TESTS: configure codecov, add tests for directory initialization and …

…probability calculations (#2)

.coveragerc

@@ -0,0 +1,10 @@
+[run]
+source = 
+    ChemSpaceAL/InitializeWorkspace.py
+
+omit =
+    ChemSpaceAL/Model.py
+    ChemSpaceAL/Dataset.py
+    ChemSpaceAL/Docking.py
+    ChemSpaceAL/Generation.py
+    ChemSpaceAL/Training.py

.github/workflows/main.yml

@@ -2,37 +2,31 @@ name: Python application test with pytest
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main, sandbox ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
 
     steps:
-    - name: Checkout code
-      uses: actions/checkout@v2
+    - name: Checkout
+      uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v2
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v4
       with:
-        python-version: '3.x'
+        python-version: '3.10'
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install pytest
+        pip install pandas numpy torch rdkit
+        pip install pytest pytest-cov
 
-    - name: Install package
-      run: |
-        python setup.py install
-
-    - name: Run pytest
-      run: |
-        pytest --cov tests/
-
-    - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+    - name: Run tests and collect coverage
+      run: pytest --cov=ChemSpaceAL
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4-beta
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-

ChemSpaceAL/ALConstruction.py

@@ -1,7 +1,6 @@
 import pandas as pd
 import numpy as np
 import pickle
-import plotly.graph_objects as go
 
 from ChemSpaceAL.Configuration import Config
 from typing import Union, Dict, List, Callable, Optional, cast
@@ -67,7 +66,6 @@ def _preprocess_scores_linearly(
     normalized = {k: v / total for k, v in negated.items()}
     return normalized
 
-
 def _preprocess_scores_softmax(
     scores: Dict[int, Number],
     do_negation: bool = False,
@@ -90,7 +88,6 @@ def _preprocess_scores_softmax(
     softmax = {k: v / total for k, v in exponentiate.items()}
     return softmax
 
-
 def balance_cluster_to_n(
     cluster_to_n: Dict[int, int], cluster_to_len: Dict[int, int]
 ) -> Dict[int, int]:

ChemSpaceAL/requirements.txt

@@ -1,9 +1,9 @@
 numpy==1.24.3
 pandas==1.5.3
 prolif==2.0.1
+scikit_learn==1.3.2
 PyYAML
 rdkit==2023.3.1
-scikit_learn==1.3.2
 torch
 tqdm==4.64.1
-wandb==0.15.4
+wandb==0.15.4

ChemSpaceAL/tests/test_al_construction.py

@@ -0,0 +1,75 @@
+from ..ALConstruction import _preprocess_scores_linearly, _preprocess_scores_softmax
+import pytest
+
+
+@pytest.mark.parametrize(
+    "scores, do_negation, expected",
+    [
+        (
+            {1: 2, 2: 2, 3: 2},
+            False,
+            {1: 1 / 3, 2: 1 / 3, 3: 1 / 3},
+        ),
+        (
+            {1: 1, 2: 0, 3: 0},
+            False,
+            {1: 1, 2: 0, 3: 0},
+        ),
+        ({}, False, {}),
+        (
+            {1: 0, 2: -2, 3: -2},
+            True,
+            {1: 0, 2: 0.5, 3: 0.5},
+        ),
+    ],
+)
+def test_preprocess_scores_linearly(scores, do_negation, expected):
+    result = _preprocess_scores_linearly(scores, do_negation)
+    for k, v in expected.items():
+        assert result[k] == pytest.approx(v)
+
+
+@pytest.mark.parametrize(
+    "scores, do_negation, divide, divide_factor, expected",
+    [
+        (
+            {1: 2, 2: 2, 3: 2},
+            False,
+            False,
+            None,
+            {1: 1 / 3, 2: 1 / 3, 3: 1 / 3},
+        ),
+        (
+            {1: 1, 2: 0, 3: 0},
+            False,
+            False,
+            None,
+            {1: 0.5761168847658291, 2: 0.21194155761708544, 3: 0.21194155761708544},
+        ),
+        (
+            {1: 1, 2: 0, 3: 0},
+            False,
+            True,
+            0.5,
+            {1: 0.7869860421615985, 2: 0.10650697891920075, 3: 0.10650697891920075},
+        ),
+        (
+            {1: -1, 2: -1, 3: 0},
+            True,
+            True,
+            0.5,
+            {1: 0.4683105308334812, 2: 0.4683105308334812, 3: 0.06337893833303762},
+        ),
+    ],
+)
+def test_preprocess_scores_softmax(
+    scores, do_negation, divide, divide_factor, expected
+):
+    result = _preprocess_scores_softmax(scores, do_negation, divide, divide_factor)
+    for k, v in expected.items():
+        assert result[k] == pytest.approx(v)
+
+
+def test_preprocess_scores_softmax_exception():
+    with pytest.raises(AssertionError):
+        _preprocess_scores_softmax({1: 2, 2: 3, 3: 4}, False, True, None)

ChemSpaceAL/tests/test_initialize_workspace.py

@@ -0,0 +1,26 @@
+import os
+import tempfile
+from unittest.mock import patch
+from .. import InitializeWorkspace as iw
+
+
+def test_create_default_folders():
+    # Using a temporary directory for testing
+    with tempfile.TemporaryDirectory() as tempdir:
+        iw.create_folders(base_path=tempdir)
+
+        # Check if the main folders are created
+        assert os.path.exists(os.path.join(tempdir, "1_Pretraining"))
+        assert os.path.exists(os.path.join(tempdir, "2_Generation"))
+
+        # Check if subfolders are created
+        assert os.path.exists(os.path.join(tempdir, "1_Pretraining", "datasets"))
+        # ... (add more assertions for other subfolders)
+    assert isinstance(iw.FOLDER_STRUCTURE, dict)
+
+
+@patch("builtins.input", return_value="Y")
+def test_create_folders_without_base_path(mock_input):
+    with tempfile.TemporaryDirectory() as tempdir:
+        os.chdir(tempdir)  # Change working directory
+        iw.create_folders()

README.md

@@ -1,9 +1,8 @@
-# ChemSpaceAL
+ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein- Specific Molecular Generation
+=======================================
 
-## An Efficient Active Learning Methodology Applied to Protein- Specific Molecular Generation
-
-<p align="center">
-<a href="https://github.com/psf/black"><img alt="Code style: black" src="https://img.shields.io/badge/code%20style-black-000000.svg"></a>
-</p>
+[![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![codecov](https://codecov.io/gh/batistagroup/ChemSpaceAL/graph/badge.svg?token=ROJSISYJWC)](https://codecov.io/gh/batistagroup/ChemSpaceAL)
 
 ![A description of the active learning methodology](media/toc_figure.jpg)

codecov.yml

@@ -0,0 +1,27 @@
+coverage:
+  precision: 2
+  round: down
+  range: "0...90"
+
+  status:
+    project: yes
+    patch: yes
+    changes: no
+
+comment:
+  layout: "header, diff, components"
+
+component_management:
+  default_rules:
+    statuses:
+      - type: patch
+        target: auto
+  individual_components:
+    - component_id: module_iw
+      name: InitializeWorkspace
+      paths:
+        - "ChemSpaceAL/InitializeWorkspace.py"
+    - component_id: module_al_construct
+      name: AL Training Set Construction
+      paths:
+        - "ChemSpaceAL/ALConstruction.py"

setup.py

@@ -31,6 +31,9 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-    install_requires=required,
+    # install_requires=required,
+    # install_requires=[
+    #     # "pytest"
+    # ]
     python_requires=">=3.10",
 )