chore: Sync 'master' into 'devel'

.editorconfig

@@ -10,7 +10,7 @@ indent_size = 4
 insert_final_newline = true
 trim_trailing_whitespace = true
 
-[*.{md,toml,yml,yaml,nix,html,css}]
+[{*.{md,toml,yml,yaml,nix,html,css,just},justfile}]
 indent_size = 2
 
 [{**/Makefile,**/CMakeLists.txt}]

CMakeLists.txt

@@ -121,43 +121,48 @@ add_subdirectory (3rdparty/re2 EXCLUDE_FROM_ALL)
 add_subdirectory (3rdparty/simlib EXCLUDE_FROM_ALL)
 add_subdirectory (3rdparty/cudd EXCLUDE_FROM_ALL)
 
-if (MATA_BUILD_EXAMPLES)
+if ((CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME) AND MATA_BUILD_EXAMPLES)
+	message ("-- Building examples")
 	add_subdirectory (examples)
 endif ()
 
 # Build tests only if Mata is the main project and we enabled testing
 if ((CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME) AND BUILD_TESTING)
+	message ("-- Building tests")
 	add_subdirectory (tests)
 	add_subdirectory (tests-integration)
 endif ()
 
 
 ##### INSTALLING AND UNINSTALLING #####
-install (TARGETS libmata cudd_headers simlib_headers
-    EXPORT mataTargets
+install (
+	TARGETS libmata cudd_headers simlib_headers
+	EXPORT mataTargets
 	ARCHIVE DESTINATION lib
 )
 # TODO: should headers be installed in some nicer way? there is something called FILE_SET in cmake, but I do not feel it will make it better
 install(
-    DIRECTORY
-        ${PROJECT_SOURCE_DIR}/include/
-        ${PROJECT_SOURCE_DIR}/3rdparty/cudd/include/ # TODO remove this after we remove PUBLIC dependency on CUDD
-        ${PROJECT_SOURCE_DIR}/3rdparty/simlib/include/ # TODO remove this after we remove PUBLIC dependency on simlib
-    DESTINATION include
+	DIRECTORY
+		${PROJECT_SOURCE_DIR}/include/
+		${PROJECT_SOURCE_DIR}/3rdparty/cudd/include/ # TODO remove this after we remove PUBLIC dependency on CUDD
+		${PROJECT_SOURCE_DIR}/3rdparty/simlib/include/ # TODO remove this after we remove PUBLIC dependency on simlib
+	DESTINATION include
 )
-install(EXPORT mataTargets
-    # NAMESPACE mata:: # for modern cmake, commented out because I am not sure what could break with it
-    DESTINATION lib/cmake/mata
+install(
+	EXPORT mataTargets
+	# NAMESPACE mata:: # for modern cmake, commented out because I am not sure what could break with it
+	DESTINATION lib/cmake/mata
 )
 
 include(CMakePackageConfigHelpers)
-configure_package_config_file(
-    cmake/mataConfig.cmake.in       # your template
-    "${CMAKE_CURRENT_BINARY_DIR}/mataConfig.cmake"  # output
-    INSTALL_DESTINATION lib/cmake/mata
+configure_package_config_file(cmake/mataConfig.cmake.in
+	"${CMAKE_CURRENT_BINARY_DIR}/mataConfig.cmake"
+	INSTALL_DESTINATION lib/cmake/mata
+)
+install(
+	FILES "${CMAKE_CURRENT_BINARY_DIR}/mataConfig.cmake"
+	DESTINATION lib/cmake/mata
 )
-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/mataConfig.cmake"
-        DESTINATION lib/cmake/mata)
 
 
 # Uninstall target from https://gitlab.kitware.com/cmake/community/-/wikis/FAQ#can-i-do-make-uninstall-with-cmake

README.md

@@ -49,34 +49,34 @@ The Mata library further depends on the following libraries, included in the `./
 
 To build the library, run the following:
 
