custom devcontainer

Avoid default with NumPy 2.x

.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": {
+        // Run commands after the container is created.
+        "command": "./.devcontainer/postCreateCommands.sh"
+    }
+}

.devcontainer/postCreateCommands.sh

@@ -0,0 +1,3 @@
+pip install --upgrade pip > /tmp/pip.stdout.log 2> /tmp/pip.stderr.log
+pip install uv > /tmp/uv.stdout.log 2> /tmp/uv.stderr.log
+uv tool install tox --with tox-uv > /tmp/tox.stdout.log 2> /tmp/tox.stderr.log

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ exclude: '^(\.tox|ci/templates|\.bumpversion\.cfg)(/|$)'
 # Note the order is intentional to avoid multiple passes of the hooks
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.7.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --show-fixes]

.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 +20,5 @@ include LICENSE
 include README.rst
 include README.MD
 
+recursive-exclude .devcontainer *
 global-exclude *.py[cod] __pycache__/* *.so *.dylib

README.rst

@@ -14,7 +14,7 @@ Overview
     * - package
       - |version| |wheel| |supported-versions| |supported-implementations| |commits-since|
 .. |docs| image:: https://readthedocs.org/projects/laser-cholera/badge/?style=flat
-    :target: https://laser-cholera.readthedocs.org/en/latest/
+    :target: https://laser-cholera.readthedocs.io/en/latest/
     :alt: Documentation Status
 
 .. |github-actions| image:: https://github.com/InstituteforDiseaseModeling/laser-cholera/actions/workflows/github-actions.yml/badge.svg

tox.ini

@@ -24,7 +24,7 @@ basepython =
     py310: {env:TOXPYTHON:python3.10}
     py311: {env:TOXPYTHON:python3.11}
     py312: {env:TOXPYTHON:python3.12}
-    {bootstrap,clean,check,report,docs,codecov}: {env:TOXPYTHON:python3}
+    {bootstrap,clean,check,report,docs,codecov}: {env:TOXPYTHON:python3.9}
 setenv =
     PYTHONPATH={toxinidir}/tests
     PYTHONUNBUFFERED=yes