diff --git a/.circleci/config.yml b/.circleci/config.yml
index f0bfeaa0..be226fcf 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -23,9 +23,6 @@ jobs:
             # Run tests
             sudo python setup.py test
 
-            # Install requirements
-            sudo pip3 install pylint==2.3.0
-
             # Run pylint tests
             pylint setup.py
             find surround/ -iname "*.py" | xargs pylint
diff --git a/examples/file-adapter/main.py b/examples/file-adapter/main.py
index a2353e8c..776bd8e8 100644
--- a/examples/file-adapter/main.py
+++ b/examples/file-adapter/main.py
@@ -13,8 +13,7 @@ def load_data(self, mode, config):
         input_path = prefix + self.assembler.config.get_path("Surround.Loader.input")
 
         with open(input_path) as csv_file:
-            state.rows = csv.DictReader(csv_file, delimiter=',', quotechar='"')
-            state.rows = [row for row in state.rows]
+            state.rows = list(csv.DictReader(csv_file, delimiter=',', quotechar='"'))
 
         return state
 
diff --git a/requirements.txt b/requirements.txt
index 7e0ccebe..972174f2 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,4 +3,5 @@ doit==0.31.1
 pandas==0.25.2
 numpy==1.17.3
 tornado==6.0.2
-google-cloud-storage==1.20.0
\ No newline at end of file
+google-cloud-storage==1.20.0
+pylint==2.4.3
\ No newline at end of file
diff --git a/surround/cli.py b/surround/cli.py
index d6c0eb7a..a79a094e 100644
--- a/surround/cli.py
+++ b/surround/cli.py
@@ -242,13 +242,11 @@ def parse_lint_args(parser, args, extra_args):
 
     linter = Linter()
     if args.list:
-        print(linter.dump_checks())
+        linter.dump_checks()
+    elif remote_cli.get_project_root(os.path.abspath(args.path)):
+        linter.check_project(args.path, extra_args, verbose=True)
     else:
-        errors, warnings = linter.check_project(PROJECTS, args.path)
-        for e in errors + warnings:
-            print(e)
-        if not errors and not warnings:
-            print("All checks passed")
+        print("error: .surround does not exist")
 
 def parse_run_args(parser, args, extra_args):
     """
diff --git a/surround/config.py b/surround/config.py
index 78f4e68e..b961bbb6 100644
--- a/surround/config.py
+++ b/surround/config.py
@@ -214,7 +214,7 @@ def __get_project_root(self, current_directory):
             parent_directory = os.path.dirname(current_directory)
             if current_directory in (home, parent_directory):
                 break
-            elif ".surround" in list_:
+            if ".surround" in list_:
                 return current_directory
             current_directory = parent_directory
 
diff --git a/surround/data/util.py b/surround/data/util.py
index ff81e2b0..9a955660 100644
--- a/surround/data/util.py
+++ b/surround/data/util.py
@@ -50,7 +50,8 @@ def prompt(question, required=True, answer_type=str, error_msg='Invalid answer,
         if answer == "" and required:
             print('This field is required!\n')
             continue
-        elif answer == "" and not required:
+
+        if answer == "" and not required:
             print()
             return default
 
diff --git a/surround/linter.py b/surround/linter.py
index 01165599..dc2dbb68 100644
--- a/surround/linter.py
+++ b/surround/linter.py
@@ -1,234 +1,6 @@
 import os
-import io
-from .stage import Filter, Estimator, Validator
-from .state import State
-from .assembler import Assembler
-
-
-class LinterStage(Filter):
-    """
-    Base class for a check in the Surround :class:`Linter`.
-
-    Provides functions for creating warnings and errors that are
-    found during the linting process.
-
-    Example::
-
-        class CheckExists(LinterStage):
-            def operate(self, data, config):
-                if not os.path.isdir(data.project_root):
-                    self.add_error(data, "Project doesn't exist!")
-    """
-
-    def __init__(self, key, description):
-        """
-        Constructor for a linter stage.
-
-        :param key: identifier of the linter stage
-        :type key: str
-        :param description: short description of the linter stage
-        :type description: str
-        """
-
-        self.key = key
-        self.description = description
-
-    def add_error(self, data, string):
-        """
-        Creates an error which will be displayed and stop the :class:`Linter`.
-
-        :param data: the data being passed between stages
-        :type data: :class:`ProjectData`
-        :param string: description of the error
-        :type string: str
-        """
-
-        data.errors.append("ERROR: %s_CHECK: %s" % (self.key, string))
-
-    def add_warning(self, data, string):
-        """
-        Creates a warning that will be displayed but the :class:`Linter` will continue.
-
-        :param data: the data being passed between stages
-        :type data: :class:`ProjectData`
-        :param string: description of the warning
-        :type string: str
-        """
-
-        data.warnings.append("WARNING: %s_CHECK: %s" % (self.key, string))
-
-    def operate(self, state, config):
-        """
-        Executed by the :class:`Linter`, performs the linting specific to this stage.
-        **Must** be implemented in extended versions of this class.
-
-        :param state: the data being passed between stages
-        :type state: :class:`ProjectData`
-        :param config: the configuration data for the linter
-        :type config: :class:`surround.config.Config`
-        """
-
-
-class CheckData(LinterStage):
-    """
-    :class:`Linter` stage that checks the data folder in the surround project for files.
-    """
-
-    def __init__(self):
-        LinterStage.__init__(self, "DATA", "Check data files")
-
-    def operate(self, state, config):
-        """
-        Executed by the :class:`Linter`, checks if there is any files in the project's data folder.
-        If there is none then a warning will be issued.
-
-        :param state: the data being passed between stages
-        :type state: :class:`surround.State`
-        :param config: the linter's configuration data
-        :type config: :class:`surround.config.Config`
-        """
-
-        path = os.path.join(state.project_root, "data")
-        if os.path.exists(path) and not os.listdir(path):
-            self.add_warning(state, "No data available, data directory is empty")
-
-
-class CheckFiles(LinterStage):
-    """
-    :class:`Linter` stage that checks the surround project files exist.
-    """
-
-    def __init__(self):
-        LinterStage.__init__(self, "FILES", "Check for Surround project files")
-
-    def operate(self, state, config):
-        """
-        Executed by the :class:`Linter`, checks if the files in the project structure exist.
-        Will create errors if required surround project files are missing in the root directory.
-
-        :param state: the data being passed between stages
-        :type state: :class:`surround.State`
-        :param config: the linter's configuation data
-        :type config: :class:`surround.config.Config`
-        """
-
-        for result in state.project_structure["new"]["files"] + state.project_structure["new"]["templates"]:
-            file_name = result[0]
-            path = os.path.join(
-                state.project_root,
-                file_name.format(project_name=state.project_name))
-            if not os.path.isfile(path):
-                self.add_error(state, "Path %s does not exist" % path)
-
-
-class CheckDirectories(LinterStage):
-    """
-    :class:`Linter` stage that checks the surround project directories exist.
-    """
-
-    def __init__(self):
-        LinterStage.__init__(
-            self, "DIRECTORIES",
-            "Check for validating Surround's directory structure")
-
-    def operate(self, state, config):
-        """
-        Executed by the :class:`Linter`, checks whether the project directories exist.
-        If the expected directories don't exist then errors will be created.
-
-        :param state: the data being passed between stages
-        :type state: :class:`surround.State`
-        :param config: the linter's configuration data
-        :type config: :class:`surround.config.Config`
-        """
-
-        for d in state.project_structure["new"]["dirs"]:
-            path = os.path.join(state.project_root,
-                                d.format(project_name=state.project_name))
-            if not os.path.isdir(path):
-                self.add_error(state, "Directory %s does not exist" % path)
-
-class LinterValidator(Validator):
-    """
-    Linter's validator stage, checks the data given in the ProjectData is valid.
-    """
-
-    def validate(self, state, config):
-        """
-        Executed by the :class:`Linter`, checks whther the paths contained are valid.
-
-        :param state: the data being passed between linter stages
-        :type state: :class:`surround.State`
-        :param config: the linter's configuration data
-        :type config: :class:`surround.config.Config`
-        """
-
-        if not isinstance(state.project_name, str):
-            state.errors.append("ERROR: PROJECT_CHECK: Project name is not a string")
-
-        if not isinstance(state.project_structure, dict):
-            state.errors.append("ERROR: PROJECT_CHECK: Project structure invalid format")
-
-        if not isinstance(state.project_root, str):
-            state.errors.append("ERROR: PROJECT_CHECK: Project root path is not a string")
-
-class Main(Estimator):
-    """
-    Class responsible for executing all of the :class:`LinterStage`'s in the Surround Linter.
-    """
-
-    def __init__(self, filters):
-        """
-        :param filters: list of stages in the linter
-        :type filters: list of :class:`LinterStage`
-        """
-
-        self.filters = filters
-
-    def estimate(self, state, config):
-        """
-        Execute each stage in the linter.
-        """
-
-        for filters in self.filters:
-            filters.operate(state, config)
-
-    def fit(self, state, config):
-        """
-        Should never be called.
-        """
-
-        print("No training implemented")
-
-
-class ProjectData(State):
-    """
-    Class containing the data passed between each :class:`LinterStage`.
-
-    **Attributes:**
-
-    - :attr:`project_structure` - expected file structure of the surround project (:class:`dict`)
-    - :attr:`project_root` - path to the root of the surround project (:class:`str`)
-    - :attr:`project_name` - name of the surround project (:class:`str`)
-    """
-
-    def __init__(self, project_structure, project_root, project_name):
-        """
-        Constructor for the ProjectData class.
-
-        :param project_structure: the expected file structure of the project
-        :type project_structure: dict
-        :param project_root: path to the root of the project
-        :type project_root: str
-        :param project_name: name of the project
-        :type project_name: str
-        """
-
-        super().__init__()
-        self.project_structure = project_structure
-        self.project_root = project_root
-        self.project_name = project_name
-
+from pathlib import Path
+from pylint.lint import Run
 
