diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index ac734c5..c05b408 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.10"]
 
     steps:
     - uses: actions/checkout@v3.3.0
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a5f6686..7b368c1 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,5 @@
 default_language_version:
-  python: python3.8
+  python: python3.10
 
 default_stages: [commit, push]
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0bcff85..c926b12 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.0] - 2023-07-13
+
+### Change
+
+- Update dependencies
+- Adjust functions to use updated `typer` syntax
+- Increase required python version to 3.10
+- Switch from using `poetry` to `hatchling`/`huak`
+
+
 ## [0.3.0] - 2022-02-17
 
 ### Added
diff --git a/LICENSE b/LICENSE
deleted file mode 100755
index dab65fe..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,27 +0,0 @@
-Copyright (c) 2013, 
-
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-    * Redistributions of source code must retain the above copyright notice,
-      this list of conditions and the following disclaimer.
-    * Redistributions in binary form must reproduce the above copyright notice,
-      this list of conditions and the following disclaimer in the documentation
-      and/or other materials provided with the distribution.
-    * Neither the name of lice nor the names of its contributors
-      may be used to endorse or promote products derived from this software
-      without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
-CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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-LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100755
index 0000000..1110e89
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,595 @@
+GNU General Public License
+==========================
+
+_Version 3, 29 June 2007_
+_Copyright © 2007 Free Software Foundation, Inc. &lt;<http://fsf.org/>&gt;_
+
+Everyone is permitted to copy and distribute verbatim copies of this license
+document, but changing it is not allowed.
+
+## Preamble
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+licensed is called the contributor's “contributor version”.
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+Source to be so available, or **(2)** arrange to deprive yourself of the benefit of the
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+recipient's use of the covered work in a country, would infringe one or more
+identifiable patents in that country that you have reason to believe are valid.
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+If, pursuant to or in connection with a single transaction or arrangement, you
+convey, or propagate by procuring conveyance of, a covered work, and grant a patent
+license to some of the parties receiving the covered work authorizing them to use,
+propagate, modify or convey a specific copy of the covered work, then the patent
+license you grant is automatically extended to all recipients of the covered work and
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+A patent license is “discriminatory” if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on the
+non-exercise of one or more of the rights that are specifically granted under this
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+was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting any implied
+license or other defenses to infringement that may otherwise be available to you
+under applicable patent law.
+
+### 12. No Surrender of Others' Freedom
+
+If conditions are imposed on you (whether by court order, agreement or otherwise)
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+conditions of this License. If you cannot convey a covered work so as to satisfy
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+agree to terms that obligate you to collect a royalty for further conveying from
+those to whom you convey the Program, the only way you could satisfy both those terms
+and this License would be to refrain entirely from conveying the Program.
+
+### 13. Use with the GNU Affero General Public License
+
+Notwithstanding any other provision of this License, you have permission to link or
+combine any covered work with a work licensed under version 3 of the GNU Affero
+General Public License into a single combined work, and to convey the resulting work.
+The terms of this License will continue to apply to the part which is the covered
+work, but the special requirements of the GNU Affero General Public License, section
+13, concerning interaction through a network will apply to the combination as such.
+
+### 14. Revised Versions of this License
+
+The Free Software Foundation may publish revised and/or new versions of the GNU
+General Public License from time to time. Such new versions will be similar in spirit
+to the present version, but may differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program specifies that
+a certain numbered version of the GNU General Public License “or any later
+version” applies to it, you have the option of following the terms and
+conditions either of that numbered version or of any later version published by the
+Free Software Foundation. If the Program does not specify a version number of the GNU
+General Public License, you may choose any version ever published by the Free
+Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions of the GNU
+General Public License can be used, that proxy's public statement of acceptance of a
+version permanently authorizes you to choose that version for the Program.
+
+Later license versions may give you additional or different permissions. However, no
+additional obligations are imposed on any author or copyright holder as a result of
+your choosing to follow a later version.
+
+### 15. Disclaimer of Warranty
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.
+EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE
+QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+### 16. Limitation of Liability
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS
+PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE
+WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16
+
+If the disclaimer of warranty and limitation of liability provided above cannot be
+given local legal effect according to their terms, reviewing courts shall apply local
+law that most closely approximates an absolute waiver of all civil liability in
+connection with the Program, unless a warranty or assumption of liability accompanies
+a copy of the Program in return for a fee.
+
+_END OF TERMS AND CONDITIONS_
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest possible use to
+the public, the best way to achieve this is to make it free software which everyone
+can redistribute and change under these terms.
+
+To do so, attach the following notices to the program. It is safest to attach them
+to the start of each source file to most effectively state the exclusion of warranty;
+and each file should have at least the “copyright” line and a pointer to
+where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program does terminal interaction, make it output a short notice like this
+when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type 'show c' for details.
+
+The hypothetical commands `show w` and `show c` should show the appropriate parts of
+the General Public License. Of course, your program's commands might be different;
+for a GUI interface, you would use an “about box”.
+
+You should also get your employer (if you work as a programmer) or school, if any, to
+sign a “copyright disclaimer” for the program, if necessary. For more
+information on this, and how to apply and follow the GNU GPL, see
+&lt;<http://www.gnu.org/licenses/>&gt;.
+
+The GNU General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may consider it
+more useful to permit linking proprietary applications with the library. If this is
+what you want to do, use the GNU Lesser General Public License instead of this
+License. But first, please read
+&lt;<http://www.gnu.org/philosophy/why-not-lgpl.html>&gt;.
diff --git a/README.md b/README.md
index 39e8b8a..17256f3 100755
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ another.
 ## Installation
 
