diff --git a/.github/workflows/unit-tests.yml b/.github/workflows/tests.yml
similarity index 67%
rename from .github/workflows/unit-tests.yml
rename to .github/workflows/tests.yml
index 864ce7d1..cf26fabd 100644
--- a/.github/workflows/unit-tests.yml
+++ b/.github/workflows/tests.yml
@@ -1,9 +1,15 @@
-name: Unit Tests
+name: Tests
 
-on: [push, pull_request]
+on: push
 
 jobs:
-  test:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/action@v3.0.1
+  tox-tests:
     runs-on: ubuntu-latest
 
     strategy:
@@ -11,6 +17,7 @@ jobs:
         python-version: [3.9]
 
     steps:
+
       - name: Checkout repository
         uses: actions/checkout@v2
 
@@ -30,12 +37,16 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          pip install -e .[dev]
 
       - name: Start ScienceBeam Docker container
         run: |
-          docker run -d --rm -p 8082:8070 elifesciences/sciencebeam-parser
+          docker run -d --rm -p 8070 elifesciences/sciencebeam-parser
 
       - name: Run tests
         run: |
-          tox
\ No newline at end of file
+          tox
+
+      - name: Test packaging
+        run: |
+          tox -e .package
diff --git a/.gitignore b/.gitignore
index 811c2ace..861b62ba 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,6 @@
 # Ignore the virtual environment directory
+_version.py
+node_modules
 venv/
 *coverage*
 .idea
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a4e07126..8fb49dff 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,6 +1,35 @@
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.257
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: "v0.4.9"
     hooks:
       - id: ruff
         args: ["--fix"]
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+        files: ".*\\.py"
+        exclude: "examples|docs/examples"
+      - id: check-added-large-files
+      - id: check-toml
+      - id: end-of-file-fixer
+        exclude: "examples|docs/examples"
+
+  # - repo: https://github.com/pre-commit/mirrors-prettier
+  #   rev: v4.0.0-alpha.8
+  #   hooks:
+  #     - id: prettier
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: isort
+        args: ["--profile", "black"]
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..71eec60b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,35 @@
+# Use the official Debian Docker image as the base
+FROM debian:latest
+
+# Set working directory
+WORKDIR /app
+
+# Install system dependencies, Python, pip, networking, and debugging tools
+RUN apt-get update && apt-get install -y \
+    git \
+    python3 \
+    python3-pip \
+    python3-venv \
+    curl \
+    iputils-ping \
+    net-tools \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy your project files
+COPY . /app
+
+# Create and activate virtual environment
+RUN python3 -m venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Upgrade pip in the virtual environment
+RUN pip install --upgrade pip
+
+# Install the package and its dependencies
+RUN pip install -e .
+
+# Install pre-commit (optional, remove if not needed in the container)
+RUN pip install pre-commit
+
+# Set the command to the osm command
+CMD ["osm", "--help"]
diff --git a/README.md b/README.md
index ffcfa641..fda883be 100644
--- a/README.md
+++ b/README.md
@@ -2,18 +2,35 @@
 OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.
 
 # How to setup and run the application
-- After cloning the repo, navigate into the project's root directory by running `cd osm_cli`
+- After cloning the repo, navigate into the project's root directory by running `cd osm`
 - Run `python -m venv venv` to create a Virtual Environment
 - Depending on your system, run the approriate command to Activate the Virtual Environment
 Windows: `venv\Scripts\activate`<br>
 macOS and Linux: `source venv/bin/activate`
 
-- Next, run `pip install -r requirements.txt && pre-commit install` to install all the dependencies.
-- Open a terminal tab and run the image `docker run --rm -p 8082:8070 elifesciences/sciencebeam-parser` and keep it running for the rest of the testing period
-- Go back to terminal(root folder)
-- Finally, run `python -m osm.cli pdf-xml "path_to_file_name.pdf" file_id`
+- Next, run `pip install -e .` to install the package with its dependencies.
+- Open a terminal tab and run the image `docker run --rm -p 8070:8070 elifesciences/sciencebeam-parser` and keep it running
+
+**Note:** The ScienceBeam image is not supported by all apple silicon chips. You may need to consider using an alternative systems.
+- Finally, run `osm pdf-xml "path_to_file_name.pdf" output_file_path`
 
 # How to run tests of the application
 Run `tox`
+
 # How to run the unit tests
-- Navigate to the project's root directory and run `python -m pytest`
+- Navigate to the project's root directory and run `pytest`
+
+# Using pre-commit for commit checks
+
+Pre-commit will run all of its hooks on every commit you make. To install
+pre-commit and its hooks, run the following commands:
+
+```
+pip install pre-commit
+pre-commit install
+```
+# How to build the Docker image and run the Docker container
+- Navigate to the project's root directory and run `docker-compose up --build`
+- When the image is built and the containers are running, open another terminal and start osm container in interactive mode using the command `docker-compose run osm bash`
+- You can do file conversions in the container using this command `osm pdf-xml "path_to_file_name.pdf" output_file_path`
+- Or use the command `docker-compose run --rm osm osm pdf-xml "path_to_file_name.pdf" output_file_path` to convert files in non-interactive mode
diff --git a/commands/converters/converter.py b/commands/converters/converter.py
deleted file mode 100644
index 4bf98da7..00000000
--- a/commands/converters/converter.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from abc import ABC, abstractmethod
-
-from pydantic import FilePath, BaseModel
-
-
-class Converter(ABC, BaseModel):
-    @abstractmethod
-    def convert(self, pdf_path: FilePath) -> str:
-        pass
diff --git a/commands/converters/pdf_converter.py b/commands/converters/pdf_converter.py
deleted file mode 100644
index f2f3ad71..00000000
--- a/commands/converters/pdf_converter.py
+++ /dev/null
@@ -1,62 +0,0 @@
-import socket
-
-import docker
-from docker.errors import DockerException
-from pydantic import FilePath
-import requests
-
-from commands.converters.converter import Converter
-from commands.utils.config import config
-
-
-class PDFConverter(Converter):
-    protocol: str = config.PROTOCAL
-    host: str = config.HOST
-    port: int = config.PORT
-
-    def convert(self, pdf_path: FilePath) -> str:
-        """Convert a PDF file to XML using ScienceBeam Parser.
-
-        Args:
-            pdf_path: Path to the PDF file
-        Returns:
-            XML content as a string
-        """
-        sciencebeam_url: str = f'{self.protocol}://{self.host}:{self.port}/api/convert'
-        with open(pdf_path, 'rb') as pdf_file:
-            files = {'file': pdf_file}
-            headers = {'Accept': 'application/tei+xml'}
-            response = requests.post(
-                sciencebeam_url, files=files, headers=headers)
-
-            if response.status_code == 200:
-                return response.text
-            else:
-                response.raise_for_status()
-
-    def is_host_ready(self, timeout=3) -> bool:
-        """Check if the host is ready to accept requests.
-        Args:
-            timeout: Timeout in seconds
-        Returns:
-            True if the docker is host is ready, False otherwise
-        """
-        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:
-            sock.settimeout(timeout)
-            try:
-                sock.connect((self.host, self.port))
-            except (socket.timeout, socket.error):
-                return False
-            return True
-
-    def is_docker_running(self):
-        """Check if the docker image exists.
-        Returns:
-            True if the docker image exists, False otherwise
-        """
-        try:
-            client = docker.from_env()
-            client.images.get('elifesciences/sciencebeam-parser')
-            return True
-        except DockerException:
-            return False
diff --git a/commands/file_processing.py b/commands/file_processing.py
deleted file mode 100644
index f37d0866..00000000
--- a/commands/file_processing.py
+++ /dev/null
@@ -1,42 +0,0 @@
-import click
-import requests
-from pydantic import ValidationError
-
-from commands.converters.pdf_converter import PDFConverter
-from logs.logger import logger
-
-
-@click.command()
-@click.argument('file_path', type=click.Path(exists=True))
-@click.argument('file_id', type=str)
-def pdf_xml(file_path, file_id):
-    """This function converts a file from PDF
-        to XML
-
-    Args:
-        file_path (file path): First parameter
-        file_id (string): Second parameter
-    Returns:
-        Creates an XML file in the directory xmls_sciencebeam
-    """
-    try:
-        converter = PDFConverter()
-
-        if not converter.is_docker_running():
-            raise click.ClickException('Please make sure the docker is running')
-
-        if not converter.is_host_ready():
-            raise click.ClickException('The converter server is offline')
-
-        xml_content = converter.convert(file_path)
-        # Save the converted xml contents
-        output_file: str = f'docs/examples/sciencebeam_xml_outputs/{file_id}.xml'
-        with open(output_file, 'w', encoding='utf-8') as xml_file:
-            xml_file.write(xml_content)
-            logger.info(f'Converted: {file_path} with ID: {file_id} to XML')
-
-    except ValidationError as error:
-        logger.error("Validation error:", error)
-
-    except requests.RequestException as error:
-        logger.error("Request error:", error)
diff --git a/commands/utils/config.py b/commands/utils/config.py
deleted file mode 100644
index ac7ace90..00000000
--- a/commands/utils/config.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from pydantic.v1 import BaseSettings
-
-
-class AppConfig(BaseSettings):
-    PORT:int = 8082
-    HOST: str = 'localhost'
-    PROTOCAL: str = 'http'
-
-
-config = AppConfig()
diff --git a/docker-compose.yml b/docker-compose.yml
new file mode 100644
index 00000000..c2a885a1
--- /dev/null
+++ b/docker-compose.yml
@@ -0,0 +1,30 @@
+version: '3.8'
+
+services:
+  sciencebeam:
+    image: elifesciences/sciencebeam-parser
+    ports:
+      - "8070:8070"
+    networks:
+      - app-network
+
+  osm:
+    build: 
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "8081:8070"
+    volumes:
+      - .:/app
+    depends_on:
+      - sciencebeam
+    environment:
+      - SCIENCEBEAM_URL=http://sciencebeam:8070
+    tty: true
+    stdin_open: true
+    networks:
+      - app-network
+
+networks:
+  app-network:
+    driver: bridge
diff --git a/osm/__init__.py b/osm/__init__.py
index e69de29b..eb23a131 100644
--- a/osm/__init__.py
+++ b/osm/__init__.py
@@ -0,0 +1,3 @@
+from . import _version
+
+__version__ = _version.version
diff --git a/osm/cli.py b/osm/cli.py
deleted file mode 100644
index ea7045cd..00000000
--- a/osm/cli.py
+++ /dev/null
@@ -1,15 +0,0 @@
-import click
-from commands.file_processing import pdf_xml
-
-
-@click.group()
-def cli():
-    """Main command group."""
-    pass
-
-
-# Add commands to the main group
-cli.add_command(pdf_xml)
-
-if __name__ == '__main__':
-    cli()
diff --git a/osm/cli/main.py b/osm/cli/main.py
new file mode 100644
index 00000000..183c5d57
--- /dev/null
+++ b/osm/cli/main.py
@@ -0,0 +1,27 @@
+import click
+
+from osm.converters.converter import convert_pdf_to_xml
+
+
+@click.group()
+def osm():
+    """Main command for OSM"""
+    pass
+
+
+@osm.command()
+@click.argument("file_path", type=click.Path(exists=True))
+@click.argument("output_file", type=str)
+def pdf_xml(file_path, output_file):
+    """This function converts a file from PDF to XML
+    Args:
+        file_path (string): an input file path
+        output_file (string): an output file path
+    Returns:
+        Creates an XML file and saves it in the output file path
+    """
+    try:
+        convert_pdf_to_xml(file_path, output_file)
+    except Exception as e:
+        click.echo(f"Error: {str(e)}", err=True)
+        exit(1)
diff --git a/commands/__init__.py b/osm/converters/__init__.py
similarity index 100%
rename from commands/__init__.py
rename to osm/converters/__init__.py
diff --git a/osm/converters/converter.py b/osm/converters/converter.py
new file mode 100644
index 00000000..8a9842dd
--- /dev/null
+++ b/osm/converters/converter.py
@@ -0,0 +1,87 @@
+import socket
+from abc import ABC, abstractmethod
+from pathlib import Path
+
+import requests
+
+from osm.logging.logger import logger
+from osm.utils.config import config
+
+
+class Converter(ABC):
+    @abstractmethod
+    def convert(self, pdf_path) -> str:
+        pass
+
+    def handle_error(self, error):
+        if isinstance(error, requests.RequestException):
+            logger.error("Request error:", exc_info=error)
+        else:
+            logger.error("An error occurred:", exc_info=error)
+
+        raise error
+
+
+class PDFConverter(Converter):
+    protocol: str = config.PROTOCOL
+    host: str = config.HOST
+    port: int = config.PORT
+
+    def convert(self, pdf_path) -> str:
+        """Convert a PDF file to XML using ScienceBeam Parser.
+
+        Args:
+            pdf_path: Path to the PDF file
+        Returns:
+            XML content as a string
+        """
+        sciencebeam_url: str = f"{self.protocol}://{self.host}:{self.port}/api/convert"
+        with Path(pdf_path).open("rb") as pdf_file:
+            files = {"file": pdf_file}
+            headers = {"Accept": "application/tei+xml"}
+            response = requests.post(sciencebeam_url, files=files, headers=headers)
+
+            if response.status_code == 200:
+                return response.text
+            else:
+                response.raise_for_status()
+
+    def is_host_ready(self, timeout=3) -> bool:
+        """Check if the host is ready to accept requests.
+        Args:
+            timeout: Timeout in seconds
+        Returns:
+            True if the docker is host is ready, False otherwise
+        """
+        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:
+            sock.settimeout(timeout)
+            try:
+                sock.connect((self.host, self.port))
+            except (socket.timeout, socket.error):
+                return False
+            return True
+
+
+def convert_pdf_to_xml(file_path, output_file_path):
+    """Converts a PDF file to XML and saves the output.
+
+    Args:
+        file_path (str): Path to the input PDF file.
+        output_file_path (str): Path to the output XML file.
+    """
+    converter = PDFConverter()
+    try:
+        if not converter.is_host_ready():
+            raise Exception("The converter server is offline")
+
+        xml_content = converter.convert(file_path)
+
+        # Save the converted xml contents
+        Path(output_file_path).write_text(xml_content)
+        logger.info(f"Converted: {file_path} to XML. Output file: {output_file_path}")
+
+    except requests.RequestException as error:
+        converter.handle_error(error)
+
+    except Exception as error:
+        converter.handle_error(error)
diff --git a/commands/converters/__init__.py b/osm/logging/__init__.py
similarity index 100%
rename from commands/converters/__init__.py
rename to osm/logging/__init__.py
diff --git a/logs/logger.py b/osm/logging/logger.py
similarity index 53%
rename from logs/logger.py
rename to osm/logging/logger.py
index d5880999..bdfadba1 100644
--- a/logs/logger.py
+++ b/osm/logging/logger.py
@@ -1,11 +1,9 @@
-from rich.logging import RichHandler
 import logging
 
+from rich.logging import RichHandler
+
 logging.basicConfig(
-    level=logging.INFO,
-    format="%(message)s",
-    datefmt="[%X]",
-    handlers=[RichHandler()]
+    level=logging.INFO, format="%(message)s", datefmt="[%X]", handlers=[RichHandler()]
 )
 
 logger = logging.getLogger("rich")
diff --git a/logs/__init__.py b/osm/utils/__init__.py
similarity index 100%
rename from logs/__init__.py
rename to osm/utils/__init__.py
diff --git a/osm/utils/config.py b/osm/utils/config.py
new file mode 100644
index 00000000..c658e687
--- /dev/null
+++ b/osm/utils/config.py
@@ -0,0 +1,7 @@
+class AppConfig:
+    PORT: int = 8070
+    HOST: str = "sciencebeam"
+    PROTOCOL: str = "http"
+
+
+config = AppConfig()
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..1668aa35
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,57 @@
+[project]
+name = "osm"
+description = "Open Science Metrics (OSM) client for tracking scientific transparency and reproducibility metrics"
+readme = "README.md"
+requires-python = ">=3.8"
+keywords = [
+  "open science",
+  "altmetrics",
+  "scientific transparency",
+  "reproducibility"
+]
+dynamic = ["version"]
+
+dependencies = [
+    "click>=8.1.7",
+    "docker>=7.1.0",
+    "rich>=13.7.1",
+    "requests>=2.32.3",
+]
+
+[project.optional-dependencies]
+dev = [
+    "tox>=4.15.0",
+    "pytest>=8.2.1",
+    "pytest-cov",
+    "ruff>=0.4.9",
+    "build",
+    "twine",
+    "pre-commit",
+    "pkginfo>=1.10"
+]
+
+[project.urls]
+homepage = "https://website"
+source = "https://github.com/nimh-dsst/osm"
+issues = "https://github.com/nimh-dsst/osm/issues"
+
+[build-system]
+requires = ["setuptools>=42", "wheel", "setuptools_scm[toml]>=3.4"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "osm/_version.py"
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[project.scripts]
+osm = "osm.cli.main:osm"
+
+[tool.black]
+line-length = 88
+target-version = ["py38", "py39", "py310"]
+
+[tool.ruff]
+line-length = 88
+indent-width = 4
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 1ff11364..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-click==8.1.7
-docker==7.1.0
-pre_commit==3.5.0
-pydantic==2.7.3
-pytest==8.2.1
-requests==2.32.3
-rich==13.7.1
-ruff==0.4.9
-tox==4.15.0
\ No newline at end of file
diff --git a/tests/test_file_processing.py b/tests/test_file_processing.py
index 30185079..0ee2576e 100644
--- a/tests/test_file_processing.py
+++ b/tests/test_file_processing.py
@@ -1,32 +1,33 @@
+from pathlib import Path
+
 import pytest
 from click.testing import CliRunner
-import os
 