 class Linter():
     """
@@ -237,46 +9,50 @@ class Linter():
 
     This class is used by the Surround CLI to perform the linting of a project via the
     `lint` sub-command.
-
-    To add a new check to the linter, append an instance of it to the ``filters`` list.
     """
 
-    filters = [CheckDirectories(), CheckFiles(), CheckData()]
-
     def dump_checks(self):
         """
-        Dumps a list of the checks in this linter.
-        The list is compiled using the :attr:`LinterStage.key` and :attr:`LinterStage.description`
-        attributes of each check.
+        Dumps a list of the checks in this linter to the terminal.
 
         :return: formatted list of the checkers in the linter
         :rtype: str
         """
-        with io.StringIO() as s:
-            s.write("Checkers in Surround's linter\n")
-            s.write("=============================")
-            for stage in self.filters:
-                s.write("\n%s - %s" % (stage.key, stage.description))
-            output = s.getvalue()
-        return output
 
+        print("Checkers in Surround's linter")
+        print("=============================")
+
+        try:
+            Run(['--list-msgs-enabled'])
+        except SystemExit:
+            pass
 
-    def check_project(self, project, project_root=os.curdir):
+    def check_project(self, project_root=os.curdir, extra_args=None, verbose=False):
         """
-        Runs the linter against the project specified, returning any warnings/errors.
+        Runs the linter against the project specified, returning zero on success
 
-        :param project: expected file structure of the project
-        :type project: dict
         :param project_root: path to the root of the project (default: current directory)
         :type project_root: str
         :return: errors and warnings found (if any)
         :rtype: (list of error strings, list of warning strings)
         """
 
-        root = os.path.abspath(project_root)
-        project_name = os.path.basename(root)
-        data = ProjectData(project, root, project_name)
-        assembler = Assembler("Linting").set_validator(LinterValidator()).set_estimator(Main(self.filters))
-        assembler.init_assembler()
-        assembler.run(data)
-        return data.errors, data.warnings
+        ignore_dirs = ['scripts', 'spikes', 'notebooks']
+        args = [str(p) for p in Path(project_root).glob("**/*.py")]
+        args = [p for p in args if os.path.basename(os.path.dirname(p)) not in ignore_dirs]
+
+        if extra_args:
+            args.extend(extra_args)
+
+        disable_msgs = [
+            'missing-class-docstring',
+            'missing-function-docstring',
+            'abstract-method',
+            'attribute-defined-outside-init'
+        ]
+
+        for msg in disable_msgs:
+            args.append('--disable=%s' % msg)
+
+        result = Run(args, do_exit=False)
+        return result.linter.msg_status == 0
diff --git a/surround/remote/cli.py b/surround/remote/cli.py
index ef9b389e..a0d86695 100644
--- a/surround/remote/cli.py
+++ b/surround/remote/cli.py
@@ -49,7 +49,7 @@ def get_project_root(current_directory):
         parent_directory = os.path.dirname(current_directory)
         if current_directory in (home, parent_directory):
             break
-        elif ".surround" in list_:
+        if ".surround" in list_:
             return current_directory
         current_directory = parent_directory
 
diff --git a/surround/tests/cli/data_cli/create_test.py b/surround/tests/cli/data_cli/create_test.py
index bff57187..4c9d568d 100644
--- a/surround/tests/cli/data_cli/create_test.py
+++ b/surround/tests/cli/data_cli/create_test.py
@@ -40,7 +40,7 @@ def test_happy_path(self):
         std_input += "Test group description\n"
         std_input += "1\n"
 
