diff --git a/.gitignore b/.gitignore
index 0a4262b7..50a2aeb0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,10 +1,7 @@
 # Ignore cache files
 __pycache__/
 *.py[cod]
-output_npz_for_testing
-!experiments/original_inputs/output_npz_for_testing
 
 src/vesuvio_analysis/core_functions/bootstrap_ws/
-running_times.txt
 figures/
-mvesuvio/tests/analysis/system/data/input/sample_input
+tests/analysis/data/inputs/sample_test/output_files/
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index eb898661..95d392de 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,15 +8,15 @@ repos:
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
-        exclude: 'mvesuvio/vesuvio_analysis/scribles|mvesuvio/experiments/original_inputs|mvesuvio/original_inputs.py|unpackaged'
+        exclude: 'unpackaged|legacy'
         types: ['python']
       - id: check-added-large-files
         args: ['--maxkb=4096']
-        exclude: 'mvesuvio/experiments/original_inputs|unpackaged'
+        exclude: 'unpackaged|legacy'
 
   - repo: https://github.com/PyCQA/flake8.git
     rev: 6.1.0
     hooks:
       - id: flake8
         args: ['--config', 'config.flake8']
-        exclude: 'mvesuvio/vesuvio_analysis/scribles|mvesuvio/experiments/original_inputs|mvesuvio/original_inputs.py|unpackaged'
+        exclude: 'unpackaged|legacy'
diff --git a/environment.yml b/environment.yml
index 803de10b..1a14c970 100644
--- a/environment.yml
+++ b/environment.yml
@@ -10,9 +10,10 @@ dependencies:
   - conda-wrappers
   - pre-commit==2.15 #review this
   - coverage
-  - mantid==6.8
+  - mantid
   - matplotlib
   - iminuit
   - h5py
   - mock
+  - pytest
   - jacobi==0.4.2 #pinned until newer versions functionality confirmed
diff --git a/pyproject.toml b/pyproject.toml
index 954e776d..61096068 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -40,7 +40,7 @@ tests_require = [
 "Bug Tracker" = "https://github.com/mantidproject/vesuvio/issues"
 
 [project.entry-points]
-console_scripts = { mvesuvio = "mvesuvio.scripts:main" }
+console_scripts = { mvesuvio = "mvesuvio.main:main" }
 
 [tool.setuptools.packages.find]
 where = ["src"]
@@ -51,19 +51,23 @@ namespaces = false
 "mvesuvio.config" = ["*.properties"]
 
 [tool.pytest.ini_options]
-pythonpath = ["."]
-testpaths = ["tests/system_tests"]
+pythonpath = [
+    ".",
+    "./src"
+]
+testpaths = ["tests"]
 filterwarnings = ["error"]
 
 [tool.coverage.report]
 include = [
     "*/src/mvesuvio/*",
+    "*/tools/calibration_scripts/*"
 ]
 
 omit = [
     "*tests*",
     "*unpackaged*",
-    "*legacy"
+    "*legacy*"
 ]
 
 fail_under = 0
diff --git a/src/mvesuvio/__init__.py b/src/mvesuvio/__init__.py
index e93fa026..a7af0ba3 100644
--- a/src/mvesuvio/__init__.py
+++ b/src/mvesuvio/__init__.py
@@ -9,7 +9,7 @@
 from mvesuvio._version import __version__
 __project_url__ = "https://github.com/mantidproject/vesuvio"
 
-from mvesuvio.scripts import main
+from mvesuvio.main import main
 
 class ArgInputs:
     def __init__(self, command):
diff --git a/src/mvesuvio/fit_in_yspace.py b/src/mvesuvio/analysis_fitting.py
similarity index 100%
rename from src/mvesuvio/fit_in_yspace.py
rename to src/mvesuvio/analysis_fitting.py
diff --git a/src/mvesuvio/analysis_functions.py b/src/mvesuvio/analysis_reduction.py
similarity index 99%
rename from src/mvesuvio/analysis_functions.py
rename to src/mvesuvio/analysis_reduction.py
index b56c5000..aec5ce7a 100644
--- a/src/mvesuvio/analysis_functions.py
+++ b/src/mvesuvio/analysis_reduction.py
@@ -3,7 +3,7 @@
 from mantid.simpleapi import *
 from scipy import optimize
 
-from .fit_in_yspace import passDataIntoWS, replaceZerosWithNCP
+from .analysis_fitting import passDataIntoWS, replaceZerosWithNCP
 
 # Format print output of arrays
 np.set_printoptions(suppress=True, precision=4, linewidth=100, threshold=sys.maxsize)
diff --git a/src/mvesuvio/procedures.py b/src/mvesuvio/analysis_routines.py
similarity index 99%
rename from src/mvesuvio/procedures.py
rename to src/mvesuvio/analysis_routines.py
index e50e412e..aa9283f8 100644
--- a/src/mvesuvio/procedures.py
+++ b/src/mvesuvio/analysis_routines.py
@@ -1,4 +1,4 @@
-from .analysis_functions import iterativeFitForDataReduction
+from .analysis_reduction import iterativeFitForDataReduction
 from mantid.api import AnalysisDataService
 from mantid.simpleapi import CreateEmptyTableWorkspace
 import numpy as np
diff --git a/src/mvesuvio/scripts/__init__.py b/src/mvesuvio/main/__init__.py
similarity index 96%
rename from src/mvesuvio/scripts/__init__.py
rename to src/mvesuvio/main/__init__.py
index 723ac21d..7a53562b 100644
--- a/src/mvesuvio/scripts/__init__.py
+++ b/src/mvesuvio/main/__init__.py
@@ -2,7 +2,7 @@
 """
 import argparse
 from os import environ, path
-from mvesuvio.scripts import handle_config
+from mvesuvio.util import handle_config
 
 
 def main(manual_args=None):
@@ -87,7 +87,7 @@ def __run_analysis(yes_to_all):
     environ["MANTIDPROPERTIES"] = path.join(
         handle_config.VESUVIO_CONFIG_PATH, "Mantid.user.properties"
     )
-    from mvesuvio import analysis_runner
+    from mvesuvio.main import analysis_runner
 
     analysis_runner.run(yes_to_all)
 
diff --git a/src/mvesuvio/analysis_runner.py b/src/mvesuvio/main/analysis_runner.py
similarity index 91%
rename from src/mvesuvio/analysis_runner.py
rename to src/mvesuvio/main/analysis_runner.py
index 309068c4..44997ad6 100644
--- a/src/mvesuvio/analysis_runner.py
+++ b/src/mvesuvio/main/analysis_runner.py
@@ -2,8 +2,8 @@
 from pathlib import Path
 import importlib
 import sys
-from mvesuvio.run_script import runScript
-from mvesuvio.scripts import handle_config
+from mvesuvio.run_routine import runRoutine
+from mvesuvio.util import handle_config
 
 
 def run(yes_to_all=False):
@@ -21,7 +21,7 @@ def run(yes_to_all=False):
     yFitIC = ai.YSpaceFitInitialConditions
     userCtr = ai.UserScriptControls
 
-    runScript(
+    runRoutine(
         userCtr,
         wsBackIC,
         wsFrontIC,
diff --git a/src/mvesuvio/run_script.py b/src/mvesuvio/run_routine.py
similarity index 95%
rename from src/mvesuvio/run_script.py
rename to src/mvesuvio/run_routine.py
index 7af71e0a..65a84282 100644
--- a/src/mvesuvio/run_script.py
+++ b/src/mvesuvio/run_routine.py
@@ -1,10 +1,10 @@
-from mvesuvio.ICHelpers import (
+from mvesuvio.util.process_inputs import (
     buildFinalWSName,
     completeICFromInputs,
     completeYFitIC,
 )
-from mvesuvio.fit_in_yspace import fitInYSpaceProcedure
-from mvesuvio.procedures import (
+from mvesuvio.analysis_fitting import fitInYSpaceProcedure
+from mvesuvio.analysis_routines import (
     runIndependentIterativeProcedure,
     runJointBackAndForwardProcedure,
     runPreProcToEstHRatio,
@@ -13,7 +13,7 @@
 )
 from mantid.api import mtd
 
-def runScript(
+def runRoutine(
     userCtr,
     wsBackIC,
     wsFrontIC,
diff --git a/tests/analysis/data/outputs/__init__.py b/src/mvesuvio/util/__init__.py
similarity index 100%
rename from tests/analysis/data/outputs/__init__.py
rename to src/mvesuvio/util/__init__.py
diff --git a/src/mvesuvio/scripts/handle_config.py b/src/mvesuvio/util/handle_config.py
similarity index 100%
rename from src/mvesuvio/scripts/handle_config.py
rename to src/mvesuvio/util/handle_config.py
diff --git a/src/mvesuvio/ICHelpers.py b/src/mvesuvio/util/process_inputs.py
similarity index 99%
rename from src/mvesuvio/ICHelpers.py
rename to src/mvesuvio/util/process_inputs.py
index 3be984bb..0a6d7411 100644
--- a/src/mvesuvio/ICHelpers.py
+++ b/src/mvesuvio/util/process_inputs.py
@@ -1,6 +1,6 @@
 from mantid.simpleapi import Load, LoadVesuvio, SaveNexus, DeleteWorkspace
 from pathlib import Path
-from mvesuvio.scripts import handle_config
+from mvesuvio.util import handle_config
 from mantid.kernel import logger
 import ntpath
 
