From f2dbad637185ea403cf096ca373ea27b9f40c038 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Wed, 24 Sep 2025 14:28:17 +0300
Subject: [PATCH 01/15] style(workflows): fix formatting

---
 .github/workflows/build-and-publish.yml | 102 ++++++++++++------------
 .github/workflows/build-and-test.yml    |   5 +-
 .github/workflows/codacy-analysis.yml   |   6 +-
 .github/workflows/codeql-analysis.yml   |  70 ++++++++--------
 4 files changed, 91 insertions(+), 92 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index 626bbc7..3fb2804 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -1,4 +1,4 @@
-name: Build and publish pyfactxx 
+name: Build and publish pyfactxx
 
 on:
   release:
@@ -16,60 +16,60 @@ jobs:
         working-directory: ./FaCT++.Python
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: ilammy/msvc-dev-cmd@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel auditwheel scikit-build cmake cython
-    - name: Build a wheel
-      run: |
-        python setup.py bdist_wheel
-    - name: Audit a wheel
-      if: runner.os == 'Linux'
-      run: |
-        auditwheel repair --plat manylinux_2_27_x86_64 dist/*
-        rm -rf dist/*
-        mv wheelhouse/* dist
-    - name: Upload artifact
-      uses: actions/upload-artifact@v3
-      with:
-        name: ${{ runner.os }}-${{ matrix.python-version }}
-        path: FaCT++.Python/dist/pyfactxx*
+      - uses: actions/checkout@v3
+      - uses: ilammy/msvc-dev-cmd@v1
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel auditwheel scikit-build cmake cython
+      - name: Build a wheel
+        run: |
+          python setup.py bdist_wheel
+      - name: Audit a wheel
+        if: runner.os == 'Linux'
+        run: |
+          auditwheel repair --plat manylinux_2_27_x86_64 dist/*
+          rm -rf dist/*
+          mv wheelhouse/* dist
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: ${{ runner.os }}-${{ matrix.python-version }}
+          path: FaCT++.Python/dist/pyfactxx*
 
   publish:
     runs-on: ubuntu-latest
-    needs: build 
+    needs: build
     defaults:
       run:
         working-directory: ./FaCT++.Python
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.8
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel auditwheel scikit-build cmake cython
-    - name: Build a source distribution
-      run: |
-        python setup.py sdist
-    - name: Download artifacts
-      uses: actions/download-artifact@v3
-      with:
-        path: FaCT++.Python/wheels/
-    - name: Move wheels
-      run: |
-        mv wheels/*/*.whl dist/
-    - name: Publish packages
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
-        packages_dir: FaCT++.Python/dist
\ No newline at end of file
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install setuptools wheel auditwheel scikit-build cmake cython
+      - name: Build a source distribution
+        run: |
+          python setup.py sdist
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: FaCT++.Python/wheels/
+      - name: Move wheels
+        run: |
+          mv wheels/*/*.whl dist/
+      - name: Publish packages
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          packages_dir: FaCT++.Python/dist
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index 31dc8e8..e1649d1 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -3,13 +3,12 @@ name: Build and test pyfactxx
 on:
   workflow_dispatch:
   push:
-    branches: [ $default-branch, "wheels" ]
+    branches: [master, "wheels"]
   pull_request:
-    branches: [ $default-branch, "wheels" ]
+    branches: [master, "wheels"]
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
     defaults:
       run:
diff --git a/.github/workflows/codacy-analysis.yml b/.github/workflows/codacy-analysis.yml
index e2eba20..f6f94ef 100644
--- a/.github/workflows/codacy-analysis.yml
+++ b/.github/workflows/codacy-analysis.yml
@@ -2,12 +2,12 @@ name: Codacy Security Scan
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ master ]
+    branches: [master]
   schedule:
-    - cron: '32 23 * * 5'
+    - cron: "32 23 * * 5"
 
 jobs:
   codacy-security-scan:
diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 0c5194d..0fb60a9 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -2,12 +2,12 @@ name: "CodeQL"
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
     # The branches below must be a subset of the branches above
-    branches: [ master ]
+    branches: [master]
   schedule:
-    - cron: '30 3 * * 0'
+    - cron: "30 3 * * 0"
 
 jobs:
   analyze:
@@ -21,37 +21,37 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        language: [ 'cpp', 'java', 'python' ]
+        language: ["cpp", "java", "python"]
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file.
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
-
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v1
-
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
-
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
-
-    #- run: |
-    #   make bootstrap
-    #   make release
-
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v1
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+          # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v1
+
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
+
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
+
+      #- run: |
+      #   make bootstrap
+      #   make release
+
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v1