-        process = subprocess.run(['surround', 'data', 'create', '-d', 'temp', '-o', 'temp.data.zip'], input=std_input, encoding='ascii')
+        process = subprocess.run(['surround', 'data', 'create', '-d', 'temp', '-o', 'temp.data.zip'], input=std_input, encoding='ascii', check=True)
 
         self.assertEqual(process.returncode, 0)
         self.assertTrue(os.path.exists("temp.data.zip"))
diff --git a/surround/tests/cli/project_cli/generated_project_test.py b/surround/tests/cli/project_cli/generated_project_test.py
index f0dc4939..61951a54 100644
--- a/surround/tests/cli/project_cli/generated_project_test.py
+++ b/surround/tests/cli/project_cli/generated_project_test.py
@@ -7,106 +7,106 @@
 class InitTest(unittest.TestCase):
 
     def setUp(self):
-        subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
 
         os.makedirs('remote')
         os.makedirs('temp/test_remote')
         Path('temp/test_remote/a.txt').touch()
 
     def test_run_from_subdir(self):
-        process = subprocess.run(['surround', 'run'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'run'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: not a surround project\n")
 
-        process = subprocess.run(['surround', 'run'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'run'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertIn("batch", process.stdout)
         self.assertIn("Run batch mode inside the container", process.stdout)
 
-        process = subprocess.run(['surround', 'run'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'run'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertIn("batch", process.stdout)
         self.assertIn("Run batch mode inside the container", process.stdout)
 
     def test_remote_from_subdir(self):
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: not a surround project\n")
 
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "info: no remote found\n")
 
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "info: no remote found\n")
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', '~'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', '~'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "test_remote\n")
 
     def test_pull_from_subdir(self):
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: not a surround project\n")
 
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named test_remote\n")
 
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named test_remote\n")
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
 
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "error: file does not exist\n")
 
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "error: file does not exist\n")
 
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertRegex(process.stdout, r'info: test_remote[/\\]{1,2}a.txt already exists\n')
 
     def test_push_from_subdir(self):
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: not a surround project\n")
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named test_remote\n")
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named test_remote\n")
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "error: file does not exist\n")
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.jpg'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "error: file does not exist\n")
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "info: a.txt pushed successfully\n")
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertRegex(process.stdout, r'info: remote[/\\]{1,2}temp[/\\]{1,2}a.txt already exists\n')
 
-        process = subprocess.run(['rm', 'test_remote/a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
-        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['rm', 'test_remote/a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
+        process = subprocess.run(['surround', 'store', 'pull', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "info: a.txt pulled successfully\n")
 
     def test_list_from_subdir(self):
-        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: not a surround project\n")
 
-        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named test_remote\n")
 
-        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named test_remote\n")
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'test_remote', '-u', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
 
-        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'push', 'test_remote', '-k', 'a.txt'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "info: a.txt pushed successfully\n")
 
-        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "a.txt\n")
 
-        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp')
+        process = subprocess.run(['surround', 'store', 'list', 'test_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp/temp', check=True)
         self.assertEqual(process.stdout, "a.txt\n")
 
     def tearDown(self):
diff --git a/surround/tests/cli/project_cli/init_test.py b/surround/tests/cli/project_cli/init_test.py
index e884bad8..6bd73c0a 100644
--- a/surround/tests/cli/project_cli/init_test.py
+++ b/surround/tests/cli/project_cli/init_test.py
@@ -9,13 +9,13 @@
 class InitTest(unittest.TestCase):
 
     def test_happy_path(self):
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertRegex(process.stdout, 'info: project created at .*temp\\n')
 
         is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp"))
         self.assertEqual(is_temp, True)
 
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: directory ./temp already exists\n")
 
     def tearDown(self):
diff --git a/surround/tests/cli/project_cli/linter_test.py b/surround/tests/cli/project_cli/linter_test.py
index 8d47ad5b..3acf0128 100644
--- a/surround/tests/cli/project_cli/linter_test.py
+++ b/surround/tests/cli/project_cli/linter_test.py
@@ -28,6 +28,7 @@ def test_lint_valid_project(self):
 
         # Linter should be able to locate .surround folder if project valid
         self.assertNotIn(".surround does not exist", output, "Current directory not a Surround project")
+        self.assertIn("Your code has been rated at 10.00/10", output, "The generated code is not lint error free!")
 
     def test_lint_invalid_project(self):
         """
diff --git a/surround/tests/cli/remote_cli/add_test.py b/surround/tests/cli/remote_cli/add_test.py
index 1e264214..9654ecd2 100644
--- a/surround/tests/cli/remote_cli/add_test.py
+++ b/surround/tests/cli/remote_cli/add_test.py
@@ -11,7 +11,7 @@
 class AddTest(unittest.TestCase):
 
     def test_rejecting_path(self):
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertIn("info: project created at", process.stdout)
         self.assertIn("temp", process.stdout)
 
@@ -25,7 +25,7 @@ def test_rejecting_path(self):
         os.chdir("../")
         self.assertEqual(result, "error: no remote named data")
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'data', '-u', os.getcwd()], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'data', '-u', os.getcwd()], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
 
         os.chdir("temp")
         result = local_remote.add('data', 'temp.jpg')
@@ -33,14 +33,14 @@ def test_rejecting_path(self):
         self.assertEqual(result, "error: temp.jpg not found.")
 
     def test_happy_path(self):
-        process = subprocess.run(['surround', 'init', os.getcwd(), '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', os.getcwd(), '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertIn("info: project created at", process.stdout)
         self.assertIn("temp", process.stdout)
 
         is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp"))
         self.assertEqual(is_temp, True)
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'data', '-u', os.getcwd()], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'data', '-u', os.getcwd()], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
 
         local_remote = Local()
 
diff --git a/surround/tests/cli/remote_cli/list_test.py b/surround/tests/cli/remote_cli/list_test.py
index 97c3f989..6042b788 100644
--- a/surround/tests/cli/remote_cli/list_test.py
+++ b/surround/tests/cli/remote_cli/list_test.py
@@ -9,29 +9,29 @@
 class ListTest(unittest.TestCase):
 
     def test_rejecting_path(self):
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertRegex(process.stdout, 'info: project created at .*temp\\n')
 
         is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp"))
         self.assertEqual(is_temp, True)
 
-        process = subprocess.run(['surround', 'store', 'list', 'temp'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'list', 'temp'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "error: no remote named temp\n")
 
     def test_happy_path(self):
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertRegex(process.stdout, 'info: project created at .*temp\\n')
 
         is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp"))
         self.assertEqual(is_temp, True)
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'temp_remote', '-u', os.getcwd() + '/temp'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'temp_remote', '-u', os.getcwd() + '/temp'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, '')
 
-        process = subprocess.run(['surround', 'store', 'remote', '-v'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-v'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertRegex(process.stdout, 'temp_remote: .*temp\\n')
 