 PLINKLiftOver requires
-* Python 3.8 
+* Python 3.10
 * The command line version of [liftOver](http://genome.ucsc.edu/cgi-bin/hgLiftOver),
 installed and on the system path
 * An appropriate [chain file](http://hgdownload.soe.ucsc.edu/downloads.html#liftover)
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 5e33936..0000000
--- a/poetry.lock
+++ /dev/null
@@ -1,1268 +0,0 @@
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-
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-
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-
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-    {file = "wrapt-1.13.3-cp39-cp39-win_amd64.whl", hash = "sha256:81bd7c90d28a4b2e1df135bfbd7c23aee3050078ca6441bead44c42483f9ebfb"},
-    {file = "wrapt-1.13.3.tar.gz", hash = "sha256:1fea9cd438686e6682271d36f3481a9f3636195578bab9ca3382e2f5f01fc185"},
-]
diff --git a/pyproject.toml b/pyproject.toml
index 217f622..3c9c890 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,73 +1,60 @@
-# Poetry pyproject.toml: https://python-poetry.org/docs/pyproject/
-
 [build-system]
-requires = ["poetry>=1.0"]
-build-backend = "poetry.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
-[tool.poetry]
+[project]
 name = "plinkliftover"
-version = "0.3.0"
+version = "0.4.0"
 description = "Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver"
 readme = "README.md"
-authors = [
-  "Miles Smith <miles-smith@omrf.org>"
+keywords = []
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Developers",
+    "Operating System :: OS Independent",
+    "Topic :: Software Development :: Libraries :: Python Modules",
 ]
-license = "GNU GPL v3.0"
-repository = "https://github.com/milescsmith/plinkliftover"
-homepage = "https://github.com/milescsmith/plinkliftover"
-
-# Keywords description https://python-poetry.org/docs/pyproject/#keywords
-keywords = []  # Update me
-
-# Pypi classifiers: https://pypi.org/classifiers/
-classifiers = [  # Update me
-  "Development Status :: 3 - Alpha",
-  "Intended Audience :: Developers",
-  "Operating System :: OS Independent",
-  "Topic :: Software Development :: Libraries :: Python Modules",
+dependencies = [
+    "psutil ==5.9.5",
+    "rich ==13.4.2",
+    "typer ==0.9.0",
+    "loguru ==0.7.0",
 ]
 
-[tool.poetry.scripts]
-# Entry points for the package https://python-poetry.org/docs/pyproject/#scripts
-"plinkliftover" = "plinkliftover.__main__:app"
-"map2bed"= "plinkliftover.map2bed:map2bedapp"
-"bed2map"= "plinkliftover.bed2map:bed2mapapp"
+[[project.authors]]
+name = "Miles Smith"
+email = "miles-smith@omrf.org"
 
-[tool.poetry.dependencies]
-python = ">=3.8.3,<4.0"
-typer = "^0.4.0"
-rich = "^10.2.1"
-psutil = "^5.8.0"
+[project.urls]
+repository = "https://github.com/milescsmith/plinkliftover"
+homepage = "https://github.com/milescsmith/plinkliftover"
 
-[tool.poetry.dev-dependencies]
-darglint = "^1.5.8"
-isort = "^5.7.0"
-pyupgrade = "^2.17"
-black = "^21.12b0"
-mypy = "0.921"
-bandit = "^1.7.0"
-safety = "^1.10.3"
-pytest = "^6.2"
-pylint = "^2.8.2"
-pydocstyle = "^6.1.1"
-pre-commit = "^2.12.1"
-flakehell = "^0.9.0"
-flake8-broken-line = "^0.6.0"
-flake8-bugbear = "^21.4"
-flake8-builtins = "^1.5.3"
-flake8-comprehensions = "^3.5.0"
-flake8-eradicate = "^1.0.0"
-flake8-isort = "^4.0.0"
-pycodestyle = "^2.6.0"
-pyflakes = "^2.2.0"
+[project.scripts]
+plinkliftover = "plinkliftover.__main__:app"
+map2bed = "plinkliftover.map2bed:map2bedapp"
+bed2map = "plinkliftover.bed2map:bed2mapapp"
 
