From 3049fe312f62adde86902d030d0893ecb0d81767 Mon Sep 17 00:00:00 2001
From: Graham Neubig <neubig@gmail.com>
Date: Tue, 18 Mar 2025 19:00:32 +0000
Subject: [PATCH 1/6] Initial commit: Create Python project starter template

---
 .github/workflows/lint.yml    | 21 ++++++++
 .github/workflows/test.yml    | 22 ++++++++
 .gitignore                    | 37 ++++++++++++++
 .pre-commit-config.yaml       | 12 +++++
 README.md                     | 95 ++++++++++++++++++++++++++++++++++-
 data/sample.csv               | 12 +++++
 pyproject.toml                | 40 +++++++++++++++
 src/starter_repo/plot_data.py | 62 +++++++++++++++++++++++
 tests/test_plot_data.py       | 33 ++++++++++++
 9 files changed, 332 insertions(+), 2 deletions(-)
 create mode 100644 .github/workflows/lint.yml
 create mode 100644 .github/workflows/test.yml
 create mode 100644 .gitignore
 create mode 100644 .pre-commit-config.yaml
 create mode 100644 data/sample.csv
 create mode 100644 pyproject.toml
 create mode 100644 src/starter_repo/plot_data.py
 create mode 100644 tests/test_plot_data.py