-        process = subprocess.run(['surround', 'store', 'list', 'temp_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'list', 'temp_remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertListEqual(sorted(str(process.stdout).splitlines()), sorted('config.yaml\n__main__.py\n__init__.py\nfile_system_runner.py\nweb_runner.py\nstages'.splitlines()))
 
     def tearDown(self):
diff --git a/surround/tests/cli/remote_cli/remote_test.py b/surround/tests/cli/remote_cli/remote_test.py
index 3d8d29e6..9a453153 100644
--- a/surround/tests/cli/remote_cli/remote_test.py
+++ b/surround/tests/cli/remote_cli/remote_test.py
@@ -9,31 +9,31 @@
 class RemoteTest(unittest.TestCase):
 
     def test_remote(self):
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertEqual(process.stdout, "error: not a surround project\n")
 
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertRegex(process.stdout, 'info: project created at .*temp\\n')
 
         is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp"))
         self.assertEqual(is_temp, True)
 
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "info: no remote found\n")
 
     def test_remote_add(self):
-        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE)
+        process = subprocess.run(['surround', 'init', './', '-p', 'temp', '-d', 'temp', '-w', 'no'], encoding='utf-8', stdout=subprocess.PIPE, check=True)
         self.assertRegex(process.stdout, 'info: project created at .*temp\\n')
 
         is_temp = os.path.isdir(os.path.join(os.getcwd() + "/temp"))
         self.assertEqual(is_temp, True)
 
-        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'data', '-u', os.getcwd()], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-a', '-n', 'data', '-u', os.getcwd()], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
 
-        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "data\n")
 
-        process = subprocess.run(['surround', 'store', 'remote', '-v'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp')
+        process = subprocess.run(['surround', 'store', 'remote', '-v'], encoding='utf-8', stdout=subprocess.PIPE, cwd='temp', check=True)
         self.assertEqual(process.stdout, "data: " + os.getcwd() + "\n")
 
     def tearDown(self):
diff --git a/templates/new/assembler_state.py.txt b/templates/new/assembler_state.py.txt
index f1fda47f..bf8ff61d 100644
--- a/templates/new/assembler_state.py.txt
+++ b/templates/new/assembler_state.py.txt
@@ -1,3 +1,8 @@
+"""
+This module defines the state object that is passed between each stage
+in the pipeline.
+"""
+
 from surround import State
 
 class AssemblerState(State):
diff --git a/templates/new/baseline.py.txt b/templates/new/baseline.py.txt
index 5d729a29..5ee8a144 100644
--- a/templates/new/baseline.py.txt
+++ b/templates/new/baseline.py.txt
@@ -1,3 +1,7 @@
+"""
+This module defines the baseline estimator in the pipeline.
+"""
+
 import logging
 from surround import Estimator
 
diff --git a/templates/new/batch_main.py.txt b/templates/new/batch_main.py.txt
index 5cca5372..8c800212 100644
--- a/templates/new/batch_main.py.txt
+++ b/templates/new/batch_main.py.txt
@@ -1,15 +1,19 @@
+"""
+Main entry-point for the Surround project.
+Runners and assemblies are defined in here.
+"""
+
 import os
 import argparse
 from surround import Surround, Assembler, Config
-from surround.experiment import ExperimentWriter
-from stages import Baseline, InputValidator, ReportGenerator
-from file_system_runner import FileSystemRunner
+from .stages import Baseline, InputValidator, ReportGenerator
+from .file_system_runner import FileSystemRunner
 
-runners = [
+RUNNERS = [
     FileSystemRunner()
 ]
 
-assemblies = [
+ASSEMBLIES = [
     Assembler("baseline")
         .set_validator(InputValidator())
         .set_estimator(Baseline())
@@ -21,19 +25,42 @@ def main():
     default_runner = config.get_path('runner.default')
     default_assembler = config.get_path('assembler.default')
 
-    parser = argparse.ArgumentParser(prog='{project_name}', description="Surround mode(s) available to run this module")
-    parser.set_defaults(experiment=True)
-    
-    parser.add_argument('-r', '--runner', help="Runner for the Assembler (index or name)", default=default_runner if default_runner is not None else "0")
-    parser.add_argument('-a', '--assembler', help="Assembler to run (index or name)", default=default_assembler if default_assembler is not None else "0")
-    parser.add_argument('-ne', '--no-experiment', dest='experiment', help="Don't consider this run an experiment", action="store_false")
+    parser = argparse.ArgumentParser(
+        prog='{project_name}',
+        description="Surround mode(s) available to run this module")
+
+    parser.add_argument(
+        '-r',
+        '--runner',
+        help="Runner for the Assembler (index or name)",
+        default=default_runner if default_runner is not None else "0")
+    parser.add_argument(
+        '-a',
+        '--assembler',
+        help="Assembler to run (index or name)",
+        default=default_assembler if default_assembler is not None else "0")
+    parser.add_argument(
+        '-ne',
+        '--no-experiment',
+        dest='experiment',
+        help="Don't consider this run an experiment",
+        action="store_false")
+    parser.add_argument(
+        '--status',
+        help="Display information about the project such as available RUNNERS and assemblers",
+        action="store_true")
     parser.add_argument('-n', '--note', help="Add a note to the experiment", type=str)
     parser.add_argument('--mode', help="Mode to run (train, batch)", default="batch")
-    parser.add_argument('--status', help="Display information about the project such as available runners and assemblers", action="store_true")
 
     args = parser.parse_args()
 
-    surround = Surround(runners, assemblies, "{project_name}", "{project_description}", os.path.dirname(os.path.dirname(__file__)))
+    surround = Surround(
+        RUNNERS,
+        ASSEMBLIES,
+        "{project_name}",
+        "{project_description}",
+        os.path.dirname(os.path.dirname(__file__))
+    )
 
     if args.status:
         surround.show_info()
diff --git a/templates/new/dodo.py.txt b/templates/new/dodo.py.txt
index 5e74af7e..7bbcffba 100644
--- a/templates/new/dodo.py.txt
+++ b/templates/new/dodo.py.txt
@@ -1,3 +1,7 @@
+"""
+This module defines the tasks that can be executed using `surround run [task name]`
+"""
+
 import os
 import sys
 import subprocess
@@ -46,15 +50,35 @@ def task_remove():
 
 def task_dev():
     """Run the main task for the project"""
+    cmd = [
+        "docker",
+        "run",
+        "--volume",
+        "\"%s/\":/app" % CONFIG["volume_path"],
+        "%s" % IMAGE,
+        "python3 -m %s %s" % (PACKAGE_PATH, "%(args)s")
+    ]
     return {{
-        'actions': ["docker run --volume \"%s/\":/app %s python3 -m %s %s" % (CONFIG["volume_path"], IMAGE, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_interactive():
     """Run the Docker container in interactive mode"""
     def run():
-        process = subprocess.Popen(['docker', 'run', '-it', '--rm', '-w', '/app', '--volume', '%s/:/app' % CONFIG['volume_path'], IMAGE, 'bash'], encoding='utf-8')
+        cmd = [
+            'docker',
+            'run',
+            '-it',
+            '--rm',
+            '-w',
+            '/app',
+            '--volume',
+            '%s/:/app' % CONFIG['volume_path'],
+            IMAGE,
+            'bash'
+        ]
+        process = subprocess.Popen(cmd, encoding='utf-8')
         process.wait()
 
     return {{
@@ -79,19 +103,30 @@ def task_train():
     # Inject user's name and email into the env variables of the container
     user_name = global_config.get_path("user.name")
     user_email = global_config.get_path("user.email")
-    experiment_args = "-e \"SURROUND_USER_NAME=%s\" -e \"SURROUND_USER_EMAIL=%s\"" % (user_name, user_email)
+    experiment_args = "-e \"SURROUND_USER_NAME=%s\" " % user_name
+    experiment_args += "-e \"SURROUND_USER_EMAIL=%s\"" % user_email
 
     experiment_path = os.path.join(str(Path.home()), ".experiments")
     experiment_volume_path = generate_docker_volume_path(experiment_path)
 