From 16aa4b82e5f15f786801fbdae9fcfaf8940cf3b4 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Wed, 24 Sep 2025 14:30:40 +0300
Subject: [PATCH 02/15] ci: bump actions/checkout to v5

---
 .github/workflows/build-and-publish.yml | 2 +-
 .github/workflows/build-and-test.yml    | 2 +-
 .github/workflows/codacy-analysis.yml   | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index 3fb2804..fa091c0 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -16,7 +16,7 @@ jobs:
         working-directory: ./FaCT++.Python
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
       - uses: ilammy/msvc-dev-cmd@v1
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index e1649d1..7533f26 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -18,7 +18,7 @@ jobs:
         python-version: ["3.7", "3.8", "3.9", "3.10"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v5
       - uses: ilammy/msvc-dev-cmd@v1
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v3
diff --git a/.github/workflows/codacy-analysis.yml b/.github/workflows/codacy-analysis.yml
index f6f94ef..fb22813 100644
--- a/.github/workflows/codacy-analysis.yml
+++ b/.github/workflows/codacy-analysis.yml
@@ -16,7 +16,7 @@ jobs:
     steps:
       # Checkout the repository to the GitHub Actions runner
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v5
 
       # Execute Codacy Analysis CLI and generate a SARIF output with the security issues identified during the analysis
       - name: Run Codacy Analysis CLI

From baf7b8beffaf1477dfd60b21f089f6cd0a035a08 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Fri, 10 Oct 2025 20:04:16 +0300
Subject: [PATCH 03/15] fix: find Python interpreter in virtual env first

---
 FaCT++.Python/CMakeLists.txt | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/FaCT++.Python/CMakeLists.txt b/FaCT++.Python/CMakeLists.txt
index d372039..20bf5af 100644
--- a/FaCT++.Python/CMakeLists.txt
+++ b/FaCT++.Python/CMakeLists.txt
@@ -1,7 +1,9 @@
 set(CMAKE_VERBOSE_MAKEFILE ON)
-cmake_minimum_required(VERSION 3.13.0)
+cmake_minimum_required(VERSION 3.15)
 set(CMAKE_CXX_STANDARD 11)
-find_program(PYTHON "python")
+
+set(Python_FIND_VIRTUALENV FIRST)
+find_package(Python3 COMPONENTS Interpreter)
 
 if (PYTHON)
 
@@ -19,4 +21,4 @@ if (PYTHON)
     add_custom_target(pyfactxx-build ALL DEPENDS ${OUTPUT})
 
     install(CODE "execute_process(COMMAND ${PYTHON} ${SETUP_PY} install)")
-endif()
\ No newline at end of file
+endif()

From 27de5aed904a7a199a2fbbe1b75e2c614d0ccd43 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Fri, 17 Oct 2025 16:20:05 +0300
Subject: [PATCH 04/15] fix: wrong module loading

