Python 3.12 support (#1238)

* add Python 3.12 to all Github work flows
* update max supported py version in setup.cfg
* remove use of pandas in example script
* Update manylinux_2_28 tag for wheel builds
* don't install setuptools/wheel for macOS CI

.github/workflows/docs.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         compiler: [gcc]
-        python-version: ["3.10"]
+        python-version: ["3.12"]
         rust: [1.62.1]
     defaults:
       run:

.github/workflows/macos_x86.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.8, 3.9, "3.10", "3.11" ]
+        python: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
         os:  [ macos-latest ]
         rust: [1.62.1]
     defaults:
@@ -46,7 +46,7 @@ jobs:
           python -m venv venv
           source venv/bin/activate
           python -m pip install --upgrade pip
-          python -m pip install setuptools wheel build
+          python -m pip install wheel
           python -m pip install -r requirements/development.txt
       - name: Build extension module
         run: |

.github/workflows/ubuntu.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: [ 3.8, 3.9, "3.10", "3.11" ]
+        python: [ 3.8, 3.9, "3.10", "3.11", "3.12" ]
         os:  [ ubuntu-22.04 ]
         compiler: [gcc, clang14]
         rust: [1.62.1]
@@ -154,7 +154,9 @@ jobs:
             python -m venv venv
             source venv/bin/activate
             which python
-            python -m pip install --no-cache-dir ./fwdpy11*-linux*.whl
+            # The CPPFLAGS contain stuff for C++ that makes no sense for C.
+            # The flags are also too strict for tskit to build under Py 3.12
+            CPPFLAGS= python -m pip install --no-cache-dir ./fwdpy11*-linux*.whl
             python -m fwdpy11 --includes
             python -c "import fwdpy11;print(fwdpy11.__version__)"
             python -c "import fwdpy11;print(fwdpy11.__file__)"

.github/workflows/wheels.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11"]
+        python: [3.8, 3.9, "3.10", "3.11", "3.12"]
     steps:
       - name: Cancel Previous Runs
         uses: styfle/[email protected]
@@ -102,7 +102,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: ["python3.8", "python3.9", "python3.10", "python3.11"]
+        python: ["python3.8", "python3.9", "python3.10", "python3.11", "python3.12"]
     steps:
       - name: Cancel Previous Runs
         uses: styfle/[email protected]
@@ -133,7 +133,7 @@ jobs:
     needs: ['build_sdist']
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11"]
+        python: [3.8, 3.9, "3.10", "3.11", "3.12"]
     steps:
       - name: Cancel Previous Runs
         uses: styfle/[email protected]
@@ -182,7 +182,7 @@ jobs:
     runs-on: macos-latest
     strategy:
       matrix:
-        python: [3.8, 3.9, "3.10", "3.11"]
+        python: [3.8, 3.9, "3.10", "3.11", "3.12"]
     steps:
       - name: Cancel Previous Runs
         uses: styfle/[email protected]

deployment/linux_wheels/run_wheel_workflow.sh

@@ -1,3 +1,3 @@
 PYTHON=$1
 
-docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux_2_28_x86_64:2022-10-02-69a0972 /bin/sh ./deployment/linux_wheels/wheel_workflow.sh $PYTHON
+docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux_2_28_x86_64:2023-11-29-1ba608e /bin/sh ./deployment/linux_wheels/wheel_workflow.sh $PYTHON

doc/misc/changelog.md

@@ -3,6 +3,10 @@
 Major changes are listed below.  Each release likely contains fiddling with back-end code,
 updates to latest `fwdpp` version, etc.
 
+## 0.21.5
+
+Add support for Python 3.12
+
 ## 0.21.4
 
 Behavior changes:

examples/gss_divergent_optima/gss_divergent_optima.py

@@ -1,7 +1,6 @@
 import sys
 
 import numpy as np
-import pandas as pd
 
 import fwdpy11
 
@@ -82,6 +81,8 @@
 fwdpy11.evolvets(rng, pop, params, 100)
 assert pop.generation == 10 * N + 200
 md = np.array(pop.diploid_metadata, copy=False)
-df = pd.DataFrame.from_records(md[["deme", "g", "w"]])
-g = df.groupby(["deme"])
-print(g.mean())
+
+for deme in np.unique(md["deme"]):
+    mean_genetic_value = md["g"][np.where(md["deme"] == deme)].mean()
+    mean_fitness = md["w"][np.where(md["deme"] == deme)].mean()
+    print(f"{deme} {mean_genetic_value} {mean_fitness}")

setup.cfg

@@ -15,7 +15,7 @@ classifiers =
 [options]
 zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.html
 include_package_data = True
-python_requires = >=3.8, <3.12
+python_requires = >=3.8, <3.13
 # NOTE: any pinning should also be coordinated
 # with requirements.in and doc/requirements.in
 # and may require regenerating the .txt files.