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
new file mode 100644
index 00000000..a687adb7
--- /dev/null
+++ b/.github/workflows/lint.yml
@@ -0,0 +1,21 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ".[dev]"
+    - name: Run ruff
+      run: ruff check .
+    - name: Run mypy
+      run: mypy src tests
\ No newline at end of file
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
new file mode 100644
index 00000000..e88e1b24
--- /dev/null
+++ b/.github/workflows/test.yml
@@ -0,0 +1,22 @@
+name: Test
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ".[dev]"
+    - name: Run tests
+      run: pytest
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 00000000..316c25f8
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,37 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Virtual Environment
+venv/
+env/
+ENV/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Project specific
+*.png
+*.csv
+!data/sample.csv
\ No newline at end of file
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
new file mode 100644
index 00000000..c04a62cc
--- /dev/null
+++ b/.pre-commit-config.yaml
@@ -0,0 +1,12 @@
+repos:
+-   repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: v0.1.6
+    hooks:
+    -   id: ruff
+        args: [--fix]
+    -   id: ruff-format
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.7.1
+    hooks:
+    -   id: mypy
+        additional_dependencies: [types-all]
\ No newline at end of file
diff --git a/README.md b/README.md
index 0139dc2e..e9e7cfe3 100644
--- a/README.md
+++ b/README.md
@@ -1,2 +1,93 @@
-# starter-repo
-An example starter repo for Python projects
+# Python Project Starter Repository
+
+This repository serves as a template demonstrating Python best practices for data analysis projects. It includes examples of:
+- CSV data processing
+- Data visualization with matplotlib
+- Command-line argument parsing
+- Type annotations
+- Testing
+- Code quality tools
+- Continuous Integration
+
+## Features
+
+### 1. Data Processing and Visualization
+The main script ([src/starter_repo/plot_data.py](src/starter_repo/plot_data.py)) demonstrates:
+- Reading CSV files using pandas
+- Creating plots with matplotlib
+- Modern Python type annotations
+- Command-line argument parsing with argparse
+
+Example usage:
+```bash
+# Install the package
+pip install .
+
+# Create a plot from the sample data
+python -m starter_repo.plot_data data/sample.csv year population --title "Population Growth" -o population.png
+```
+
+### 2. Testing
+The project uses pytest for testing. Test files are located in the [tests/](tests/) directory.
+
+To run tests:
+```bash
+pip install ".[dev]"  # Install development dependencies
+pytest
+```
+
+### 3. Code Quality Tools
+This project uses several tools to maintain code quality:
+
+#### Pre-commit Hooks
+We use [pre-commit](.pre-commit-config.yaml) with:
+- [Ruff](https://github.com/charliermarsh/ruff) for linting and formatting
+- [mypy](https://mypy.readthedocs.io/) for static type checking
+
+To set up pre-commit:
+```bash
+pip install pre-commit
+pre-commit install
+```
+
+### 4. Continuous Integration
+GitHub Actions workflows are set up for:
+- [Linting](.github/workflows/lint.yml): Runs Ruff and mypy
+- [Testing](.github/workflows/test.yml): Runs pytest on multiple Python versions
+
+### 5. Project Structure
+```
+.
+|- src/
+|  |- starter_repo/      # Source code
+|     |- plot_data.py   # Main script
+|- tests/                 # Test files
+|  |- test_plot_data.py
+|- data/                  # Sample data
+|  |- sample.csv
+|- .github/workflows/     # CI configuration
+|- pyproject.toml        # Project metadata and dependencies
+|- .pre-commit-config.yaml # Pre-commit hook configuration
+|- README.md
+```
+
+## Installation
+
+```bash
+# For users
+pip install .
+
+# For developers
+pip install -e ".[dev]"
+```
+
+## Contributing
+1. Fork the repository
+2. Install development dependencies: `pip install -e ".[dev]"`
+3. Install pre-commit hooks: `pre-commit install`
+4. Make your changes
+5. Run tests: `pytest`
+6. Submit a pull request
+
+## Author
+Graham Neubig (neubig@gmail.com)
\ No newline at end of file
diff --git a/data/sample.csv b/data/sample.csv
new file mode 100644
index 00000000..c1fe84b9
--- /dev/null
+++ b/data/sample.csv
@@ -0,0 +1,12 @@
+year,population
+2000,6115
+2001,6214
+2002,6312
+2003,6411
+2004,6510
+2005,6609
+2006,6709
+2007,6809
+2008,6909
+2009,7009
+2010,7109
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 00000000..2a15676e
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,40 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "starter-repo"
+version = "0.1.0"
+authors = [
+    { name="Graham Neubig", email="neubig@gmail.com" },
+]
+description = "A starter repository demonstrating Python best practices"
+readme = "README.md"
+requires-python = ">=3.8"
+dependencies = [
+    "pandas",
+    "matplotlib",
+]
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "ruff",
+    "mypy",
+    "pre-commit",
+]
+
+[tool.ruff]
+select = ["E", "F", "I"]
+line-length = 100
+
+[tool.mypy]
+python_version = "3.8"
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+check_untyped_defs = true
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+python_files = ["test_*.py"]
\ No newline at end of file
diff --git a/src/starter_repo/plot_data.py b/src/starter_repo/plot_data.py
new file mode 100644
index 00000000..70d2eb7e
--- /dev/null
+++ b/src/starter_repo/plot_data.py
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+from pathlib import Path
+import argparse
+import pandas as pd
+import matplotlib.pyplot as plt
+from typing import list, tuple
+
+def read_csv_data(file_path: Path, x_col: str, y_col: str) -> tuple[list[float], list[float]]:
+    """Read data from a CSV file and return specified columns.
+    
+    Args:
+        file_path: Path to the CSV file
+        x_col: Name of the column to use for x-axis
+        y_col: Name of the column to use for y-axis
+        
+    Returns:
+        Tuple of x and y data as lists
+    """
+    df = pd.read_csv(file_path)
+    return df[x_col].tolist(), df[y_col].tolist()
+
+def create_plot(x_data: list[float], y_data: list[float], 
+                x_label: str, y_label: str, title: str) -> plt.Figure:
+    """Create a plot from the provided data.
+    
+    Args:
+        x_data: Data for x-axis
+        y_data: Data for y-axis
+        x_label: Label for x-axis
+        y_label: Label for y-axis
+        title: Plot title
+        
+    Returns:
+        matplotlib Figure object
+    """
+    fig, ax = plt.subplots()
+    ax.plot(x_data, y_data)
+    ax.set_xlabel(x_label)
+    ax.set_ylabel(y_label)
+    ax.set_title(title)
+    return fig
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="Create plots from CSV data")
+    parser.add_argument("file_path", type=Path, help="Path to the CSV file")
+    parser.add_argument("x_column", type=str, help="Column name for x-axis")
+    parser.add_argument("y_column", type=str, help="Column name for y-axis")
+    parser.add_argument("--output", "-o", type=Path, default=Path("plot.png"),
+                       help="Output file path (default: plot.png)")
+    parser.add_argument("--title", "-t", type=str, default="Data Plot",
+                       help="Plot title (default: Data Plot)")
+    
+    args = parser.parse_args()
+    
+    x_data, y_data = read_csv_data(args.file_path, args.x_column, args.y_column)
+    fig = create_plot(x_data, y_data, args.x_column, args.y_column, args.title)
+    fig.savefig(args.output)
+    plt.close(fig)
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file
diff --git a/tests/test_plot_data.py b/tests/test_plot_data.py
new file mode 100644
index 00000000..ddbcb609
--- /dev/null
+++ b/tests/test_plot_data.py
@@ -0,0 +1,33 @@
+from pathlib import Path
+import pandas as pd
+import pytest
+from starter_repo.plot_data import read_csv_data, create_plot
+
+@pytest.fixture
+def sample_csv(tmp_path: Path) -> Path:
+    """Create a sample CSV file for testing."""
+    df = pd.DataFrame({
+        'x': [1, 2, 3, 4, 5],
+        'y': [2, 4, 6, 8, 10]
+    })
+    file_path = tmp_path / "test.csv"
+    df.to_csv(file_path, index=False)
+    return file_path
+
+def test_read_csv_data(sample_csv: Path) -> None:
+    """Test reading data from CSV file."""
+    x_data, y_data = read_csv_data(sample_csv, 'x', 'y')
+    assert x_data == [1, 2, 3, 4, 5]
+    assert y_data == [2, 4, 6, 8, 10]
+
+def test_create_plot() -> None:
+    """Test plot creation."""
+    x_data = [1, 2, 3]
+    y_data = [2, 4, 6]
+    fig = create_plot(x_data, y_data, "X", "Y", "Test Plot")
+    assert fig is not None
+    # Basic check that the figure contains the expected elements
+    ax = fig.axes[0]
+    assert ax.get_xlabel() == "X"
+    assert ax.get_ylabel() == "Y"
+    assert ax.get_title() == "Test Plot"
\ No newline at end of file

From 800c2f2b3b26ae7155ad0c274768e81acec1a58f Mon Sep 17 00:00:00 2001
From: Graham Neubig <neubig@gmail.com>
Date: Tue, 18 Mar 2025 19:03:03 +0000
Subject: [PATCH 2/6] Fix formatting with pre-commit hooks

---
 .pre-commit-config.yaml       |  3 +--
 pyproject.toml                |  3 +++
 src/starter_repo/plot_data.py | 46 ++++++++++++++++++++++-------------
 tests/test_plot_data.py       | 15 ++++++------
 4 files changed, 41 insertions(+), 26 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c04a62cc..89d12d53 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,5 +8,4 @@ repos:
 -   repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.7.1
     hooks:
-    -   id: mypy
-        additional_dependencies: [types-all]
\ No newline at end of file
+    -   id: mypy
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 2a15676e..9fe4c3e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,6 +2,9 @@
 requires = ["hatchling"]
 build-backend = "hatchling.build"
 
+[tool.hatch.build.targets.wheel]
+packages = ["src/starter_repo"]
+
 [project]
 name = "starter-repo"
 version = "0.1.0"
diff --git a/src/starter_repo/plot_data.py b/src/starter_repo/plot_data.py
index 70d2eb7e..e6f1c414 100644
--- a/src/starter_repo/plot_data.py
+++ b/src/starter_repo/plot_data.py
@@ -1,36 +1,40 @@
 #!/usr/bin/env python3
 
-from pathlib import Path
 import argparse
-import pandas as pd
+from pathlib import Path
+from typing import List, Tuple
+
 import matplotlib.pyplot as plt
-from typing import list, tuple
+import pandas as pd
+
 
-def read_csv_data(file_path: Path, x_col: str, y_col: str) -> tuple[list[float], list[float]]:
+def read_csv_data(file_path: Path, x_col: str, y_col: str) -> Tuple[List[float], List[float]]:
     """Read data from a CSV file and return specified columns.
-    
+
     Args:
         file_path: Path to the CSV file
         x_col: Name of the column to use for x-axis
         y_col: Name of the column to use for y-axis
-        
+
     Returns:
         Tuple of x and y data as lists
     """
     df = pd.read_csv(file_path)
     return df[x_col].tolist(), df[y_col].tolist()
 
-def create_plot(x_data: list[float], y_data: list[float], 
-                x_label: str, y_label: str, title: str) -> plt.Figure:
+
+def create_plot(
+    x_data: List[float], y_data: List[float], x_label: str, y_label: str, title: str
+) -> plt.Figure:
     """Create a plot from the provided data.
-    
+
     Args:
         x_data: Data for x-axis
         y_data: Data for y-axis
         x_label: Label for x-axis
         y_label: Label for y-axis
         title: Plot title
-        
+
     Returns:
         matplotlib Figure object
     """
@@ -41,22 +45,30 @@ def create_plot(x_data: list[float], y_data: list[float],
     ax.set_title(title)
     return fig
 
+
 def main() -> None:
     parser = argparse.ArgumentParser(description="Create plots from CSV data")
     parser.add_argument("file_path", type=Path, help="Path to the CSV file")
     parser.add_argument("x_column", type=str, help="Column name for x-axis")
     parser.add_argument("y_column", type=str, help="Column name for y-axis")
-    parser.add_argument("--output", "-o", type=Path, default=Path("plot.png"),
-                       help="Output file path (default: plot.png)")
-    parser.add_argument("--title", "-t", type=str, default="Data Plot",
-                       help="Plot title (default: Data Plot)")
-    
+    parser.add_argument(
+        "--output",
+        "-o",
+        type=Path,
+        default=Path("plot.png"),
+        help="Output file path (default: plot.png)",
+    )
+    parser.add_argument(
+        "--title", "-t", type=str, default="Data Plot", help="Plot title (default: Data Plot)"
+    )
+
     args = parser.parse_args()
-    
+
     x_data, y_data = read_csv_data(args.file_path, args.x_column, args.y_column)
     fig = create_plot(x_data, y_data, args.x_column, args.y_column, args.title)
     fig.savefig(args.output)
     plt.close(fig)
 
+
 if __name__ == "__main__":
-    main()
\ No newline at end of file
+    main()
diff --git a/tests/test_plot_data.py b/tests/test_plot_data.py
index ddbcb609..c1236940 100644
--- a/tests/test_plot_data.py
+++ b/tests/test_plot_data.py
@@ -1,25 +1,26 @@
 from pathlib import Path
+
 import pandas as pd
 import pytest
-from starter_repo.plot_data import read_csv_data, create_plot
+from starter_repo.plot_data import create_plot, read_csv_data
+
 
 @pytest.fixture
 def sample_csv(tmp_path: Path) -> Path:
     """Create a sample CSV file for testing."""
-    df = pd.DataFrame({
-        'x': [1, 2, 3, 4, 5],
-        'y': [2, 4, 6, 8, 10]
-    })
+    df = pd.DataFrame({"x": [1, 2, 3, 4, 5], "y": [2, 4, 6, 8, 10]})
     file_path = tmp_path / "test.csv"
     df.to_csv(file_path, index=False)
     return file_path
 
+
 def test_read_csv_data(sample_csv: Path) -> None:
     """Test reading data from CSV file."""
-    x_data, y_data = read_csv_data(sample_csv, 'x', 'y')
+    x_data, y_data = read_csv_data(sample_csv, "x", "y")
     assert x_data == [1, 2, 3, 4, 5]
     assert y_data == [2, 4, 6, 8, 10]
 
+
 def test_create_plot() -> None:
     """Test plot creation."""
     x_data = [1, 2, 3]
@@ -30,4 +31,4 @@ def test_create_plot() -> None:
     ax = fig.axes[0]
     assert ax.get_xlabel() == "X"
     assert ax.get_ylabel() == "Y"
-    assert ax.get_title() == "Test Plot"
\ No newline at end of file
+    assert ax.get_title() == "Test Plot"

From 79ba8a2bc3016bdd367576fb2edaf1e7fda8834b Mon Sep 17 00:00:00 2001
From: Graham Neubig <neubig@gmail.com>
Date: Tue, 18 Mar 2025 19:10:48 +0000
Subject: [PATCH 3/6] Move starter_repo directory to root level

---
 README.md                                       | 7 +++----
 pyproject.toml                                  | 2 +-
 {src/starter_repo => starter_repo}/plot_data.py | 0
 3 files changed, 4 insertions(+), 5 deletions(-)
 rename {src/starter_repo => starter_repo}/plot_data.py (100%)

diff --git a/README.md b/README.md
index e9e7cfe3..1cd36c90 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@ This repository serves as a template demonstrating Python best practices for dat
 ## Features
 
 ### 1. Data Processing and Visualization
-The main script ([src/starter_repo/plot_data.py](src/starter_repo/plot_data.py)) demonstrates:
+The main script ([starter_repo/plot_data.py](starter_repo/plot_data.py)) demonstrates:
 - Reading CSV files using pandas
 - Creating plots with matplotlib
 - Modern Python type annotations
@@ -58,9 +58,8 @@ GitHub Actions workflows are set up for:
 ### 5. Project Structure
 ```
 .
-|- src/
-|  |- starter_repo/      # Source code
-|     |- plot_data.py   # Main script
+|- starter_repo/         # Source code
+|  |- plot_data.py      # Main script
 |- tests/                 # Test files
 |  |- test_plot_data.py
 |- data/                  # Sample data
diff --git a/pyproject.toml b/pyproject.toml
index 9fe4c3e1..63e0f734 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [tool.hatch.build.targets.wheel]
-packages = ["src/starter_repo"]
+packages = ["starter_repo"]
 
 [project]
 name = "starter-repo"
diff --git a/src/starter_repo/plot_data.py b/starter_repo/plot_data.py
similarity index 100%
rename from src/starter_repo/plot_data.py
rename to starter_repo/plot_data.py

From 0faeb618c27a9c1f67be0dc2a4521cf96e0eb2f1 Mon Sep 17 00:00:00 2001
From: Graham Neubig <neubig@gmail.com>
Date: Tue, 18 Mar 2025 19:20:11 +0000
Subject: [PATCH 4/6] Use lower-case type hints and fix test data types

---
 .github/workflows/lint.yml |  4 ++--
 .github/workflows/test.yml |  4 ++--
 LICENSE                    | 21 +++++++++++++++++++++
 README.md                  | 22 +++++++++++++++++++++-
 mypy.ini                   | 10 ++++++++++
 pyproject.toml             | 15 +++++++--------
 starter_repo/__init__.py   |  3 +++
 starter_repo/plot_data.py  |  5 ++---
 tests/test_plot_data.py    | 11 ++++++-----
 9 files changed, 74 insertions(+), 21 deletions(-)
 create mode 100644 LICENSE
 create mode 100644 mypy.ini
 create mode 100644 starter_repo/__init__.py

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index a687adb7..1083b0a2 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -1,6 +1,6 @@
 name: Lint
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   lint:
@@ -10,7 +10,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e88e1b24..7ae3c4a6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,13 +1,13 @@
 name: Test
 
-on: [push, pull_request]
+on: [pull_request]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.11', '3.12']
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 00000000..25c11fa0
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Graham Neubig
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
\ No newline at end of file
diff --git a/README.md b/README.md
index 1cd36c90..8fae1d57 100644
--- a/README.md
+++ b/README.md
@@ -88,5 +88,25 @@ pip install -e ".[dev]"
 5. Run tests: `pytest`
 6. Submit a pull request
 
+## License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+> **Note**: Without a license, the code is under exclusive copyright by default. This means no one can copy, distribute, or modify your work without facing potential legal consequences. Adding a license (like MIT) explicitly grants these permissions, making it clear how others can use your code.
+
 ## Author
-Graham Neubig (neubig@gmail.com)
\ No newline at end of file
+Graham Neubig (neubig@gmail.com)
+
+## Citation
+
+If you use this repository in your research, please cite it using the following BibTeX entry:
+
+```bibtex
+@misc{neubig2025starter,
+  author = {Graham Neubig},
+  title = {Python Project Starter Repository},
+  year = {2025},
+  publisher = {GitHub},
+  journal = {GitHub Repository},
+  howpublished = {\url{https://github.com/neubig/starter-repo}}
+}
\ No newline at end of file
diff --git a/mypy.ini b/mypy.ini
new file mode 100644
index 00000000..95ace867
--- /dev/null
+++ b/mypy.ini
@@ -0,0 +1,10 @@
+[mypy]
+python_version = 3.12
+warn_return_any = true
+warn_unused_configs = true
+disallow_untyped_defs = true
+check_untyped_defs = true
+namespace_packages = true
+
+[mypy.plugins.numpy.*]
+ignore_errors = true
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 63e0f734..25c05f2a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,8 @@ authors = [
 ]
 description = "A starter repository demonstrating Python best practices"
 readme = "README.md"
-requires-python = ">=3.8"
+license = "MIT"
+requires-python = ">=3.11"
 dependencies = [
     "pandas",
     "matplotlib",
@@ -25,18 +26,16 @@ dev = [
     "ruff",
     "mypy",
     "pre-commit",
+    "pandas-stubs",
 ]
 
 [tool.ruff]
-select = ["E", "F", "I"]
 line-length = 100
 
-[tool.mypy]
-python_version = "3.8"
-warn_return_any = true
-warn_unused_configs = true
-disallow_untyped_defs = true
-check_untyped_defs = true
+[tool.ruff.lint]
+select = ["E", "F", "I"]
+
+
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
diff --git a/starter_repo/__init__.py b/starter_repo/__init__.py
new file mode 100644
index 00000000..0c2751dc
--- /dev/null
+++ b/starter_repo/__init__.py
@@ -0,0 +1,3 @@
+"""A starter repository demonstrating Python best practices."""
+
+__version__ = "0.1.0"
diff --git a/starter_repo/plot_data.py b/starter_repo/plot_data.py
index e6f1c414..921ef635 100644
--- a/starter_repo/plot_data.py
+++ b/starter_repo/plot_data.py
@@ -2,13 +2,12 @@
 
 import argparse
 from pathlib import Path
-from typing import List, Tuple
 
 import matplotlib.pyplot as plt
 import pandas as pd
 
 
-def read_csv_data(file_path: Path, x_col: str, y_col: str) -> Tuple[List[float], List[float]]:
+def read_csv_data(file_path: Path, x_col: str, y_col: str) -> tuple[list[float], list[float]]:
     """Read data from a CSV file and return specified columns.
 
     Args:
@@ -24,7 +23,7 @@ def read_csv_data(file_path: Path, x_col: str, y_col: str) -> Tuple[List[float],
 
 
 def create_plot(
-    x_data: List[float], y_data: List[float], x_label: str, y_label: str, title: str
+    x_data: list[float], y_data: list[float], x_label: str, y_label: str, title: str
 ) -> plt.Figure:
     """Create a plot from the provided data.
 
diff --git a/tests/test_plot_data.py b/tests/test_plot_data.py
index c1236940..32bdb060 100644
--- a/tests/test_plot_data.py
+++ b/tests/test_plot_data.py
@@ -2,13 +2,14 @@
 
 import pandas as pd
 import pytest
+
 from starter_repo.plot_data import create_plot, read_csv_data
 
 
 @pytest.fixture
 def sample_csv(tmp_path: Path) -> Path:
     """Create a sample CSV file for testing."""
-    df = pd.DataFrame({"x": [1, 2, 3, 4, 5], "y": [2, 4, 6, 8, 10]})
+    df = pd.DataFrame({"x": [1.0, 2.0, 3.0, 4.0, 5.0], "y": [2.0, 4.0, 6.0, 8.0, 10.0]})
     file_path = tmp_path / "test.csv"
     df.to_csv(file_path, index=False)
     return file_path
@@ -17,14 +18,14 @@ def sample_csv(tmp_path: Path) -> Path:
 def test_read_csv_data(sample_csv: Path) -> None:
     """Test reading data from CSV file."""
     x_data, y_data = read_csv_data(sample_csv, "x", "y")
-    assert x_data == [1, 2, 3, 4, 5]
-    assert y_data == [2, 4, 6, 8, 10]
+    assert x_data == [1.0, 2.0, 3.0, 4.0, 5.0]
+    assert y_data == [2.0, 4.0, 6.0, 8.0, 10.0]
 
 
 def test_create_plot() -> None:
     """Test plot creation."""
-    x_data = [1, 2, 3]
-    y_data = [2, 4, 6]
+    x_data = [1.0, 2.0, 3.0]
+    y_data = [2.0, 4.0, 6.0]
     fig = create_plot(x_data, y_data, "X", "Y", "Test Plot")
     assert fig is not None
     # Basic check that the figure contains the expected elements

From 8d0481e98effcdd5b37a1ce47b24bbdaa6ffb86b Mon Sep 17 00:00:00 2001
From: Graham Neubig <neubig@gmail.com>
Date: Thu, 20 Mar 2025 09:40:33 -0400
Subject: [PATCH 5/6] Fix README

---
 README.md | 71 ++++++++++++++++++++++---------------------------------
 1 file changed, 28 insertions(+), 43 deletions(-)

diff --git a/README.md b/README.md
index 8fae1d57..2f5f5f1b 100644
--- a/README.md
+++ b/README.md
@@ -1,24 +1,25 @@
 # Python Project Starter Repository
 
-This repository serves as a template demonstrating Python best practices for data analysis projects. It includes examples of:
-- CSV data processing
-- Data visualization with matplotlib
-- Command-line argument parsing
-- Type annotations
-- Testing
-- Code quality tools
-- Continuous Integration
+This repository serves as a template demonstrating Python best practices for data analysis projects. It includes:
+
+- An example Python program (reading in data and plotting)
+- Command-line argument parsing ([argparse](https://docs.python.org/3/library/argparse.html))
+- Code style checking, aka "linting" (with [ruff](https://github.com/astral-sh/ruff))
+- Static type checking (with [mypy](https://mypy.readthedocs.io/))
+- Pre-commit hooks that run these checks automatically (with [pre-commit](https://pre-commit.com/))
+- Testing (with [pytest](https://docs.pytest.org/))
+- Continuous Integration (with [GitHub Actions](https://github.com/features/actions))
+- Package management (with [pip](https://pip.pypa.io/) and [pyproject.toml](https://pip.pypa.io/en/stable/reference/build-system/pyproject-toml/))
+- An open source license ([MIT](https://opensource.org/licenses/MIT))
 
 ## Features
 
 ### 1. Data Processing and Visualization
-The main script ([starter_repo/plot_data.py](starter_repo/plot_data.py)) demonstrates:
-- Reading CSV files using pandas
-- Creating plots with matplotlib
-- Modern Python type annotations
-- Command-line argument parsing with argparse
 
-Example usage:
+The main script ([starter_repo/plot_data.py](starter_repo/plot_data.py)) can be replaced with any code that you want to write.
+
+Installation can be done as follows:
+
 ```bash
 # Install the package
 pip install .
@@ -28,59 +29,44 @@ python -m starter_repo.plot_data data/sample.csv year population --title "Popula
 ```
 
 ### 2. Testing
-The project uses pytest for testing. Test files are located in the [tests/](tests/) directory.
+
+Writing unit tests is a good way to ensure that your code behaves as expected, and you can write unit tests before you write the code that you want to test (aka "test-driven development"). Test files are located in the [tests/](tests/) directory.
 
 To run tests:
+
 ```bash
 pip install ".[dev]"  # Install development dependencies
 pytest
 ```
 
 ### 3. Code Quality Tools
+
 This project uses several tools to maintain code quality:
 
 #### Pre-commit Hooks
+
 We use [pre-commit](.pre-commit-config.yaml) with:
+
 - [Ruff](https://github.com/charliermarsh/ruff) for linting and formatting
 - [mypy](https://mypy.readthedocs.io/) for static type checking
 
 To set up pre-commit:
+
 ```bash
 pip install pre-commit
 pre-commit install
 ```
 
 ### 4. Continuous Integration
+
 GitHub Actions workflows are set up for:
+
 - [Linting](.github/workflows/lint.yml): Runs Ruff and mypy
 - [Testing](.github/workflows/test.yml): Runs pytest on multiple Python versions
 
-### 5. Project Structure
-```
-.
-|- starter_repo/         # Source code
-|  |- plot_data.py      # Main script
-|- tests/                 # Test files
-|  |- test_plot_data.py
-|- data/                  # Sample data
-|  |- sample.csv
-|- .github/workflows/     # CI configuration
-|- pyproject.toml        # Project metadata and dependencies
-|- .pre-commit-config.yaml # Pre-commit hook configuration
-|- README.md
-```
-
-## Installation
-
-```bash
-# For users
-pip install .
-
-# For developers
-pip install -e ".[dev]"
-```
 
 ## Contributing
+
 1. Fork the repository
 2. Install development dependencies: `pip install -e ".[dev]"`
 3. Install pre-commit hooks: `pre-commit install`
@@ -94,11 +80,9 @@ This project is licensed under the MIT License - see the [LICENSE](LICENSE) file
 
 > **Note**: Without a license, the code is under exclusive copyright by default. This means no one can copy, distribute, or modify your work without facing potential legal consequences. Adding a license (like MIT) explicitly grants these permissions, making it clear how others can use your code.
 
-## Author
-Graham Neubig (neubig@gmail.com)
-
 ## Citation
 
+This was created by [Graham Neubig](https://phontron.com) primarily as an example for student researchers.
 If you use this repository in your research, please cite it using the following BibTeX entry:
 
 ```bibtex
@@ -109,4 +93,5 @@ If you use this repository in your research, please cite it using the following
   publisher = {GitHub},
   journal = {GitHub Repository},
   howpublished = {\url{https://github.com/neubig/starter-repo}}
-}
\ No newline at end of file
+}
+```

From 4e69b7525ea7178e36c7521954d9843f0f11c184 Mon Sep 17 00:00:00 2001
From: Graham Neubig <neubig@gmail.com>
Date: Thu, 20 Mar 2025 09:42:32 -0400
Subject: [PATCH 6/6] Update linting

---
 .github/workflows/lint.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index 1083b0a2..aa29c8b7 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -18,4 +18,4 @@ jobs:
     - name: Run ruff
       run: ruff check .
     - name: Run mypy
-      run: mypy src tests
\ No newline at end of file
+      run: mypy starter_repo tests
\ No newline at end of file