Rename python package dir to "src" to be different from installed package.
---
 FaCT++.Python/.gitignore                      |  6 ++--
 FaCT++.Python/CMakeLists.txt                  |  2 +-
 FaCT++.Python/MANIFEST.in                     |  5 ++-
 FaCT++.Python/setup.cfg                       |  2 +-
 FaCT++.Python/setup.py                        | 32 ++++++++-----------
 .../{pyfactxx => src}/CMakeLists.txt          |  2 +-
 FaCT++.Python/{pyfactxx => src}/__init__.py   |  3 +-
 FaCT++.Python/{pyfactxx => src}/coras         |  0
 .../{pyfactxx => src}/lib_factxx.pyx          |  0
 .../{pyfactxx => }/tests/__init__.py          |  0
 .../{pyfactxx => }/tests/conftest.py          |  0
 .../{pyfactxx => }/tests/test_concept.py      |  0
 .../{pyfactxx => }/tests/test_d_role.py       |  0
 .../{pyfactxx => }/tests/test_instance.py     |  0
 .../{pyfactxx => }/tests/test_o_role.py       |  0
 .../{pyfactxx => }/tests/test_one_to_one.py   |  0
 .../tests/test_query_instances.py             |  0
 .../{pyfactxx => }/tests/test_set_op.py       |  0
 18 files changed, 22 insertions(+), 30 deletions(-)
 rename FaCT++.Python/{pyfactxx => src}/CMakeLists.txt (93%)
 rename FaCT++.Python/{pyfactxx => src}/__init__.py (99%)
 rename FaCT++.Python/{pyfactxx => src}/coras (100%)
 rename FaCT++.Python/{pyfactxx => src}/lib_factxx.pyx (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/__init__.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/conftest.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_concept.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_d_role.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_instance.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_o_role.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_one_to_one.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_query_instances.py (100%)
 rename FaCT++.Python/{pyfactxx => }/tests/test_set_op.py (100%)

diff --git a/FaCT++.Python/.gitignore b/FaCT++.Python/.gitignore
index 77b9fe4..5db6e40 100644
--- a/FaCT++.Python/.gitignore
+++ b/FaCT++.Python/.gitignore
@@ -5,9 +5,9 @@ __pycache__/
 dist/
 MANIFEST
 
-# cythonized files  
-pyfactxx/*.cpp
-pyfactxx/*.so
+# cythonized files
+src/*.cpp
+src/*.so
 
 # scikit-build files
 _skbuild/
diff --git a/FaCT++.Python/CMakeLists.txt b/FaCT++.Python/CMakeLists.txt
index 20bf5af..154d6e0 100644
--- a/FaCT++.Python/CMakeLists.txt
+++ b/FaCT++.Python/CMakeLists.txt
@@ -10,7 +10,7 @@ if (PYTHON)
     file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
 
     set(SETUP_PY    "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
-    set(DEPS        "${CMAKE_CURRENT_SOURCE_DIR}/pyfactxx/__init__.py")
+    set(DEPS        "${CMAKE_CURRENT_SOURCE_DIR}/src/__init__.py")
     set(OUTPUT      "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp")
 
     add_custom_command(OUTPUT ${OUTPUT}
diff --git a/FaCT++.Python/MANIFEST.in b/FaCT++.Python/MANIFEST.in
index 4f3040a..7fff1be 100644
--- a/FaCT++.Python/MANIFEST.in
+++ b/FaCT++.Python/MANIFEST.in
@@ -1,6 +1,5 @@
 global-include CMakeLists.txt
-prune _skbuild/ 
-recursive-include pyfactxx *.py *.pyx
-prune pyfactxx/tests
+prune _skbuild/
+recursive-include src *.py *.pyx
 graft lib
 include COPYING pyproject.toml README.md setup.py
diff --git a/FaCT++.Python/setup.cfg b/FaCT++.Python/setup.cfg
index 8c70520..4aa14c2 100644
--- a/FaCT++.Python/setup.cfg
+++ b/FaCT++.Python/setup.cfg
@@ -36,7 +36,7 @@ tests_require = pytest, pytest-cov
 formats = zip
 
 [tool:pytest]
-addopts = --cov=pyfactxx
+addopts = --cov=src
 
 [coverage:report]
 show_missing = 1
diff --git a/FaCT++.Python/setup.py b/FaCT++.Python/setup.py
index a7f7996..01cc5e9 100644
--- a/FaCT++.Python/setup.py
+++ b/FaCT++.Python/setup.py
@@ -19,35 +19,29 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-import re
 import ast
 import pathlib
-from skbuild import setup
+import re
 
+from skbuild import setup
 
 root = pathlib.Path(__file__).parent.resolve()
 DEBUG = False
 
-_version_re = re.compile(r'__version__\s+=\s+(.*)')
+_version_re = re.compile(r"__version__\s+=\s+(.*)")
 
-with open('pyfactxx/__init__.py', 'rb') as f:
-    version = str(ast.literal_eval(_version_re.search(
-        f.read().decode('utf-8')).group(1)))
+with open("src/__init__.py", "rb") as f:
+    version = str(
+        ast.literal_eval(_version_re.search(f.read().decode("utf-8")).group(1))
+    )
 
-config = 'Debug' if DEBUG else 'Release'
-cmake_args = [
-    f'-DCMAKE_BUILD_TYPE={config}',
-    f'-DPYFACTXX_ROOT={root.as_posix()}'
-]
+config = "Debug" if DEBUG else "Release"
+cmake_args = [f"-DCMAKE_BUILD_TYPE={config}", f"-DPYFACTXX_ROOT={root.as_posix()}"]
 
 setup(
     version=version,
-    packages=[
-        "pyfactxx",
-        "pyfactxx.coras"],
-    package_dir={
-        "pyfactxx": "pyfactxx", 
-        "pyfactxx.coras": "pyfactxx/coras"},
-    cmake_source_dir=str(root/'pyfactxx'),
-    cmake_args=cmake_args
+    packages=["pyfactxx", "pyfactxx.coras"],
+    package_dir={"pyfactxx": "src", "pyfactxx.coras": "src/coras"},
+    cmake_source_dir=str(root / "src"),
+    cmake_args=cmake_args,
 )
diff --git a/FaCT++.Python/pyfactxx/CMakeLists.txt b/FaCT++.Python/src/CMakeLists.txt
similarity index 93%
rename from FaCT++.Python/pyfactxx/CMakeLists.txt
rename to FaCT++.Python/src/CMakeLists.txt
index 72243ab..39aa55a 100644
--- a/FaCT++.Python/pyfactxx/CMakeLists.txt
+++ b/FaCT++.Python/src/CMakeLists.txt
@@ -18,7 +18,7 @@ target_include_directories(lib_factxx PRIVATE ${FACT_DIR} Kernel)
 target_link_libraries(lib_factxx Kernel)
 python_extension_module(lib_factxx)
 
-install(TARGETS lib_factxx LIBRARY DESTINATION pyfactxx)
+install(TARGETS lib_factxx LIBRARY DESTINATION src)
 
 set(CPACK_PROJECT_NAME ${PROJECT_NAME})
 set(CPACK_PROJECT_VERSION ${PROJECT_VERSION})
diff --git a/FaCT++.Python/pyfactxx/__init__.py b/FaCT++.Python/src/__init__.py
similarity index 99%
rename from FaCT++.Python/pyfactxx/__init__.py
rename to FaCT++.Python/src/__init__.py
index 3a64261..51019c5 100644
--- a/FaCT++.Python/pyfactxx/__init__.py
+++ b/FaCT++.Python/src/__init__.py
@@ -17,9 +17,8 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
-from .lib_factxx import Reasoner  # pylint: disable=no-name-in-module
 from .coras import Coras
-
+from .lib_factxx import Reasoner  # pylint: disable=no-name-in-module
 
 __version__ = "1.8.1"
 
diff --git a/FaCT++.Python/pyfactxx/coras b/FaCT++.Python/src/coras
similarity index 100%
rename from FaCT++.Python/pyfactxx/coras
rename to FaCT++.Python/src/coras
diff --git a/FaCT++.Python/pyfactxx/lib_factxx.pyx b/FaCT++.Python/src/lib_factxx.pyx
similarity index 100%
rename from FaCT++.Python/pyfactxx/lib_factxx.pyx
rename to FaCT++.Python/src/lib_factxx.pyx
diff --git a/FaCT++.Python/pyfactxx/tests/__init__.py b/FaCT++.Python/tests/__init__.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/__init__.py
rename to FaCT++.Python/tests/__init__.py
diff --git a/FaCT++.Python/pyfactxx/tests/conftest.py b/FaCT++.Python/tests/conftest.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/conftest.py
rename to FaCT++.Python/tests/conftest.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_concept.py b/FaCT++.Python/tests/test_concept.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_concept.py
rename to FaCT++.Python/tests/test_concept.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_d_role.py b/FaCT++.Python/tests/test_d_role.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_d_role.py
rename to FaCT++.Python/tests/test_d_role.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_instance.py b/FaCT++.Python/tests/test_instance.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_instance.py
rename to FaCT++.Python/tests/test_instance.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_o_role.py b/FaCT++.Python/tests/test_o_role.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_o_role.py
rename to FaCT++.Python/tests/test_o_role.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_one_to_one.py b/FaCT++.Python/tests/test_one_to_one.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_one_to_one.py
rename to FaCT++.Python/tests/test_one_to_one.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_query_instances.py b/FaCT++.Python/tests/test_query_instances.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_query_instances.py
rename to FaCT++.Python/tests/test_query_instances.py
diff --git a/FaCT++.Python/pyfactxx/tests/test_set_op.py b/FaCT++.Python/tests/test_set_op.py
similarity index 100%
rename from FaCT++.Python/pyfactxx/tests/test_set_op.py
rename to FaCT++.Python/tests/test_set_op.py

From d9e0210d9d2ef6f188da160c0d893265804468b4 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Fri, 17 Oct 2025 16:26:19 +0300
Subject: [PATCH 05/15] fix: do not use editable install

Editable install is broken since Setuptools 64
https://github.com/pypa/setuptools/issues/3504 Not supported by scikit-build
https://github.com/scikit-build/scikit-build/issues/740
https://github.com/scikit-build/scikit-build/issues/770
https://github.com/scikit-build/scikit-build/issues/939
---
 .github/workflows/build-and-test.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index 7533f26..3160b59 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -29,9 +29,8 @@ jobs:
           python -m pip install --upgrade pip
           pip install scikit-build cmake cython pytest pytest-cov
       - name: Install package
-        working-directory: ./FaCT++.Python
         run: |
-          pip install -e .
+          pip install .
       - name: Test with pytest
         run: |
-          pytest FaCT++.Python
+          pytest

From 9f7e05e35029dd69ed865b97d131be7842986b9f Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Fri, 17 Oct 2025 16:28:55 +0300
Subject: [PATCH 06/15] fix: bump versions of build tools and supported
 interpreters

---
 FaCT++.Python/pyproject.toml |  8 ++++----
 FaCT++.Python/setup.cfg      | 16 ++++++++--------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/FaCT++.Python/pyproject.toml b/FaCT++.Python/pyproject.toml
index a203ce9..bc76eb3 100644
--- a/FaCT++.Python/pyproject.toml
+++ b/FaCT++.Python/pyproject.toml
@@ -1,10 +1,10 @@
 [build-system]
-requires = [  
-  "setuptools>=42",
+requires = [
+  "setuptools>=64",
   "cython>0.25",
   "wheel",
   "scikit-build",
-  "cmake",
+  "cmake>=3.15",
   "ninja; platform_system!='Windows'"
 ]
-build-backend = "setuptools.build_meta"
\ No newline at end of file
+build-backend = "setuptools.build_meta"
diff --git a/FaCT++.Python/setup.cfg b/FaCT++.Python/setup.cfg
index 4aa14c2..cf97b83 100644
--- a/FaCT++.Python/setup.cfg
+++ b/FaCT++.Python/setup.cfg
@@ -8,27 +8,28 @@ maintainer_email = ir@tilde.pro
 url = https://github.com/tilde-lab/pyfactxx
 long_description = file: README.md
 long_description_content_type = text/markdown
-license = GNU GPL 3.0
-license_files = file: COPYING
+license = GPL-3.0-only
+license_files =
+    COPYING
 classifiers =
     Development Status :: 4 - Beta
     Intended Audience :: Science/Research
     Topic :: Scientific/Engineering :: Artificial Intelligence
-    License :: OSI Approved :: GNU General Public License v3 (GPLv3)
     Programming Language :: C++
     Programming Language :: Cython
     Programming Language :: Lisp
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.6
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.8
     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 :: 3.14
 
 [options]
 zip_safe = False
 include_package_data = True
-python_requires = >=3.7
+python_requires = >=3.9
 install_requires = rdflib
 tests_require = pytest, pytest-cov
 
@@ -41,4 +42,3 @@ addopts = --cov=src
 [coverage:report]
 show_missing = 1
 partial_branches = 1
-

From 9a7a3f08a988d19b6838fc0b15af8987e935d642 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Fri, 17 Oct 2025 16:29:21 +0300
Subject: [PATCH 07/15] ci: bump versions of actions and supported interpreters

---
 .github/workflows/build-and-test.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index 3160b59..79db93a 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -7,6 +7,9 @@ on:
   pull_request:
     branches: [master, "wheels"]
 
+permissions:
+  contents: read # access to check out code and install dependencies
+
 jobs:
   build:
     runs-on: ubuntu-latest
@@ -15,13 +18,13 @@ jobs:
         working-directory: ./FaCT++.Python
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
       - uses: actions/checkout@v5
       - uses: ilammy/msvc-dev-cmd@v1
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies

From a1c0c367a1f6538bf1838839edc9cc83b71c1118 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Fri, 17 Oct 2025 17:39:49 +0300
Subject: [PATCH 08/15] ci: no need to install deps manually

---
 .github/workflows/build-and-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index 79db93a..0d71e68 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -30,7 +30,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install scikit-build cmake cython pytest pytest-cov
+          pip install pytest pytest-cov
       - name: Install package
         run: |
           pip install .

From 0208e7e7c5eab44a228ce971b642a0906a16c513 Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Wed, 22 Oct 2025 23:16:49 +0300
Subject: [PATCH 09/15] ci: update build matrix

---
 .github/workflows/build-and-publish.yml | 8 ++++----
 .github/workflows/build-and-test.yml    | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index fa091c0..f38d6b4 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -9,8 +9,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: ["ubuntu-20.04", "windows-latest"]
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: ["ubuntu-22.04", "windows-2025"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
     defaults:
       run:
         working-directory: ./FaCT++.Python
@@ -32,7 +32,7 @@ jobs:
       - name: Audit a wheel
         if: runner.os == 'Linux'
         run: |
-          auditwheel repair --plat manylinux_2_27_x86_64 dist/*
+          auditwheel repair --plat manylinux_2_34_x86_64 dist/*whl
           rm -rf dist/*
           mv wheelhouse/* dist
       - name: Upload artifact
@@ -52,7 +52,7 @@ jobs:
       - name: Set up Python 3.8
         uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: 3.14
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
diff --git a/.github/workflows/build-and-test.yml b/.github/workflows/build-and-test.yml
index 0d71e68..0f7ddae 100644
--- a/.github/workflows/build-and-test.yml
+++ b/.github/workflows/build-and-test.yml
@@ -12,7 +12,7 @@ permissions:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     defaults:
       run:
         working-directory: ./FaCT++.Python

From cf3d4afd4c097b12a61eef6fb39cce902a47141c Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Wed, 22 Oct 2025 23:19:42 +0300
Subject: [PATCH 10/15] ci: update action versions

---
 .github/workflows/build-and-publish.yml | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index f38d6b4..26bbff7 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -17,9 +17,13 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
-      - uses: ilammy/msvc-dev-cmd@v1
+      - uses: actions/setup-node@v6
+        with:
+          node-version: "24"
+      # TODO: migrate to the upstream
+      - uses: knopki/msvc-dev-cmd@221ec3af3b87c0c8189236347c1c0788d2022272
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
@@ -36,7 +40,7 @@ jobs:
           rm -rf dist/*
           mv wheelhouse/* dist
       - name: Upload artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ runner.os }}-${{ matrix.python-version }}
           path: FaCT++.Python/dist/pyfactxx*
@@ -48,9 +52,9 @@ jobs:
       run:
         working-directory: ./FaCT++.Python
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v3
+      - uses: actions/checkout@v5
+      - name: Set up Python
+        uses: actions/setup-python@v6
         with:
           python-version: 3.14
       - name: Install dependencies
@@ -61,14 +65,14 @@ jobs:
         run: |
           python setup.py sdist
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v5
         with:
           path: FaCT++.Python/wheels/
       - name: Move wheels
         run: |
           mv wheels/*/*.whl dist/
       - name: Publish packages
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}

From 796d9efc92b8c48746bc7aa0309dfd36852ebc1b Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Thu, 23 Oct 2025 00:14:42 +0300
Subject: [PATCH 11/15] ci: fixes

---
 .github/workflows/build-and-publish.yml | 27 +++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build-and-publish.yml b/.github/workflows/build-and-publish.yml
index 26bbff7..7d8e642 100644
--- a/.github/workflows/build-and-publish.yml
+++ b/.github/workflows/build-and-publish.yml
@@ -4,6 +4,9 @@ on:
   release:
     types: [created]
 
+permissions:
+  contents: read # access to check out code and install dependencies
+
 jobs:
   build:
     runs-on: ${{ matrix.os }}
@@ -29,7 +32,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel auditwheel scikit-build cmake cython
+          pip install setuptools wheel scikit-build cmake cython
+      - name: Install Linux-only dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pip install auditwheel patchelf
       - name: Build a wheel
         run: |
           python setup.py bdist_wheel
@@ -46,11 +53,16 @@ jobs:
           path: FaCT++.Python/dist/pyfactxx*
 
   publish:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs: build
     defaults:
       run:
         working-directory: ./FaCT++.Python
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pyfactxx
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - uses: actions/checkout@v5
       - name: Set up Python
@@ -60,7 +72,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install setuptools wheel auditwheel scikit-build cmake cython
+          pip install setuptools wheel scikit-build cmake cython
       - name: Build a source distribution
         run: |
           python setup.py sdist
@@ -74,6 +86,9 @@ jobs:
       - name: Publish packages
         uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
-          user: __token__
-          password: ${{ secrets.PYPI_API_TOKEN }}
-          packages_dir: FaCT++.Python/dist
+          packages-dir: FaCT++.Python/dist/
+          # # useful for testing:
+          # verbose: true
+          # repository-url: https://test.pypi.org/legacy/
+          # user: __token__
+          # password: ${{ secrets.PYPI_API_TOKEN }}

From 897e434e49620564aea932bab3e3734145e6dd6f Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Thu, 23 Oct 2025 00:26:24 +0300
Subject: [PATCH 12/15] fix: bump min cmake version to 3.15

---
 CMakeLists.txt                   | 2 +-
 FaCT++.C/CMakeLists.txt          | 2 +-
 FaCT++.JNI/CMakeLists.txt        | 2 +-
 FaCT++.Python/src/CMakeLists.txt | 2 +-
 FaCT++/CMakeLists.txt            | 2 +-
 Kernel/CMakeLists.txt            | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 550231d..1b81c7f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.15)
 project(factplusplus)
 
 # global definition
diff --git a/FaCT++.C/CMakeLists.txt b/FaCT++.C/CMakeLists.txt
index 93455fd..fec14d4 100644
--- a/FaCT++.C/CMakeLists.txt
+++ b/FaCT++.C/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 3.15)
 
 set(SOURCE_FILES
 	fact.cpp
diff --git a/FaCT++.JNI/CMakeLists.txt b/FaCT++.JNI/CMakeLists.txt
index 3c146d9..56a9b27 100644
--- a/FaCT++.JNI/CMakeLists.txt
+++ b/FaCT++.JNI/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 3.15)
 
 # We are using JNI and need to #include <jni.h>
 find_package(JNI REQUIRED)
diff --git a/FaCT++.Python/src/CMakeLists.txt b/FaCT++.Python/src/CMakeLists.txt
index 39aa55a..6147375 100644
--- a/FaCT++.Python/src/CMakeLists.txt
+++ b/FaCT++.Python/src/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.13.0)
+cmake_minimum_required(VERSION 3.15)
 project(pyfactxx)
 set(CMAKE_CXX_STANDARD 11)
 include(CMakePrintHelpers)
diff --git a/FaCT++/CMakeLists.txt b/FaCT++/CMakeLists.txt
index 040bf38..305a317 100644
--- a/FaCT++/CMakeLists.txt
+++ b/FaCT++/CMakeLists.txt
@@ -1,5 +1,5 @@
 project(FaCT++)
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 3.15)
 
 set(SOURCE_FILES
 	AD.cpp
diff --git a/Kernel/CMakeLists.txt b/Kernel/CMakeLists.txt
index f287b74..1422d7e 100644
--- a/Kernel/CMakeLists.txt
+++ b/Kernel/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 3.15)
 
 set(SOURCE_FILES
 	Actor.cpp

From 072e8189a5534aaec97e22fb1e52f8e6a67cfa0d Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Thu, 23 Oct 2025 14:40:36 +0300
Subject: [PATCH 13/15] ci: fix codacy

---
 .github/workflows/codacy-analysis.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/codacy-analysis.yml b/.github/workflows/codacy-analysis.yml
index fb22813..2ade04b 100644
--- a/.github/workflows/codacy-analysis.yml
+++ b/.github/workflows/codacy-analysis.yml
@@ -36,6 +36,10 @@ jobs:
 
       # Upload the SARIF file generated in the previous step
       - name: Upload SARIF results file
-        uses: github/codeql-action/upload-sarif@v1
+        uses: github/codeql-action/upload-sarif@v4
+        # Codacy is broken now
+        # https://github.com/codacy/codacy-analysis-cli/issues/541
+        continue-on-error: true
         with:
           sarif_file: results.sarif
+          wait-for-processing: true

From eb2edd704a740eaac91c0b4fd8043154e7bed3ed Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Thu, 23 Oct 2025 14:40:44 +0300
Subject: [PATCH 14/15] ci: fix codeql

---
 .github/workflows/codeql-analysis.yml | 22 +++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml
index 0fb60a9..3826736 100644
--- a/.github/workflows/codeql-analysis.yml
+++ b/.github/workflows/codeql-analysis.yml
@@ -12,7 +12,7 @@ on:
 jobs:
   analyze:
     name: Analyze
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     permissions:
       actions: read
       contents: read
@@ -29,7 +29,7 @@ jobs:
 
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v1
+        uses: github/codeql-action/init@v3
         with:
           languages: ${{ matrix.language }}
           # If you wish to specify custom queries, you can do so here or in a config file.
@@ -40,7 +40,8 @@ jobs:
       # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
       # If this step fails, then you should remove it and run the build manually (see below)
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v1
+        if: matrix.language != 'cpp'
+        uses: github/codeql-action/autobuild@v3
 
       # ℹ️ Command-line programs to run using the OS shell.
       # 📚 https://git.io/JvXDl
@@ -49,9 +50,16 @@ jobs:
       #    and modify them (or add more) to build your code if your project
       #    uses a compiled language
 
-      #- run: |
-      #   make bootstrap
-      #   make release
+      - name: Install dependencies
+        if: matrix.language == 'cpp'
+        run: |
+          sudo apt-get update
+          sudo apt-get install cmake default-jdk
+      - name: Build
+        if: matrix.language == 'cpp'
+        run: |
+          cmake .
+          make
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v1
+        uses: github/codeql-action/analyze@v3

From f5cff44fc53713409a3426c7d3b6050acd9accbb Mon Sep 17 00:00:00 2001
From: Sergei Korolev <knopki@duck.com>
Date: Thu, 23 Oct 2025 16:23:13 +0300
Subject: [PATCH 15/15] fix: port to GCC 13 (Ubuntu 24.04)

---
 Kernel/flags.h | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Kernel/flags.h b/Kernel/flags.h
index 418577a..213197b 100644
--- a/Kernel/flags.h
+++ b/Kernel/flags.h
@@ -16,6 +16,7 @@ You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 */
+#include <cstdint>
 
 #ifndef FLAGS_H
 #define FLAGS_H