diff --git a/tests/analysis/data/benchmark/__init__.py b/tests/analysis/data/benchmark/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/analysis/data/outputs/stored_spec_144-182_iter_3_GC_MS.npz b/tests/analysis/data/benchmark/stored_spec_144-182_iter_3_GC_MS.npz
similarity index 100%
rename from tests/analysis/data/outputs/stored_spec_144-182_iter_3_GC_MS.npz
rename to tests/analysis/data/benchmark/stored_spec_144-182_iter_3_GC_MS.npz
diff --git a/tests/analysis/data/outputs/stored_yspace_fit.npz b/tests/analysis/data/benchmark/stored_yspace_fit.npz
similarity index 100%
rename from tests/analysis/data/outputs/stored_yspace_fit.npz
rename to tests/analysis/data/benchmark/stored_yspace_fit.npz
diff --git a/tests/analysis/data/outputs/stored_yspace_fit_GC.npz b/tests/analysis/data/benchmark/stored_yspace_fit_GC.npz
similarity index 100%
rename from tests/analysis/data/outputs/stored_yspace_fit_GC.npz
rename to tests/analysis/data/benchmark/stored_yspace_fit_GC.npz
diff --git a/tests/analysis/data/inputs/sample_test/output_files/spec_144-182_iter_3_GC_MS.npz b/tests/analysis/data/inputs/sample_test/output_files/spec_144-182_iter_3_GC_MS.npz
deleted file mode 100644
index feadfcb0..00000000
Binary files a/tests/analysis/data/inputs/sample_test/output_files/spec_144-182_iter_3_GC_MS.npz and /dev/null differ
diff --git a/tests/analysis/system/test_analysis.py b/tests/analysis/system/test_analysis.py
index 8c29826e..185599af 100644
--- a/tests/analysis/system/test_analysis.py
+++ b/tests/analysis/system/test_analysis.py
@@ -2,8 +2,8 @@
 import numpy as np
 import numpy.testing as nptest
 from pathlib import Path
-from mvesuvio.run_script import runScript
-from mvesuvio.scripts import handle_config
+from mvesuvio.run_routine import runRoutine
+from mvesuvio.util import handle_config
 from tests.analysis.data.inputs.sample_test import (
     LoadVesuvioBackParameters,
     LoadVesuvioFrontParameters,
@@ -13,10 +13,9 @@
     UserScriptControls,
 )
 import mvesuvio
-sample_test_dir = Path(__file__).absolute().parent.parent / "data" / "inputs" / "sample_test.py" 
 mvesuvio.set_config(
     ip_folder=str(Path(handle_config.VESUVIO_PACKAGE_PATH).joinpath("config", "ip_files")),
-    inputs_file=str(sample_test_dir)
+    inputs_file=str(Path(__file__).absolute().parent.parent / "data" / "inputs" / "sample_test.py")
 )
 
 ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder"))
@@ -40,7 +39,7 @@ def get_current_result(cls):
 
     @classmethod
     def _run(cls):
-        scattRes, yfitRes = runScript(
+        scattRes, yfitRes = runRoutine(
             UserScriptControls(),
             LoadVesuvioBackParameters(ipFilesPath),
             LoadVesuvioFrontParameters(ipFilesPath),
@@ -60,9 +59,9 @@ def _run(cls):
 
     @classmethod
     def _load_benchmark_results(cls):
-        testPath = Path(__file__).absolute().parent.parent / "data" / "outputs"
+        benchmarkPath = Path(__file__).absolute().parent.parent / "data" / "benchmark"
         benchmarkResults = np.load(
-            str(testPath / "stored_spec_144-182_iter_3_GC_MS.npz")
+            str(benchmarkPath / "stored_spec_144-182_iter_3_GC_MS.npz")
         )
         AnalysisRunner._benchmarkResults = benchmarkResults
 
diff --git a/tests/analysis/system/test_yspace_fit.py b/tests/analysis/system/test_yspace_fit.py
index 4d714dba..fea1ad79 100644
--- a/tests/analysis/system/test_yspace_fit.py
+++ b/tests/analysis/system/test_yspace_fit.py
@@ -1,11 +1,11 @@
-from mvesuvio.run_script import runScript
+from mvesuvio.run_routine import runRoutine 
 from mantid.simpleapi import Load
 from mantid.api import AnalysisDataService
 from pathlib import Path
 import numpy as np
 import unittest
 import numpy.testing as nptest
-from mvesuvio.scripts import handle_config
+from mvesuvio.util import handle_config
 from tests.analysis.data.inputs.sample_test import (
     LoadVesuvioBackParameters,
     LoadVesuvioFrontParameters,
@@ -14,10 +14,9 @@
     YSpaceFitInitialConditions,
 )
 import mvesuvio
-sample_test_dir = Path(__file__).absolute().parent.parent / "data" / "inputs" / "sample_test.py" 
 mvesuvio.set_config(
     ip_folder=str(Path(handle_config.VESUVIO_PACKAGE_PATH).joinpath("config", "ip_files")),
-    inputs_file=str(sample_test_dir)
+    inputs_file=str(Path(__file__).absolute().parent.parent / "data" / "inputs" / "sample_test.py")
 )
 np.set_printoptions(suppress=True, precision=8, linewidth=150)
 