-[tool.black]
-# https://github.com/psf/black
-line-length = 80
-target-version = ["py38"]
+[project.optional-dependencies]
+dev = [
+    "bandit ==1.7.5",
+    "black ==23.7.0",
+    "darglint ==1.8.1",
+    "flakehell ==0.9.0",
+    "isort ==5.12.0",
+    "jupyterlab ==4.0.3",
+    "mypy ==1.4.1",
+    "nox ==2023.4.22",
+    "pre-commit ==3.3.3",
+    "pycodestyle ==2.10.0",
+    "pydocstyle ==6.3.0",
+    "pyflakes ==3.0.1",
+    "pylint ==2.17.4",
+    "pytest ==7.4.0",
+    "pyupgrade ==3.9.0",
+    "safety ==2.3.4",
+]
 
 [tool.isort]
-# https://github.com/timothycrosley/isort/
 known_typing = "typing,types,typing_extensions,mypy,mypy_extensions"
 sections = "FUTURE,TYPING,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER"
 include_trailing_comma = true
@@ -78,48 +65,86 @@ force_grid_wrap = 0
 use_parentheses = true
 line_length = 80
 
+[tool.hatch.build.targets.wheel]
+packages = ["src/plinkliftover"]
 
-[tool.flakehell]
-# optionally inherit from remote config (or local if you want)
-base = "https://raw.githubusercontent.com/life4/flakehell/master/pyproject.toml"
-# specify any flake8 options. For example, exclude "example.py":
-exclude = ["example.py"]
-# make output nice
-# format = "grouped"
-# 80 chars aren't enough in 21 century
-max_line_length = 90
-# show line of source code in output
-show_source = true
+[tool.black]
+line-length = 120
+target-version = ["py310"]
+skip-string-normalization = true
 
-[tool.flakehell.plugins]
-flake8-bandit = ["+*"]
-flake8-bugbear = ["-B950"]
-flake8-builtins = ["+*"]
-pylint = ["+*", "-C0103", "-C0116", "-C901", "-E203", "-E401", "-E501", "-E266", "-F401", "-F403", "-R0913", "-R0914", "-W503", "-W1203", "-W1309"]
-# wemake-python-styleguide = ["+*", "-WPS305", "-WPS221", "-WPS111", "-WPS231", "-WPS326", "-WPS337", "-WPS336", "-WPS528", "-WPS529"]
-flake8-broken-line = ["+*"]
-flake8-commas = ["+*"]
-flake8-comprehensions = ["+*"]
-# flake8-darglint = ["+*", "-DAR101"]
-flake8-debugger = ["+*"]
-# flake8-docstrings = ["+*"]
-flake8-eradicate = ["+*", "-E800"]
-flake8-isort = ["+*"]
-# flake8-rst-docstrings = ["+*"]
-# flake8-string-format = ["+*"]
-# mccabe = ["+*"]
-# pep8-naming = ["+*"]
-pycodestyle = ["+*","-E203", "-E401", "-E501", "-E266", "-W503", "-W1203", "-W1309"]
-pyflakes = ["+*"]
+[tool.ruff]
+target-version = "py310"
+line-length = 120
+select = [
+    "A",
+    "ARG",
+    "B",
+    "C",
+    "DTZ",
+    "E",
+    "EM",
+    "F",
+    "FBT",
+    "I",
+    "I001",
+    "ICN",
+    "ISC",
+    "N",
+    "PLC",
+    "PLE",
+    "PLR",
+    "PLW",
+    "Q",
+    "RUF",
+    "S",
+    "T",
+    "TID",
+    "UP",
+    "W",
+    "YTT",
+]
+ignore = [
+    "B027",
+    "FBT003",
+    "S105",
+    "S106",
+    "S107",
+    "C901",
+    "PLR0911",
+    "PLR0912",
+    "PLR0913",
+    "PLR0915",
+]
+unfixable = [
+    "F401",
+    "UP007",
+]
+exclude = [
+    ".git",
+    ".hg",
+    "__pycache__",
+    "_bin/*",
+    "_build/*",
+    "_ig_fbcode_wheel/*",
+    "buck-out/*",
+    "third-party-buck/*",
+    "third-party2/*",
+    "dist",
+    ".venv",
+    ".nox",
+    ".mypy_cache",
+    ".pytype",
+    ".svn",
+    "__pypackages__",
+]
+src = ["src"]
 
-# match by prefix
-[tool.flakehell.exceptions."tests/"]
-pycodestyle = ["-*"]     # disable a check
-pyflakes = ["-*"]           # disable a plugin
+[tool.ruff.mccabe]
+max-complexity = 50
 
-[tool.flakehell.exceptions."tests/test_example.py"]
-pyflakes = ["+*"]           # enable a plugin
+[tool.ruff.isort]
+known-first-party = ["readcounts"]
 
-# match by glob
-[tool.flakehell.exceptions."**/test_*.py"]
-pyflakes = ["-*"]
+[tool.ruff.flake8-tidy-imports]
+ban-relative-imports = "all"
diff --git a/setup.cfg b/setup.cfg
index a82165c..b45aae9 100755
--- a/setup.cfg
+++ b/setup.cfg
@@ -10,7 +10,7 @@ docstring_style = google
 
