build: drop support for py 3.8 and lock at py 3.9 for development (#265)

.devcontainer.json

@@ -4,25 +4,26 @@
 	"name": "Ubuntu",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
 	"image": "mcr.microsoft.com/devcontainers/base:jammy",
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
 	"features": {
 		"ghcr.io/rocker-org/devcontainer-features/miniforge:2": {}
 	},
 
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-
 	// Use 'forwardPorts' to make a list of ports inside the container available locally.
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "mamba env create -n haptools -f dev-env.yml && conda run -n haptools poetry config virtualenvs.in-project true && conda run -n haptools poetry install",
+	"postCreateCommand": "mamba env create -y -n haptools -f dev-env.yml && conda run -n haptools poetry config virtualenvs.in-project true && conda run -n haptools poetry install",
 
 	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
 			"extensions": [
 				"ms-python.python",
-				"ms-python.black-formatter"
+				"ms-vscode.live-server",
+				"ms-python.black-formatter",
+				"GitHub.vscode-github-actions"
 			],
 			"settings": {
 				"python.analysis.typeCheckingMode": "off", // TODO: set to "strict"
@@ -37,9 +38,17 @@
 				"python.testing.pytestEnabled": true,
 				"python.testing.unittestEnabled": false,
 				"terminal.integrated.environmentChangesRelaunch": true,
-				"editor.defaultFormatter": "ms-python.black-formatter",
+				"[python]": {
+					"editor.defaultFormatter": "ms-python.black-formatter",
+					"editor.formatOnSave": true
+				},
+				"black-formatter.importStrategy": "fromEnvironment",
+				"black-formatter.showNotification": "always",
 				"terminal.integrated.hideOnStartup": "always",
-				"files.eol": "\n"
+				"files.eol": "\n",
+				"git.autofetch": true,
+				"git.enableSmartCommit": true,
+				"git.confirmSync": false
 			}
 		}
 	}

.github/workflows/release.yml

@@ -26,7 +26,7 @@ jobs:
         if: ${{ steps.release.outputs.release_created }}
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8' # keep synced with dev-env.yml
+          python-version: '3.9' # keep synced with dev-env.yml
 
       - name: Upgrade pip
         if: ${{ steps.release.outputs.release_created }}
@@ -37,7 +37,7 @@ jobs:
       - name: Install Poetry
         if: ${{ steps.release.outputs.release_created }}
         run: |
-          pip install 'poetry==1.8.3'  # keep version synced with dev-env.yml
+          pip install 'poetry==1.8.5'  # keep version synced with dev-env.yml
           poetry --version
 
       - name: Bump version for developmental release

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { python: "3.8", os: "ubuntu-latest", session: "lint" }
+          - { python: "3.9", os: "ubuntu-latest", session: "lint" }
           - { python: "3.7", os: "ubuntu-latest", session: "tests" }
           - { python: "3.8", os: "ubuntu-latest", session: "tests" }
           - { python: "3.9", os: "ubuntu-latest", session: "tests" }
@@ -20,8 +20,8 @@ jobs:
           - { python: "3.13", os: "ubuntu-latest", session: "tests" }
           # - { python: "3.11", os: "windows-latest", session: "tests" }
           - { python: "3.9", os: "macos-13", session: "tests" }
-          - { python: "3.11", os: "macos-latest", session: "tests" }
-          - { python: "3.8", os: "ubuntu-latest", session: "size" }
+          - { python: "3.12", os: "macos-latest", session: "tests" }
+          - { python: "3.9", os: "ubuntu-latest", session: "size" }
 
     env:
       NOXSESSION: ${{ matrix.session }}

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.8"
+    python: "3.9" # should keep this in sync with version in dev-env.yml
   jobs:
     post_create_environment:
       # Install poetry

dev-env.yml

@@ -3,11 +3,11 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - conda-forge::python=3.8 # the lowest version of python that we formally support; keep in sync with release.yml
-  - conda-forge::pip==24.0
-  - conda-forge::poetry==1.8.3 # should keep this in sync with version in release.yml
-  - conda-forge::nox==2024.4.15
+  - conda-forge::python=3.9 # the lowest version of python that we formally support; keep in sync with release.yml, tests.yml, .readthedocs.yaml, and noxfile.py
+  - conda-forge::pip==24.3.1
+  - conda-forge::poetry==1.8.5 # should keep this in sync with version in release.yml
+  - conda-forge::nox==2024.10.9
   - conda-forge::poetry-plugin-export==1.8.0
   - pip:
     - nox-poetry==1.0.3
-    - poetry-conda==0.1.1
+    - poetry-conda==0.1.3

noxfile.py

@@ -10,7 +10,7 @@
 
 package = "haptools"
 python_versions = ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
-locked_python_version = "3.8"
+locked_python_version = "3.9"  # keep in sync with dev-env.yml
 nox.needs_version = ">= 2022.11.21"
 nox.options.sessions = (
     "docs",