Merge branch 'issue_483' into integrate_llm

Author: tturocy

.clang-tidy

@@ -7,15 +7,12 @@ Checks: |
   -modernize-avoid-c-arrays,
   -modernize-pass-by-value,
   -modernize-use-nodiscard,
-  -modernize-concat-nested-namespaces,
   cppcoreguidelines-pro-type-cstyle-cast,
   cppcoreguidelines-pro-type-member-init,
   cppcoreguidelines-prefer-member-initializer,
   misc-const-correctness
 WarningsAsErrors: '*'
-# Don't bother with wxWidgets headers
-HeaderFilterRegex: '^((?!labenski).)*$'
-AnalyzeTemporaryDtors: false
+HeaderFilterRegex: '.*'
 FormatStyle:     none
 User:            arbiter
 CheckOptions:

.github/workflows/python.yml

@@ -10,7 +10,7 @@ jobs:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
     strategy:
       matrix:
-        python-version: ['3.9', '3.12']
+        python-version: ['3.9', '3.13']
 
     steps:
       - uses: actions/checkout@v4
@@ -21,10 +21,10 @@ jobs:
       - name: Set up dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools cython pytest wheel lxml numpy scipy
+          pip install setuptools build cython pytest pytest-skip-slow wheel lxml numpy scipy
       - name: Build source distribution
         run:
-          python setup.py sdist
+          python -m build
       - name: Build from source distribution
         run: |
           cd dist
@@ -37,7 +37,7 @@ jobs:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
     strategy:
       matrix:
-        python-version: ['3.12']
+        python-version: ['3.13']
 
     steps:
       - uses: actions/checkout@v4
@@ -48,7 +48,7 @@ jobs:
       - name: Set up dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install cython pytest wheel lxml numpy scipy
+          pip install cython pytest pytest-skip-slow wheel lxml numpy scipy
       - name: Build extension
         run: |
           python -m pip install -v .
@@ -60,7 +60,7 @@ jobs:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
     strategy:
       matrix:
-        python-version: ['3.12']
+        python-version: ['3.13']
 
     steps:
       - uses: actions/checkout@v4
@@ -71,7 +71,7 @@ jobs:
       - name: Set up dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install cython pytest wheel lxml numpy scipy
+          pip install cython pytest pytest-skip-slow wheel lxml numpy scipy
       - name: Build extension
         run: |
           python -m pip install -v .
@@ -83,7 +83,7 @@ jobs:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
     strategy:
       matrix:
-        python-version: ['3.12']
+        python-version: ['3.13']
 
     steps:
       - uses: actions/checkout@v4
@@ -94,7 +94,7 @@ jobs:
       - name: Set up dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install cython pytest wheel lxml numpy scipy
+          pip install cython pytest pytest-skip-slow wheel lxml numpy scipy
       - name: Build extension
         run: |
           python -m pip install -v .

ChangeLog

@@ -2,8 +2,10 @@
 
 ## [16.4.0] - unreleased
 
-### Removed
+### General
+- Officially added support for Python 3.13.
 
+### Removed
 - The deprecated functions `Game.read_game`, `Game.parse_game` and `Game.write` functions have
   been removed as planned. (#357)
 
@@ -57,6 +59,12 @@
   Explorer, as GTE no longer reads files in this format.
 
 
+## [16.2.2] - unreleased
+
+### Fixed
+- `Game.copy_tree` and `Game.move_tree` implementations reversed the roles of the
+  `src` and `dest` nodes (#499)
+
 ## [16.2.1] - 2025-01-06
 
 ### Fixed
@@ -67,7 +75,6 @@
 - Attempting to call the default constructor on Game objects (rather than one of the factory
   functions) now raises a more informative exception (#463)
 
-
 ## [16.2.0] - 2024-04-05
 
 ### Fixed

Makefile.am

@@ -245,6 +245,8 @@ EXTRA_DIST = \
 	src/README.rst
 
 core_SOURCES = \
+    src/core/core.h \
+    src/core/util.h \
 	src/core/array.h \
 	src/core/list.h \
 	src/core/vector.h \
@@ -636,8 +638,7 @@ msw-msi:
 	light -ext WixUIExtension gambit.wixobj
 
 clang-tidy:
-	clang-tidy ${top_srcdir}/src/core/*.cc -- --std=c++17 -I ${top_srcdir}/src -I ${top_srcdir}/src/labenski/include -DVERSION="" ${WX_CXXFLAGS}
-	clang-tidy ${top_srcdir}/src/games/*.cc ${top_srcdir}/src/games/*/*.cc -- --std=c++17 -I ${top_srcdir}/src -I ${top_srcdir}/src/labenski/include -DVERSION="" ${WX_CXXFLAGS}
-	clang-tidy ${top_srcdir}/src/solvers/*/*.cc -- --std=c++17 -I ${top_srcdir}/src -I ${top_srcdir}/src/labenski/include -DVERSION="" ${WX_CXXFLAGS}
-	clang-tidy ${top_srcdir}/src/tools/*/*.cc -- --std=c++17 -I ${top_srcdir}/src -I ${top_srcdir}/src/labenski/include -DVERSION="" ${WX_CXXFLAGS}
-	clang-tidy ${top_srcdir}/src/gui/*.cc -- --std=c++17 -I ${top_srcdir}/src -I ${top_srcdir}/src/labenski/include -DVERSION="" ${WX_CXXFLAGS}
+	clang-tidy ${top_srcdir}/src/core/*.cc -- --std=c++17 -I ${top_srcdir}/src -DVERSION=""
+	clang-tidy ${top_srcdir}/src/games/*.cc ${top_srcdir}/src/games/*/*.cc -- --std=c++17 -I ${top_srcdir}/src -DVERSION=""
+	clang-tidy ${top_srcdir}/src/solvers/*/*.cc -- --std=c++17 -I ${top_srcdir}/src -DVERSION=""
+	clang-tidy ${top_srcdir}/src/tools/*/*.cc -- --std=c++17 -I ${top_srcdir}/src -DVERSION=""