 [mypy]
 # mypy configurations: http://bit.ly/2zEl9WI
-python_version = 3.7
+python_version = 3.10
 pretty = True
 allow_redefinition = False
 check_untyped_defs = True
diff --git a/src/plinkliftover/__init__.py b/src/plinkliftover/__init__.py
index 23680b2..dcb2f6a 100755
--- a/src/plinkliftover/__init__.py
+++ b/src/plinkliftover/__init__.py
@@ -1,6 +1,11 @@
-# type: ignore[attr-defined]
-"""`plinkliftover` Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver"""
+"""
+`plinkliftover` Converts genotype data stored in plink's PED+MAP
+format from one genome build to another, using liftOver
+"""
 from importlib.metadata import PackageNotFoundError, version
+from typing import Annotated
+
+from loguru import logger
 
 try:
     __version__ = version(__name__)
@@ -11,19 +16,38 @@
 from rich.console import Console
 
 console = Console()
+logger.disable("readcounts")
+
+app = typer.Typer(
+    name="plinkliftover",
+    help="Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver",
+    add_completion=False,
+)
+
+verbosity_level = 0
 
 
-def version_callback(value: bool):
+def version_callback(value: bool) -> None:  # noqa FBT001
     """Prints the version of the package."""
     if value:
-        console.print(
-            f"[yellow]plinkliftover[/] version: [bold blue]{__version__}[/]"
-        )
+        console.print(f"[yellow]plinkliftover[/] version: [bold blue]{__version__}[/]")
         raise typer.Exit()
 
 
-app = typer.Typer(
-    name="plinkliftover",
-    help="Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver",
-    add_completion=False,
-)
+@app.callback()
+def verbosity(
+    verbose: Annotated[
+        int,
+        typer.Option(
+            "-v",
+            "--verbose",
+            help="Control output verbosity. Pass this argument multiple times to increase the amount of output.",
+            count=True,
+        ),
+    ] = 0
+) -> None:
+    verbosity_level = verbose  # noqa: F841
+
+
+if __name__ == "main":
+    app()
diff --git a/src/plinkliftover/__main__.py b/src/plinkliftover/__main__.py
index 90a9312..b8e99cd 100755
--- a/src/plinkliftover/__main__.py
+++ b/src/plinkliftover/__main__.py
@@ -1,50 +1,57 @@
-# type: ignore[attr-defined]
-from typing import Optional
-
 from distutils.spawn import find_executable
 from pathlib import Path
+from typing import Annotated, Optional
 
 import typer
+from loguru import logger
 
-from . import __version__, app, console, version_callback
-from .bed2map import bed2map
-from .liftover import liftBed, liftDat, liftPed
-from .logger import plo_logger as logger
-from .map2bed import map2bed
+from plinkliftover import app, console, verbosity_level, version_callback
+from plinkliftover.bed2map import bed2map
+from plinkliftover.liftover import lift_bed, lift_dat, lift_ped
+from plinkliftover.logger import init_logger
+from plinkliftover.map2bed import map2bed
 
 
-@app.command(name="")
+@app.command(name="liftover")
 def liftover(
-    mapfile: str = typer.Argument(
-        ..., help="The plink MAP file to `liftOver`."
-    ),
-    chainfile: str = typer.Argument(
-        ..., help="The location of the chain files to provide to `liftOver`."
-    ),
-    pedfile: Optional[str] = typer.Option(
-        None,
-        help='Optionally remove "unlifted SNPs" from the plink PED file after running `liftOver`.',
-        show_default=False,
-    ),
-    datfile: Optional[str] = typer.Option(
-        None,
-        help="Optionally remove 'unlifted SNPs' from a data file containing a list of SNPs (e.g. for  --exclude or --include in `plink`)",
-        show_default=False,
-    ),
-    prefix: Optional[str] = typer.Option(
-        None, help="The prefix to give to the output files.", show_default=False
-    ),
-    liftoverexecutable: Optional[str] = typer.Option(
-        None, help="The location of the `liftOver` executable."
-    ),
-    version: bool = typer.Option(
-        None,
-        "-v",
-        "--version",
-        callback=version_callback,
-        is_eager=True,
-        help="Prints the version of the plinkliftover package.",
-    ),
+    mapfile: Annotated[
+        Path,
+        typer.Argument(help="The plink MAP file to `liftOver`."),
+    ],
+    chainfile: Annotated[Path, typer.Argument(help="The location of the chain files to provide to `liftOver`.")],
+    pedfile: Annotated[
+        Optional[Path],  # noqa UP007
+        typer.Option(
+            help='Optionally remove "unlifted SNPs" from the plink PED file after running `liftOver`.',
+            show_default=False,
+        ),
+    ] = None,
+    datfile: Annotated[
+        Optional[Path],  # noqa UP007
+        typer.Option(
+            help=(
+                "Optionally remove 'unlifted SNPs' from a data file containing a list of SNPs "
+                "(e.g. for  --exclude or --include in `plink`)"
+            ),
+            show_default=False,
+        ),
+    ] = None,
+    prefix: Annotated[
+        Optional[str], typer.Option(help="The prefix to give to the output files.", show_default=False)  # noqa UP007
+    ] = None,
+    liftoverexecutable: Annotated[
+        Optional[str], typer.Option(help="The location of the `liftOver` executable.")  # noqa UP007
+    ] = None,
+    version: Annotated[  # noqa ARG007
+        bool,
+        typer.Option(
+            "-V",
+            "--version",
+            callback=version_callback,
+            is_eager=True,
+            help="Prints the version of the plinkliftover package.",
+        ),
+    ] = False,  # noqa FBT002
 ) -> None:
     """Converts genotype data stored in plink's PED+MAP format from one genome
     build to another, using liftOver.
@@ -52,36 +59,33 @@ def liftover(
     # Show usage message if user hasn't provided any arguments, rather
     # than giving a non-descript error message with the usage()
 
-    mapfile = Path(mapfile)
+    init_logger(verbose=verbosity_level)
+
     oldbed = mapfile.with_suffix(".bed")
     map2bed(mapfile, oldbed)
 
     # If a location is not specified for the liftOver executable.
     # assume it is in the User's $PATH.
     if liftoverexecutable is None:
-        try:
-            liftOverPath = Path(find_executable("liftOver"))
-        except TypeError as e:
-            logger.exception(
-                "The `liftOver` executable was not found.  Please make sure it is installed and in the PATH"
-            )
-            logger.error(e)
+        if (lop := find_executable("liftOver")) is not None:
+            lift_over_path = Path(lop)
+            if not lift_over_path.exists():
+                msg = "The `liftOver` executable was not found.  Please make sure it is installed and in the PATH"
+                logger.exception(msg)
+                raise FileNotFoundError(msg)
     else:
-        liftOverPath = Path(liftoverexecutable)
-        if not liftOverPath.exists():
-            logger.exception(
-                "The `liftOver` executable was not found.  Please make sure it is installed and in the PATH"
-            )
-            raise FileNotFoundError(
-                "The `liftOver` executable was not found.  Please make sure it is installed and in the PATH"
-            )
+        lift_over_path = Path(liftoverexecutable)
+        if not lift_over_path.exists():
+            msg = "The `liftOver` executable was not found.  Please make sure it is installed and in the PATH"
+            logger.exception(msg)
+            raise FileNotFoundError(msg)
 
     newbed = Path(f"{mapfile}.bed")
-    lifted_set, unlifted_set, lb_status = liftBed(
+    lifted_set, unlifted_set, lb_status = lift_bed(
         fin=oldbed,
         fout=newbed,
         chainfile=chainfile,
-        liftOverPath=liftOverPath,
+        lift_over_path=lift_over_path,
     )
 
     if lb_status:
@@ -99,9 +103,7 @@ def liftover(
         console.print(f"[pink]{datfile.name}[/]")
         newdat = Path(f"{prefix}.dat")
 
-        ld_status = liftDat(fin=datfile, fout=newdat, lifted_set=lifted_set)
-
-        if ld_status:
+        if lift_dat(fin=datfile, fout=newdat, lifted_set=lifted_set):
             console.print("lifting [purple]dat[/] file: [green]SUCCESS[/]")
             logger.info(f"lifting map file: {newmap} - SUCCESS")
         else:
@@ -111,27 +113,16 @@ def liftover(
     if pedfile is not None:
         pedfile = Path(pedfile)
         console.print(f"[pink]{pedfile.name}[/]")
-        newPed = Path(f"{prefix}.ped")
-        lp_status = liftPed(
-            fin=pedfile, fout=newPed, fOldMap=mapfile, unlifted_set=unlifted_set
-        )
+        new_ped = Path(f"{prefix}.ped")
 
-        if lp_status:
-            console.print(
-                "lifting [dark_orange3]ped[/] file: [bold green]SUCCESS[/]"
-            )
+        if lift_ped(fin=pedfile, fout=new_ped, foldmap=mapfile, unlifted_set=unlifted_set):
+            console.print("lifting [dark_orange3]ped[/] file: [bold green]SUCCESS[/]")
             logger.info("lifting ped file: SUCCESS")
         else:
-            console.print(
-                "lifting [dark_orange3]ped[/] file: [bold red]FAILED[/]"
-            )
+            console.print("lifting [dark_orange3]ped[/] file: [bold red]FAILED[/]")
             logger.info("lifting ped file: FAILED")
 
     console.print("cleaning up BED files...")
     logger.info("cleaning up BED files...")
     newbed.unlink()
     oldbed.unlink()
-
-
-if __name__ == "__main__":
-    typer.run(main)
diff --git a/src/plinkliftover/bed2map.py b/src/plinkliftover/bed2map.py
index b103078..92078ad 100644
--- a/src/plinkliftover/bed2map.py
+++ b/src/plinkliftover/bed2map.py
@@ -1,29 +1,26 @@
-from typing import Optional
-
 from pathlib import Path
+from typing import Annotated, Optional
 
 import typer
+from loguru import logger
 
-from . import app, console, version_callback
-from .logger import plo_logger as logger
+from plinkliftover import app, console, verbosity_level, version_callback
+from plinkliftover.logger import init_logger
 
