diff --git a/.flake8 b/.flake8
deleted file mode 100644
index dcaf688..0000000
--- a/.flake8
+++ /dev/null
@@ -1,9 +0,0 @@
-[flake8]
-select = B,C,E,F,W,B001,B003,B006,B007,B301,B305,B306,B902,Q000,Q001,Q002,Q003,I252
-ignore = E203,E722,W503
-max-line-length = 120
-ban-relative-imports = true
-per-file-ignores =
-    # tests can use relative imports
-    tests/*: I252
-    tests/**/*: I252
\ No newline at end of file
diff --git a/.github/workflows/build-laplaciannb.yml b/.github/workflows/build-laplaciannb.yml
new file mode 100644
index 0000000..07aa166
--- /dev/null
+++ b/.github/workflows/build-laplaciannb.yml
@@ -0,0 +1,120 @@
+name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI
+
+## from packaging tutorial: https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution 📦
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.x"
+    - name: Install pdm
+      run: >-
+        python3 -m
+        pip install
+        pdm
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: pdm build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/laplaciannb  # Replace <package-name> with your PyPI project name
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v3.0.0
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Create GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      run: >-
+        gh release create
+        '${{ github.ref_name }}'
+        --repo '${{ github.repository }}'
+        --notes ""
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+  publish-to-testpypi:
+    name: Publish Python 🐍 distribution 📦 to TestPyPI
+    needs:
+    - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/laplaciannb
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution 📦 to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        repository-url: https://test.pypi.org/legacy/
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
\ No newline at end of file
diff --git a/.github/workflows/build-lmnb.yml b/.github/workflows/build-lmnb.yml
deleted file mode 100644
index ff4a433..0000000
--- a/.github/workflows/build-lmnb.yml
+++ /dev/null
@@ -1,48 +0,0 @@
-name: build lmnb
-
-on:
-  push:
-    tags:
-    - lmnb-v*
-
-concurrency:
-  group: build-lmnb-${{ github.head_ref }}
-
-jobs:
-  build:
-    name: Build wheels and source distribution
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - name: Install build dependencies
-      run: python -m pip install --upgrade build
-
-    - name: Build source distribution
-      run: python -m build
-
-    - uses: actions/upload-artifact@v3
-      with:
-        name: artifacts
-        path: dist/*
-        if-no-files-found: error
-
-  publish:
-    name: Publish release
-    needs:
-    - build
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/download-artifact@v3
-      with:
-        name: artifacts
-        path: dist
-
-    - name: Push build artifacts to PyPI
-      uses: pypa/gh-action-pypi-publish@v1.5.1
-      with:
-        skip_existing: true
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN_LMNB }}
\ No newline at end of file
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
new file mode 100644
index 0000000..cf7600a
--- /dev/null
+++ b/.github/workflows/ruff.yml
@@ -0,0 +1,11 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: astral-sh/ruff-action@v1
+        with:
+          args: 'format --check'
+          src: './src'
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
deleted file mode 100644
index 790f4c2..0000000
--- a/.github/workflows/tests.yml
+++ /dev/null
@@ -1,45 +0,0 @@
-name: tests
-
-on: [push]
-
-concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.sha }}
-  cancel-in-progress: true
-
-env:
-  PYTHONUNBUFFERED: "1"
-  FORCE_COLOR: "1"
-
-jobs:
-  run:
-    name: Python ${{ matrix.python-version }} on ${{ startsWith(matrix.os, 'macos-') && 'macOS' || startsWith(matrix.os, 'windows-') && 'Windows' || 'Linux' }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ['3.8', '3.9', '3.10']
-
-    steps:
-    - uses: actions/checkout@v3
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Ensure latest pip
-      run: python -m pip install --upgrade pip
-
-    - name: Install ourself
-      run: |
-        pip install -e .
-
-    - name: Install Hatch
-      run: pip install --upgrade --pre hatch
-
-    - name: Run lint
-      run: hatch run lint:all
-    
-    - name: Run tests
-      run: hatch run full
diff --git a/.gitignore b/.gitignore
index d5e913c..308d44e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -67,3 +67,6 @@ _configtest.o.d
 
 # Used by mypy
 .mypy_cache/
+
+# Pdm
+.pdm-python
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 247ac1e..b4460da 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,26 +1,20 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
-    hooks:
-    -   id: check-yaml
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
--   repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-    -   id: black
-        exclude: tests/
-        args: [--check]
--   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-    -   id: flake8
-        additional_dependencies: [
-            'flake8-blind-except',
-            'flake8-docstrings',
-            'flake8-bugbear',
-            'flake8-comprehensions',
-            'flake8-docstrings',
-            'flake8-implicit-str-concat',
-            'pydocstyle>=5.0.0',
-        ]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.7.2
+  hooks:
+    # Run the linter.
