Merge pull request #55 from cavalab/island_GA

(py)Brush v1.0: islands!

.gitignore

@@ -1,6 +1,9 @@
 *.vscode 
 *.html
 
+# files generated by running the test suite
+tests/cpp/__*
+
 tags
 build/
 operon/

README.md

@@ -98,13 +98,16 @@ In addition, Brush provides functionality that allows you to feed in more compli
 ```python
 # load data
 import pandas as pd
+
 df = pd.read_csv('docs/examples/datasets/d_enc.csv')
 X = df.drop(columns='label')
 y = df['label']
 
 # import and make a regressor
-from brush import BrushRegressor
-est = BrushRegressor()
+from pybrush import BrushRegressor
+
+# you can set verbosity=1 to see the progress bar
+est = BrushRegressor(verbosity=1)
 
 # use like you would a sklearn regressor
 est.fit(X,y)
@@ -118,15 +121,18 @@ print('score:', est.score(X,y))
 ```python
 # load data
 import pandas as pd
+
 df = pd.read_csv('docs/examples/datasets/d_analcatdata_aids.csv')
 X = df.drop(columns='target')
 y = df['target']
 
 # import and make a classifier
-from brush import BrushClassifier
-est = BrushClassifier()
+from pybrush import BrushClassifier
+est = BrushClassifier(verbosity=1)
+
 # use like you would a sklearn classifier
 est.fit(X,y)
+
 y_pred = est.predict(X)
 y_pred_proba = est.predict_proba(X)
 
@@ -237,4 +243,30 @@ If you are developing the cpp code and want to build the cpp tests, run the foll
 ./install tests
 ```
 
+## Building the docs locally
+
+To build the documentation you will need some additional requirements.
+Before proceeding, make sure you have the python wrapper installed, as the documentation have some sample notebooks that will run the code.
+
+First go to the `docs` folder:
+
+```bash
+cd docs/
+```
+
+Then, install additional python packages in the same environemnt as brush is intalled with:
+
+```bash
+conda activate brush
+pip install -r requirements.txt
+```
+
+Now just run:
+
+```bash
+make html
+```
+
+The static website is located in `-build/html`
+
 <!-- end development -->

docs/conf.py

@@ -37,7 +37,6 @@ def configureDoxyfile(input_dir, output_dir):
 	with open('Doxyfile', 'w') as fp2:
 		fp2.write(filedata)
 
-
 ## Only trigger readthedocs build if running on readthedocs servers:
 # read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
 
@@ -58,7 +57,7 @@ def configureDoxyfile(input_dir, output_dir):
 author = 'William La Cava and Joseph D. Romano'
 
 # The full version, including alpha/beta/rc tags
-release = '0.1a'
+release = '0.1a' # TODO: use versionstr here
 
 
 # -- General configuration ---------------------------------------------------
@@ -112,7 +111,8 @@ def configureDoxyfile(input_dir, output_dir):
 breathe_default_project = "brush"
 breathe_default_members = ('members', 'undoc-members')
 breathe_projects_source = {
-	"brush": ("../src/", list(glob('../src/', recursive=True)))
+	"brush"  : ("../src/",     list(glob('../src/', recursive=True)) ),
+	"pybrush": ("../pybrush/", list(glob('../pybrush/', recursive=True)) ),
 }
 
 html_theme_options = {

docs/cpp_api/archive.rst

@@ -0,0 +1,5 @@
+Archive
+=======
+
+.. doxygenstruct:: Brush::Pop::Archive
+   :members:

docs/cpp_api/engine.rst

@@ -0,0 +1,9 @@
+Engine (and parameters)
+=======================
+
+.. doxygenstruct:: Brush::Parameters
+   :members:
+
+.. doxygenclass:: Brush::Engine
+   :members:
+

docs/cpp_api/evaluation.rst

@@ -0,0 +1,8 @@
+Evaluation
+==========
+
+.. doxygenclass:: Brush::Eval::Evaluation
+   :members:
+
+.. doxygenclass:: Brush::Eval::Scorer
+   :members:

docs/cpp_api/index.md

@@ -13,5 +13,11 @@ search_space
 program
 node
 nodetypes
+individual
+evaluation
+population
 variation
+selection
+archive
+engine
 ```

docs/cpp_api/individual.rst

@@ -0,0 +1,8 @@
+Individual and Fitness
+======================
+
+.. doxygenclass:: Brush::Pop::Individual
+   :members:
+
+.. doxygenstruct:: Brush::Fitness
+   :members:

docs/cpp_api/population.rst

@@ -0,0 +1,5 @@
+Population
+==========
+
+.. doxygenclass:: Brush::Pop::Population
+   :members:

docs/cpp_api/selection.rst

@@ -0,0 +1,14 @@
+Selection
+=========
+
+.. doxygenclass:: Brush::Sel::Selection
+   :members:
+
+.. doxygenclass:: Brush::Sel::SelectionOperator
+   :members:
+
+.. doxygenclass:: Brush::Sel::NSGA2
+   :members:
+
+.. doxygenclass:: Brush::Sel::Lexicase
+   :members:

docs/cpp_api/variation.rst

@@ -1,4 +1,8 @@
 Variation (Crossover/Mutation)
 ==============================
 
-.. doxygenfile:: variation.h
+.. doxygenclass:: Brush::Var::MutationBase
+   :members:
+
+.. doxygenclass:: Brush::Var::Variation
+   :members: