Add pytest and tests for CLI and Python module

- Add pytest configuration for test management
- Implement test suite for CLI functionality and Python module
- Update README with testing instructions and badge
- Fix Dockerfile
- Create .dockerignore to exclude unnecessary files from Docker builds
- Add GitHub Actions workflows for testing
- Clean up makefile to include test commands

Author: jgoedeke

.dockerignore

@@ -0,0 +1,27 @@
+# Build artifacts
+*.o
+*.so
+*.pyc
+imctermite
+main.cpp.cpp
+
+# Python build
+python/build/
+python/dist/
+python/*.so
+python/*.cpp
+python/lib/
+python/LICENSE
+python/README.md
+python/*.egg-info/
+__pycache__/
+
+# Git and editor
+.git/
+.venv/
+*.swp
+*.swo
+*~
+
+# Test outputs
+.pytest_cache/

.github/workflows/pypi-deploy.yml

@@ -8,9 +8,13 @@ on:
 
 jobs:
 
+  test:
+    uses: ./.github/workflows/test.yml
+
   build_setup:
     name: Prepare environment for wheel builds
     runs-on: ubuntu-24.04
+    needs: [test]
     steps:
       - uses: actions/checkout@v2
       - name: Prepare wheel build

.github/workflows/test.yml

@@ -0,0 +1,21 @@
+name: Run Tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v3
+    
+    - name: Build Docker image
+      run: docker build -t imctermite .
+    
+    - name: Run tests in container
+      run: docker run --rm imctermite make test

.gitignore

@@ -43,3 +43,6 @@ python/*.soc
 python/lib/
 python/*.cpp
 python/wheelhouse/
+
+__pycache__/
+.pytest_cache/

Dockerfile

@@ -1,21 +1,22 @@
-
-FROM debian:bullseye-20210111
+FROM debian:bullseye
 
 USER root
 
 RUN apt-get update && apt-get install -y \
     build-essential git vim \
     python3 python3-pip
-RUN python3 -m pip install cython
+RUN python3 -m pip install cython pytest
+RUN ln -s /usr/bin/python3 /usr/bin/python
 
 RUN g++ -v
 
-COPY ./ /IMCtermite/
+WORKDIR /IMCtermite
+COPY ./ .
 
 # install CLI tool
-RUN cd /IMCtermite && ls -lh && make install && ls -lh /usr/local/bin/imctermite
+RUN make install
 
 # install Python module
-RUN cd /IMCtermite && ls -lh && make cython-install
+RUN make python-build
 
 CMD ["sleep","infinity"]

README.md

@@ -1,6 +1,7 @@
 
 [![LICENSE](https://img.shields.io/github/license/RecordEvolution/IMCtermite)](https://img.shields.io/github/license/RecordEvolution/IMCtermite)
 [![STARS](https://img.shields.io/github/stars/RecordEvolution/IMCtermite)](https://img.shields.io/github/stars/RecordEvolution/IMCtermite)
+![Tests](https://github.com/RecordEvolution/IMCtermite/actions/workflows/test.yml/badge.svg)
 ![CI Build Wheel](https://github.com/RecordEvolution/IMCtermite/actions/workflows/pypi-deploy.yml/badge.svg?branch=&event=push)
 [![PYPI](https://img.shields.io/pypi/v/IMCtermite.svg)](https://pypi.org/project/imctermite/)
 
@@ -27,6 +28,7 @@ Python module to integrate the _.raw_  format into any ETL workflow.
 * [File format](#Fileformat)
 * [Build and Installation](#Installation)
 * [Usage and Examples](#Usage)
+* [Testing](#Testing)
 * [References](#References)
 
 ## File format
@@ -217,6 +219,12 @@ A more complete [example](python/examples/usage.py), including the methods for
 obtaining the channels, i.a. their data and/or directly printing them to files,
 can be found in the `python/examples` folder.
 
+## Testing
+
+Run end-to-end tests: `make test`
+
+See [tests/README.md](tests/README.md) for details.
+
 ## References
 
 ### IMC

makefile

@@ -35,7 +35,7 @@ INST := /usr/local/bin
 # C++ and CLI tool
 
 # build executable
-$(EXE): check-tags $(GVSN) main.o
+$(EXE): check-tags main.o
 	$(CC) $(OPT) main.o -o $@
 
 # build main.cpp and include git version/commit tag
@@ -86,7 +86,7 @@ docker-run:
 #-----------------------------------------------------------------------------#
 # python
 
-python-build: check-tags $(GVSN)
+python-build: check-tags
 	make -C python/ build-inplace
 	cp python/imctermite*.so ./ -v
 
@@ -97,10 +97,29 @@ python-clean:
 python-test:
 	PYTHONPATH=./ python python/examples/usage.py
 
+#-----------------------------------------------------------------------------#
+# tests
+
+test: $(EXE) python-build
+	@echo "Running all tests..."
+	@PYTHONPATH=./ pytest
+
+test-cli: $(EXE)
+	@echo "Running CLI tests..."
+	@PYTHONPATH=./ pytest tests/test_cli.py
+
+test-python: python-build
+	@echo "Running Python tests..."
+	@PYTHONPATH=./ pytest tests/test_python.py
+
 #-----------------------------------------------------------------------------#
 # clean
 
-clean: cpp-clean python-clean
+test-clean:
+	rm -rf .pytest_cache
+	find tests/ -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
+
+clean: cpp-clean python-clean test-clean
 
 #-----------------------------------------------------------------------------#
 # github actions

pytest.ini

@@ -0,0 +1,9 @@
+[pytest]
+testpaths = tests
+pythonpath = .
+python_files = test_*.py
+python_classes = Test*
+python_functions = test_*
+addopts = -v --strict-markers --tb=short
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')

tests/README.md

@@ -0,0 +1,30 @@
+# IMCtermite Tests
+
+End-to-end tests for both the CLI tool and Python module.
+
+
+## Running Tests
+
+### All Tests
+```bash
+make test              # Via makefile (builds if needed)
+pytest                 # Direct pytest
+```
+
+### CLI Tests Only
+```bash
+make test-cli
+pytest tests/test_cli.py
+```
+
+### Python Module Tests Only
+```bash
+make test-python
+pytest tests/test_python.py
+```
+
+## Prerequisites
+
+```bash
+pip install cython pytest setuptools
+```