+    - id: ruff
+      types_or: [ python, pyi ]
+      args: [ --fix ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi ]
+- repo: local
+  hooks:
+    - id: pytest-check
+      name: pytest-check
+      entry: pytest
+      language: system
+      pass_filenames: false
+      always_run: true
\ No newline at end of file
diff --git a/README.md b/README.md
index c97b1f1..04fda50 100644
--- a/README.md
+++ b/README.md
@@ -34,28 +34,12 @@ https://doi.org/10.1002/cbic.201900741
 Authors
 --------
 
-Huge thanks to **Florian Nigsch** (florian.nigsch@novartis.com) for the first implementation of the algorithm in python and **Peter Kutchukian** (peter.kutchukian@novartis.net) for scientific guidance and validation.
-
-
 Author and maintainer: **Bartosz Baranowski** (bartosz.baranowski@novartis.com)
 
 
 Installation
 ------------
 
-Dependencies:
-
-```
-- Python       (>= 3.8)
-- pandas       (>=1.4.2)
-- numpy        (>=1.22.4)
-- scikit-learn (>=1.1.1)
-- scipy        (>=1.8.1)
-```
-
-=======
-
-
 User installation:
 
 ```pip install laplaciannb```
@@ -64,4 +48,5 @@ User installation:
 
 Changelog
 ---------
+`v0.6.0` - Move to pdm build
 `v0.5.0` - Initial release
diff --git a/bayes/__about__.py b/bayes/__about__.py
deleted file mode 100644
index 93b60a1..0000000
--- a/bayes/__about__.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = '0.5.1'
diff --git a/examples/bayes_tutorial.ipynb b/examples/bayes_tutorial.ipynb
index ee803eb..001bc70 100644
--- a/examples/bayes_tutorial.ipynb
+++ b/examples/bayes_tutorial.ipynb
@@ -7,7 +7,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import joblib\n",
     "import pandas as pd"
    ]
   },
@@ -61,7 +60,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bayes.LaplacianNB import LaplacianNB"
+    "from laplaciannb.LaplacianNB import LaplacianNB"
    ]
   },
   {
@@ -82,6 +81,7 @@
     "from rdkit import Chem\n",
     "from rdkit.Chem import AllChem\n",
     "\n",
+    "\n",
     "def get_fp(smiles: str) -> set:\n",
     "    \"\"\"Function to calculate MorganFingerprint from smiles.\n",
     "    It returns index of all '1' bits of not-folded fingerprint.\n",
diff --git a/hatch.toml b/hatch.toml
deleted file mode 100644
index 67e3216..0000000
--- a/hatch.toml
+++ /dev/null
@@ -1,96 +0,0 @@
-[envs.default]
-dependencies = [
-  "coverage[toml]>=6.2",
-  "hatchling",
-  "filelock>=3.7.1",
-  "pytest",
-  "pytest-cov",
-  "pytest-mock",
-  "pytest-randomly",
-  "pytest-rerunfailures",
-  "pytest-xdist",
-  "trustme",
-  "rdkit",
-  "pre-commit"
-]
-
-[envs.default.scripts]
-full = "pytest -n auto --reruns 5 --reruns-delay 3 -r aR --cov-report=term-missing --cov-config=pyproject.toml --cov=bayes/ --cov=tests {args:tests}"
-dev = "pytest -p no:randomly --no-cov {args:tests}"
-
-[envs.test.overrides]
-env.HERMETIC_TESTS.type = [
-  { value = "container", if = ["true"] },
-  "virtual",
-]
-
-[[envs.test.matrix]]
-python = ["38", "39", "310"]
-
-[envs.lint]
-detached = true
-dependencies = [
-  "bandit>=1.7.4",
-  "black>=23.3.0",
-  "flake8>=6.0.0",
-  "flake8-bugbear>=22.7.1",
-  "flake8-quotes>=3.3.1",
-  "flake8-tidy-imports>=4.8.0",
-  "isort>=5.10.1",
-  "mypy>=0.971",
