Clean up directory, update install docs, and fix readthedocs

.coveragerc

@@ -9,4 +9,6 @@ exclude_lines =
     def __repr__
     raise AssertionError
     raise NotImplementedError
-    if __name__ == .__main__.:
+    if __name__ == .__main__.:
+
+# Migrate to pyproject.toml when: https://github.com/nedbat/coveragepy/issues/664

.flake8

@@ -2,3 +2,5 @@
 exclude = .git,__pycache__
 per-file-ignores =
 	foreshadow/transformers/externals.py:F401
+
+# Migrate to pyproject.toml when: https://gitlab.com/pycqa/flake8/issues/428

.readthedocs.yml

@@ -0,0 +1,4 @@
+# .readthedocs.yml
+python:
+  version: 3.6
+  pip_install: true

doc/developers.rst

@@ -39,14 +39,14 @@ General Setup
          fi
          eval "$(pyenv virtualenv-init -)"
       
-      Restart your shell session for the changes to take effect and perform the following setup *in the root directory of the project*. This sets up a convenient virtualenv that automatically activates in the root of your project.
+      Restart your shell session for the changes to take effect and perform the following setup **in the root directory of the project**. This sets up a convenient virtualenv that automatically activates in the root of your project.
 
       .. code-block:: console
       
-         $ pyenv install 3.6.5
-         $ pyenv global 3.6.5
-         $ pyenv virtualenv -p python3.6 3.6.5 venv
-         $ pyenv local venv 3.6.5
+         $ pyenv install 3.6.8
+         $ pyenv global 3.6.8
+         $ pyenv virtualenv -p python3.6 3.6.8 venv
+         $ pyenv local venv 3.6.8
    
    3. Install poetry package manager
 
@@ -75,7 +75,7 @@ Prepare for Autosklearn install
 
       .. code-block:: console
       
-         (venv) $ brew install gcc # (or apt-get)
+         (venv) $ brew install gcc@5 # (or apt-get)
 
 Install all the packages and commit hooks
    When the project is installed through poetry both project requirements and development requirements are installed. Install commit-hooks using the `pre-commit`_ utility.
@@ -85,6 +85,8 @@ Install all the packages and commit hooks
    .. code-block:: console
    
       (venv) $ poetry install -v
+      (venv) $ export CC=gcc-5; export CXX=g++-5;
+      (venv) $ poetry install -E dev
       (venv) $ poetry run pre-commit install
 
 Making sure everything works

pyproject.toml

@@ -103,6 +103,7 @@ exclude = '''
 
 [tool.isort]
 known_first_party = 'foreshadow'
+known_third_party = ["category_encoders", "numpy", "pandas", "pytest", "scipy", "sklearn", "tpot"]
 multi_line_output = 3
 lines_after_imports = 2
 force_grid_wrap = 0

scripts/macos.sh

@@ -1,3 +1,4 @@
+# macos.sh
 
 echo Checking for Brew....
 
@@ -22,7 +23,7 @@ fi
 
 echo Installing neccesary python versions
 
-pyenv install -s 3.6.5
+pyenv install -s 3.6.8
 
 echo Installing pyenv-virtualenv
 
@@ -45,9 +46,9 @@ source ~/.bash_profile
 echo Setting up virtual environment
 
 if [[ -z "${DEPLOY_ENV}" ]]; then
-  pyenv local 3.6.5
+  pyenv local 3.6.8
   pyenv virtualenv venv
-  pyenv local venv 3.6.5
+  pyenv local venv 3.6.8
 else
   echo Already in virutalenv skipping setup...
 fi
@@ -67,14 +68,15 @@ else
   brew install gcc@5
 fi
 
+pyenv shell system
+curl -sSL https://raw.githubusercontent.com/sdispater/poetry/master/get-poetry.py | python
+pyenv shell --unset
+poetry install -v
+
+# Install optional dependencies
 export CC=gcc-5
 export CXX=g++-5
+poetry install -v -E dev
 
-if [ ! -f requirements.txt ]; then
-    echo "Could not find requirements will now exit"
-    exit 2
-fi
-
-pip install -r pre_requirements.txt
-pip install -r test_requirements.txt
-pip install -r requirements.txt
+# Run tests
+pytest