Merge pull request #55 from ecrl/dev

3.0.1 - updated install method, GitHub workflows, unit testing

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,30 @@
+name: Upload new PaDELPy version to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package to PyPI
+      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/run_tests.yml

@@ -0,0 +1,26 @@
+name: Run ECabc tests
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+            python -m pip install --upgrade pip
+            pip install build
+            pip install pytest pytest-md
+      - name: Install package
+        run: python -m pip install .
+      - name: Run tests
+        uses: pavelzw/pytest-action@v2
+        with:
+          emoji: false
+          report-title: 'ECabc test report'

README.md

@@ -5,7 +5,6 @@
 [![PyPI version](https://badge.fury.io/py/ecabc.svg)](https://badge.fury.io/py/ecabc)
 [![GitHub license](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/ECRL/ecabc/blob/master/LICENSE)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.01420/status.svg)](https://doi.org/10.21105/joss.01420)
-[![Build Status](https://dev.azure.com/uml-ecrl/package-management/_apis/build/status/ECRL.ecabc?branchName=master)](https://dev.azure.com/uml-ecrl/package-management/_build/latest?definitionId=5&branchName=master)
 
 **ECabc** is an open source Python package used to tune parameters for user-supplied functions based on the [Artificial Bee Colony by D. Karaboğa](http://scholarpedia.org/article/Artificial_bee_colony_algorithm). ECabc optimizes user supplied functions, or **fitness function**s, using a set of variables that exist within a search space. The bee colony consists of three types of bees: employers, onlookers and scouts. An **employer bee** exploits a solution comprised of a permutation of the variables in the search space, and evaluates the viability of the solution. An **onlooker bee** chooses an employer bee with an optimal solution and searches for new solutions near them. The **scout bee**, a variant of the employer bee, will search for a new solution if it has stayed too long at its current solution.
 
@@ -43,7 +42,7 @@ Note: if multiple Python releases are installed on your system (e.g. 2.7 and 3.7
 ### Method 2: From source
 - Download the ECabc repository, navigate to the download location on the command line/terminal, and execute:
 ```
-python setup.py install
+pip install .
 ```
 
 There are currently no additional dependencies for ECabc.

pyproject.toml

@@ -0,0 +1,27 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+exclude = ["paper*"]
+
+[project]
+name = "ecabc"
+version = "3.0.1"
+authors = [
+    { name="Sanskriti Sharma", email="[email protected]" },
+    { name="Hernan Gelaf-Romer", email="[email protected]" },
+    { name="Travis Kessler", email="[email protected]" },
+]
+description = "Artificial bee colony for function parameter optimization"
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/ecrl/ecabc"
+"Bug Tracker" = "https://github.com/ecrl/ecabc/issues"

tests/test_all.py

@@ -1,11 +1,235 @@
-import unittest
+import pytest
 
-from unit_tests.bee import TestBee
-from unit_tests.colony import TestColony
-from unit_tests.parameter import TestParameter
-from unit_tests.utils import TestUtils
+import ecabc.utils as abc_utils
+from ecabc import ABC, Bee, Parameter
 
 
-if __name__ == '__main__':
+def _objective_function(params):
+    return sum(params)
 
-    unittest.main()
+
+def _objective_function_kwargs(params, my_kwarg):
+    return sum(params) + my_kwarg
+
+
+# utils.py
+
+
+def test_apply_mutation():
+    params = [Parameter(0, 10, True) for _ in range(3)]
+    curr_params = [5, 5, 5]
+    mut_params = abc_utils.apply_mutation(curr_params, params)
+    assert curr_params != mut_params
+
+
+def test_call_obj_fn():
+    param_vals = [2, 2, 2]
+    ret_params, result = abc_utils.call_obj_fn(
+        param_vals, _objective_function, {}
+    )
+    assert result == 6
+    assert ret_params == param_vals
+    fn_args = {'my_kwarg': 2}
+    ret_params, result = abc_utils.call_obj_fn(
+        param_vals, _objective_function_kwargs, fn_args
+    )
+    assert result == 8
+    assert param_vals == ret_params
+
+
+def test_choose_bee():
+
+    bee_1 = Bee([0], 100000000000000000000, 0)
+    bee_2 = Bee([0], 0, 0)
+    chosen_bee = abc_utils.choose_bee([bee_1, bee_2])
+    assert chosen_bee == bee_2
+
+
+def test_determine_best_bee():
+
+    bee_1 = Bee([10], 10, 0)
+    bee_2 = Bee([0], 0, 0)
+    bee_2_fitness = bee_2._fitness_score
+    bee_2_ret_val = bee_2._obj_fn_val
+    bee_2_params = bee_2._params
+    _fit, _ret, _param = abc_utils.determine_best_bee([bee_1, bee_2])
+    assert _fit == bee_2_fitness
+    assert _ret == bee_2_ret_val
+    assert _param == bee_2_params
+
+
+# parameter.py
+
+
+def test_param_init():
+    param = Parameter(0, 10, False)
+    assert param._restrict is False
+    param = Parameter(0, 10)
+    assert param._restrict is True
+    assert param._dtype == int
+    assert param._min_val == 0
+    assert param._max_val == 10
+
+
+def test_rand_val():
+    for _ in range(100):
+        param = Parameter(0, 10)
+        rand_val = param.rand_val
+        assert rand_val >= 0
+        assert rand_val <= 10
+        assert type(rand_val) == int
+    param = Parameter(0.0, 10.0)
+    rand_val = param.rand_val
+    assert type(rand_val) == float
+
+
+def test_mutate():
+    param = Parameter(0, 10)
+    rand_val = param.rand_val
+    for _ in range(1000):
+        mutation = param.mutate(rand_val)
+        if mutation < 0 or mutation > 10:
+            raise ValueError('Mutation outside min/max bounds')
+    param = Parameter(0, 3, False)
+    rand_val = param.rand_val
+    outside_bounds = False
+    mutation = param.mutate(rand_val)
+    while True:
+        if mutation < 0 or mutation > 3:
+            outside_bounds = True
+            break
+        mutation = param.mutate(mutation)
+    assert outside_bounds is True
+
+
+# abc.py
+
+
+def test_colony_init():
+    c = ABC(10, _objective_function)
+    assert c._num_employers == 10
+    assert c._obj_fn == _objective_function
+    kwargs = {'my_kwarg': 2}
+    c = ABC(10, _objective_function_kwargs, kwargs)
+    assert c._obj_fn_args == kwargs
+    c = ABC(10, _objective_function, num_processes=8)
+    assert c._num_processes == 8
+    with pytest.raises(ReferenceError):
+        c = ABC(10, None)
+
+
+def test_no_bees():
+    c = ABC(10, _objective_function)
+    assert c.best_fitness == 0
+    assert c.best_ret_val is None
+    assert c.best_params == {}
+    assert c.average_fitness is None
+    assert c.average_ret_val is None
+    with pytest.raises(RuntimeError):
+        c.search()
+
+
+def test_add_parameter():
+    c = ABC(10, _objective_function)
+    c.add_param(0, 1)
+    c.add_param(2, 3)
+    c.add_param(4, 5)
+    assert len(c._params) == 3
+    assert c._params[0]._min_val == 0
+    assert c._params[0]._max_val == 1
+    assert c._params[1]._min_val == 2
+    assert c._params[1]._max_val == 3
+    assert c._params[2]._min_val == 4
+    assert c._params[2]._max_val == 5
+    assert c._params[0]._dtype == int
+    c.add_param(0.0, 1.0)
+    assert c._params[3]._dtype == float
+    assert c._params[0]._restrict is True
+    c.add_param(0, 1, False)
+    assert c._params[4]._restrict is False
+
+
+def test_initialize():
+    c = ABC(10, _objective_function)
+    c.add_param(0, 10)
+    c.add_param(0, 10)
+    c.initialize()
+    assert len(c._bees) == 20
+
+
+def test_search_and_stats():
+    c = ABC(10, _objective_function)
+    c.add_param(0, 0)
+    c.add_param(0, 0)
+    c.initialize()
+    for _ in range(50):
+        c.search()
+    assert c.best_fitness == 1
+    assert c.best_ret_val == 0
+    assert c.best_params == {'P0': 0, 'P1': 0}
+
+
+def test_kwargs():
+    c = ABC(10, _objective_function_kwargs, {'my_kwarg': 2})
+    c.add_param(0, 0)
+    c.add_param(0, 0)
+    c.initialize()
+    for _ in range(50):
+        c.search()
+    assert c.best_ret_val == 2
+
+
+def test_multiprocessing():
+    c = ABC(20, _objective_function, num_processes=4)
+    assert c._num_processes == 4
+    c.add_param(0, 10)
+    c.add_param(0, 10)
+    c.initialize()
+    c.search()
+
+
+def test_custom_param_name():
+    c = ABC(20, _objective_function)
+    c.add_param(0, 10, name='int1')
+    c.add_param(0, 10, name='int2')
+    c.initialize()
+    for _ in range(50):
+        c.search()
+    assert c.best_params == {'int1': 0, 'int2': 0}
+
+
+# bee.py
+
+
+def test_bee_init():
+    bee = Bee([0, 0, 0], 0, 1, True)
+    assert bee._is_employer is True
+    bee = Bee([0, 0, 0], 0, 1)
+    assert bee._is_employer is False
+    assert bee._params == [0, 0, 0]
+    assert bee._obj_fn_val == 0
+    assert bee._fitness_score == 1
+    assert bee._stay_limit == 1
+
+
+def test_abandon():
+    bee = Bee([0, 0, 0], 0, 2)
+    result = bee.abandon
+    assert result is False
+    result = bee.abandon
+    assert result is True
+
+
+def test_calc_fitness():
+    result = Bee.calc_fitness(0)
+    assert result == 1
+    result = Bee.calc_fitness(-1)
+    assert result == 2
+
+
+def test_is_better_food():
+    bee = Bee([0, 0, 1], 1, 1)
+    result = bee.is_better_food(0)
+    assert result is True
+    result = bee.is_better_food(2)
+    assert result is False