From b05300522a3e316a5c4ea055c3bfc923895171ee Mon Sep 17 00:00:00 2001
From: Jeremy Muhlich <jmuhlich@bitflood.org>
Date: Wed, 21 Feb 2024 17:26:00 -0500
Subject: [PATCH] Add python 3.12 to CI matrix (#586)

* Use raw strings for strings with incidental backslashes
* Correct spelling of now-renamed assert_raises_regex
* Work around Python 3.12 OrderedDict repr in doctest:
Python 3.12 changed the OrderedDict repr to emit a dict literal as the
constructor argument instead of a list of tuples. We have one doctest
that returns an OrderedDict, failing on 3.12 without this workaround.
This change adds a temporary monkeypatch to collections.OrderedDict
in the nose module-level fixture, but I don't like it.
---
 .github/workflows/ci.yml     |  2 +-
 pysb/bng.py                  |  2 +-
 pysb/export/stochkit.py      |  6 +++---
 pysb/importers/bngl.py       |  2 +-
 pysb/kappa.py                |  2 +-
 pysb/pattern.py              | 24 ++++++++++++++++++++++++
 pysb/tests/test_bng.py       |  4 ++--
 pysb/tests/test_importers.py |  4 ++--
 8 files changed, 35 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index dec1f2a0d..ab1b4fc27 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     defaults:
       run:
         shell: bash -l {0}
diff --git a/pysb/bng.py b/pysb/bng.py
index ba3b49254..2cf116a2d 100644
--- a/pysb/bng.py
+++ b/pysb/bng.py
@@ -850,7 +850,7 @@ def _parse_reaction(model, line, reaction_cache):
     rule_list = rule_list.split(',')  # BNG lists all rules that generate a rxn
     # Support new (BNG 2.2.6-stable or greater) and old BNG naming convention
     # for reverse rules
-    rule_name, is_reverse = zip(*[re.subn('^_reverse_|\(reverse\)$', '', r)
+    rule_name, is_reverse = zip(*[re.subn(r'^_reverse_|\(reverse\)$', '', r)
                                   for r in rule_list])
     is_reverse = tuple(bool(i) for i in is_reverse)
     r_names = ['__s%d' % r for r in reactants]
diff --git a/pysb/export/stochkit.py b/pysb/export/stochkit.py
index 7f4f2f731..1cf1fd42b 100644
--- a/pysb/export/stochkit.py
+++ b/pysb/export/stochkit.py
@@ -225,7 +225,7 @@ def export(self, initials=None, param_values=None):
 
         # Reactions
         reacs = etree.Element('ReactionsList')
-        pattern = re.compile("(__s\d+)\*\*(\d+)")
+        pattern = re.compile(r"(__s\d+)\*\*(\d+)")
         for rxn_id, rxn in enumerate(self.model.reactions):
             rxn_name = 'Rxn%d' % rxn_id
             rxn_desc = 'Rules: %s' % str(rxn["rule"])
@@ -325,6 +325,6 @@ def export(self, initials=None, param_values=None):
             doc = etree.tostring(document)
             xmldoc = xml.dom.minidom.parseString(doc)
             uglyXml = xmldoc.toprettyxml(indent='  ')
-            text_re = re.compile(">\n\s+([^<>\s].*?)\n\s+</", re.DOTALL)
-            prettyXml = text_re.sub(">\g<1></", uglyXml)
+            text_re = re.compile(r">\n\s+([^<>\s].*?)\n\s+</", re.DOTALL)
+            prettyXml = text_re.sub(r">\g<1></", uglyXml)
             return prettyXml
diff --git a/pysb/importers/bngl.py b/pysb/importers/bngl.py
index ff6e12d98..d6718d729 100644
--- a/pysb/importers/bngl.py
+++ b/pysb/importers/bngl.py
@@ -238,7 +238,7 @@ def _parse_initials(self):
             try:
                 value = float(value_param)
                 # Need to create a new parameter for the initial conc. literal
-                name = re.sub('[^\w]+', '_', i.get('name').replace(
+                name = re.sub(r'[^\w]+', '_', i.get('name').replace(
                     ')', '').replace('(', '')) + '_0'
                 try:
                     value_param = self.parameter(name, value)
diff --git a/pysb/kappa.py b/pysb/kappa.py
index b2f74eb75..c5950591c 100644
--- a/pysb/kappa.py
+++ b/pysb/kappa.py
@@ -1,4 +1,4 @@
-"""
+r"""
 Wrapper functions for running the Kappa programs *KaSim* and *KaSa*.
 
 The path to the directory containing the KaSim and KaSa executables can be
diff --git a/pysb/pattern.py b/pysb/pattern.py
index 95af8cf4e..464800fbf 100644
--- a/pysb/pattern.py
+++ b/pysb/pattern.py
@@ -1090,3 +1090,27 @@ def __cmp__(self, other):
     def _repr_species_dict(self, species_dict):
         return '{%s}' % ', '.join(["'__s%d': %s" % (k, self.species[k])
                                    for k in sorted(species_dict.keys())])
+
+
+# doctest fixtures
+
+
+def setup_module(module):
+    # Patch OrderedDict repr to match Python 3.11 and earlier.
+    global _old_od
+    _old_od = collections.OrderedDict
+    class OrderedDict(_old_od):
+        def __repr__(self):
+            if not self:
+                return '%s()' % (self.__class__.__name__,)
+            return '%s(%r)' % (self.__class__.__name__, list(self.items()))
+    collections.OrderedDict = OrderedDict
+setup_module.__test__ = False
+
+
+def teardown_module(module):
+    # Restore OrderedDict.
+    global _old_od
+    collections.OrderedDict = _old_od
+    del _old_od
+teardown_module.__test__ = False
diff --git a/pysb/tests/test_bng.py b/pysb/tests/test_bng.py
index ac24ee738..4cfc697dd 100644
--- a/pysb/tests/test_bng.py
+++ b/pysb/tests/test_bng.py
@@ -4,7 +4,7 @@
 from pysb.bng import *
 import os
 import unittest
-from nose.tools import assert_raises_regexp
+from nose.tools import assert_raises_regex
 from pysb.generator.bng import BngPrinter
 import sympy
 import math
@@ -249,7 +249,7 @@ def test_bng_error():
     Parameter('kf', 1)
     # The following rule does not specify A's site on the RHS, so should generate a BNG error
     Rule('r1', A(a='s1') >> A(), kf)
-    assert_raises_regexp(
+    assert_raises_regex(
         BngInterfaceError,
         'Molecule created in reaction rule: Component\(s\) a missing from molecule A\(\)',
         generate_equations,
diff --git a/pysb/tests/test_importers.py b/pysb/tests/test_importers.py
index 8a8da6bfd..e5f5b5c30 100644
--- a/pysb/tests/test_importers.py
+++ b/pysb/tests/test_importers.py
@@ -4,7 +4,7 @@
 from pysb.importers.bngl import model_from_bngl, BnglImportError
 from pysb.importers.sbml import model_from_sbml, model_from_biomodels
 import numpy
-from nose.tools import assert_raises_regexp, raises
+from nose.tools import assert_raises_regex, raises
 import warnings
 import mock
 import tempfile
@@ -203,7 +203,7 @@ def test_bngl_import_expected_errors():
 
     for filename, errmsg in expected_errors.items():
         full_filename = _bngl_location(filename)
-        yield (assert_raises_regexp,
+        yield (assert_raises_regex,
                BnglImportError,
                errmsg,
                bngl_import_compare_simulations,