Workflow for mlflow added

.github/workflows/ci-tests.yml

@@ -34,9 +34,13 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           pip install --upgrade --upgrade-strategy eager -r dev-requirements.txt -e .
-      - name: Test with pytest
+      - name: Unit test with pytest
         run: |
-          pytest sklearn_genetic/ --verbose --color=yes --assert=plain --cov-fail-under=95 --cov-config=.coveragerc --cov=./ -p no:warnings
+          pytest sklearn_genetic/tests/unit --verbose --color=yes --assert=plain --cov-fail-under=89 --cov-config=.coveragerc --cov=./ -p no:warnings
+      - name: MLflow test with pytest
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          pytest sklearn_genetic/tests/mlflow --verbose --color=yes --assert=plain --cov-fail-under=6 --cov-config=.coveragerc --cov=./ -p no:warnings
       - name: "Upload coverage to Codecov"
         uses: codecov/codecov-action@v1
         with:

dev-requirements.txt

@@ -16,3 +16,4 @@ numpydoc
 nbsphinx
 tensorflow>=2.0.0
 tqdm>=4.61.1
+testcontainers

sklearn_genetic/tests/mlflow/Dockerfile

@@ -0,0 +1,7 @@
+FROM python:3.9-slim-bullseye
+
+RUN pip install --no-cache mlflow psycopg2-binary
+
+EXPOSE 5000
+
+CMD ["mlflow", "ui", "--host", "0.0.0.0", "--backend-store-uri", "postgresql+psycopg2://postgres@postgres:5432/mlflow", "--default-artifact-root", "./mlruns"]

sklearn_genetic/tests/mlflow/conftest.py

@@ -0,0 +1,20 @@
+import os
+import pytest
+import mlflow
+import logging
+from testcontainers.compose import DockerCompose
+
+
+@pytest.fixture(scope="module", autouse=True)
+def setup_mlflow():
+    path = os.path.abspath(os.path.dirname(__file__))
+    with DockerCompose(
+        path, compose_file_name=["docker-compose.yml"], pull=True
+    ) as compose:
+        host = compose.get_service_host("mlflow", 5000)
+        if host == "0.0.0.0":
+            host = "localhost"
+        port = compose.get_service_port("mlflow", 5000)
+        logging.info(f"MLflow started @http://{host}:{port}")
+        mlflow.set_tracking_uri(f"http://{host}:{port}")
+        yield

sklearn_genetic/tests/mlflow/docker-compose.yml

@@ -0,0 +1,19 @@
+version: '3'
+
+services:
+  mlflow:
+    build:
+      context: ""
+      dockerfile: Dockerfile
+    ports:
+      - "5000"
+    depends_on:
+      - postgres
+
+  postgres:
+    image: postgres:13.1-alpine
+    environment:
+      POSTGRES_DB: mlflow
+      POSTGRES_HOST_AUTH_METHOD: trust
+    ports:
+      - 5432

sklearn_genetic/tests/test_mlflow.py → sklearn_genetic/tests/mlflow/test_mlflow.py

@@ -1,14 +1,12 @@
 import pytest
-import shutil
-import os
+import requests
 
 import mlflow
 from mlflow.tracking import MlflowClient
 from mlflow.entities import ViewType
 from sklearn.datasets import load_digits
 from sklearn.tree import DecisionTreeClassifier
 from sklearn.model_selection import train_test_split
-from sklearn.metrics import accuracy_score
 from sklearn.model_selection import StratifiedKFold
 
 from ..genetic_search import GASearchCV
@@ -141,11 +139,3 @@ def test_mlflow_after_run(mlflow_resources, mlflow_run):
     assert 2 <= int(params["max_depth"]) <= 20
     assert 2 <= int(params["max_leaf_nodes"]) <= 30
     assert client.get_metric_history(run_id, "score")[0].key == "score"
-
-
-def test_cleanup():
-    """
-    Ensure resources are cleaned up.
-    """
-    shutil.rmtree("mlruns")
-    assert "mlruns" not in os.listdir(os.getcwd())

sklearn_genetic/tests/test_plots.py → sklearn_genetic/tests/unit/test_plots.py

@@ -4,7 +4,11 @@
 from sklearn.tree import DecisionTreeRegressor
 
 from .. import GASearchCV
-from ..plots import plot_fitness_evolution, plot_search_space, plot_parallel_coordinates
+from ..plots import (
+    plot_fitness_evolution,
+    plot_search_space,
+    plot_parallel_coordinates,
+)
 from ..space import Integer, Categorical, Continuous