pyproject.toml

@@ -1,5 +1,42 @@
 [build-system]
 requires = ["setuptools", "wheel", "Cython"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pygambit"
+version = "16.3.0"
+description = "The package for computation in game theory"
+readme = "src/README.rst"
+requires-python = ">=3.9"
+license = "GPL-2.0-or-later"
+authors = [
+    {name = "Theodore Turocy", email = "ted.turocy@gmail.com"},
+    {name = "Rahul Savani", email = "rahul.savani@liverpool.ac.uk"}
+]
+keywords = ["game theory", "Nash equilibrium"]
+classifiers=[
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering :: Mathematics"
+]
+dependencies = [
+    "numpy",
+    "scipy",
+]
+
+[project.urls]
+Homepage = "https://www.gambit-project.org"
+Documentation = "https://gambitproject.readthedocs.io"
+Repository = "https://github.com/gambitproject/gambit.git"
+Issues = "https://github.com/gambitproject/gambit/issues"
+Changelog = "https://github.com/gambitproject/gambit/blob/master/ChangeLog"
+
 
 [tool.ruff]
 line-length = 99
@@ -33,3 +70,16 @@ indent-style = "space"
 
 [tool.cython-lint]
 max-line-length = 99
+
+
+[tool.pytest.ini_options]
+addopts = "--strict-markers"
+markers = [
+    "nash_enummixed_strategy: tests of enummixed_solve in strategies",
+    "nash_lcp_strategy: tests of lcp_solve in strategies",
+    "nash_lcp_behavior: tests of lcp_solve in behaviors",
+    "nash_lp_strategy: tests of lp_solve in strategies",
+    "nash_lp_behavior: tests of lp_solve in behaviors",
+    "nash: all tests of Nash equilibrium solvers",
+    "slow: all time-consuming tests",
+]

setup.py

@@ -99,44 +99,7 @@ def solver_library_config(library_name: str, paths: list) -> tuple:
     )
 )
 
-
-def readme():
-    with open("src/README.rst") as f:
-        return f.read()
-
-
 setuptools.setup(
-    name="pygambit",
-    version="16.3.0",
-    description="The package for computation in game theory",
-    long_description=readme(),
-    classifiers=[
-        "Development Status :: 5 - Production/Stable",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Programming Language :: Python :: Implementation :: CPython",
-        "Topic :: Scientific/Engineering :: Mathematics"
-    ],
-    keywords="game theory Nash equilibrium",
-    license="GPL2+",
-    author="Theodore Turocy",
-    author_email="ted.turocy@gmail.com",
-    url="https://www.gambit-project.org",
-    project_urls={
-        "Documentation": "https://gambitproject.readthedocs.io/",
-        "Source": "https://github.com/gambitproject/gambit",
-        "Tracker": "https://github.com/gambitproject/gambit/issues",
-    },
-    python_requires=">=3.9",
-    install_requires=[
-        "numpy",
-        "scipy",
-        "deprecated",
-    ],
     libraries=[cppgambit_bimatrix, cppgambit_liap, cppgambit_logit, cppgambit_simpdiv,
                cppgambit_gtracer, cppgambit_enumpoly,
                cppgambit_games, cppgambit_core],

src/core/array.h

@@ -2,7 +2,7 @@
 // This file is part of Gambit
 // Copyright (c) 1994-2025, The Gambit Project (https://www.gambit-project.org)
 //
-// FILE: src/libgambit/array.h
+// FILE: src/core/array.h
 // A basic bounds-checked array type
 //
 // This program is free software; you can redistribute it and/or modify
@@ -20,12 +20,14 @@
 // Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
 //
 
-#ifndef LIBGAMBIT_ARRAY_H
-#define LIBGAMBIT_ARRAY_H
+#ifndef GAMBIT_CORE_ARRAY_H
+#define GAMBIT_CORE_ARRAY_H
 
 #include <vector>
 #include <iterator>
 
+#include "util.h"
+
 namespace Gambit {
 
 /// \brief An extension of std::vector to have arbitrary offset index
@@ -282,4 +284,4 @@ template <class T> void erase_atindex(Array<T> &p_array, int p_index)
 
 } // end namespace Gambit
 
-#endif // LIBGAMBIT_ARRAY_H
+#endif // GAMBIT_CORE_ARRAY_H

src/core/core.h

@@ -0,0 +1,34 @@
+//
+// This file is part of Gambit
+// Copyright (c) 1994-2025, The Gambit Project (https://www.gambit-project.org)
+//
+// FILE: src/core/core.h
+// Core (game theory-independent) declarations and utilities for Gambit
+//
+// This program is free software; you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation; either version 2 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program; if not, write to the Free Software
+// Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+//
+
+#ifndef GAMBIT_CORE_CORE_H
+#define GAMBIT_CORE_CORE_H
+
+#include "util.h"
+#include "array.h"
+#include "list.h"
+#include "recarray.h"
+#include "vector.h"
+#include "matrix.h"
+#include "rational.h"
+
+#endif // GAMBIT_CORE_CORE_H