-]
-[envs.lint.scripts]
-typing = "mypy --install-types --non-interactive {args:bayes tests}"
-security = "bandit --quiet --recursive --skip B101,B102,B105,B110,B112,B301,B307,B324,B403,B404,B603,B604,B606,B607 {args:.}"
-style = [
-  "flake8 {args:.}",
-  "black --check --diff {args:.} --exclude tests/",
-  "isort --check-only --diff {args:.}",
-]
-fmt = [
-  "isort {args:.}",
-  "black {args:.}",
-  "style",
-]
-all = [
-  "style",
-  "typing",
-  "security",
-]
-
-[envs.docs]
-dependencies = [
-  "mkdocs~=1.3.0",
-  "mkdocs-material~=8.3.9",
-  # Plugins
-  "mkdocs-minify-plugin~=0.5.0",
-  "mkdocs-git-revision-date-localized-plugin~=1.0.1",
-  "mkdocstrings-python~=0.7.1",
-  "mkdocs-redirects~=1.0.4",
-  # https://github.com/jimporter/mike/issues/82#issuecomment-1172913929
-  "mike @ https://github.com/jimporter/mike/archive/392d57b8bb9d14bcedf2451a0dc302709f8055eb.zip",
-  # Extensions
-  "mkdocs-click~=0.8.0",
-  "pymdown-extensions~=9.5.0",
-  "mkdocs-material-extensions~=1.0.3",
-  # Necessary for syntax highlighting in code blocks
-  "pygments~=2.12.0",
-]
-
-[envs.docs.scripts]
-build = "mkdocs build --clean --strict {args}"
-serve = "mkdocs serve --dev-addr localhost:8000 {args}"
-ci-build = "mike deploy --update-aliases {args}"
-
-[envs.backend]
-detached = true
-dependencies = [
-  "build~=0.7.0",
-  "httpx",
-]
-
-[envs.backend.env-vars]
-HATCH_BUILD_CLEAN = "true"
-[envs.backend.scripts]
-build = "python -m build ."
-publish = "hatch publish dist"
diff --git a/pdm.lock b/pdm.lock
new file mode 100644
index 0000000..f22bb15
--- /dev/null
+++ b/pdm.lock
@@ -0,0 +1,656 @@
+# This file is @generated by PDM.
+# It is not intended for manual editing.
+
+[metadata]
+groups = ["default", "ruff", "test"]
+strategy = ["inherit_metadata"]
+lock_version = "4.5.0"
+content_hash = "sha256:e25b9aaba95744648858ced98bafafb5c87ad7d49bb69a3793c9c3bf46ce612d"
+
+[[metadata.targets]]
+requires_python = ">=3.9"
+
+[[package]]
+name = "cfgv"
+version = "3.4.0"
+requires_python = ">=3.8"
+summary = "Validate configuration and produce human readable error messages."
+groups = ["test"]
+files = [
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
+]
+
+[[package]]
+name = "colorama"
+version = "0.4.6"
+requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+summary = "Cross-platform colored terminal text."
+groups = ["test"]
+marker = "sys_platform == \"win32\""
+files = [
+    {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
+    {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
+]
+
+[[package]]
+name = "distlib"
+version = "0.3.9"
+summary = "Distribution utilities"
+groups = ["test"]
+files = [
+    {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"},
+    {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"},
+]
+
+[[package]]
+name = "exceptiongroup"
+version = "1.2.2"
+requires_python = ">=3.7"
+summary = "Backport of PEP 654 (exception groups)"
+groups = ["test"]
+marker = "python_version < \"3.11\""
+files = [
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
+]
+
+[[package]]
+name = "filelock"
+version = "3.16.1"
+requires_python = ">=3.8"
+summary = "A platform independent file lock."
