Fix Master/Dev

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: It's broken ¯\_(ツ)_/¯
+
+---
+
+**File**: org/iconic/file.java
+**Lines**:
+**Branch**:
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Additional context**
+Add any other context about the problem here. (eg. **Stacktraces**)

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,14 @@
+---
+name: Feature Request
+about: Improvements and TODOs
+
+---
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

CONTRIBUTING.md

@@ -0,0 +1,28 @@
+# How to contribute
+I'm really glad you're reading this.
+
+## Merges into higher branches
+This section is for merging your changes into the development branch (and later the master branch).
+Make sure you run every unit test in the suite before creating your pull request. We don't want any regressions. Once you've done this, you're good to make your very own Pull Request!
+
+### Creating a Pull Request (PR)
+- Merges from any branch into *development* and *master* must go through a GitHub PR.
+- Each PR must be assigned to me ([@scottwalkerau](https://github.com/scottwalkerau)) and have someone relevant as a reviewer. (Try not to add too many people as reviewers, at most 2)
+- If you cannot think of someone relevant, leave it blank and I will do it myself or assign someone.
+- Add any relevant comments for reviewers and myself on the PR. (There is a very small template for this)
+
+### Reviewing a PR
+- Read through every line changed so you understand **why** the PR is there.
+- Flag any overall questions you have as a **Comment**
+- Flag anything general you think should be done differently as **Request Changes** (For specific sections of the code, see below)
+- If you think **every file** is good, select **Approve**
+
+*NOTE:*
+- You can select individual lines for single comments or starting a review.
+- Selecting one of the three radio buttons applies the action to every file and doesn't reference a specific line.
+
+## Coding conventions
+I'm hoping you all adhere to these when writing your code. It will increase readability for your reviewers and maintainability later on...
+- No single line *if*, *while*, *for*, etc. structures without curly braces. Use curly braces.
+- Each method that does not call a subroutine should perform at most 1 function. (eg. A method to translate numbers to excel headers should not be buried within another function, it should be its own)
+- If your methods are too long, create a private subroutine.

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 Iconic
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,2 @@
+**Changes**
+Describe what this merge will change

api/src/main/java/org/iconic/ea/chromosome/Chromosome.java

@@ -1,5 +1,6 @@
 package org.iconic.ea.chromosome;
 
+import org.iconic.ea.data.DataManager;
 import org.iconic.ea.operator.evolutionary.mutation.Mutator;
 
 import java.util.LinkedList;
@@ -96,7 +97,7 @@ public void setChanged(boolean changed) {
      * @param input The input samples to evaluate
      * @return A list of outputs, one for each input sample
      */
-    public abstract List<T> evaluate(List<List<T>> input);
+    public abstract List<T> evaluate(final DataManager<T> input);
 
     /**
      * <p>

api/src/main/java/org/iconic/ea/chromosome/expression/ExpressionChromosome.java

@@ -1,9 +1,12 @@
 package org.iconic.ea.chromosome.expression;
 
+import lombok.extern.log4j.Log4j2;
 import org.iconic.ea.chromosome.Chromosome;
 import org.iconic.ea.chromosome.LinearChromosome;
-import org.iconic.ea.chromosome.graph.Node;
 import org.iconic.ea.chromosome.TreeChromosome;
+import org.iconic.ea.chromosome.graph.Node;
+import org.iconic.ea.data.DataManager;
+import org.iconic.ea.data.FeatureClass;
 
 import java.util.LinkedList;
 import java.util.List;
@@ -13,6 +16,7 @@
  * {@inheritDoc}
  * <p>A chromosome that encodes an expression tree.</p>
  */
+@Log4j2
 public class ExpressionChromosome<T> extends Chromosome<T> implements TreeChromosome<T>, LinearChromosome<Node<T>>, Cloneable {
     private List<Node<T>> genome;
     private Node<T> root;
@@ -91,11 +95,24 @@ private Node<T> recursivelyGenerateTree(Node<T> root) {
      * {@inheritDoc}
      */
     @Override
-    public List<T> evaluate(List<List<T>> input) {
+    public List<T> evaluate(final DataManager<T> dataManager) {
         List<T> calculatedValues = new LinkedList<>();
+        List<String> headers = dataManager.getSampleHeaders();
+        int numSamples = dataManager.getSampleSize();
+
+        for (int i = 0; i < numSamples; ++i) {
+            List<T> row = new LinkedList<>();
+
+            for (String header : headers) {
+                FeatureClass<Number> feature = dataManager.getDataset().get(header);
+
+                row.add(
+                        (T) feature.getSampleValue(i)
+                );
+            }
 
-        for (List<T> row : input) {
-            calculatedValues.add(getRoot().apply(row));
+            T output = getRoot().apply(row);
+            calculatedValues.add(output);
         }
 
         return calculatedValues;