     # Ensure experiments will work if using a local storage location (not in the cloud)
     if os.path.join(experiment_path, "local") == global_config.get_path("experiment.url"):
-        experiment_args += " --volume \"%s\":/experiments -e \"SURROUND_EXPERIMENT_URL=/experiments/local\"" % experiment_volume_path
+        experiment_args += " --volume \"%s\":/experiments " % experiment_volume_path
+        experiment_args += "-e \"SURROUND_EXPERIMENT_URL=/experiments/local\""
     else:
-        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % global_config.get_path("experiment.url")
+        current_url = global_config.get_path("experiment.url")
+        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % current_url
+
+    cmd = [
+        "docker run %s" % experiment_args,
+        "--volume \"%s\":/app/output" % output_path,
+        "--volume \"%s\":/app/input" % data_path,
+        IMAGE,
+        "python3 -m {project_name} --mode train --experiment %(args)s"
+    ]
 
     return {{
-        'actions': ["docker run %s --volume \"%s\":/app/output --volume \"%s\":/app/input %s python3 -m {project_name} --mode train %s" % (experiment_args, output_path, data_path, IMAGE, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
@@ -105,58 +140,111 @@ def task_batch():
     # Inject user's name and email into the env variables of the container
     user_name = global_config.get_path("user.name")
     user_email = global_config.get_path("user.email")
-    experiment_args = "-e \"SURROUND_USER_NAME=%s\" -e \"SURROUND_USER_EMAIL=%s\"" % (user_name, user_email)
+    experiment_args = "-e \"SURROUND_USER_NAME=%s\" " % user_name
+    experiment_args += "-e \"SURROUND_USER_EMAIL=%s\"" % user_email
 
     experiment_path = os.path.join(str(Path.home()), ".experiments")
     experiment_volume_path = generate_docker_volume_path(experiment_path)
 
     # Ensure experiments will work if using a local storage location (not in the cloud)
     if os.path.join(experiment_path, "local") == global_config.get_path("experiment.url"):
-        experiment_args += " --volume \"%s\":/experiments -e \"SURROUND_EXPERIMENT_URL=/experiments/local\"" % experiment_volume_path
+        experiment_args += " --volume \"%s\":/experiments " % experiment_volume_path
+        experiment_args += "-e \"SURROUND_EXPERIMENT_URL=/experiments/local\""
     else:
-        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % global_config.get_path("experiment.url")
+        current_url = global_config.get_path("experiment.url")
+        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % current_url
+
+    cmd = [
+        "docker run %s" % experiment_args,
+        "--volume \"%s\":/app/output" % output_path,
+        "--volume \"%s\":/app/input" % data_path,
+        IMAGE,
+        "python3 -m {project_name} --mode batch %(args)s"
+    ]
 
     return {{
-        'actions': ["docker run %s --volume \"%s\":/app/output --volume \"%s\":/app/input %s python3 -m {project_name} --mode batch %s" % (experiment_args, output_path, data_path, IMAGE, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_train_local():
     """Run training mode locally"""
+    cmd = [
+        sys.executable,
+        "-m %s" % PACKAGE_PATH,
+        "--mode train",
+        "%(args)s"
+    ]
+
     return {{
         'basename': 'trainLocal',
-        'actions': ["%s -m %s --mode train %s" % (sys.executable, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_batch_local():
     """Run batch mode locally"""
+    cmd = [
+        sys.executable,
+        "-m %s" % PACKAGE_PATH,
+        "--mode batch",
+        "%(args)s"
+    ]
+
     return {{
         'basename': 'batchLocal',
-        'actions': ["%s -m %s --mode batch %s" % (sys.executable, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_jupyter():
-    command = "pip install -r /app/requirements.txt; mkdir /etc/ipython; echo \"c.InteractiveShellApp.extensions.append('autoreload')\nc.InteractiveShellApp.exec_lines = ['%autoreload 2', 'import sys', 'sys.path.append(\\'../\\')']\" > /etc/ipython/ipython_config.py; /usr/local/bin/start.sh jupyter notebook --NotebookApp.token=''"
-    
+    # Allow for auto reload to be enabled and import modules from project package
+    ipython_config = "c.InteractiveShellApp.extensions.append('autoreload')\n"
+    ipython_config += "c.InteractiveShellApp.exec_lines = "
+    ipython_config += "['%autoreload 2', 'import sys', 'sys.path.append(\\'../\\')']"
+
+    # Build the command for running jupyter
+    command = [
+        "pip install -r /app/requirements.txt",
+        "mkdir /etc/ipython",
+        "echo \"%s\" > /etc/ipython/ipython_config.py" % ipython_config,
+        "/usr/local/bin/start.sh jupyter notebook --NotebookApp.token=''"
+    ]
+    command = "; ".join(command)
+
     def run_command():
-        process = subprocess.Popen([
-            "docker", 
-            "run",
-            "--rm",
-            "--name", "{project_name}_surround_notebook",
-            "--volume", "%s:/app" % CONFIG['volume_path'], 
-            "-p", "55910:8888",
-            "--user", "root",
-            "-w", "/app",
-            "jupyter/base-notebook:307ad2bb5fce", 
-            "bash",  "-c", command], stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding='utf-8')
+        process = subprocess.Popen(
+            [
+                "docker",
+                "run",
+                "--rm",
+                "--name",
+                "{project_name}_surround_notebook",
+                "--volume",
+                "%s:/app" % CONFIG['volume_path'],
+                "-p",
+                "55910:8888",
+                "--user",
+                "root",
+                "-w",
+                "/app",
+                "jupyter/base-notebook:307ad2bb5fce",
+                "bash",
+                "-c",
+                command
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            encoding='utf-8')
 
         print("Starting jupyter notbook server...\n")
-        
+
         # Get the IP address of the container, otherwise use localhost
-        ip_process = subprocess.Popen(['docker-machine', 'ip'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding='utf-8')
+        ip_process = subprocess.Popen(
+            ['docker-machine', 'ip'],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            encoding='utf-8')
         ip_process.wait()
 
         ip_output = ip_process.stdout.readline().rstrip()
@@ -168,14 +256,22 @@ def task_jupyter():
 
         # Wait for the notebook server to be up before loading browser
         while True:
-            line = process.stderr.readline().rstrip() 
+            line = process.stderr.readline().rstrip()
             if line and 'Serving notebooks from local directory' in line:
                 break
-            elif process.poll():
+
+            if process.poll():
                 print("Failed to start the server, check if its not running somewhere else!")
 