+groups = ["test"]
+files = [
+    {file = "filelock-3.16.1-py3-none-any.whl", hash = "sha256:2082e5703d51fbf98ea75855d9d5527e33d8ff23099bec374a134febee6946b0"},
+    {file = "filelock-3.16.1.tar.gz", hash = "sha256:c249fbfcd5db47e5e2d6d62198e565475ee65e4831e2561c8e313fa7eb961435"},
+]
+
+[[package]]
+name = "identify"
+version = "2.6.1"
+requires_python = ">=3.8"
+summary = "File identification library for Python"
+groups = ["test"]
+files = [
+    {file = "identify-2.6.1-py2.py3-none-any.whl", hash = "sha256:53863bcac7caf8d2ed85bd20312ea5dcfc22226800f6d6881f232d861db5a8f0"},
+    {file = "identify-2.6.1.tar.gz", hash = "sha256:91478c5fb7c3aac5ff7bf9b4344f803843dc586832d5f110d672b19aa1984c98"},
+]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+requires_python = ">=3.7"
+summary = "brain-dead simple config-ini parsing"
+groups = ["test"]
+files = [
+    {file = "iniconfig-2.0.0-py3-none-any.whl", hash = "sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374"},
+    {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"},
+]
+
+[[package]]
+name = "joblib"
+version = "1.4.2"
+requires_python = ">=3.8"
+summary = "Lightweight pipelining with Python functions"
+groups = ["default"]
+files = [
+    {file = "joblib-1.4.2-py3-none-any.whl", hash = "sha256:06d478d5674cbc267e7496a410ee875abd68e4340feff4490bcb7afb88060ae6"},
+    {file = "joblib-1.4.2.tar.gz", hash = "sha256:2382c5816b2636fbd20a09e0f4e9dad4736765fdfb7dca582943b9c1366b3f0e"},
+]
+
+[[package]]
+name = "nodeenv"
+version = "1.9.1"
+requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+summary = "Node.js virtual environment builder"
+groups = ["test"]
+files = [
+    {file = "nodeenv-1.9.1-py2.py3-none-any.whl", hash = "sha256:ba11c9782d29c27c70ffbdda2d7415098754709be8a7056d79a737cd901155c9"},
+    {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"},
+]
+
+[[package]]
+name = "numpy"
+version = "2.0.2"
+requires_python = ">=3.9"
+summary = "Fundamental package for array computing in Python"
+groups = ["default"]
+files = [
+    {file = "numpy-2.0.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:51129a29dbe56f9ca83438b706e2e69a39892b5eda6cedcb6b0c9fdc9b0d3ece"},
+    {file = "numpy-2.0.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:f15975dfec0cf2239224d80e32c3170b1d168335eaedee69da84fbe9f1f9cd04"},
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+version = "1.13.1"
+requires_python = ">=3.9"
+summary = "Fundamental algorithms for scientific computing in Python"
+groups = ["default"]
+dependencies = [
+    "numpy<2.3,>=1.22.4",
+]
+files = [
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+name = "six"
+version = "1.16.0"
+requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+summary = "Python 2 and 3 compatibility utilities"
+groups = ["default"]
+files = [
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+version = "3.5.0"
+requires_python = ">=3.8"
+summary = "threadpoolctl"
+groups = ["default"]
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+]
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+version = "2.0.2"
+requires_python = ">=3.8"
+summary = "A lil' TOML parser"
+groups = ["test"]
+marker = "python_version < \"3.11\""
+files = [
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+]
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+version = "2024.2"
+requires_python = ">=2"
+summary = "Provider of IANA time zone data"
+groups = ["default"]
+files = [
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+]
+
+[[package]]
+name = "virtualenv"
+version = "20.27.1"
+requires_python = ">=3.8"
+summary = "Virtual Python Environment builder"
+groups = ["test"]
+dependencies = [
+    "distlib<1,>=0.3.7",
+    "filelock<4,>=3.12.2",
+    "importlib-metadata>=6.6; python_version < \"3.8\"",
+    "platformdirs<5,>=3.9.1",
+]
+files = [
+    {file = "virtualenv-20.27.1-py3-none-any.whl", hash = "sha256:f11f1b8a29525562925f745563bfd48b189450f61fb34c4f9cc79dd5aa32a1f4"},
+    {file = "virtualenv-20.27.1.tar.gz", hash = "sha256:142c6be10212543b32c6c45d3d3893dff89112cc588b7d0879ae5a1ec03a47ba"},
+]
diff --git a/pyproject.toml b/pyproject.toml
index 3ee769e..b60045c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,83 +1,53 @@
-[build-system]
-requires = ["hatchling>=1.4.1"]
-build-backend = "hatchling.build"
-
 [project]
 name = "laplaciannb"
-description = 'TBD'
-readme = "README.md"
-requires-python = ">=3.8"
-license = "MIT"
-keywords = []
+version = "0.6.0"
+description = "**LaplacianNB** is a Python module developed at **Novartis AG** for Naive Bayes classifier for laplacian modified models based on scikit-learn Naive Bayes implementation."
