Merge pull request #31 from perib/dev

Dev
EpistasisLab · Aug 1, 2023 · e19efb6 · e19efb6
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diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 TPOT stands for Tree-based Pipeline Optimization Tool. TPOT2 is a Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming. Consider TPOT2 your Data Science Assistant.
 
 TPOT2 is a rewrite of TPOT with some additional functionality. Notably, we added support for graph-based pipelines and additional parameters to better specify the desired search space. 
-TPOT2 is currently in Alpha. This means that there will likely be some backwards incompatible changes to the API as we develop. Some implemented features may be buggy. There is a list of known issues written at the bottom of this README. Some features have placeholder names or are listed as "Experimental" in the doc string. These are features that may not be fully implemented and may or may work with all other features.
+TPOT2 is currently in Alpha. This means that there will likely be some backwards incompatible changes to the API as we develop. Some implemented features may be buggy. There is a list of known issues written at the bottom of this README. Some features have placeholder names or are listed as "Experimental" in the doc string. These are features that may not be fully implemented and may or may not work with all other features.
 
 If you are interested in using the current stable release of TPOT, you can do that here: [https://github.com/EpistasisLab/tpot/](https://github.com/EpistasisLab/tpot/). 
 
@@ -136,7 +136,7 @@ Setting `verbose` to 5 can be helpful during debugging as it will print out the
 
 ## Contributing to TPOT2
 
-We welcome you to check the existing issues for bugs or enhancements to work on. If you have an idea for an extension to TPOT, please file a new issue so we can discuss it.
+We welcome you to check the existing issues for bugs or enhancements to work on. If you have an idea for an extension to TPOT2, please file a new issue so we can discuss it.
 
 
 ### Known issues

diff --git a/Tutorial/1_Estimators_Overview.ipynb b/Tutorial/1_Estimators_Overview.ipynb
diff --git a/Tutorial/2_Defining_Search_Space_(config_dicts).ipynb b/Tutorial/2_Defining_Search_Space_(config_dicts).ipynb
diff --git a/Tutorial/3_Genetic_Feature_Set_Selectors.ipynb b/Tutorial/3_Genetic_Feature_Set_Selectors.ipynb
diff --git a/Tutorial/4_Symbolic_Regression_and_Classification.ipynb b/Tutorial/4_Symbolic_Regression_and_Classification.ipynb
diff --git a/Tutorial/5_GraphPipeline.ipynb b/Tutorial/5_GraphPipeline.ipynb
diff --git a/Tutorial/6_SH_and_early_termination.ipynb b/Tutorial/6_SH_and_early_termination.ipynb
diff --git a/Tutorial/7_dask_parallelization.ipynb b/Tutorial/7_dask_parallelization.ipynb
@@ -273,7 +273,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.10.11"
   },
   "orig_nbformat": 4,
   "vscode": {

diff --git a/Tutorial/8_Genetic_Algorithm_Overview.ipynb b/Tutorial/8_Genetic_Algorithm_Overview.ipynb
diff --git a/setup.py b/setup.py
@@ -44,7 +44,7 @@ def calculate_version():
                       'jupyter>=1.0.0',
                       'networkx>=3.0',
                       'dask>=2023.3.1',
-                      'distributed>=2023.3.1',
+                      'distributed>=2023.7.0',
                       'dask-ml>=2022.5.27',
                       'dask-jobqueue>=0.8.1',
                       'func_timeout>=4.3.5',

diff --git a/tpot2/__init__.py b/tpot2/__init__.py
@@ -1,17 +1,18 @@
 
 #TODO: are all the imports in the init files done correctly?
 #TODO clean up import organization
-from ._version import __version__
-from .graphsklearn import *
-from .individual import *
-from .logbook import *
-from .population import *
-from .base_evolver import *
-from .objectives import *
-from .evolutionary_algorithms import *
-from .tpot_estimator import *
-from .builtin_modules import *
-from .config import *
-from .representations import *
-from .parent_selectors import *
-from .utils import *
+
+from .graphsklearn import GraphPipeline
+from .population import Population
+
+from . import builtin_modules
+from . import utils
+from . import config
+from . import individual_representations
+from . import evolvers
+from . import objectives
+from . import selectors
+from . import tpot_estimator
+
+
+from .tpot_estimator import TPOTClassifier, TPOTRegressor, TPOTEstimator, TPOTEstimatorSteadyState
diff --git a/tpot2/builtin_modules/__init__.py b/tpot2/builtin_modules/__init__.py
@@ -4,4 +4,5 @@
 from .column_one_hot_encoder import ColumnOneHotEncoder
 from .arithmetictransformer import ArithmeticTransformer
 from .passthrough import Passthrough
-from .imputer import ColumnSimpleImputer
+from .imputer import ColumnSimpleImputer
+from .selector_wrappers import RFE_ExtraTreesClassifier, SelectFromModel_ExtraTreesClassifier, RFE_ExtraTreesRegressor, SelectFromModel_ExtraTreesRegressor