                 # Stop any containers that might be running
-                process = subprocess.Popen(['docker', 'stop', '{project_name}_surround_notebook'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                process = subprocess.Popen(
+                    [
+                        'docker',
+                        'stop',
+                        '{project_name}_surround_notebook'
+                    ],
+                    stdout=subprocess.PIPE,
+                    stderr=subprocess.PIPE)
                 process.wait()
                 return
 
@@ -191,9 +287,16 @@ def task_jupyter():
             pass
         finally:
             print("Closing server...")
-            process = subprocess.Popen(['docker', 'stop', '{project_name}_surround_notebook'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            process = subprocess.Popen(
+                [
+                    'docker',
+                    'stop',
+                    '{project_name}_surround_notebook'
+                ],
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE)
             process.wait()
-    
+
     return {{
         'actions': [run_command]
     }}
diff --git a/templates/new/file_system_runner.py.txt b/templates/new/file_system_runner.py.txt
index c8a6a15b..529bd901 100644
--- a/templates/new/file_system_runner.py.txt
+++ b/templates/new/file_system_runner.py.txt
@@ -1,6 +1,10 @@
+"""
+This module is responsible for loading the data and running the pipeline.
+"""
+
 import logging
-from surround import Runner, RunMode
-from stages import AssemblerState
+from surround import Runner
+from .stages import AssemblerState
 
 logging.basicConfig(level=logging.INFO)
 
diff --git a/templates/new/init.py.txt b/templates/new/init.py.txt
index cc2c489b..4cfc0097 100644
--- a/templates/new/init.py.txt
+++ b/templates/new/init.py.txt
@@ -1,3 +1,7 @@
+"""
+This file is required for the project to be considered a python package.
+"""
+
 import os
 import sys
 
diff --git a/templates/new/input_validator.py.txt b/templates/new/input_validator.py.txt
index da4ef782..91bf58a5 100644
--- a/templates/new/input_validator.py.txt
+++ b/templates/new/input_validator.py.txt
@@ -1,3 +1,9 @@
+"""
+This module defines the input validator which is executed
+before all other stages in the pipeline and checks whether
+the data contained in the State object is valid.
+"""
+
 from surround import Validator
 
 class InputValidator(Validator):
diff --git a/templates/new/report_generator.py.txt b/templates/new/report_generator.py.txt
index d7f78330..6ba69d41 100644
--- a/templates/new/report_generator.py.txt
+++ b/templates/new/report_generator.py.txt
@@ -1,7 +1,13 @@
+"""
+This module generates the HTML report which uses the
+template in the templates folder. This report can then
+be viewed in the experimentation web application.
+"""
+
 import os
-import surround
 import tornado.template
 
+import surround
 from surround.experiment.util import get_surround_config
 
 class ReportGenerator(surround.Visualiser):
@@ -11,7 +17,11 @@ class ReportGenerator(surround.Visualiser):
         self.global_config = get_surround_config()
 
     def visualise(self, state, config):
-        results_page = self.results_template.generate(config=config, state=state, global_config=self.global_config, surround_version=surround.__version__)
+        results_page = self.results_template.generate(
+            config=config,
+            state=state,
+            global_config=self.global_config,
+            surround_version=surround.__version__)
 
-        with open(os.path.join(config["output_path"], "results.html"), "wb+") as f:
-            f.write(results_page)
+        with open(os.path.join(config["output_path"], "results.html"), "wb+") as out:
+            out.write(results_page)
diff --git a/templates/new/stages_init.py.txt b/templates/new/stages_init.py.txt
index 3441b98f..338ffde3 100644
--- a/templates/new/stages_init.py.txt
+++ b/templates/new/stages_init.py.txt
@@ -1,3 +1,8 @@
+"""
+Import each stage you create in this file so they can be imported
+directly from the stages package e.g. `from .stages import Baseline`.
+"""
+
 from .baseline import Baseline
 from .input_validator import InputValidator
 from .assembler_state import AssemblerState
diff --git a/templates/new/web_dodo.py.txt b/templates/new/web_dodo.py.txt
index 89c09171..fa3fbe16 100644
--- a/templates/new/web_dodo.py.txt
+++ b/templates/new/web_dodo.py.txt
@@ -1,3 +1,7 @@
+"""
+This module defines the tasks that can be executed using `surround run [task name]`
+"""
+
 import os
 import sys
 import subprocess
@@ -46,15 +50,38 @@ def task_remove():
 
 def task_dev():
     """Run the main task for the project"""
+    cmd = [
+        "docker",
+        "run",
+        "-p 8080:8080",
+        "--volume",
+        "\"%s/\":/app" % CONFIG["volume_path"],
+        "%s" % IMAGE,
+        "python3 -m %s %s" % (PACKAGE_PATH, "%(args)s")
+    ]
     return {{
-        'actions': ["docker run -p 8080:8080 --volume \"%s/\":/app %s python3 -m %s %s" % (CONFIG["volume_path"], IMAGE, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_interactive():
     """Run the Docker container in interactive mode"""
     def run():
-        process = subprocess.Popen(['docker', 'run', '-p', '8080:8080', '-it', '--rm', '-w', '/app', '--volume', '%s/:/app' % CONFIG['volume_path'], IMAGE, 'bash'], encoding='utf-8')
+        cmd = [
+            'docker',
+            'run',
+            '-p',
+            '8080:8080',
+            '-it',
+            '--rm',
+            '-w',
+            '/app',
+            '--volume',
+            '%s/:/app' % CONFIG['volume_path'],
+            IMAGE,
+            'bash'
+        ]
+        process = subprocess.Popen(cmd, encoding='utf-8')
         process.wait()
 
     return {{
@@ -63,8 +90,17 @@ def task_interactive():
 
 def task_prod():
     """Run the main task inside a Docker container for use in production """
+    cmd = [
+        "docker",
+        "run",
+        "-p 8080:8080",
+        IMAGE,
+        "python3 -m %s" % PACKAGE_PATH,
+        "%(args)s"
+    ]
+
     return {{
-        'actions': ["docker run -p 8080:8080 %s python3 -m %s %s" % (IMAGE, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'task_dep': ["build"],
         'params': PARAMS
     }}
@@ -79,19 +115,30 @@ def task_train():
     # Inject user's name and email into the env variables of the container
     user_name = global_config.get_path("user.name")
     user_email = global_config.get_path("user.email")
-    experiment_args = "-e \"SURROUND_USER_NAME=%s\" -e \"SURROUND_USER_EMAIL=%s\"" % (user_name, user_email)
+    experiment_args = "-e \"SURROUND_USER_NAME=%s\" " % user_name
+    experiment_args += "-e \"SURROUND_USER_EMAIL=%s\"" % user_email
 
     experiment_path = os.path.join(str(Path.home()), ".experiments")
     experiment_volume_path = generate_docker_volume_path(experiment_path)
 