-# bed2mapapp = typer.Typer(
-#     name="bed2map",
-#     help="Converts BED files to PLINK MAP format",
-#     add_completion=False,
-# )
+BED_LINES_LENGTH: int = 4
 
 
 def bed2map(fin: Path, fout: Path) -> bool:
+    init_logger(verbosity_level)
     logger.info(f"fin: {fin}, fout: {fout}")
     console.print(
         f"Converting lifted [green]BED[/] [blue]{fin.name}[/] file back to [green]MAP[/] [yellow]{fout.name}[/]..."
     )
     lines = fin.read_text().split("\n")
-    output = list()
+    output = []
     with typer.progressbar(lines) as bed_lines:
         for line in bed_lines:
-            if len(x := line.split()) == 4:
+            if len(x := line.split()) == BED_LINES_LENGTH:
                 chrom, _, pos1, rs = x
                 chrom = chrom.replace("chr", "")
                 output.append(f"{chrom}\t{rs}\t0.0\t{pos1}")
@@ -33,23 +30,29 @@ def bed2map(fin: Path, fout: Path) -> bool:
 
 @app.command(name="bed2map")
 def bed2mapapp(
-    bedfile: Path = typer.Argument(..., help="A BED file."),
-    output: Optional[Path] = typer.Option(
-        None,
-        "-o",
-        "--output",
-        help=f"Location to save MAP file to.  If one is not provided, "
-        f"then it will be saved to where the BED file is.",
-        show_default=True,
-    ),
-    version: bool = typer.Option(
-        None,
-        "-v",
-        "--version",
-        callback=version_callback,
-        is_eager=True,
-        help="Prints the version of the plinkliftover package.",
-    ),
+    bedfile: Annotated[Path, typer.Argument(help="A BED file.")],
+    output: Annotated[
+        Optional[Path],  # noqa UP007
+        typer.Option(
+            "-o",
+            "--output",
+            help=(
+                "Location to save MAP file to.  If one is not provided, "
+                "then it will be saved to where the BED file is."
+            ),
+            show_default=True,
+        ),
+    ] = None,
+    version: Annotated[  # noqa ARG001
+        Optional[bool],  # noqa UP007
+        typer.Option(
+            "-v",
+            "--version",
+            callback=version_callback,
+            is_eager=True,
+            help="Prints the version of the plinkliftover package.",
+        ),
+    ] = None,
 ) -> None:
     """Convert genotype data stored in a PLINK MAP file into a BED file,
     allowing one to use the online version of liftOver should the local
diff --git a/src/plinkliftover/liftover.py b/src/plinkliftover/liftover.py
index 873e14f..a3427d4 100755
--- a/src/plinkliftover/liftover.py
+++ b/src/plinkliftover/liftover.py
@@ -14,98 +14,85 @@
  - to generally be slightly more PEP compliant.
 
 Modified by Miles Smith:
- - Update to work with python >=3.7
+ - Update to work with python >= 3.10
 """
 
-from typing import Set, Tuple
-
 import sys
 from pathlib import Path
 from subprocess import check_output
 
+from loguru import logger
 from typer import progressbar
 
-from . import console
-from .logger import plo_logger as logger
+from plinkliftover import console
+
+DAT_LINE_LENGTH: int = 2
 
 
-def liftBed(
+def lift_bed(
     fin: Path,
     fout: Path,
     chainfile: Path,
-    liftOverPath: Path,
-) -> Tuple[Set[str]]:
+    lift_over_path: Path,
+) -> tuple[set[str], set[str], bool]:
     console.print(f"Lifting [green]BED[/] file [blue]{fin.name}[/]...")
-    params = {
-        "LIFTOVER_BIN": liftOverPath.resolve(),
+    params: dict[str, str | Path] = {
+        "LIFTOVER_BIN": lift_over_path.resolve(),
         "OLD": fin,
         "CHAIN": chainfile,
         "NEW": fout,
         "UNLIFTED": f"{fout}.unlifted",
     }
 
