From 3b34f31d97016a9b61b2f029d9414530b4de4668 Mon Sep 17 00:00:00 2001
From: Christopher Lorton <christopher.lorton@gatesfoundation.org>
Date: Fri, 22 Nov 2024 00:54:50 +0000
Subject: [PATCH] custom devcontainer Avoid default with NumPy 2.x

---
 .devcontainer/devcontainer.json     | 25 +++++++++++++++++++++++++
 .devcontainer/postCreateCommands.sh |  3 +++
 .pre-commit-config.yaml             |  2 +-
 .readthedocs.yml                    |  2 +-
 MANIFEST.in                         |  1 +
 README.rst                          |  2 +-
 tox.ini                             |  2 +-
 7 files changed, 33 insertions(+), 4 deletions(-)
 create mode 100644 .devcontainer/devcontainer.json
 create mode 100755 .devcontainer/postCreateCommands.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
new file mode 100644
index 0000000..5424256
--- /dev/null
+++ b/.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/postCreateCommand.sh"
+    }
+}
diff --git a/.devcontainer/postCreateCommands.sh b/.devcontainer/postCreateCommands.sh
new file mode 100755
index 0000000..e82ad61
--- /dev/null
+++ b/.devcontainer/postCreateCommands.sh
@@ -0,0 +1,3 @@
+pip install --upgrade pip
+pip install uv
+uv tool install tox --with tox-uv
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f253289..2124ee7 100644
--- a/.pre-commit-config.yaml
+++ b/.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]
diff --git a/.readthedocs.yml b/.readthedocs.yml
index ab1ac0c..0c69ac3 100644
--- a/.readthedocs.yml
+++ b/.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
diff --git a/MANIFEST.in b/MANIFEST.in
index f6c406c..97b8e7c 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -20,4 +20,5 @@ include LICENSE
 include README.rst
 include README.MD
 
+recursive-exclude .devcontainer *
 global-exclude *.py[cod] __pycache__/* *.so *.dylib
diff --git a/README.rst b/README.rst
index a661cf5..525218f 100644
--- a/README.rst
+++ b/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
diff --git a/tox.ini b/tox.ini
index 50fa9be..d4c318d 100644
--- a/tox.ini
+++ b/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