-from osm.cli import cli
+from osm.cli.main import pdf_xml
 
 
 @pytest.fixture
 def setup_and_teardown():
     # Setup: Create a temporary PDF file for testing
-    pdfs_folder = 'docs/examples/pdf_inputs'
-    file = 'test_sample.pdf'
-    file_id = 'test_file_id'
-    output_file = f'docs/examples/sciencebeam_xml_outputs/{file_id}.xml'
+    pdfs_folder = "docs/examples/pdf_inputs"
+    file = "test_sample.pdf"
+    output_file = "test_output_file.xml"
 
-    yield pdfs_folder, file, file_id, output_file
+    yield pdfs_folder, file, output_file
 
     # Teardown: Remove the generated XML file
-    if os.path.exists(output_file):
-        os.remove(output_file)
+    output_file_path = Path(output_file)
+    if output_file_path.exists():
+        output_file_path.unlink()
 
 
 def test_pdf_xml_command(setup_and_teardown):
-    pdfs_folder, file, file_id, output_file = setup_and_teardown
+    pdfs_folder, file, output_file = setup_and_teardown
 
     runner = CliRunner()
-    pdf_path = f'{pdfs_folder}/{file}'
-    result = runner.invoke(cli, ['pdf-xml', pdf_path, file_id])
+    pdf_path = f"{pdfs_folder}/{file}"
+    result = runner.invoke(pdf_xml, [str(pdf_path), output_file])
 
     # Check that the command executed successfully
     assert result.exit_code == 0
-    assert os.path.exists(output_file)
+    assert Path(output_file).exists()
diff --git a/tox.ini b/tox.ini
index 2831f21c..4420e676 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,13 +1,11 @@
 [tox]
-envlist = py39, py310, py311, py312, lint
+envlist = py39, py310, py311, py312, lint, format
 
 [testenv]
 deps =
-    pytest
-    pytest-cov
-    -r requirements.txt
+    .[dev]
 commands =
-    python -m pytest --cov=commands --cov-report=term-missing --cov-report=html --cov-report=xml
+    python -m pytest --cov=osm --cov-report=term-missing --cov-report=html --cov-report=xml
 
 [testenv:lint]
 description = Run ruff to lint the code
@@ -15,6 +13,11 @@ commands =
     ruff check .
 
 [testenv:format]
-description = Run ruff to format the code
+description = Check that code is formatted with ruff
 commands =
-    ruff check --fix .
\ No newline at end of file
+    ruff format --check
+
+[testenv:.package]
+description = Generate distribution package
+basepython = python3
+commands = python -m build --sdist --wheel --outdir packaged