ["static", "ci/templates"]
@@ -144,7 +148,7 @@ search = 'version = release = "{current_version}"'
 replace = 'version = release = "{new_version}"'
 
 [[tool.bumpversion.files]]
-filename = "src/laser_measles/__init__.py"
+filename = "src/laser_cholera/__init__.py"
 search = '__version__ = "{current_version}"'
 replace = '__version__ = "{new_version}"'