-```
+```shell
 git clone https://github.com/VeriFIT/mata
 cd mata
 make release
 ```
 
 In order to install the library, you can run
 
-```
+```shell
 sudo make install
 ```
 
 In order to verify the functionality of the library, you can run the test suite:
 
-```
+```shell
 make test
 ```
 
 You might, need to install the dependencies to measure the coverage of the tests.
 Run the following to install the dependencies for MacOS:
 
-```
+```shell
 brew install lcov gcovr
 ```
 
 Run the following to install the dependencies for Ubuntu:
 
-```
+```shell
 sudo apt install -y build-essential lcov gcovr xdg-utils
 ```
 
@@ -87,9 +87,12 @@ package on your system as follows.
 
 ### Installation from PyPI
 
-To install a latest version from the PyPI repository, run
+To install a latest version from the PyPI repository, run:
 
-```
+```shell
+# Using uv:
+uv add libmata
+# Or using pip:
 pip3 install libmata
 ```
 
@@ -98,7 +101,15 @@ pip3 install libmata
 To build from sources first, install the necessary requirements for Python and your
 system. We recommend using the virtual environemnt (`venv`) to install and use the library.
 
+Using `uv`:
+
+```shell
+uv sync --python 3.13
 ```
+
+Or using `pip`:
+
+```shell
 python -m pip install --upgrade pip
 make -C bindings/python init
 
@@ -108,13 +119,13 @@ sudo apt -qq install -y graphviz graphviz-dev
 
 Now, you can install the library.
 
-```
+```shell
 make -C bindings/python install
 ```
 
 Finally, you can verify the binding woks as expected by running the test suite:
 
-```
+```shell
 make -C bindings/python test
 ```
 
@@ -125,21 +136,21 @@ This directory contains examples of various usage in form of:
 
 1. C/C++ example programs. By default, they are built with the library. To run for example the first example:
 
-```
+```shell
 ./build/examples/example01-simple
 ```
 
 3. Python example scripts. To run the scripts run the following.
 
-```
-python examples/example01-python-binding.py
+```shell
+python3 examples/example01-python-binding.py
 ```
 
 4. Python jupyter notebooks. To run the jupyter notebook, one needs to have jupyter installed as
    a prerequisite. The run the jupyter notebook, that creates an instance on your local server.
    Navigate to generated link to see the available jupyter notebooks:
 
-```
+```shell
 pip3 install jupyter
 jupyter notebook
 ```

bindings/python/libmata/nfa/nfa.pyx

@@ -326,17 +326,17 @@ cdef class Nfa:
         """
         self.thisptr.get().final.erase(state)
 
-    def clear_final(self) -> Self:
+    def clear_final(self) -> Nfa:
         """Clears final state set of the automaton."""
         self.thisptr.get().final.clear()
         return self
 
-    def unify_initial(self, bool force_new_state = False) -> Self:
+    def unify_initial(self, bool force_new_state = False) -> Nfa:
         """Unify initial states into a single new initial state."""
         self.thisptr.get().unify_initial(force_new_state)
         return self
 
-    def unify_final(self, bool force_new_state = False) -> Self:
+    def unify_final(self, bool force_new_state = False) -> Nfa:
         """Unify final states into a single new final state."""
         self.thisptr.get().unify_final(force_new_state)
 
@@ -518,7 +518,7 @@ cdef class Nfa:
         Remove states which are not accessible (unreachable; state is accessible when the state is the endpoint of a path
          starting from an initial state) or not co-accessible (non-terminating; state is co-accessible when the state is
          the starting point of a path ending in a final state).
-        :return: Self.
+        :return: Nfa.
         """
         self.thisptr.get().trim(NULL)
         return self
@@ -530,7 +530,7 @@ cdef class Nfa:
          starting from an initial state) or not co-accessible (non-terminating; state is co-accessible when the state is
          the starting point of a path ending in a final state).
 
-        :return: Self, State map of original to new states.
+        :return: Nfa, State map of original to new states.
         """
         cdef StateRenaming state_map
         self.thisptr.get().trim(&state_map)
@@ -539,15 +539,15 @@ cdef class Nfa:
     def concatenate(self, Nfa other) -> Nfa:
         """Concatenate 'self' with 'other' in-place.
 
-        :return: Self
+        :return: Nfa
         """
         self.thisptr.get().concatenate(dereference(other.thisptr.get()))
         return self
 
     def union(self, Nfa other) -> Nfa:
         """Make union of 'self' with 'other' in-place.
 
-        :return: Self
+        :return: Nfa
         """
         self.thisptr.get().unite_nondet_with(dereference(other.thisptr.get()))
         return self

bindings/python/pyproject.toml

@@ -1,24 +1,40 @@
 [project]
 name = "libmata"
 dynamic = ["version"]
-description = "Mata Python bindings"
+description = "Python bindings for Mata: A fast and simple automata library"
 readme = "README.md"
 requires-python = ">=3.13"
+keywords = ["automata", "finite automata", "alternating automata"]
+authors = [
+  { name = "Lukáš Holík", email = "holik@fit.vutbr.cz" },
+  { name = "Ondřej Lengál", email = "lengal@fit.vutbr.cz" },
+  { name = "Martin Hruška", email = "ihruskam@fit.vutbr.cz" },
+  { name = "Tomáš Fiedor", email = "ifiedortom@fit.vutbr.cz" },
+  { name = "David Chocholatý", email = "chocholaty.david@protonmail.com" },
+  { name = "Juraj Síč", email = "sicjuraj@fit.vutbr.cz" },
+  { name = "Tomáš Vojnar", email = "vojnar@fit.vutbr.cz" },
+]
 dependencies = [
   "coverage>=6.4.1",
   "cython>=0.29.32",
-  "graphviz>=0.20.0",
-  "ipykernel>=7.2.0",
+  "graphviz>=0.20.1",
+  "ipykernel>=7.1.0",
   "ipython>=7.9.0",
   "networkx>=2.6.3",
   "pandas>=1.3.5",
-  "papermill>=2.7.0",
+  "papermill>=2.6.0",
   "pytest>=3.6.4",
   "pytest-cov>=3.0.0",
   "seaborn>=0.13.2",
-  "setuptools>=82.0.1",
   "tabulate>=0.8.10",
 ]
+
+[project.urls]
+Homepage = "https://github.com/VeriFIT/mata"
+
+[tool.setuptools]
+packages = ["libmata", "libmata.nfa"]
+
 [build-system]
 requires = ["setuptools", "wheel", "Cython>=0.29.32"]
 build-backend = "setuptools.build_meta"

bindings/python/setup.py

@@ -249,38 +249,7 @@ def run_safely_external_command(
 
 
 setup(
-    name="libmata",
-    packages=["libmata", "libmata.nfa"],
-    package_dir={'libmata': 'libmata', 'libmata.nfa': os.path.join('libmata', 'nfa')},
     version=get_version(),
-    ext_modules=cythonize(
-        extensions,
-        compiler_directives={'language_level': "3"}
-    ),
-    description="The automata library",
-    author="Lukáš Holík <holik@fit.vutbr.cz>, "
-                "Ondřej Lengál <lengal@fit.vutbr.cz>, "
-                "Martin Hruška <ihruskam@fit.vutbr.cz>, "
-                "Tomáš Fiedor <ifiedortom@fit.vutbr.cz>, "
-                "David Chocholatý <chocholaty.david@protonmail.com>, "
-                "Juraj Síč <sicjuraj@fit.vutbr.cz>, "
-                "Tomáš Vojnar <vojnar@fit.vutbr.cz>",
-    author_email="holik@fit.vutbr.cz",
-    long_description=README_MD,
-    long_description_content_type="text/markdown",
-    keywords="automata, finite automata, alternating automata",
-    url="https://github.com/verifit/mata",
-    cmdclass={
-        'sdist': sdist,
-        'build_ext': build_ext
-    },
-    # Requirements from install for pip
-    install_requires=[
-        'Cython>=0.29.32',
-        'tabulate>=0.8.10',
-        'ipython>=7.9.0',
-        'pandas>=1.3.5',
-        'networkx>=2.6.3',
-        'graphviz>=0.10.1',
-    ]
+    ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}),
+    cmdclass={"sdist": sdist, "build_ext": build_ext},
 )

examples/CMakeLists.txt

@@ -1,6 +1,8 @@
-file(GLOB MATA_EXAMPLES "${CMAKE_CURRENT_SOURCE_DIR}/*.cc")
+file(GLOB_RECURSE MATA_EXAMPLES CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/*.cc")
 foreach(MATA_EXAMPLE ${MATA_EXAMPLES})
-    get_filename_component(MATA_EXAMPLE_NAME ${MATA_EXAMPLE} NAME_WE)
-    add_executable(${MATA_EXAMPLE_NAME} ${MATA_EXAMPLE})
-    target_link_libraries(${MATA_EXAMPLE_NAME} PRIVATE libmata)
-endforeach()
+	file(RELATIVE_PATH MATA_EXAMPLE_REL "${CMAKE_CURRENT_SOURCE_DIR}" "${MATA_EXAMPLE}")
+	string(REPLACE "/" "-" MATA_EXAMPLE_NAME "${MATA_EXAMPLE_REL}")
+	string(REPLACE ".cc" "" MATA_EXAMPLE_NAME "${MATA_EXAMPLE_NAME}")
+	add_executable(${MATA_EXAMPLE_NAME} ${MATA_EXAMPLE})
+	target_link_libraries(${MATA_EXAMPLE_NAME} PRIVATE libmata)
+endforeach()

examples/Makefile

@@ -0,0 +1,24 @@
+# Makefile wrapper for building/running selected MATA examples via CMake.
+
+ROOT_DIR ?= ..
+BUILD_DIR ?= $(ROOT_DIR)/build
+CMAKE_BUILD_TYPE ?= Debug
+JOBS ?= 6
+
+EXAMPLE ?= example01-simple
+
+.PHONY: all configure build run clean
+
+all: build
+
+configure:
+	cmake -S $(ROOT_DIR) -B $(BUILD_DIR) -DCMAKE_BUILD_TYPE=$(CMAKE_BUILD_TYPE)
+
+build: configure
+	cmake --build $(BUILD_DIR) --parallel $(JOBS)
+
+run: build
+	$(BUILD_DIR)/examples/$(EXAMPLE)
+
+clean:
+	rm -f $(BUILD_DIR)/examples/$(EXAMPLE)

examples/notebooks/jupytext.toml

@@ -0,0 +1 @@
+formats = "ipynb,py:percent"

examples/notebooks/run_papermill_examples.sh

@@ -1,9 +1,13 @@
-#!/usr/bin/env sh
+#!/usr/bin/env bash
 
 set -euo pipefail
 
-papermill ./example-01-ws1s-formulae.ipynb tmp_out.ipynb
-papermill ./example-02-redos-attacks.ipynb tmp_out.ipynb
-papermill ./example-03-exploring-maze.ipynb tmp_out.ipynb
-papermill ./example-04-visualization.ipynb tmp_out.ipynb
-rm tmp_out.ipynb
+SCRIPT_DIR="$(dirname "$0")"
+
+TMP_OUT="$(mktemp --tmpdir mata-papermill-XXXXXX.ipynb)"
+trap 'rm -f "$TMP_OUT"' EXIT
+
+for file in "$SCRIPT_DIR"/*.ipynb; do
+    echo "Running: $file."
+    papermill "$file" "$TMP_OUT"
+done