@@ -47,7 +46,7 @@ class AnalysisRunner:
     _benchmarkResults = None
     _currentResults = None
     _input_data_path = Path(__file__).absolute().parent.parent / "data" / "inputs"
-    _output_data_path = Path(__file__).absolute().parent.parent / "data" / "outputs"
+    _benchmark_path = Path(__file__).absolute().parent.parent / "data" / "benchmark"
     _workspaces_loaded = False
 
     @classmethod
@@ -86,14 +85,14 @@ def _load_workspaces(cls):
     def _run(cls):
         cls.load_workspaces()   # Load data to skip run of routine
 
-        scattRes, yfitRes = runScript(
+        scattRes, yfitRes = runRoutine(
             userCtr, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, True
         )
         cls._currentResults = yfitRes
 
     @classmethod
     def _load_benchmark_results(cls):
-        cls._benchmarkResults = np.load(str(cls._output_data_path / "stored_yspace_fit.npz"))
+        cls._benchmarkResults = np.load(str(cls._benchmark_path / "stored_yspace_fit.npz"))
 
 
 class TestSymSumYSpace(unittest.TestCase):
diff --git a/tests/analysis/system/test_yspace_fit_GC.py b/tests/analysis/system/test_yspace_fit_GC.py
index 10bf805b..06520725 100644
--- a/tests/analysis/system/test_yspace_fit_GC.py
+++ b/tests/analysis/system/test_yspace_fit_GC.py
@@ -1,11 +1,11 @@
-from mvesuvio.run_script import runScript
+from mvesuvio.run_routine import runRoutine
 from mantid.simpleapi import Load
 from mantid.api import AnalysisDataService
 from pathlib import Path
 import numpy as np
 import unittest
 import numpy.testing as nptest
-from mvesuvio.scripts import handle_config
+from mvesuvio.util import handle_config
 from tests.analysis.data.inputs.sample_test import (
     LoadVesuvioBackParameters,
     LoadVesuvioFrontParameters,
@@ -14,10 +14,9 @@
     YSpaceFitInitialConditions,
 )
 import mvesuvio
-sample_test_dir = Path(__file__).absolute().parent.parent / "data" / "inputs" / "sample_test.py" 
 mvesuvio.set_config(
     ip_folder=str(Path(handle_config.VESUVIO_PACKAGE_PATH).joinpath("config", "ip_files")),
-    inputs_file=str(sample_test_dir)
+    inputs_file=str(Path(__file__).absolute().parent.parent / "data" / "inputs" / "sample_test.py")
 )
 np.set_printoptions(suppress=True, precision=8, linewidth=150)
 
@@ -48,7 +47,7 @@ class AnalysisRunner:
     _benchmarkResults = None
     _currentResults = None
     _input_data_path = Path(__file__).absolute().parent.parent / "data" / "inputs"
-    _output_data_path = Path(__file__).absolute().parent.parent / "data" / "outputs"
+    _benchmark_path = Path(__file__).absolute().parent.parent / "data" / "benchmark"
     _workspaces_loaded = False
 
     @classmethod
@@ -87,7 +86,7 @@ def _load_workspaces(cls):
     def _run(cls):
         cls.load_workspaces()
         
-        scattRes, yfitRes = runScript(
+        scattRes, yfitRes = runRoutine(
             userCtr, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, True
         )
         cls._currentResults = yfitRes
@@ -95,7 +94,7 @@ def _run(cls):
     @classmethod
     def _load_benchmark_results(cls):
         cls._benchmarkResults = np.load(
-            str(cls._output_data_path / "stored_yspace_fit_GC.npz")
+            str(cls._benchmark_path / "stored_yspace_fit_GC.npz")
         )
 
 
diff --git a/tests/analysis/unit/test_analysis_functions.py b/tests/analysis/unit/test_analysis_functions.py
index bf898b58..08283e8b 100644
--- a/tests/analysis/unit/test_analysis_functions.py
+++ b/tests/analysis/unit/test_analysis_functions.py
@@ -1,6 +1,6 @@
 import unittest
 from mock import MagicMock
-from mvesuvio.analysis_functions import extractWS
+from mvesuvio.analysis_reduction import extractWS
 
 
 class TestAnalysisFunctions(unittest.TestCase):
diff --git a/tests/analysis/system/tests_IC.py b/unpackaged/test_bootstrap/tests_IC.py
similarity index 100%
rename from tests/analysis/system/tests_IC.py
rename to unpackaged/test_bootstrap/tests_IC.py