Merge pull request #37 from rodrigo-arenas/0.6.Xdev

[PR] Installation dependencies

README.rst

@@ -57,6 +57,11 @@ It's advised to install sklearn-genetic using a virtual env, inside the env use:
 
    pip install sklearn-genetic-opt
 
+If you want to get all the features, including plotting and mlflow logging capabilities,
+install all the extra packages::
+
+    pip install sklearn-genetic-opt[all]
+
 Example
 #######
 

docs/index.rst

@@ -22,6 +22,10 @@ It's advised to install sklearn-genetic using a virtual env, inside the env use:
 
    pip install sklearn-genetic-opt
 
+Or install with the extra packages to get the full functionalities::
+
+   pip install sklearn-genetic-opt[all]
+
 .. |PythonMinVersion| replace:: 3.7
 .. |ScikitLearnMinVersion| replace:: 0.21.3
 .. |NumPyMinVersion| replace:: 1.14.5
@@ -34,9 +38,15 @@ sklearn-genetic-opt requires:
 - Python (>= |PythonMinVersion|)
 - scikit-learn (>= |ScikitLearnMinVersion|)
 - NumPy (>= |NumPyMinVersion|)
-- Seaborn (>= |SeabornMinVersion|)
 - DEAP (>= |DEAPMinVersion|)
+
+extra requirements:
+
+These requirements are necessary to use the
+:mod:`~sklearn_genetic.plots` and :class:`~sklearn_genetic.mlflow.MLflowConfig` modules
+
 - MLflow (>= |MLflowMinVersion|)
+- Seaborn (>= |SeabornMinVersion|)
 
 .. toctree::
    :maxdepth: 2
@@ -48,7 +58,6 @@ sklearn-genetic-opt requires:
    tutorials/custom_callback
    tutorials/understand_cv
    tutorials/mlflow
-   release_notes
 
 .. toctree::
    :maxdepth: 2
@@ -60,6 +69,11 @@ sklearn-genetic-opt requires:
    notebooks/Digits_decision_tree.ipynb
    notebooks/MLflow_logger.ipynb
 
+.. toctree::
+   :maxdepth: 2
+   :caption: Release Notes
+
+   release_notes
 
 .. toctree::
    :maxdepth: 2

docs/release_notes.rst

@@ -19,12 +19,21 @@ Features:
 * Added support for extra methods coming from scikit-learn's BaseSearchCV, it is
   still partial support, missing properties like `cv_results_`, `best_index_` and `multimetric_`.
 
+^^^^^^^^^^^^
+API Changes:
+^^^^^^^^^^^^
+
+* The modules :mod:`~sklearn_genetic.plots` and :class:`~sklearn_genetic.mlflow.MLflowConfig`
+  now requires an explicit installation of seaborn and mlflow, now those
+  are optionally installed using ``pip install sklearn-genetic-opt[all].``
+
 ^^^^^
 Docs:
 ^^^^^
 
 * Edited all demos to be in the jupyter notebook format.
 * Added embedded jupyter notebooks examples
+* The modules of the package now have a summary of their classes/functions in the docs
 
 What's new in 0.5.0
 -------------------

setup.py

@@ -33,15 +33,19 @@
         "Documentation": "https://sklearn-genetic-opt.readthedocs.io/en/stable/",
         "Source Code": "https://github.com/rodrigo-arenas/Sklearn-genetic-opt",
     },
-    packages=find_packages(include=["sklearn_genetic", "sklearn_genetic.*"]),
+    packages=find_packages(
+        include=["sklearn_genetic", "sklearn_genetic.*"], exclude=["*tests*"]
+    ),
     install_requires=[
         "scikit-learn>=0.21.3",
         "numpy>=1.14.5",
-        "seaborn>=0.9.0",
         "deap>=1.3.1",
-        "pydantic>=1.8.2",
-        "mlflow>=1.17.0",
     ],
+    extras_require={
+        "mlflow": ["mlflow>=1.17.0"],
+        "seaborn": ["seaborn>=0.9.0"],
+        "all": ["mlflow>=1.17.0", "seaborn>=0.9.0"],
+    },
     python_requires=">=3.7",
     include_package_data=True,
 )

sklearn_genetic/__init__.py

@@ -1,23 +1,20 @@
 from .genetic_search import GASearchCV
-from .plots import plot_fitness_evolution, plot_search_space
+
 from .callbacks import (
     ThresholdStopping,
     ConsecutiveStopping,
     DeltaThreshold,
     LogbookSaver,
 )
-from .mlflow import MLflowConfig
+
 
 from ._version import __version__
 
 __all__ = [
     "GASearchCV",
-    "plot_fitness_evolution",
-    "plot_search_space",
     "ThresholdStopping",
     "ConsecutiveStopping",
     "DeltaThreshold",
     "LogbookSaver",
-    "MLflowConfig",
     "__version__",
 ]

sklearn_genetic/mlflow.py

@@ -1,4 +1,11 @@
-import mlflow
+import logging
+
+# Check if mlflow is installed as an extra requirement
+try:
+    import mlflow
+except ModuleNotFoundError:  # noqa
+    logger = logging.getLogger(__name__)  # noqa
+    logger.error("MLflow not found, pip install mlflow to use MLflowConfig")  # noqa
 
 
 class MLflowConfig:

sklearn_genetic/plots.py

@@ -1,9 +1,17 @@
-import seaborn as sns
+import logging
+
+# Check if seaborn is installed as an extra requirement
+try:
+    import seaborn as sns
+except ModuleNotFoundError:  # noqa
+    logger = logging.getLogger(__name__)  # noqa
+    logger.error(
+        "seaborn not found, pip install seaborn to use plots functions"
+    )  # noqa
 
 from .utils import logbook_to_pandas
 from .parameters import Metrics
 
-
 """
 This module contains some useful function to explore the results of the optimization routines
 """

sklearn_genetic/tests/test_genetic_search.py

@@ -80,8 +80,8 @@ def test_expected_ga_results():
         ("eaSimple", ThresholdStopping(threshold=0.01)),
         ("eaMuPlusLambda", ThresholdStopping(threshold=0.01)),
         ("eaMuCommaLambda", ThresholdStopping(threshold=0.01)),
-        ("eaSimple", TimerStopping(total_seconds=5)),
-        ("eaMuPlusLambda", TimerStopping(total_seconds=5)),
+        ("eaSimple", TimerStopping(total_seconds=0.5)),
+        ("eaMuPlusLambda", TimerStopping(total_seconds=2)),
         ("eaMuCommaLambda", TimerStopping(total_seconds=5)),
         ("eaSimple", ConsecutiveStopping(generations=5, metric="fitness")),
         ("eaMuPlusLambda", ConsecutiveStopping(generations=5, metric="fitness")),