 authors = [
-  { name = "Baranowski, Bartosz", email = "bartosz.baranowski@novartis.com" },
+    {name = "Bartosz Baranowski",email = "bartosz.baranowski@novartis.com"},
 ]
-classifiers = [
-  "Development Status :: 5 - Production/Stable",
-  "Programming Language :: Python",
-  "Programming Language :: Python :: 3.8",
-  "Programming Language :: Python :: 3.9",
-  "Programming Language :: Python :: 3.10",
-]
-dependencies = [
-  "pandas>=1.4.2",
-  "numpy>=1.22.4",
-  "scikit-learn>=1.1.1",
-  "scipy>=1.8.1",]
-dynamic = ["version"]
+dependencies = ["rdkit>=2024.3.5", "scikit-learn>=1.5.2", "pandas>=2.2.3"]
+requires-python = ">=3.9"
+readme = "README.md"
+license = {text = "BSD 3"}
 
-[tool.hatch.build.targets.sdist]
-exclude = [
-  "/.github",
-  "/.git",
-]
+[build-system]
+requires = ["pdm-backend"]
+build-backend = "pdm.backend"
 
-[tool.hatch.build.targets.wheel]
 
-[project.urls]
-Documentation = "https://github.com/unknown/laplaciannb#readme"
-Issues = "https://github.com/unknown/laplaciannb/issues"
-Source = "https://github.com/unknown/laplaciannb"
+[dependency-groups]
+test = ["ruff>=0.7.2", "pytest>=8.3.3", "pre-commit>=4.0.1"]
 
-[tool.hatch.version]
-path = "bayes/__about__.py"
+[tool.ruff]
+line-length = 119
 
-[tool.mypy]
-disallow_untyped_defs = false
-follow_imports = "normal"
-ignore_missing_imports = true
-pretty = true
-show_column_numbers = true
-warn_no_return = false
-warn_unused_ignores = true
+[tool.ruff.lint]
+# Never enforce `E501` (line length violations).
+ignore = ["C901", "E501", "E741", "F402", "F823" ]
+select = ["C", "E", "F", "I", "W"]
+exclude = ["*.ipynb"]
 
-[tool.bandit]
-recursive = true
-skip = ["B101", "B102", "B105", "B110", "B112", "B301", "B307", "B324", "B403", "B404", "B603", "B604", "B606", "B607"]
+# Ignore import violations in all `__init__.py` files.
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401", "F403", "F811"]
 
-[tool.black]
-include = '\.pyi?$'
-line-length = 120
-skip-string-normalization = true
-target-version = ["py38"]
+[tool.ruff.lint.isort]
+lines-after-imports = 2
 
-[tool.isort]
-default_section = "THIRDPARTY"
-force_grid_wrap = 0
-include_trailing_comma = true
-known_first_party = ["hatch", "hatchling"]
-line_length = 120
-multi_line_output = 3
-use_parentheses = true
+[tool.ruff.format]
+# Like Black, use double quotes for strings.
+quote-style = "double"
+exclude = ["*.ipynb"]
 
-[tool.coverage.run]
-branch = true
-omit = [
-]
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false
+
+# Like Black, automatically detect the appropriate line ending.
+line-ending = "auto"
+
+[tool.pdm]
+distribution = true
 
-[tool.coverage.report]
-exclude_lines = [
-  "no cov",
-  "if __name__ == .__main__.:",
-  "if TYPE_CHECKING:",
-]
diff --git a/bayes/LaplacianNB.py b/src/laplaciannb/LaplacianNB.py
similarity index 98%
rename from bayes/LaplacianNB.py
rename to src/laplaciannb/LaplacianNB.py
index 57e8c92..7d3446a 100644
--- a/bayes/LaplacianNB.py
+++ b/src/laplaciannb/LaplacianNB.py
@@ -96,11 +96,11 @@ def __init__(self, *, alpha=1.0, fit_prior=True, class_prior=None):
 
     def _check_X(self, X):
         """Validate X, used only in predict* methods."""
-        X = super()._validate_data(X, reset=False, dtype='object', ensure_2d=False)
+        X = super()._validate_data(X, reset=False, dtype="object", ensure_2d=False)
         return X
 
     def _check_X_y(self, X, y, reset=True):
-        X, y = super()._validate_data(X, y, reset=True, dtype='object', ensure_2d=False)
+        X, y = super()._validate_data(X, y, reset=True, dtype="object", ensure_2d=False)
         return X, y
 
     def _sum_sets(self, set_list):
@@ -152,7 +152,7 @@ def _update_feature_log_prob(self, alpha):
         self.feature_names_ = dict(zip(self.feature_names_, range(len(self.feature_names_))))
         prior = self.feature_count_ / self.feature_all_
         self.feature_prob_ = (classc + alpha) / (np.outer(prior, total) + alpha)
-        self.feature_log_prob_ = np.log(self.feature_prob_).astype('float32')
+        self.feature_log_prob_ = np.log(self.feature_prob_).astype("float32")
 
     def _joint_log_likelihood(self, X):
         """Calculate the posterior log probability of the samples X"""
diff --git a/bayes/__init__.py b/src/laplaciannb/__init__.py
similarity index 100%
rename from bayes/__init__.py
rename to src/laplaciannb/__init__.py
diff --git a/tests/bayes_test.py b/tests/bayes_test.py
index 078c36f..5264936 100644
--- a/tests/bayes_test.py
+++ b/tests/bayes_test.py
@@ -5,7 +5,7 @@
 import pandas as pd
 from numpy.testing import assert_array_equal
 
-from bayes.LaplacianNB import LaplacianNB
+from laplaciannb.LaplacianNB import LaplacianNB
 
 
 def test_bayes():
@@ -43,7 +43,7 @@ def test_rdkit():
     from rdkit import Chem
     from rdkit.Chem import AllChem
 
-    from bayes.LaplacianNB import LaplacianNB
+    from src.laplaciannb.LaplacianNB import LaplacianNB
 
     def get_fp(smiles: str) -> set:
         """Function to calculate MorganFingerprint from smiles.
@@ -60,14 +60,14 @@ def get_fp(smiles: str) -> set:
         fp = AllChem.GetMorganFingerprint(mol, 2)
         return set(fp.GetNonzeroElements().keys())
 
-    DATA_PATH = Path(__file__).parent.parent.joinpath('tests/data/')
-    file = str(DATA_PATH.joinpath('smiles_test.csv'))
+    DATA_PATH = Path(__file__).parent.parent.joinpath("tests/data/")
+    file = str(DATA_PATH.joinpath("smiles_test.csv"))
     df = pd.read_csv(file)
-    df['sets'] = df['smiles'].apply(
+    df["sets"] = df["smiles"].apply(
         lambda x: get_fp(x),
     )
-    X = df['sets']
-    y = df['activity']
+    X = df["sets"]
+    y = df["activity"]
     clf = LaplacianNB()
     clf.fit(X, y)
 
@@ -77,11 +77,10 @@ def get_fp(smiles: str) -> set:
 
 
 def test_joint_log_likelihood():
-
     from rdkit import Chem
     from rdkit.Chem import AllChem
 
-    from bayes.LaplacianNB import LaplacianNB
+    from src.laplaciannb.LaplacianNB import LaplacianNB
 
     def get_fp(smiles: str) -> set:
         """Function to calculate MorganFingerprint from smiles.
@@ -98,20 +97,20 @@ def get_fp(smiles: str) -> set:
         fp = AllChem.GetMorganFingerprint(mol, 2)
         return set(fp.GetNonzeroElements().keys())
 
-    DATA_PATH = Path(__file__).parent.parent.joinpath('tests/data/')
-    file = str(DATA_PATH.joinpath('smiles_test.csv'))
+    DATA_PATH = Path(__file__).parent.parent.joinpath("tests/data/")
+    file = str(DATA_PATH.joinpath("smiles_test.csv"))
     df = pd.read_csv(file)
-    df['sets'] = df['smiles'].apply(
+    df["sets"] = df["smiles"].apply(
         lambda x: get_fp(x),
     )
-    X = df['sets']
-    y = df['activity']
+    X = df["sets"]
+    y = df["activity"]
     clf = LaplacianNB()
     clf.fit(X, y)
 
     # check if algorithm can predict if index is out of range of fitted ones
-    new_df = pd.DataFrame({'sets': [{10210210310210}]})
-    new_X = new_df['sets']
+    new_df = pd.DataFrame({"sets": [{10210210310210}]})
+    new_X = new_df["sets"]
     try:
         clf._joint_log_likelihood(new_X)
     except Exception as exc: