chore: upgrade CI/CD pipeline with comprehensive testing and code qua…

.github/workflows/smoke.yml

@@ -1,25 +1,82 @@
-name: Smoke
+name: CI
 
 on:
   push:
+    branches: [ main, develop ]
   pull_request:
+    branches: [ main, develop ]
 
 jobs:
-  smoke:
+  build-and-test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y gfortran cmake ninja-build
+
+    - name: Install dependencies
+      run: make dev
+
+    - name: Compile check (smoke test)
+      run: make smoke
+
+    - name: Generate coverage report
+      run: make coverage
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4
+      with:
+        fail_ci_if_error: false
+
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install ruff
+
+    - name: Lint with ruff
+      run: ruff check pyiri2016 tests settings examples scripts
+
+    - name: Format check with ruff
+      run: ruff format pyiri2016 tests settings examples scripts --check
+
+  typecheck:
+    runs-on: ubuntu-latest
+
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+    - uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11"
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
 
-      - name: Install system dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y gfortran cmake
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install mypy numpy
 
-      - name: Install dependencies and run smoke test
-        run: make dev && make smoke
+    - name: Type check with mypy
+      run: mypy --ignore-missing-imports

.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+# Pre-commit hooks for pyIRI2016
+# Install with: pre-commit install
+# Run manually: pre-commit run --all-files
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.0
+    hooks:
+      - id: ruff
+        name: ruff check
+        args: [--fix]
+      - id: ruff-format
+        name: ruff format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.19.1
+    hooks:
+      - id: mypy
+        name: mypy type check
+        additional_dependencies: [
+          "numpy",
+        ]
+        args: [
+          --ignore-missing-imports,
+        ]
+        exclude: "^(build|dist|source|\.venv)"

CHANGELOG.md

@@ -26,6 +26,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Better separation between `make dev` (development) and `make install` (user installation)
 - **.gitignore enhancements**: Added `.venv/`, `.pytest_cache/`, `htmlcov/` for cleaner repository
 - **Updated GitHub Actions workflow**: Replaced uv package manager with system dependencies (gfortran, cmake)
+- **Comprehensive CI/CD pipeline** (issue #12): Upgraded from minimal smoke test to full testing and quality checks
+  - Initial effort towards Multi-version Python testing: Set up to 3.11
+  - Automated pytest with coverage reports
+  - Ruff linting and code formatting checks
+  - Mypy type checking
+  - Codecov coverage integration
+  - 3 parallel CI jobs: build-and-test, lint, typecheck
+- **Code quality tools**:
+  - Ruff: Integrated for linting and code formatting (configured in `pyproject.toml`)
+  - Mypy: Integrated for static type checking with NumPy support
+- **Pre-commit hooks** (issue #12): Added `.pre-commit-config.yaml` for automated local development checks
+  - Ruff check and format on commit
+  - Mypy type checking on commit
+  - Install with: `pre-commit install && pre-commit run --all-files`
+- **Enhanced Makefile targets** (issue #12): New quality assurance commands
+  - `make lint`: Check code with ruff
+  - `make lint-fix`: Auto-fix linting issues
+  - `make format`: Auto-format code with ruff
+  - `make typecheck`: Run mypy static type checking
+  - `make pre-commit`: Run all quality checks (lint + typecheck + test)
 
 ### Changed
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY : build coverage install smoke health test test-examples dev dev-plotting clean-venv
+.PHONY : build coverage install smoke health test test-examples dev dev-plotting clean-venv lint lint-fix typecheck format pre-commit
 
 export PYTHONIOENCODING=utf-8
 export LC_ALL=en_US.UTF-8
@@ -12,14 +12,14 @@ dev:
 	./.venv/bin/python -m pip install --upgrade pip wheel setuptools
 	./.venv/bin/python -m pip install 'numpy>=2.0' simple-settings beautifulsoup4 wget 'scikit-build-core' cmake ninja charset-normalizer
 	bash -c 'VIRTUAL_ENV=./.venv PYTHONIOENCODING=utf-8 LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 ./.venv/bin/python -m pip install -e .'
-	./.venv/bin/python -m pip install pre-commit coverage pytest pytest-cov parameterized
+	./.venv/bin/python -m pip install pre-commit coverage pytest pytest-cov parameterized ruff mypy
 
 dev-plotting:
 	[ -d .venv ] || python3 -m venv .venv
 	./.venv/bin/python -m pip install --upgrade pip wheel setuptools
 	./.venv/bin/python -m pip install 'numpy>=2.0' simple-settings beautifulsoup4 wget 'scikit-build-core' cmake ninja charset-normalizer
 	bash -c 'VIRTUAL_ENV=./.venv PYTHONIOENCODING=utf-8 LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 ./.venv/bin/python -m pip install -e .[plotting]'
-	./.venv/bin/python -m pip install pre-commit coverage pytest pytest-cov parameterized
+	./.venv/bin/python -m pip install pre-commit coverage pytest pytest-cov parameterized ruff mypy
 
 build:
 	[ -d .venv ] || python3 -m venv .venv
@@ -60,3 +60,18 @@ test-examples:
 	MPLBACKEND=Agg ./.venv/bin/python examples/iri1DExample08.py > /dev/null && echo "✓ iri1DExample08.py passed" || echo "✗ iri1DExample08.py failed"
 	MPLBACKEND=Agg ./.venv/bin/python scripts/iri2DExample01.py > /dev/null && echo "✓ iri2DExample01.py passed" || echo "✗ iri2DExample01.py failed"
 	MPLBACKEND=Agg ./.venv/bin/python scripts/iri2DExample02.py > /dev/null && echo "✓ iri2DExample02.py passed" || echo "✗ iri2DExample02.py failed"
+
+lint:
+	./.venv/bin/python -m ruff check pyiri2016 tests settings examples scripts
+
+lint-fix:
+	./.venv/bin/python -m ruff check pyiri2016 tests settings examples scripts --fix
+
+format:
+	./.venv/bin/python -m ruff format pyiri2016 tests settings examples scripts
+
+typecheck:
+	./.venv/bin/python -m mypy pyiri2016 tests examples scripts --ignore-missing-imports
+
+pre-commit: lint typecheck test
+	@echo "✅ All checks passed!"

README.md

@@ -1,5 +1,7 @@
 [![alt tag](https://zenodo.org/badge/DOI/10.5281/zenodo.240895.svg)](https://doi.org/10.5281/zenodo.240895)
-[![Smoke](https://github.com/rilma/pyIRI2016/actions/workflows/smoke.yml/badge.svg?branch=main)](https://github.com/rilma/pyIRI2016/actions/workflows/smoke.yml)
+[![Smoke CI](https://github.com/rilma/pyIRI2016/actions/workflows/smoke.yml/badge.svg?branch=main)](https://github.com/rilma/pyIRI2016/actions/workflows/smoke.yml)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue)](https://www.python.org/downloads/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE.md)
 
 # pyIRI2016
 
@@ -48,13 +50,31 @@ Creates source distribution and binary wheel in `dist/` directory.
 ## Test
 
 ```sh
+# Run health checks
 make health
+
+# Run syntax check (smoke test)
 make smoke
+
+# Run all tests
 make test
+
+# Run tests with coverage report
+make coverage
+
+# Code quality checks
+make lint          # Check code with ruff
+make lint-fix      # Auto-fix linting issues
+make format        # Auto-format code with ruff
+make typecheck     # Type checking with mypy
+
+# Run all quality checks
+make pre-commit    # lint + typecheck + test
 ```
 
-`make smoke` runs a fast, CI-safe syntax check without network or Fortran build requirements.
-`make health` verifies Python, gfortran, and cmake are available, then runs `make smoke`.
+**`make smoke`**: Runs fast syntax validation without network or Fortran build requirements.
+**`make health`**: Verifies Python, gfortran, and cmake are available, then runs smoke tests.
+**`make coverage`**: Runs all tests with coverage analysis and generates HTML report in `htmlcov/`.
 
 ## Examples
 
@@ -64,8 +84,10 @@ Example outputs:
 
 | | |
 |---|---|
-| ![Height Profile](figures/iri1DExample01.png) | ![Latitude Profile](figures/iri1DExample02.png) |
-| ![Time Profile](figures/iri1DExample08.png) | ![Height vs Time](figures/iri2DExample01.png) |
+| ![Height Profile](figures/iri1DExample01.png) |
+| ![Height vs Time](figures/iri2DExample01.png) |
+| ![Time Profile](figures/iri1DExample08.png) |
+| ![Latitude Profile](figures/iri1DExample02.png) |
 
 ## Reference
 

examples/example01.py

@@ -2,14 +2,13 @@
 from pyiri2016 import IRI2016
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
 
     def main1():
 
         Obj = IRI2016()
         IRIData, IRIDATAAdd = Obj.IRI()
-        print(IRIData['ne'])
-        print(IRIDATAAdd['NmF2'], IRIDATAAdd['hmF2'])
-
+        print(IRIData["ne"])
+        print(IRIDATAAdd["NmF2"], IRIDATAAdd["hmF2"])
 
     main1()

examples/example02.py

@@ -2,14 +2,11 @@
 from pyiri2016 import IRI2016Profile
 
 
-if __name__ == '__main__':
-
+if __name__ == "__main__":
 
     def main1():
 
-        iri2016Obj = IRI2016Profile(option=1, verbose=True)
-
+        IRI2016Profile(option=1, verbose=True)
 
     # Height Profile Example
     main1()
-

examples/iri1DExample01.py

@@ -2,56 +2,65 @@
 from pyiri2016 import IRI2016Profile
 from numpy import arange
 from matplotlib.pyplot import figure, legend, savefig, close
-import seaborn
 from pathlib import Path
 import uuid
 
-def example01():
 
-    """ Height Profile Example """
+def example01():
+    """Height Profile Example"""
 
-    altlim = [100., 1000.]
-    altstp = 5.
+    altlim = [100.0, 1000.0]
+    altstp = 5.0
     lat, lon = -11.95, -76.77
     year, month, dom = 2003, 11, 21
 
-    iri2016Obj = IRI2016Profile(altlim=altlim, altstp=altstp, lat=lat, \
-        lon=lon, year=year, month=month, dom=dom, option=1, verbose=False)
+    iri2016Obj = IRI2016Profile(
+        altlim=altlim,
+        altstp=altstp,
+        lat=lat,
+        lon=lon,
+        year=year,
+        month=month,
+        dom=dom,
+        option=1,
+        verbose=False,
+    )
 
     altbins = arange(altlim[0], altlim[1] + altstp, altstp)
 
     nalt = len(altbins)
     index = range(nalt)
 
-    fig = figure(figsize=(16,6))
+    fig = figure(figsize=(16, 6))
 
     pn = fig.add_subplot(121)
-    ne = iri2016Obj.a[0, index]        
-    pn.plot(ne, altbins, label='N$_e$')
+    ne = iri2016Obj.a[0, index]
+    pn.plot(ne, altbins, label="N$_e$")
     pn.set_title(iri2016Obj.title1)
-    pn.set_xlabel('Density (m$^{-3}$)')
-    pn.set_ylabel('Altitude (km)')
-    pn.set_xscale('log')
-    legend(loc='best')
+    pn.set_xlabel("Density (m$^{-3}$)")
+    pn.set_ylabel("Altitude (km)")
+    pn.set_xscale("log")
+    legend(loc="best")
 
     pn = fig.add_subplot(122)
     ti = iri2016Obj.a[2, index]
     te = iri2016Obj.a[3, index]
-    pn.plot(ti, altbins, label='T$_i$')
-    pn.plot(te, altbins, label='T$_e$')
+    pn.plot(ti, altbins, label="T$_i$")
+    pn.plot(te, altbins, label="T$_e$")
     pn.set_title(iri2016Obj.title2)
-    pn.set_xlabel('Temperature ($^\circ$)')
-    pn.set_ylabel('Altitude (km)')        
-    legend(loc='best')
+    pn.set_xlabel("Temperature ($^\circ$)")
+    pn.set_ylabel("Altitude (km)")
+    legend(loc="best")
 
     # Save to figures folder with unique UUID suffix
     output_dir = Path(__file__).parent.parent / "figures"
     output_dir.mkdir(exist_ok=True)
     unique_id = str(uuid.uuid4())[:8]
     output_file = output_dir / f"iri1DExample01_{unique_id}.png"
-    savefig(output_file, dpi=100, bbox_inches='tight')
+    savefig(output_file, dpi=100, bbox_inches="tight")
     print(f"✓ Plot saved to: {output_file}")
     close(fig)
 
-if __name__ == '__main__':
+
+if __name__ == "__main__":
     example01()