Merge pull request #583 from popsim-consortium/bump_python_CI

Update CI

.github/mergify.yml

@@ -4,15 +4,12 @@ queue_rules:
       - base=main
       - check-success=build-deploy-docs
       - check-success=lint
-      - check-success=dev-deps (macos-11, 3.11)
-      - check-success=dev-deps (ubuntu-20.04, 3.11)
-      - check-success=dev-deps (windows-2022, 3.11)
-      - check-success=tests (macos-11, 3.7)
-      - check-success=tests (macos-11, 3.11)
-      - check-success=tests (ubuntu-20.04, 3.7)
-      - check-success=tests (ubuntu-20.04, 3.11)
-      - check-success=tests (windows-2022, 3.7)
-      - check-success=tests (windows-2022, 3.11)
+      - check-success=dev-deps (macos-14, 3.12)
+      - check-success=dev-deps (ubuntu-24.04, 3.12)
+      - check-success=dev-deps (windows-2022, 3.12)
+      - check-success=tests (macos-14, 3.12)
+      - check-success=tests (ubuntu-24.04, 3.12)
+      - check-success=tests (windows-2022, 3.12)
 
 pull_request_rules:
   - name: automatic merge for Dependabot pull requests
@@ -22,15 +19,12 @@ pull_request_rules:
       - label=dependencies
       - check-success=build-deploy-docs
       - check-success=lint
-      - check-success=dev-deps (macos-11, 3.11)
-      - check-success=dev-deps (ubuntu-20.04, 3.11)
-      - check-success=dev-deps (windows-2022, 3.11)
-      - check-success=tests (macos-11, 3.7)
-      - check-success=tests (macos-11, 3.11)
-      - check-success=tests (ubuntu-20.04, 3.7)
-      - check-success=tests (ubuntu-20.04, 3.11)
-      - check-success=tests (windows-2022, 3.7)
-      - check-success=tests (windows-2022, 3.11)
+      - check-success=dev-deps (macos-14, 3.12)
+      - check-success=dev-deps (ubuntu-24.04, 3.12)
+      - check-success=dev-deps (windows-2022, 3.12)
+      - check-success=tests (macos-14, 3.12)
+      - check-success=tests (ubuntu-24.04, 3.12)
+      - check-success=tests (windows-2022, 3.12)
     actions:
       queue:
         name: default

.github/workflows/dev.yaml

@@ -15,8 +15,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-2022, macos-14]
-        python-version: ["3.11"]
+        os: [ubuntu-24.04, windows-2022, macos-14]
+        python-version: ["3.12"]
 
     steps:
       - name: checkout

.github/workflows/docs.yaml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   build-deploy-docs:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
 
     steps:
       - uses: actions/checkout@v3
@@ -20,13 +20,13 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
           pip install --upgrade pip
-          pip install -r requirements/minimal.txt
-          pip install -r requirements/docs.txt
+          pip install -r requirements_minimal_CI.txt
+          pip install -r requirements_docs_CI.txt
           python -m pip install build packaging
 
       - name: Build package

.github/workflows/lint.yaml

@@ -13,15 +13,16 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
-          pip install -r requirements/minimal.txt
-          pip install -r requirements/lint.txt
+          pip install -r requirements_minimal_CI.txt
+          pip install -r requirements_lint_CI.txt
           # Mypy also checks types in the tests/ folder
-          pip install -r requirements/tests.txt
-          python setup.py build
+          pip install -r requirements_tests_CI.txt
+          pip install build
+          python -m build .
 
       - name: black
         run: black --check .

.github/workflows/tests.yaml

@@ -24,8 +24,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, windows-2022, macos-14]
-        python-version: ["3.9", "3.11"]
+        os: [ubuntu-24.04, windows-2022, macos-14]
+        python-version: ["3.12"]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
@@ -43,8 +43,8 @@ jobs:
 
       - name: install dependencies
         run: |
-          pip install -r requirements/minimal.txt
-          pip install -r requirements/tests.txt
+          pip install -r requirements_minimal_CI.txt
+          pip install -r requirements_tests_CI.txt
 
       # Check that demes installs as expected.
       # Also check the "demes" CLI entry point.

.github/workflows/wheel.yaml

@@ -9,16 +9,16 @@ on:
 
 jobs:
   wheel_build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: install dependencies
         run: |
-          pip install -r requirements/minimal.txt
+          pip install -r requirements_minimal_CI.txt
           pip install build
 
       - name: build wheel

demes/load_dump.py

@@ -1,6 +1,7 @@
 """
 Functions to load and dump graphs in YAML and JSON formats.
 """
+
 from __future__ import annotations
 import contextlib
 import json

requirements/docs.txt

@@ -1,5 +1,5 @@
-demesdraw==0.4.0
+demesdraw
 jupyter-book==0.15.1
-piccolo_theme==0.19.0
-sphinx_issues==3.0.1
-sphinxcontrib-programoutput==0.17
+piccolo_theme
+sphinx_issues
+sphinxcontrib-programoutput

requirements/lint.txt

@@ -1,3 +1,3 @@
-black==23.11.0
-flake8==6.1.0
-mypy==1.9.0
+black
+flake8
+mypy

requirements/minimal.txt

@@ -1,2 +1,2 @@
-attrs==23.2.0
-ruamel.yaml==0.18.6
+attrs
+ruamel.yaml

requirements/tests.txt

@@ -1,5 +1,4 @@
-numpy; python_version=='3.7'
-numpy==1.26.3; python_version>='3.8'
-pytest==7.4.3
-pytest-cov==4.1.0
-pytest-xdist==3.5.0
+numpy
+pytest
+pytest-cov
+pytest-xdist