-    check_output(params.values())
+    check_output([str(params[_]) for _ in params])  # noqa: S603
     # record lifted/unliftd rs
     unlifted_lines = Path(params["UNLIFTED"]).read_text().split("\n")
     console.print(f"Processing [red]unlifted[/] {fout.name}.unlifted")
     with progressbar(unlifted_lines) as unlifted:
-        unlifted_set = {
-            ln.strip().split()[-1]
-            for ln in unlifted
-            if len(ln) > 0 and ln[0] != "#"
-        }
+        unlifted_set = {ln.strip().split()[-1] for ln in unlifted if len(ln) > 0 and ln[0] != "#"}
 
     console.print(f"Processing [red]new[/] {fout.name}")
     new_bed_lines = Path(params["NEW"]).read_text().split("\n")
     with progressbar(new_bed_lines) as new_bed:
-        lifted_set = {
-            ln.strip().split()[-1]
-            for ln in new_bed
-            if len(ln) != 0 and ln[0] != "#"
-        }
+        lifted_set = {ln.strip().split()[-1] for ln in new_bed if len(ln) != 0 and ln[0] != "#"}
 
     return lifted_set, unlifted_set, True
 
 
-def liftDat(fin: Path, fout: Path, lifted_set: Set[str]) -> bool:
+def lift_dat(fin: Path, fout: Path, lifted_set: set[str]) -> bool:
     console.print(f"Updating [green]DAT[/] file [pink]{fin.name}[/]...")
     lines = fin.read_text().split("\n")
-    output = list()
+    output = []
     with progressbar(lines) as dat_lines:
         for ln in dat_lines:
             if len(ln) == 0 or ln[0] != "M":
                 output.append(ln)
-            else:
-                if len(thing := ln.strip().split()) == 2:
-                    _, rs = thing
-                    if rs in lifted_set:
-                        output.append(ln)
+            elif len(thing := ln.strip().split()) == DAT_LINE_LENGTH:
+                _, rs = thing
+                if rs in lifted_set:
+                    output.append(ln)
     console.print(f"Writing [green]new DAT[/] file [pink]{fout.name}[/]...")
 
     return True
 
 
-def liftPed(
-    fin: Path, fout: Path, fOldMap: Path, unlifted_set: Set[str]
-) -> bool:
+def lift_ped(fin: Path, fout: Path, foldmap: Path, unlifted_set: set[str]) -> bool:
     # two ways to do it:
     # 1. write unlifted snp list
     #    use PLINK to do this job using --exclude
     # 2. alternatively, we can write our own method
     # we will use method 2
-    marker = [i.strip().split()[1] for i in open(fOldMap)]
+    marker = [i.strip().split()[1] for i in open(foldmap)]
     flag = [(x not in unlifted_set) for x in marker]
 
     console.print(f"Updating [green]PED[/] file [orange]{fin.resolve()}[/]...")
     lines = fin.read_text().split("\n")
-    output = list()
+    output = []
     with progressbar(lines) as liftped_lines:
         for ln in liftped_lines:
             if ln.strip() != "":
                 f = ln.strip().split()
-                f = f[:6] + [
-                    f[i * 2] + " " + f[i * 2 + 1] for i in range(3, len(f) // 2)
-                ]
+                f = f[:6] + [f"{f[i * 2]} {f[i * 2 + 1]}" for i in range(3, len(f) // 2)]
                 if len(f[6:]) != len(flag):
                     logger.error("Inconsistent length of ped and map files")
                     logger.error(f"{len(f[6:])} vs {len(flag)}")
@@ -115,9 +102,7 @@ def liftPed(
                 a = "\t".join(f[:6])
                 b = "\t".join(newmarker)
                 output.append(f"{a}\t{b}\n")
-    console.print(
-        f"Writing new [green]PED[/] data to [light_slate_blue]{fout.resolve()}[/]"
-    )
+    console.print(f"Writing new [green]PED[/] data to [light_slate_blue]{fout.resolve()}[/]")
     with open(fout, "w") as fo:
         fo.writelines(output)
     return True
diff --git a/src/plinkliftover/logger.py b/src/plinkliftover/logger.py
index 62f8f7e..e90b274 100755
--- a/src/plinkliftover/logger.py
+++ b/src/plinkliftover/logger.py
@@ -1,82 +1,22 @@
-# stolen wholesale from `anndata <https://github.com/theislab/anndata/blob/master/anndata/_core/anndata.py>`_
-# BSD 3-Clause License
+import datetime
+from sys import stderr
 
-# Copyright (c) 2017-2018 P. Angerer, F. Alexander Wolf, Theis Lab
-# All rights reserved.
+from loguru import logger
 
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
 
-# * Redistributions of source code must retain the above copyright notice, this
-#   list of conditions and the following disclaimer.
+def init_logger(verbose: int, msg_format: str | None = None) -> None:
+    if msg_format is None:
+        msg_format = "<cyan>{name}</cyan>:<cyan>{function}</cyan>:<cyan>{line}</cyan>·-·<level>{message}</level>"
 
-# * Redistributions in binary form must reproduce the above copyright notice,
-#   this list of conditions and the following disclaimer in the documentation
-#   and/or other materials provided with the distribution.
+    timezone = datetime.datetime.now(datetime.timezone.utc).astimezone().tzinfo
+    logger.add(f"readcounts_{datetime.datetime.now(tz=timezone).strftime('%d-%m-%Y--%H-%M-%S')}.log", level="DEBUG")
 
-# * Neither the name of the copyright holder nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-
-# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-import logging
-import os
-
-_previous_memory_usage = None
-
-plo_logger = logging.getLogger("plinkliftover")
-# Don’t pass log messages on to logging.root and its handler
-plo_logger.propagate = False
-plo_logger.setLevel("ERROR")
-plo_logger.addHandler(logging.StreamHandler())  # Logs go to stderr
-plo_logger.handlers[-1].setFormatter(logging.Formatter("%(message)s"))
-plo_logger.handlers[-1].setLevel("ERROR")
-
-
-def get_logger(name):
-    """\
-    Creates a child logger that delegates to plo_logger
-    instead to logging.root
-    """
-    return plo_logger.manager.getLogger(name)
-
-
-def get_memory_usage():
-    import psutil
-
-    process = psutil.Process(os.getpid())
-    try:
-        meminfo = process.memory_info()
-    except AttributeError:
-        meminfo = process.get_memory_info()
-    mem = meminfo[0] / 2 ** 30  # output in GB
-    mem_diff = mem
-    global _previous_memory_usage
-    if _previous_memory_usage is not None:
-        mem_diff = mem - _previous_memory_usage
-    _previous_memory_usage = mem
-    return mem, mem_diff
-
-
-def format_memory_usage(mem_usage, msg="", newline=False):
-    newline = "\n" if newline else ""
-    more = " \n... " if msg != "" else ""
-    mem, diff = mem_usage
-    return (
-        f"{newline}{msg}{more}"
-        f"Memory usage: current {mem:.2f} GB, difference {diff:+.2f} GB"
-    )
-
-
-def print_memory_usage(msg="", newline=False):
-    print(format_memory_usage(get_memory_usage(), msg, newline))
+    match verbose:
+        case 3:
+            logger.add(stderr, format=msg_format, level="DEBUG")
+        case 2:
+            logger.add(stderr, format=msg_format, level="INFO")
+        case 1:
+            logger.add(stderr, format=msg_format, level="WARNING")
+        case _:
+            logger.add(stderr, format=msg_format, level="ERROR")
diff --git a/src/plinkliftover/map2bed.py b/src/plinkliftover/map2bed.py
index 8ee65ad..2492ab9 100644
--- a/src/plinkliftover/map2bed.py
+++ b/src/plinkliftover/map2bed.py
@@ -1,17 +1,13 @@
-from typing import Optional
-
 from pathlib import Path
+from typing import Annotated, Optional
 
 import typer
+from loguru import logger
 
-from . import app, console, version_callback
-from .logger import plo_logger as logger
+from plinkliftover import app, console, verbosity_level, version_callback
+from plinkliftover.logger import init_logger
 
-# map2bedapp = typer.Typer(
-#     name="map2bed",
-#     help="Converts PLINK MAP files into BED format",
-#     add_completion=False,
-# )
+MAP_LINE_LENGTH: int = 4
 
 
 def map2bed(fin: Path, fout: Path) -> bool:
@@ -19,38 +15,43 @@ def map2bed(fin: Path, fout: Path) -> bool:
     console.print(
         f"Converting [green]MAP[/] file [yellow]{fin.name}[/] file to [green]UCSC BED[/] file [blue]{fout.name}[/]..."
     )
+    init_logger(verbosity_level)
     lines = fin.read_text().split("\n")
-    output = list()
+    output = []
     with typer.progressbar(lines) as map_lines:
         for line in map_lines:
-            if len(x := line.split()) == 4:
+            if len(x := line.split()) == MAP_LINE_LENGTH:
                 chrom, rs, _, pos = x
                 output.append(f"chr{chrom}\t{int(pos)-1}\t{int(pos)}\t{rs}")
-            else:
-                pass
     fout.write_text("\n".join(output))
     return True
 
 
 @app.command(name="map2bed")
 def map2bedapp(
-    mapfile: Path = typer.Argument(..., help="A PLINK MAP file."),
-    output: Optional[Path] = typer.Option(
-        None,
-        "-o",
-        "--output",
-        help=f"Location to save BED file to.  If one is not provided, "
-        f"then it will be saved to where the MAP file is.",
-        show_default=True,
-    ),
-    version: bool = typer.Option(
-        None,
-        "-v",
-        "--version",
-        callback=version_callback,
-        is_eager=True,
-        help="Prints the version of the plinkliftover package.",
-    ),
+    mapfile: Annotated[Path, typer.Argument(help="A PLINK MAP file.")],
+    output: Annotated[
+        Optional[Path],  # noqa UP007
+        typer.Option(
+            "-o",
+            "--output",
+            help=(
+                "Location to save BED file to.  If one is not provided, "
+                "then it will be saved to where the MAP file is."
+            ),
+            show_default=True,
+        ),
+    ] = None,
+    version: Annotated[  # noqa ARG001
+        bool,
+        typer.Option(
+            "-v",
+            "--version",
+            callback=version_callback,
+            is_eager=True,
+            help="Prints the version of the plinkliftover package.",
+        ),
+    ] = False,  # noqa FBT007
 ) -> None:
     """Convert genotype data stored in a PLINK MAP file into a BED file,
     allowing one to use the online version of liftOver should the local