diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 7270ee84..289e50d9 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -62,13 +62,8 @@ jobs:
           etc/make-doc.sh  # so that all files are generated!
           cd docs
           python -m sphinx -b doctest -d _build/doctrees source _build/doctest
-      - name: "Pip3 installing pylint + cpplint . . ."
-        run: |
-          pip3 install pylint cpplint
-      - name: "Running pylint and cpplint . . ."
-        run: |
-          python -m pylint setup.py tests/*.py libsemigroups_pybind11/*.py
-          python -m cpplint src/*.hpp src/*.cpp
+      - name: "Running ruff, pylint and cpplint . . ."
+        run: make lint
   macosx:
     strategy:
       fail-fast: false
@@ -127,10 +122,5 @@ jobs:
           etc/make-doc.sh  # so that all files are generated!
           cd docs
           python -m sphinx -b doctest -d _build/doctrees source _build/doctest
-      - name: "Pip3 installing pylint + cpplint . . ."
-        run: |
-          pip3 install pylint cpplint
-      - name: "Running pylint and cpplint . . ."
-        run: |
-          python -m pylint setup.py tests/*.py libsemigroups_pybind11/*.py
-          python -m cpplint src/*.hpp src/*.cpp
+      - name: "Running ruff, pylint and cpplint . . ."
+        run: make lint
diff --git a/.gitignore b/.gitignore
index c224cfdb..11477e00 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,3 +20,4 @@ docs/source/api/Transf.rst
 gh-pages/
 htmlcov
 .cache
+src/libsemigroups_pybind11/_version.py
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 7492f97d..ca684f8d 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -208,13 +208,14 @@ A class with no helpers or templates
 ____________________________________
 
 If the class you are binding has no templates or helper functions, then you
-need to add it to the list imports in `<libsemigroups_pybind11/__init__.py>`__.
+need to add it to the list imports in 
+`<src/libsemigroups_pybind11/__init__.py>`__.
 
 A class with helpers
 ____________________
 
 If a class has a helper namespace, this should be respected in Python by
-creating a module with the same name in the ``libsemigroups_pybind11``
+creating a module with the same name in the ``src/libsemigroups_pybind11``
 directory. In that module, all of the relevant helper functions should be
 imported from ``_libsemigroups_pybind11``.
 
@@ -226,7 +227,7 @@ will be one class for each combination of templates. Instead of calling these
 directly, a Python function should be created that acts as a constructor, that
 then calls the the corresponding ``_libsemigroups_pybind11`` constructor
 depending on the keyword arguments specified. This function should then be
-imported in `<libsemigroups_pybind11/__init__.py>`__.
+imported in `<src/libsemigroups_pybind11/__init__.py>`__.
 
 The documentation
 -----------------
@@ -439,10 +440,10 @@ whilst contributing are::
   │       └── index.rst
   ├── etc/
   │   └── replace-string-in-doc.py
-  ├── libsemigroups_pybind11/
-  │   ├── __init__.py
-  │   └── class_name.py
   ├── src/
+  |   ├──libsemigroups_pybind11/
+  │   |   ├── __init__.py
+  │   |   └── class_name.py
   │   └── class-name.cpp
   ├── tests/
   │   └── test_class_name.py
diff --git a/MANIFEST.in b/MANIFEST.in
index 5cfff31e..bcf45a12 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1 +1,2 @@
-include src/*.hpp
+graft src
+include tests/*.py
diff --git a/Makefile b/Makefile
index 152f90a7..b5110522 100644
--- a/Makefile
+++ b/Makefile
@@ -19,15 +19,13 @@ install:
 	pip3 install . --use-feature=in-tree-build
 
 black:
-	black setup.py tests/*.py libsemigroups_pybind11/*.py docs/source/conf.py
+	black setup.py tests/*.py src/libsemigroups_pybind11/*.py docs/source/conf.py
 
 check: doctest
 	pytest -vv tests/test_*.py
 
 lint:
-	ruff check --exit-zero setup.py tests/*.py libsemigroups_pybind11/*.py docs/source/*.py
-	pylint --exit-zero setup.py tests/*.py libsemigroups_pybind11/*.py libsemigroups_pybind11/**/*.py
-	cpplint src/*.hpp src/*.cpp
+	etc/make-lint.sh
 
 coverage:
 	@coverage run --source . --omit="tests/*" -m pytest tests/test_*.py
@@ -39,8 +37,8 @@ clean-doc:
 	rm -rf docs/_build
 
 clean: clean-doc
-	rm -rf __pycache__ libsemigroups_pybind11.egg-info
-	rm -rf tests/__pycache__ libsemigroups_pybind11/__pycache__
+	find . -type d -name __pycache__ -prune -exec rm -rf {} \;
+	rm -rf libsemigroups_pybind11.egg-info
 	rm -f *.whl
 	rm -rf build/
 
diff --git a/build_tools/__init__.py b/build_tools/__init__.py
new file mode 100644
index 00000000..c09fb606
--- /dev/null
+++ b/build_tools/__init__.py
@@ -0,0 +1,111 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2021-2024 J. D. Mitchell
+#
+# Distributed under the terms of the GPL license version 3.
+#
+# The full license is in the file LICENSE, distributed with this software.
+
+"""
+This module provides some tools for building libsemigroups_pybind11.
+"""
+
+import re
+from packaging import version
+import pkgconfig
+
+
+def minimum_libsemigroups_version():
+    """
+    Returns the minimum required version of libsemigroups required to make
+    this work.
+    """
+    return "3.0.0"
+
+
+def libsemigroups_version():
+    "Get the version of libsemigroups installed using pkg-config."
+
+    vers = pkgconfig.modversion("libsemigroups")
+    if re.search(r"\d+\.\d+\.\d+-\d+-\w{7}", vers):
+        # i.e. supplied is of the form: 1.1.0-6-g8b04c08
+        vers = re.search(r"\d+\.\d\.+\d+-\d+", vers).group(0)
+    return vers
+
+
+def compare_version_numbers(supplied, required):
+    """Returns True if supplied >= required"""
+
+    if isinstance(supplied, str) and isinstance(required, str):
+        if "dev" in supplied:
+            print(
+                (
+                    "\033[93mWarning: You are using a development version of libsemigroups. This "
+                    "may cause undocumented behaviour\033[0m"
+                )
+            )
+            return True
+        return version.parse(supplied) >= version.parse(required)
+    raise TypeError(
+        f"expected (string, string), got a ({supplied.__name__}, {required.__name__})"
+    )
+
+
+def extra_link_args() -> str:
+    """Find extra link args"""
+    libs_only_L = pkgconfig.libs(  # pylint: disable=invalid-name
+        "libsemigroups"
+    )
+    # The above pkgconfig query can return an empty string (this also happens on
+    # the command line). This happens, for example, using pkg-config version 1.8.0
+    # on ArchLinux. CN 27/10/2021
+
+    assert (
+        len(libs_only_L) == 0 or libs_only_L[:2] == "-L"
+    ), "The first two characters of the library path to the libsemigroups.so etc should be '-L'"
+
+    libs_only_L = [  # pylint: disable=invalid-name
+        x for x in libs_only_L.split(" ") if x.startswith("-L")
+    ]
+
+    if len(libs_only_L) == 0:
+        libs_only_L = ["-L/usr/lib"]  # pylint: disable=invalid-name
+    return libs_only_L
+
+
+def ld_library_path() -> str:
+    """Construct the LD_LIBRARY_PATH"""
+    return ":".join([x[2:] for x in extra_link_args()])
+
+
+def validate_libsemigroups():
+    DISCLAIMER = """
+    (You should not see this message unless you are installing
+    libsemigroups_pybind11 from its sources. If you are not installing from the
+    sources, please raise an issue at:
+    https://github.com/libsemigroups/libsemigroups_pybind11)"""
+
+    if not pkgconfig.exists("libsemigroups"):
+        raise ImportError(
+            f"""cannot locate the libsemigroups library.
+    For more information about installing the libsemigroups library see
+    https://libsemigroups.github.io/libsemigroups_pybind11/install.html.
+
+    If libsemigroups is installed, then it cannot be located by pkg-config,
+    perhaps you should add the directory containing `libsemigroups.pc' to the
+    \"PKG_CONFIG_PATH\". The file `libsemigroups.pc' might be in one of the
+    following directories:
+    * /usr/local/lib/pkgconfig
+    * $CONDA_PREFIX/lib/pkgconfig if your active conda environment has pkgconfig
+    installed, and libsemigroups was installed with conda/mamba in this
+    environment.
+    {DISCLAIMER}"""
+        )
+
+    if not compare_version_numbers(
+        libsemigroups_version(), minimum_libsemigroups_version()
+    ):
+        raise ImportError(
+            f"libsemigroups version at least {minimum_libsemigroups_version()}"
+            + f" is required, found {libsemigroups_version()}"
+        )
diff --git a/dev-environment.yml b/dev-environment.yml
index 193a9014..2f4f6d8e 100644
--- a/dev-environment.yml
+++ b/dev-environment.yml
@@ -5,7 +5,7 @@ channels:
   - nodefaults
 
 dependencies:
-  - python=3.12
+  - python>=3.12
   - black
   - bs4
   - codespell
@@ -14,12 +14,13 @@ dependencies:
   - ipython
   - lxml
   - pip
+  - pybind11
   - pylint
   - pytest
-  - pybind11
-  - sphinx
-  - sphinx-copybutton
+  - ruff
   - sphinx_rtd_theme
+  - sphinx-copybutton
+  - sphinx
   - sphinxcontrib-bibtex
   - pip:
       - accepts
diff --git a/docs/environment.yml b/docs/environment.yml
deleted file mode 100644
index 2cf89c92..00000000
--- a/docs/environment.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-name: libsemigroups-pybind11-doc
-
-channels:
-  - conda-forge
-  - anaconda
-
-dependencies:
-  - libsemigroups==2.0.0
-  - pip
-  - sphinx-copybutton==0.5.2
-  - sphinxcontrib-bibtex==2.6.2
-  - packaging==23.2
-  - pkgconfig
-  - pybind11==2.11.1
-  - pyparsing==3.1.1
-  
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index d42114a3..00000000
--- a/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: libsemigroups
-
-channels:
-  - conda-forge
-
-dependencies:
-  - libsemigroups
diff --git a/etc/libsemigroups_version.py b/etc/libsemigroups_version.py
index 18c75c29..c52c6c50 100755
--- a/etc/libsemigroups_version.py
+++ b/etc/libsemigroups_version.py
@@ -2,9 +2,14 @@
 import os
 import sys
 
-__dir__ = os.path.abspath(os.path.dirname(__file__))
-sys.path.insert(0, __dir__ + "/../libsemigroups_pybind11")
-
-from tools import minimum_libsemigroups_version
+sys.path.append(
+    os.path.abspath(
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+        )
+    )
+)
+from build_tools import minimum_libsemigroups_version
 
 print(minimum_libsemigroups_version())
diff --git a/etc/make-lint.sh b/etc/make-lint.sh
new file mode 100755
index 00000000..e077c3b7
--- /dev/null
+++ b/etc/make-lint.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+if [[ $# -ne 0 ]]; then
+    bold "error expected 0 arguments, got $#!"
+    exit 1
+fi
+
+exit_code=0
+python_files="setup.py tests/*.py src/libsemigroups_pybind11/*.py src/libsemigroups_pybind11/**/*.py docs/source/*.py docs/source/**/*.py"
+
+echo "Linting with ruff . . ."
+ruff check $python_files || ((exit_code = 1))
+
+echo "Linting with pylint . . ."
+pylint $python_files || ((exit_code = 1))
+
+echo "Linting with cpplint . . ."
+cpplint src/*.hpp src/*.cpp || ((exit_code = 1))
+
+exit $exit_code
diff --git a/libsemigroups_pybind11/tools.py b/libsemigroups_pybind11/tools.py
deleted file mode 100644
index 2215dcd1..00000000
--- a/libsemigroups_pybind11/tools.py
+++ /dev/null
@@ -1,99 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright (c) 2021-2024 J. D. Mitchell
-#
-# Distributed under the terms of the GPL license version 3.
-#
-# The full license is in the file LICENSE, distributed with this software.
-
-"""
-This module provides some tools for libsemigroups_pybind11.
-"""
-
-import re
-
-from packaging import version
-
-try:
-    import pkgconfig
-
-    PKGCONFIG_IMPORTED = True
-except ModuleNotFoundError:
-    PKGCONFIG_IMPORTED = False
-
-
-def ordinal(n: int):
-    """
-    Returns 1st from 1, 2nd from 2 etc.
-    From https://stackoverflow.com/questions/9647202/
-    """
-    if 11 <= (n % 100) <= 13:
-        suffix = "th"
-    else:
-        suffix = ["th", "st", "nd", "rd", "th"][min(n % 10, 4)]
-    return str(n) + suffix
-
-
-def minimum_libsemigroups_version():
-    """
-    Returns the minimum required version of libsemigroups required to make
-    this work.
-    """
-    return "2.7.0"
-    # Changed down from 2.7.1 -- do something sensible here
-
-
-if PKGCONFIG_IMPORTED:
-
-    def libsemigroups_version():
-        "Get the version of libsemigroups installed using pkg-config."
-
-        vers = pkgconfig.modversion("libsemigroups")
-        if re.search(r"\d+\.\d+\.\d+-\d+-\w{7}", vers):
-            # i.e. supplied is of the form: 1.1.0-6-g8b04c08
-            vers = re.search(r"\d+\.\d\.+\d+-\d+", vers).group(0)
-        return vers
-
-
-def compare_version_numbers(supplied, required):
-    """Returns True if supplied >= required"""
-
-    if isinstance(supplied, str) and isinstance(required, str):
-        if "dev" in supplied:
-            print(
-                (
-                    "\033[93mWarning: You are using a development version of libsemigroups. This "
-                    "may cause undocumented behaviour\033[0m"
-                )
-            )
-            return True
-        return version.parse(supplied) >= version.parse(required)
-    raise TypeError(
-        f"expected (string, string), got a ({supplied.__name__}, {required.__name__})"
-    )
-
-
-def extra_link_args() -> str:
-    """Find extra link args"""
-    # pylint: disable=invalid-name
-    libs_only_L = pkgconfig.libs("libsemigroups")
-    # The above pkgconfig query can return an empty string (this also happens on
-    # the command line). This happens, for example, using pkg-config version 1.8.0
-    # on ArchLinux. CN 27/10/2021
-
-    assert (
-        len(libs_only_L) == 0 or libs_only_L[:2] == "-L"
-    ), "The first two characters of the library path to the libsemigroups.so etc should be '-L'"
-
-    libs_only_L = [  # pylint: disable=invalid-name
-        x for x in libs_only_L.split(" ") if x.startswith("-L")
-    ]
-
-    if len(libs_only_L) == 0:
-        libs_only_L = ["-L/usr/lib"]  # pylint: disable=invalid-name
-    return libs_only_L
-
-
-def ld_library_path() -> str:
-    """Construct the LD_LIBRARY_PATH"""
-    return ":".join([x[2:] for x in extra_link_args()])
diff --git a/pyproject.toml b/pyproject.toml
index 3ad58062..882ad789 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,26 +1,116 @@
-[tool.black]
-line-length = 80
-[tool.ruff] 
-lint.select = ["E", "F", "B"]
-lint.ignore = ["F401"]
-line-length = 100
-[tool.pylint]
-disable = ["R0801", "fixme"]
+# TODO:
+#  * Run check-manifest and populate MANIFEST.in
+#  * Use ruff
+#  * Remove .codespellrc
+#  * Decide on good configurations for tools
+#  * Remove requirements.txt
+#  * Use pre-commit
+#  * Use MyPy
 [build-system]
 requires = [
-    "setuptools==75.6.0",
-    "wheel",
-    "pybind11==2.11.1",
-    "pkgconfig>=1.5.5",
-    "packaging==23.2",
+    "setuptools>=64",
+    "setuptools-scm>=8",
+    "pybind11",
+    "pkgconfig",
+    "packaging",
 ]
-
 build-backend = "setuptools.build_meta"
 
-[tool.pytest.ini_options]
-markers = [
-    "quick",
-    "standard",
-    "extreme",
-    "fail",
+[project]
+name = "libsemigroups_pybind11"
+dynamic = ["version"]
+description = "A python package for the libsemigroups C++ library."
+readme = "README.md"
+authors = [
+    { name = "Joseph Edwards", email = "jde1@st-andrews.ac.uk" },
+    { name = "James Mitchell", email = "jdm3@st-andrews.ac.uk" },
+    { name = "Maria Tsalakou", email = "mt200@st-andrews.ac.uk" },
+    { name = "Murray Whyte", email = "mw231@st-andrews.ac.uk" },
 ]
+# TODO: Uncomment and update
+# maintainers = [{ name = "My Organization", email = "myemail@email.com" }]
+requires-python = ">=3.9"
+dependencies = ["graphviz", "numpy", "typing_extensions"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python :: 3 :: Only",
+    "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",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Natural Language :: English",
+]
+license = "GPL-3.0-or-later"
+license-files = ["LICENSE"]
+
+[project.urls]
+Homepage = "https://github.com/libsemigroups/libsemigroups_pybind11"
+Documentation = "https://libsemigroups.github.io/libsemigroups_pybind11/"
+Issues = "https://github.com/libsemigroups/libsemigroups_pybind11/issues"
+Changelog = "https://libsemigroups.github.io/libsemigroups_pybind11/changelog.html"
+
+[project.optional-dependencies]
+test = ["pytest"]
+docs = [
+    "sphinx_rtd_theme",
+    "sphinx >=8.2",
+    "sphinx-copybutton",
+    "sphinxcontrib-bibtex",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools_scm]
+version_file = "src/libsemigroups_pybind11/_version.py"
+
+[tool.black]
+line-length = 80
+
+[tool.ruff]
+line-length = 100
+lint.ignore = ["F401", "E402"]
+lint.select = ["E", "F", "B"]
+# Uncomment the following to have more aggressive ruff linting
+# lint.extend-select = ["B", "I", "UP"]
+
+# [tool.ruff.format]
+# docstring-code-format = true
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = ["tests"]
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+console_output_style = "progress"
+filterwarnings = ["error"]
+markers = ["quick", "standard", "extreme", "fail"]
+verbosity_test_cases = 1
+xfail_strict = true
+
+[tool.pylint.main]
+ignore-paths = "src/libsemigroups_pybind11/_version.py"
+jobs = 0
+
+[tool.pylint.miscellaneous]
+# List of note tags to take in consideration, separated by a comma.
+# notes = ["TODO", "FIXME", "REVIEW"]
+disable = ["R0801", "fixme"]
+notes = []
+
+[tool.pylint.similarities]
+ignore-imports = "yes"
+
+# TODO: Decide if we want to use mypy
+# [tool.mypy]
+# files = "src"
+# python_version = "3.9"
+# strict = true
+# enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]
+# warn_unreachable = true
+
+# [[tool.mypy.overrides]]
+# module = [ "_libsemigroups_pybind11", ]
+# ignore_missing_imports = true
diff --git a/requirements.txt b/requirements.txt
index d6857707..2db5feda 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,14 +1,34 @@
-setuptools==75.6.0
+accepts==2020.12.3
+argcomplete==3.6.2
+beautifulsoup4==4.13.3
+colorama==0.4.6
+cpplint==2.0.0
+eventlet==0.39.1
+exceptiongroup==1.2.2
+gevent==24.11.1
 graphviz==0.20.3
-numpy==2.0.2
+greenlet==3.1.1
+numpy==2.0.2;
+ox_profile==0.2.14
 packaging==24.2
+pexpect==4.9.0
 pkgconfig==1.5.5
+pudb==2024.1.3
 pybind11==2.13.6
-pyparsing==3.2.0
+pygments==2.19.1
+pylint==3.3.5
 pytest==8.3.3
-six==1.16.0
+pyyaml==6.0.2
+ruff==0.11.2
+setuptools==75.8.2
 sphinx_rtd_theme==3.0.2
-sphinx==7.4.7
 sphinx-copybutton==0.5.2
+# We are being slightly deceptive here. Compiling with sphinx==7.4.7 will work,
+# but will cause warnings
+sphinx==8.2.3;python_version>="3.11"
+sphinx==7.4.7;python_version<="3.10"
 sphinxcontrib-bibtex==2.6.3
-typing_extensions==4.12.2
\ No newline at end of file
+tomli==2.2.1
+twisted==24.11.0
+typing_extensions==4.13.0
+zope==5.13
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 8be1ef2f..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,3 +0,0 @@
-[pylint.similarities]
-ignore-imports=yes
-notes=["TODO", "FIXME", "REVIEW"]
diff --git a/setup.py b/setup.py
index 71cdd485..1066b0da 100644
--- a/setup.py
+++ b/setup.py
@@ -14,7 +14,6 @@
 import glob
 import os
 import sys
-from pprint import pprint
 
 import pkgconfig
 from pybind11.setup_helpers import (
@@ -23,133 +22,44 @@
     build_ext,
     naive_recompile,
 )
-from setuptools import find_packages, setup
+from setuptools import setup
 
 ParallelCompile("NPY_NUM_BUILD_JOBS", needs_recompile=naive_recompile).install()
 
-__dir__ = os.path.abspath(os.path.dirname(__file__))
-sys.path.insert(0, __dir__ + "/libsemigroups_pybind11")
+sys.path.append(os.path.abspath(os.path.dirname(__file__)))
 
-from tools import (  # pylint: disable=import-error, wrong-import-position # noqa: E402
-    compare_version_numbers,
-    extra_link_args,
-    libsemigroups_version,
-    minimum_libsemigroups_version,
+from build_tools import (  # pylint: disable=wrong-import-position
+    validate_libsemigroups,
 )
 
-__version__ = "1.0.0"
+validate_libsemigroups()
 
-DISCLAIMER = """(You should not see this message unless you are installing
-libsemigroups_pybind11 from its sources. If you are not installing from the
-sources, please raise an issue at:
-https://github.com/libsemigroups/libsemigroups_pybind11)"""
-
-if not pkgconfig.exists("libsemigroups"):
-    raise ImportError(
-        f"""cannot locate the libsemigroups library.
-For more information about installing the libsemigroups library see
-https://libsemigroups.github.io/libsemigroups_pybind11/install.html.
-
-If libsemigroups is installed, then it cannot be located by pkg-config, perhaps
-you should add the directory containing `libsemigroups.pc' to the
-\"PKG_CONFIG_PATH\". The file `libsemigroups.pc' might be in one of the
-following directories:
-* /usr/local/lib/pkgconfig
-* $CONDA_PREFIX/lib/pkgconfig if your active conda environment has pkgconfig
-  installed, and libsemigroups was installed with conda/mamba in this
-  environment.
-{DISCLAIMER}"""
-    )
-
-if not compare_version_numbers(
-    libsemigroups_version(), minimum_libsemigroups_version()
-):
-    raise ImportError(
-        f"libsemigroups version at least {minimum_libsemigroups_version()}"
-        + f" is required, found {libsemigroups_version()}"
-    )
-
-
-class GetPyBind11Include:  # pylint: disable=too-few-public-methods
-    """
-    Helper class to determine the pybind11 include path
-
-    The purpose of this class is to postpone importing pybind11
-    until it is actually installed, so that the ``get_include()``
-    method can be invoked.
-    """
-
-    def __init__(self, user=False):
-        self.user = user
-
-    def __str__(self):
-        import pybind11  # pylint: disable=import-outside-toplevel
-
-        return pybind11.get_include(self.user)
-
-
-include_path = [
-    GetPyBind11Include(),
-    GetPyBind11Include(user=True),
-]
-
-for lib in ("libsemigroups", "eigen3", "fmt"):
-    try:
-        cflags_only_I = pkgconfig.cflags(lib)  # pylint: disable=invalid-name
-    except pkgconfig.pkgconfig.PackageNotFoundError:
-        continue
-
-    cflags_only_I = [
-        x[2:] for x in cflags_only_I.split(" ") if x.startswith("-I")
-    ]
-
-    include_path.extend(cflags_only_I)
-    if lib == "libsemigroups":
-        include_path.extend(
-            [os.path.join(x, "libsemigroups") for x in cflags_only_I]
-        )
+libsemigroups_info = pkgconfig.parse("libsemigroups")
+extra_libs = set(libsemigroups_info["libraries"])
+extra_libs.remove("semigroups")
+include_dirs = set(libsemigroups_info["include_dirs"])
+for lib in extra_libs:
+    include_dirs.update(set(pkgconfig.parse(lib)["include_dirs"]))
+include_dirs = sorted(list(include_dirs))
 
 print("Include directories are:")
-pprint(include_path)
+print(include_dirs)
 
-print("Extra link args are:")
-pprint(extra_link_args())
+print("Library directories args are:")
+print(libsemigroups_info["library_dirs"])
 
 ext_modules = [
     Pybind11Extension(
         "_libsemigroups_pybind11",
         glob.glob("src/*.cpp"),
-        include_dirs=include_path,
+        include_dirs=include_dirs,
+        library_dirs=libsemigroups_info["library_dirs"],
         language="c++",
         libraries=["semigroups"],
-        extra_link_args=extra_link_args(),
     ),
 ]
 
-with open(os.path.join(__dir__, "README.md"), "r", encoding="utf-8") as readme:
-    long_description = readme.read()
-
 setup(
-    name="libsemigroups_pybind11",
-    version=__version__,
-    author="Joseph Edwards, James Mitchell, Maria Tsalakou, Murray Whyte",
-    author_email="jdm3@st-andrews.ac.uk",
-    url="https://github.com/libsemigroups/libsemigroups_pybind11",
-    description="A python package for the libsemigroups C++ library",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
     ext_modules=ext_modules,
-    packages=find_packages(),
-    setup_requires=["pkgconfig>=1.5.5"],
-    install_requires=[
-        "packaging>=20.4",
-        "pkgconfig>=1.5.5",
-        "pybind11>=2.13.0",
-        "graphviz>=0.20.1",
-        "numpy>=1.26.0",
-    ],
-    tests_require=["pytest==8.0.0"],
     cmdclass={"build_ext": build_ext},
-    zip_safe=False,
-    python_requires=">=3.9.0",
 )
diff --git a/libsemigroups_pybind11/__init__.py b/src/libsemigroups_pybind11/__init__.py
similarity index 97%
rename from libsemigroups_pybind11/__init__.py
rename to src/libsemigroups_pybind11/__init__.py
index 7bde5047..b437c2d7 100644
--- a/libsemigroups_pybind11/__init__.py
+++ b/src/libsemigroups_pybind11/__init__.py
@@ -10,7 +10,7 @@
 This package provides the user-facing python part of libsemigroups_pybind11
 """
 
-import pkgconfig
+from ._version import version as __version__
 
 from .detail.dot import _Dot as Dot
 
@@ -48,8 +48,6 @@
     "https://github.com/libsemigroups/libsemigroups_pybind11)"
 )
 
-assert pkgconfig.exists("libsemigroups")
-
 try:
     from _libsemigroups_pybind11 import (  # pylint: disable=no-name-in-module
         AhoCorasick,
diff --git a/libsemigroups_pybind11/action.py b/src/libsemigroups_pybind11/action.py
similarity index 100%
rename from libsemigroups_pybind11/action.py
rename to src/libsemigroups_pybind11/action.py
diff --git a/libsemigroups_pybind11/adapters.py b/src/libsemigroups_pybind11/adapters.py
similarity index 100%
rename from libsemigroups_pybind11/adapters.py
rename to src/libsemigroups_pybind11/adapters.py
diff --git a/libsemigroups_pybind11/aho_corasick.py b/src/libsemigroups_pybind11/aho_corasick.py
similarity index 100%
rename from libsemigroups_pybind11/aho_corasick.py
rename to src/libsemigroups_pybind11/aho_corasick.py
diff --git a/libsemigroups_pybind11/bipartition.py b/src/libsemigroups_pybind11/bipartition.py
similarity index 100%
rename from libsemigroups_pybind11/bipartition.py
rename to src/libsemigroups_pybind11/bipartition.py
diff --git a/libsemigroups_pybind11/blocks.py b/src/libsemigroups_pybind11/blocks.py
similarity index 100%
rename from libsemigroups_pybind11/blocks.py
rename to src/libsemigroups_pybind11/blocks.py
diff --git a/libsemigroups_pybind11/bmat8.py b/src/libsemigroups_pybind11/bmat8.py
similarity index 100%
rename from libsemigroups_pybind11/bmat8.py
rename to src/libsemigroups_pybind11/bmat8.py
diff --git a/libsemigroups_pybind11/congruence.py b/src/libsemigroups_pybind11/congruence.py
similarity index 100%
rename from libsemigroups_pybind11/congruence.py
rename to src/libsemigroups_pybind11/congruence.py
diff --git a/libsemigroups_pybind11/detail/__init__.py b/src/libsemigroups_pybind11/detail/__init__.py
similarity index 100%
rename from libsemigroups_pybind11/detail/__init__.py
rename to src/libsemigroups_pybind11/detail/__init__.py
diff --git a/libsemigroups_pybind11/detail/congruence_common.py b/src/libsemigroups_pybind11/detail/congruence_common.py
similarity index 100%
rename from libsemigroups_pybind11/detail/congruence_common.py
rename to src/libsemigroups_pybind11/detail/congruence_common.py
diff --git a/libsemigroups_pybind11/detail/cxx_wrapper.py b/src/libsemigroups_pybind11/detail/cxx_wrapper.py
similarity index 99%
rename from libsemigroups_pybind11/detail/cxx_wrapper.py
rename to src/libsemigroups_pybind11/detail/cxx_wrapper.py
index 5a1f50cd..77c51f33 100644
--- a/libsemigroups_pybind11/detail/cxx_wrapper.py
+++ b/src/libsemigroups_pybind11/detail/cxx_wrapper.py
@@ -14,8 +14,6 @@
 
 from functools import update_wrapper
 
-import abc
-
 from types import MethodType
 from typing import Any, Callable
 from typing_extensions import Self
@@ -58,7 +56,7 @@ def register_cxx_wrapped_type(cxx_type: pybind11_type, py_type: type) -> None:
     _CXX_WRAPPED_TYPE_TO_PY_TYPE[cxx_type] = py_type
 
 
-class CxxWrapper(metaclass=abc.ABCMeta):
+class CxxWrapper:
     # pylint: disable=missing-class-docstring
     # pylint: disable=protected-access, no-member
     def __init__(
diff --git a/libsemigroups_pybind11/detail/decorators.py b/src/libsemigroups_pybind11/detail/decorators.py
similarity index 100%
rename from libsemigroups_pybind11/detail/decorators.py
rename to src/libsemigroups_pybind11/detail/decorators.py
diff --git a/libsemigroups_pybind11/detail/dot.py b/src/libsemigroups_pybind11/detail/dot.py
similarity index 100%
rename from libsemigroups_pybind11/detail/dot.py
rename to src/libsemigroups_pybind11/detail/dot.py
diff --git a/src/libsemigroups_pybind11/detail/tools.py b/src/libsemigroups_pybind11/detail/tools.py
new file mode 100644
index 00000000..2dde02de
--- /dev/null
+++ b/src/libsemigroups_pybind11/detail/tools.py
@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+
+# Copyright (c) 2021-2024 J. D. Mitchell
+#
+# Distributed under the terms of the GPL license version 3.
+#
+# The full license is in the file LICENSE, distributed with this software.
+
+"""
+This module provides some tools for libsemigroups_pybind11.
+"""
+
+
+def ordinal(n: int):
+    """
+    Returns 1st from 1, 2nd from 2 etc.
+    From https://stackoverflow.com/questions/9647202/
+    """
+    if 11 <= (n % 100) <= 13:
+        suffix = "th"
+    else:
+        suffix = ["th", "st", "nd", "rd", "th"][min(n % 10, 4)]
+    return str(n) + suffix
diff --git a/libsemigroups_pybind11/froidure_pin.py b/src/libsemigroups_pybind11/froidure_pin.py
similarity index 100%
rename from libsemigroups_pybind11/froidure_pin.py
rename to src/libsemigroups_pybind11/froidure_pin.py
diff --git a/libsemigroups_pybind11/is_obviously_infinite.py b/src/libsemigroups_pybind11/is_obviously_infinite.py
similarity index 100%
rename from libsemigroups_pybind11/is_obviously_infinite.py
rename to src/libsemigroups_pybind11/is_obviously_infinite.py
diff --git a/libsemigroups_pybind11/kambites.py b/src/libsemigroups_pybind11/kambites.py
similarity index 100%
rename from libsemigroups_pybind11/kambites.py
rename to src/libsemigroups_pybind11/kambites.py
diff --git a/libsemigroups_pybind11/knuth_bendix.py b/src/libsemigroups_pybind11/knuth_bendix.py
similarity index 100%
rename from libsemigroups_pybind11/knuth_bendix.py
rename to src/libsemigroups_pybind11/knuth_bendix.py
diff --git a/libsemigroups_pybind11/konieczny.py b/src/libsemigroups_pybind11/konieczny.py
similarity index 100%
rename from libsemigroups_pybind11/konieczny.py
rename to src/libsemigroups_pybind11/konieczny.py
diff --git a/libsemigroups_pybind11/matrix.py b/src/libsemigroups_pybind11/matrix.py
similarity index 100%
rename from libsemigroups_pybind11/matrix.py
rename to src/libsemigroups_pybind11/matrix.py
diff --git a/libsemigroups_pybind11/pbr.py b/src/libsemigroups_pybind11/pbr.py
similarity index 100%
rename from libsemigroups_pybind11/pbr.py
rename to src/libsemigroups_pybind11/pbr.py
diff --git a/libsemigroups_pybind11/presentation/__init__.py b/src/libsemigroups_pybind11/presentation/__init__.py
similarity index 100%
rename from libsemigroups_pybind11/presentation/__init__.py
rename to src/libsemigroups_pybind11/presentation/__init__.py
diff --git a/libsemigroups_pybind11/presentation/examples.py b/src/libsemigroups_pybind11/presentation/examples.py
similarity index 100%
rename from libsemigroups_pybind11/presentation/examples.py
rename to src/libsemigroups_pybind11/presentation/examples.py
diff --git a/libsemigroups_pybind11/schreier_sims.py b/src/libsemigroups_pybind11/schreier_sims.py
similarity index 100%
rename from libsemigroups_pybind11/schreier_sims.py
rename to src/libsemigroups_pybind11/schreier_sims.py
diff --git a/libsemigroups_pybind11/sims.py b/src/libsemigroups_pybind11/sims.py
similarity index 100%
rename from libsemigroups_pybind11/sims.py
rename to src/libsemigroups_pybind11/sims.py
diff --git a/libsemigroups_pybind11/stephen.py b/src/libsemigroups_pybind11/stephen.py
similarity index 100%
rename from libsemigroups_pybind11/stephen.py
rename to src/libsemigroups_pybind11/stephen.py
diff --git a/libsemigroups_pybind11/to.py b/src/libsemigroups_pybind11/to.py
similarity index 100%
rename from libsemigroups_pybind11/to.py
rename to src/libsemigroups_pybind11/to.py
diff --git a/libsemigroups_pybind11/todd_coxeter.py b/src/libsemigroups_pybind11/todd_coxeter.py
similarity index 100%
rename from libsemigroups_pybind11/todd_coxeter.py
rename to src/libsemigroups_pybind11/todd_coxeter.py
diff --git a/libsemigroups_pybind11/transf.py b/src/libsemigroups_pybind11/transf.py
similarity index 100%
rename from libsemigroups_pybind11/transf.py
rename to src/libsemigroups_pybind11/transf.py
diff --git a/libsemigroups_pybind11/ukkonen.py b/src/libsemigroups_pybind11/ukkonen.py
similarity index 100%
rename from libsemigroups_pybind11/ukkonen.py
rename to src/libsemigroups_pybind11/ukkonen.py
diff --git a/libsemigroups_pybind11/word_graph.py b/src/libsemigroups_pybind11/word_graph.py
similarity index 100%
rename from libsemigroups_pybind11/word_graph.py
rename to src/libsemigroups_pybind11/word_graph.py
diff --git a/libsemigroups_pybind11/words.py b/src/libsemigroups_pybind11/words.py
similarity index 100%
rename from libsemigroups_pybind11/words.py
rename to src/libsemigroups_pybind11/words.py