ci: run all examples including slow ones

.github/workflows/build_and_publish.yml

@@ -54,7 +54,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-24.04, macos-14, macos-15-intel ]
-        python-version: [ 310, 311 ]
+        python-version: [ 310, 311, 312, 313 ]
 
     steps:
       - name: "Checkout code"
@@ -99,7 +99,7 @@ jobs:
 
       - name: "Build sdist"
         run: |
-          pip3 install pipx ppsetuptools
+          pip3 install pipx
           pipx run build --sdist
 
       - name: "Upload build artifacts"

cibuildwheel.toml

@@ -31,18 +31,11 @@ linux.before-test = [
   "pip install 'biopython' 'matplotlib' 'numpy<2' 'pandas' 'pygments' 'scipy'"
 ]
 
-# Run examples serially (one at a time) without parallel to avoid memory issues in CI
+# Run ALL examples serially (one at a time) - including slow ones after memory fixes
 linux.test-command = [
   """cd {project}/examples && for f in *.py; do
-    case "$f" in
-      benefits_of_sex.py|genealogies_with_selection.py|measuring_fixation_probabilities.py|multi_sample_adaptive.py|mutation_selection_balance_highd.py|neutral_LD_highd.py|speed_highd.py|speed_lowd.py)
-        echo "Skipping slow example: $f"
-        ;;
-      *)
-        echo "Testing $f..."
-        MPLBACKEND=Agg python3 "$f" || exit 1
-        ;;
-    esac
+    echo "Testing $f..."
+    MPLBACKEND=Agg python3 "$f" || exit 1
   done"""
 ]
 
@@ -51,17 +44,10 @@ macos.before-test = [
   "pip install 'biopython' 'matplotlib' 'numpy<2' 'pandas' 'pygments' 'scipy'"
 ]
 
-# Run same tests as Linux for consistency - serially without parallel
+# Run ALL examples serially - including slow ones after memory fixes
 macos.test-command = [
   """cd {project}/examples && for f in *.py; do
-    case "$f" in
-      benefits_of_sex.py|genealogies_with_selection.py|measuring_fixation_probabilities.py|multi_sample_adaptive.py|mutation_selection_balance_highd.py|neutral_LD_highd.py|speed_highd.py|speed_lowd.py)
-        echo "Skipping slow example: $f"
-        ;;
-      *)
-        echo "Testing $f..."
-        MPLBACKEND=Agg python3 "$f" || exit 1
-        ;;
-    esac
+    echo "Testing $f..."
+    MPLBACKEND=Agg python3 "$f" || exit 1
   done"""
 ]

examples/mutation_selection_balance_highd.py

@@ -65,7 +65,7 @@
 for locus in range(L):
 
     # make histogram
-    y,x = np.histogram(allele_frequencies[:,locus], bins=af_bins, normed='True')
+    y,x = np.histogram(allele_frequencies[:,locus], bins=af_bins, density=True)
 
     # plot
     plt.plot(bc, y, color=plt.cm.jet(locus*4))
@@ -78,7 +78,7 @@
 # compare explicitly to diffusion theory by normalizing to the diffusion theory prediction
 plt.figure()
 for locus in range(L):
-    y,x = np.histogram(allele_frequencies[:,locus], bins=af_bins, normed='True')
+    y,x = np.histogram(allele_frequencies[:,locus], bins=af_bins, density=True)
 
     # calculate the diffusion theory single locus result
     diffusion_theory = bc**(2*N*mu-1)*(1-bc)**(2*N*mu-1)*np.exp(2*N*s[locus]*bc)

pyproject.toml

@@ -8,7 +8,7 @@ authors = [
   { name = "Ivan Aksamentov" },
 ]
 readme = "README.md"
-requires-python = ">=3.6"
+requires-python = ">=3.10"
 keywords = ["packaging", "dependency", "infer", "pyproject.toml"]
 classifiers = [
   "Programming Language :: Python :: 3",
@@ -25,8 +25,7 @@ repository = "https://github.com/neherlab/ffpopsim"
 [build-system]
 build-backend = "setuptools.build_meta"
 requires = [
-  "numpy",
-  "ppsetuptools",
+  "numpy<2",
   "setuptools",
   "wheel",
 ]

setup.py

@@ -1,17 +1,10 @@
 #!/usr/bin/env python
 # vim: fdm=indent
 
-import sys
 import subprocess
 import os
 
-# Python 3.6 compatibility: Python 3.6 has no compatible version of setuptools that supports
-# PEP-517 (the `pyproject.toml`-based config), so we use a shim package `ppsetuptools` instead.
-if sys.version_info >= (3, 7):
-  from setuptools import setup, Extension
-else:
-  from ppsetuptools import setup, Extension
-
+from setuptools import setup, Extension
 import numpy as np
 
 # Get GSL include paths