     # Ensure experiments will work if using a local storage location (not in the cloud)
     if os.path.join(experiment_path, "local") == global_config.get_path("experiment.url"):
-        experiment_args += " --volume \"%s\":/experiments -e \"SURROUND_EXPERIMENT_URL=/experiments/local\"" % experiment_volume_path
+        experiment_args += " --volume \"%s\":/experiments " % experiment_volume_path
+        experiment_args += "-e \"SURROUND_EXPERIMENT_URL=/experiments/local\""
     else:
-        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % global_config.get_path("experiment.url")
+        current_url = global_config.get_path("experiment.url")
+        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % current_url
+
+    cmd = [
+        "docker run %s" % experiment_args,
+        "--volume \"%s\":/app/output" % output_path,
+        "--volume \"%s\":/app/input" % data_path,
+        "%s" % IMAGE,
+        "python3 -m {project_name} --mode train %(args)s"
+    ]
 
     return {{
-        'actions': ["docker run %s --volume \"%s\":/app/output --volume \"%s\":/app/input %s python3 -m {project_name} --mode train  --runner 1 %s" % (experiment_args, output_path, data_path, IMAGE, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
@@ -105,74 +152,147 @@ def task_batch():
     # Inject user's name and email into the env variables of the container
     user_name = global_config.get_path("user.name")
     user_email = global_config.get_path("user.email")
-    experiment_args = "-e \"SURROUND_USER_NAME=%s\" -e \"SURROUND_USER_EMAIL=%s\"" % (user_name, user_email)
+    experiment_args = "-e \"SURROUND_USER_NAME=%s\" " % user_name
+    experiment_args += "-e \"SURROUND_USER_EMAIL=%s\"" % user_email
 
     experiment_path = os.path.join(str(Path.home()), ".experiments")
     experiment_volume_path = generate_docker_volume_path(experiment_path)
 
     # Ensure experiments will work if using a local storage location (not in the cloud)
     if os.path.join(experiment_path, "local") == global_config.get_path("experiment.url"):
-        experiment_args += " --volume \"%s\":/experiments -e \"SURROUND_EXPERIMENT_URL=/experiments/local\"" % experiment_volume_path
+        experiment_args += " --volume \"%s\":/experiments " % experiment_volume_path
+        experiment_args += "-e \"SURROUND_EXPERIMENT_URL=/experiments/local\""
     else:
-        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % global_config.get_path("experiment.url")
+        current_url = global_config.get_path("experiment.url")
+        experiment_args += " -e \"SURROUND_EXPERIMENT_URL=%s\"" % current_url
+
+    cmd = [
+        "docker run %s" % experiment_args,
+        "--volume \"%s\":/app/output" % output_path,
+        "--volume \"%s\":/app/input" % data_path,
+        "%s" % IMAGE,
+        "python3 -m {project_name} --mode batch %(args)s"
+    ]
 
     return {{
-        'actions': ["docker run %s --volume \"%s\":/app/output --volume \"%s\":/app/input %s python3 -m {project_name} --mode batch --runner 1 %s" % (experiment_args, output_path, data_path, IMAGE, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_train_local():
     """Run training mode locally"""
+    cmd = [
+        sys.executable,
+        "-m %s" % PACKAGE_PATH,
+        "--mode train",
+        "--runner 1",
+        "%(args)s"
+    ]
+
     return {{
         'basename': 'trainLocal',
-        'actions': ["%s -m %s --mode train --runner 1 %s" % (sys.executable, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_batch_local():
     """Run batch mode locally"""
+    cmd = [
+        sys.executable,
+        "-m %s" % PACKAGE_PATH,
+        "--mode batch",
+        "--runner 1",
+        "%(args)s"
+    ]
+
     return {{
         'basename': 'batchLocal',
-        'actions': ["%s -m %s --mode batch --runner 1 %s" % (sys.executable, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_web():
     """Run web mode inside the container"""
+    cmd = [
+        "docker",
+        "run",
+        "-p",
+        "8080:8080",
+        IMAGE,
+        "python3 -m %s" % PACKAGE_PATH,
+        "--runner WebRunner",
+        "%(args)s"
+    ]
+
     return {{
-        'actions': ["docker run -p 8080:8080 %s python3 -m %s --runner WebRunner %s" % (IMAGE, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 def task_web_local():
     """Run web mode locally"""
+    cmd = [
+        sys.executable,
+        "-m %s" % PACKAGE_PATH,
+        "--runner WebRunner",
+        "%(args)s"
+    ]
+
     return {{
         'basename': 'webLocal',
-        'actions': ["%s -m %s --runner WebRunner %s" % (sys.executable, PACKAGE_PATH, "%(args)s")],
+        'actions': [" ".join(cmd)],
         'params': PARAMS
     }}
 
 
 def task_jupyter():
-    command = "pip install -r /app/requirements.txt; mkdir /etc/ipython; echo \"c.InteractiveShellApp.extensions.append('autoreload')\nc.InteractiveShellApp.exec_lines = ['%autoreload 2', 'import sys', 'sys.path.append(\\'../\\')']\" > /etc/ipython/ipython_config.py; /usr/local/bin/start.sh jupyter notebook --NotebookApp.token=''"
-    
+    # Allow for auto reload to be enabled and import modules from project package
+    ipython_config = "c.InteractiveShellApp.extensions.append('autoreload')\n"
+    ipython_config += "c.InteractiveShellApp.exec_lines = "
+    ipython_config += "['%autoreload 2', 'import sys', 'sys.path.append(\\'../\\')']"
+
+    # Build the command for running jupyter
+    command = [
+        "pip install -r /app/requirements.txt",
+        "mkdir /etc/ipython",
+        "echo \"%s\" > /etc/ipython/ipython_config.py" % ipython_config,
+        "/usr/local/bin/start.sh jupyter notebook --NotebookApp.token=''"
+    ]
+    command = "; ".join(command)
+
     def run_command():
-        process = subprocess.Popen([
-            "docker", 
-            "run",
-            "--rm",
-            "--name", "{project_name}_surround_notebook",
-            "--volume", "%s:/app" % CONFIG['volume_path'], 
-            "-p", "55910:8888",
-            "--user", "root",
-            "-w", "/app",
-            "jupyter/base-notebook:307ad2bb5fce", 
-            "bash",  "-c", command], stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding='utf-8')
+        process = subprocess.Popen(
+            [
+                "docker",
+                "run",
+                "--rm",
+                "--name",
+                "{project_name}_surround_notebook",
+                "--volume",
+                "%s:/app" % CONFIG['volume_path'],
+                "-p",
+                "55910:8888",
+                "--user",
+                "root",
+                "-w",
+                "/app",
+                "jupyter/base-notebook:307ad2bb5fce",
+                "bash",
+                "-c",
+                command
+            ],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            encoding='utf-8')
 
         print("Starting jupyter notbook server...\n")
-        
+
         # Get the IP address of the container, otherwise use localhost
-        ip_process = subprocess.Popen(['docker-machine', 'ip'], stdout=subprocess.PIPE, stderr=subprocess.PIPE, encoding='utf-8')
+        ip_process = subprocess.Popen(
+            ['docker-machine', 'ip'],
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            encoding='utf-8')
         ip_process.wait()
 
         ip_output = ip_process.stdout.readline().rstrip()
@@ -184,14 +304,22 @@ def task_jupyter():
 
         # Wait for the notebook server to be up before loading browser
         while True:
-            line = process.stderr.readline().rstrip() 
+            line = process.stderr.readline().rstrip()
             if line and 'Serving notebooks from local directory' in line:
                 break
-            elif process.poll():
+
+            if process.poll():
                 print("Failed to start the server, please try again!")
 
                 # Stop any containers that might be running
-                process = subprocess.Popen(['docker', 'stop', '{project_name}_surround_notebook'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+                process = subprocess.Popen(
+                    [
+                        'docker',
+                        'stop',
+                        '{project_name}_surround_notebook'
+                    ],
+                    stdout=subprocess.PIPE,
+                    stderr=subprocess.PIPE)
                 process.wait()
                 return
 
@@ -207,9 +335,16 @@ def task_jupyter():
             pass
         finally:
             print("Closing server...")
-            process = subprocess.Popen(['docker', 'stop', '{project_name}_surround_notebook'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            process = subprocess.Popen(
+                [
+                    'docker',
+                    'stop',
+                    '{project_name}_surround_notebook'
+                ],
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE)
             process.wait()
-    
+
     return {{
         'actions': [run_command]
     }}
diff --git a/templates/new/web_main.py.txt b/templates/new/web_main.py.txt
index f4e2e9ca..7de7cb84 100644
--- a/templates/new/web_main.py.txt
+++ b/templates/new/web_main.py.txt
@@ -1,17 +1,21 @@
+"""
+Main entry-point for the Surround project.
+Runners and ASSEMBLIES are defined in here.
+"""
+
 import os
 import argparse
 from surround import Surround, Assembler, Config
-from surround.experiment import ExperimentWriter
-from stages import Baseline, InputValidator, ReportGenerator
-from file_system_runner import FileSystemRunner
-from web_runner import WebRunner
+from .stages import Baseline, InputValidator, ReportGenerator
+from .file_system_runner import FileSystemRunner
+from .web_runner import WebRunner
 
-runners = [
+RUNNERS = [
     WebRunner(),
     FileSystemRunner()
 ]
 
-assemblies = [
+ASSEMBLIES = [
     Assembler("baseline")
         .set_validator(InputValidator())
         .set_estimator(Baseline())
@@ -23,19 +27,42 @@ def main():
     default_runner = config.get_path('runner.default')
     default_assembler = config.get_path('assembler.default')
 
-    parser = argparse.ArgumentParser(prog='{project_name}', description="Surround mode(s) available to run this module")
-    parser.set_defaults(experiment=True)
-    
-    parser.add_argument('-r', '--runner', help="Runner for the Assembler (index or name)", default=default_runner if default_runner is not None else "0")
-    parser.add_argument('-a', '--assembler', help="Assembler to run (index or name)", default=default_assembler if default_assembler is not None else "0")
-    parser.add_argument('-ne', '--no-experiment', dest='experiment', help="Don't consider this run an experiment", action="store_false")
+    parser = argparse.ArgumentParser(
+        prog='{project_name}',
+        description="Surround mode(s) available to run this module")
+
+    parser.add_argument(
+        '-r',
+        '--runner',
+        help="Runner for the Assembler (index or name)",
+        default=default_runner if default_runner is not None else "0")
+    parser.add_argument(
+        '-a',
+        '--assembler',
+        help="Assembler to run (index or name)",
+        default=default_assembler if default_assembler is not None else "0")
+    parser.add_argument(
+        '-ne',
+        '--no-experiment',
+        dest='experiment',
+        help="Don't consider this run an experiment",
+        action="store_false")
+    parser.add_argument(
+        '--status',
+        help="Display information about the project such as available RUNNERS and assemblers",
+        action="store_true")
     parser.add_argument('-n', '--note', help="Add a note to the experiment", type=str)
     parser.add_argument('--mode', help="Mode to run (train, batch)", default="batch")
-    parser.add_argument('--status', help="Display information about the project such as available runners and assemblers", action="store_true")
 
     args = parser.parse_args()
 
-    surround = Surround(runners, assemblies, "{project_name}", "{project_description}", os.path.dirname(os.path.dirname(__file__)))
+    surround = Surround(
+        RUNNERS,
+        ASSEMBLIES,
+        "{project_name}",
+        "{project_description}",
+        os.path.dirname(os.path.dirname(__file__))
+    )
 
     if args.status:
         surround.show_info()
diff --git a/templates/new/web_runner.py.txt b/templates/new/web_runner.py.txt
index b9ab2e3a..b7c75e66 100644
--- a/templates/new/web_runner.py.txt
+++ b/templates/new/web_runner.py.txt
@@ -1,3 +1,7 @@
+"""
+This module is responsible for serving the pipeline via HTTP endpoints.
+"""
+
 import json
 import logging
 import tornado.httpserver
@@ -5,7 +9,7 @@ import tornado.ioloop
 import tornado.options
 import tornado.web
 from surround import Runner, RunMode
-from stages import AssemblerState
+from .stages import AssemblerState
 
 logging.basicConfig(level=logging.INFO)
 
@@ -35,20 +39,16 @@ class Application(tornado.web.Application):
 class EstimateHandler(tornado.web.RequestHandler):
     def initialize(self, assembler):
         self.assembler = assembler
-        self.data = AssemblerState()
 
     def post(self):
         req_data = json.loads(self.request.body)
 
-        # Clean output_data on every request
-        self.data.output_data = ""
-
-        # Prepare input_date for the assembler
-        self.data.input_data = req_data["message"]
+        # Prepare input_data for the assembler
+        data = AssemblerState(req_data["message"])
 
         # Execute assembler
-        self.assembler.run(self.data)
-        logging.info("Message: %s", self.data.output_data)
+        self.assembler.run(data)
+        logging.info("Message: %s", data.output_data)
 
 
 class InfoHandler(tornado.web.RequestHandler):
@@ -56,4 +56,4 @@ class InfoHandler(tornado.web.RequestHandler):
         self.assembler = assembler
 
     def get(self):
-      self.write({{'version': '0.0.1'}})
+        self.write({{'version': '0.0.1'}})