From 9aa4dfbda6fa6efc19d6722063f3d38ebcb6e77c Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Fri, 10 Nov 2023 15:05:35 +0000
Subject: [PATCH 1/8] add default config file

---
 EVSVesuvio/config/vesuvio.user.properties | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 EVSVesuvio/config/vesuvio.user.properties

diff --git a/EVSVesuvio/config/vesuvio.user.properties b/EVSVesuvio/config/vesuvio.user.properties
new file mode 100644
index 00000000..66768fd7
--- /dev/null
+++ b/EVSVesuvio/config/vesuvio.user.properties
@@ -0,0 +1 @@
+# properties that suit your particular installation.
\ No newline at end of file

From 3de46ad225dddd67f27aef580ad19fff5c5ca524 Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Fri, 10 Nov 2023 15:18:18 +0000
Subject: [PATCH 2/8] add config dir creation

---
 EVSVesuvio/scripts/__init__.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/EVSVesuvio/scripts/__init__.py b/EVSVesuvio/scripts/__init__.py
index dd64ce45..99787b72 100644
--- a/EVSVesuvio/scripts/__init__.py
+++ b/EVSVesuvio/scripts/__init__.py
@@ -1,9 +1,20 @@
 """Package defining top-level application
 and entry points.
 """
+import os
+from shutil import copyfile
 
 
 def main():
-    """Placeholder.
-    """
-    print("TEST_VESUVIO_LAUNCH")
+    make_config_dir()
+
+
+def make_config_dir():
+    config_dir = os.path.join(os.path.expanduser("~"), '.mvesuvio')
+    if not os.path.isdir(config_dir):
+        os.mkdir(config_dir)
+        copyfile('EVSVesuvio/config/vesuvio.user.properties', f'{config_dir}/vesuvio.user.properties')
+
+
+if __name__ == '__main__':
+    main()

From 292adc51647dc6332835ecd4177f243616b8a86c Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Fri, 10 Nov 2023 17:12:28 +0000
Subject: [PATCH 3/8] add ability to set up config and caching

---
 EVSVesuvio/config/vesuvio.user.properties |  4 +-
 EVSVesuvio/scripts/__init__.py            | 68 +++++++++++++++++++++--
 2 files changed, 65 insertions(+), 7 deletions(-)

diff --git a/EVSVesuvio/config/vesuvio.user.properties b/EVSVesuvio/config/vesuvio.user.properties
index 66768fd7..912419db 100644
--- a/EVSVesuvio/config/vesuvio.user.properties
+++ b/EVSVesuvio/config/vesuvio.user.properties
@@ -1 +1,3 @@
-# properties that suit your particular installation.
\ No newline at end of file
+# properties that suit your particular installation.
+caching.location =
+caching.experiment =
\ No newline at end of file
diff --git a/EVSVesuvio/scripts/__init__.py b/EVSVesuvio/scripts/__init__.py
index 99787b72..af648857 100644
--- a/EVSVesuvio/scripts/__init__.py
+++ b/EVSVesuvio/scripts/__init__.py
@@ -1,20 +1,76 @@
 """Package defining top-level application
 and entry points.
 """
+import argparse
 import os
 from shutil import copyfile
 
+VESUVIO_CONFIG_FILE = "vesuvio.user.properties"
+
 
 def main():
-    make_config_dir()
+    parser = __set_up_parser()
+    args = parser.parse_args()
+    config_dir = os.path.join(os.path.expanduser("~"), '.mvesuvio')
+    cache_dir = config_dir if not args.set_cache else args.set_cache
+    experiment = "default" if not args.set_experiment else args.set_experiment
 
+    if __setup_config_dir(config_dir):
+        __set_config_vars(config_dir, {'caching.location': cache_dir,
+                                       'caching.experiment': experiment})
+    __setup_expr_dir(cache_dir, experiment)
 
-def make_config_dir():
-    config_dir = os.path.join(os.path.expanduser("~"), '.mvesuvio')
-    if not os.path.isdir(config_dir):
-        os.mkdir(config_dir)
-        copyfile('EVSVesuvio/config/vesuvio.user.properties', f'{config_dir}/vesuvio.user.properties')
+
+def __set_up_parser():
+    parser = argparse.ArgumentParser(description="Package to analyse Vesuvio instrument data")
+    parser.add_argument("--set-cache", "-c", help="set the cache directory", default="", type=str)
+    parser.add_argument("--set-experiment", "-e", help="set the current experiment", default="", type=str)
+    return parser
+
+
+def __setup_config_dir(config_dir):
+    success = __mk_dir('config', config_dir)
+    if success:
+        copyfile('EVSVesuvio/config/vesuvio.user.properties', f'{config_dir}/{VESUVIO_CONFIG_FILE}')
+    return success
+
+
+def __setup_expr_dir(cache_dir, experiment):
+    expr_path = os.path.join(cache_dir, "experiments", experiment)
+    __mk_dir('experiment', expr_path)
+
+
+def __mk_dir(type, path):
+    success = False
+    if not os.path.isdir(path):
+        try:
+            os.makedirs(path)
+            success = True
+        except:
+            print(f'Unable to make {type} directory at location: {path}')
+    return success
+
+
+def __set_config_vars(config_dir, var_dict):
+    file_path = f'{config_dir}/{VESUVIO_CONFIG_FILE}'
+    with open(file_path, 'r') as file:
+        lines = file.readlines()
+
+    updated_lines = []
+    for line in lines:
+        match = False
+        for var in var_dict:
+            if line.startswith(var):
+                updated_lines.append(f'{var}={var_dict[var]}\n')
+                match = True
+                break
+        if not match:
+            updated_lines.append(line)
+
+    with open(file_path, 'w') as file:
+        file.writelines(updated_lines)
 
 
 if __name__ == '__main__':
+    print("test")
     main()

From 6a39a0edaa0513d71c892f843af25a707e910da5 Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Fri, 10 Nov 2023 19:21:27 +0000
Subject: [PATCH 4/8] ammend script to work with cache dir

---
 EVSVesuvio/original_inputs.py                 | 11 +++---
 EVSVesuvio/scripts/__init__.py                | 32 +++------------
 EVSVesuvio/scripts/handle_config.py           | 39 +++++++++++++++++++
 .../core_functions/ICHelpers.py               |  5 +--
 .../core_functions/bootstrap_analysis.py      |  5 ---
 5 files changed, 52 insertions(+), 40 deletions(-)
 create mode 100644 EVSVesuvio/scripts/handle_config.py

diff --git a/EVSVesuvio/original_inputs.py b/EVSVesuvio/original_inputs.py
index cde26a90..5a7cf58e 100644
--- a/EVSVesuvio/original_inputs.py
+++ b/EVSVesuvio/original_inputs.py
@@ -1,13 +1,14 @@
 import time
 import numpy as np
 from pathlib import Path
-from vesuvio_analysis.core_functions.bootstrap import runBootstrap
-from vesuvio_analysis.core_functions.bootstrap_analysis import runAnalysisOfStoredBootstrap
-from vesuvio_analysis.core_functions.run_script import runScript
+from EVSVesuvio.vesuvio_analysis.core_functions.bootstrap import runBootstrap
+from EVSVesuvio.vesuvio_analysis.core_functions.bootstrap_analysis import runAnalysisOfStoredBootstrap
+from EVSVesuvio.vesuvio_analysis.core_functions.run_script import runScript
 from mantid.api import AnalysisDataService
+from EVSVesuvio.scripts import handle_config
 
-scriptName =  Path(__file__).name.split(".")[0]  # Take out .py
-experimentPath = Path(__file__).absolute().parent / "experiments" / scriptName  # Path to the repository
+scriptName =  handle_config.read_config_var('caching.experiment')
+experimentsPath = Path(handle_config.read_config_var('caching.location')) / "experiments" / scriptName # Path to the repository
 ipFilesPath = Path(__file__).absolute().parent / "vesuvio_analysis" / "ip_files"
 
 
diff --git a/EVSVesuvio/scripts/__init__.py b/EVSVesuvio/scripts/__init__.py
index af648857..85a14ea5 100644
--- a/EVSVesuvio/scripts/__init__.py
+++ b/EVSVesuvio/scripts/__init__.py
@@ -1,22 +1,20 @@
-"""Package defining top-level application
-and entry points.
+"""Package defining entry points.
 """
 import argparse
 import os
 from shutil import copyfile
-
-VESUVIO_CONFIG_FILE = "vesuvio.user.properties"
+from EVSVesuvio.scripts import handle_config
 
 
 def main():
     parser = __set_up_parser()
     args = parser.parse_args()
-    config_dir = os.path.join(os.path.expanduser("~"), '.mvesuvio')
+    config_dir = handle_config.VESUVIO_CONFIG_PATH
     cache_dir = config_dir if not args.set_cache else args.set_cache
     experiment = "default" if not args.set_experiment else args.set_experiment
 
     if __setup_config_dir(config_dir):
-        __set_config_vars(config_dir, {'caching.location': cache_dir,
+        handle_config.set_config_vars({'caching.location': cache_dir,
                                        'caching.experiment': experiment})
     __setup_expr_dir(cache_dir, experiment)
 
@@ -31,7 +29,7 @@ def __set_up_parser():
 def __setup_config_dir(config_dir):
     success = __mk_dir('config', config_dir)
     if success:
-        copyfile('EVSVesuvio/config/vesuvio.user.properties', f'{config_dir}/{VESUVIO_CONFIG_FILE}')
+        copyfile('EVSVesuvio/config/vesuvio.user.properties', f'{config_dir}/{handle_config.VESUVIO_CONFIG_FILE}')
     return success
 
 
@@ -51,26 +49,6 @@ def __mk_dir(type, path):
     return success
 
 
-def __set_config_vars(config_dir, var_dict):
-    file_path = f'{config_dir}/{VESUVIO_CONFIG_FILE}'
-    with open(file_path, 'r') as file:
-        lines = file.readlines()
-
-    updated_lines = []
-    for line in lines:
-        match = False
-        for var in var_dict:
-            if line.startswith(var):
-                updated_lines.append(f'{var}={var_dict[var]}\n')
-                match = True
-                break
-        if not match:
-            updated_lines.append(line)
-
-    with open(file_path, 'w') as file:
-        file.writelines(updated_lines)
-
-
 if __name__ == '__main__':
     print("test")
     main()
diff --git a/EVSVesuvio/scripts/handle_config.py b/EVSVesuvio/scripts/handle_config.py
new file mode 100644
index 00000000..7ea62272
--- /dev/null
+++ b/EVSVesuvio/scripts/handle_config.py
@@ -0,0 +1,39 @@
+import os
+
+VESUVIO_CONFIG_PATH = os.path.join(os.path.expanduser("~"), '.mvesuvio')
+VESUVIO_CONFIG_FILE = "vesuvio.user.properties"
+
+
+def set_config_vars(var_dict):
+    file_path = f'{VESUVIO_CONFIG_PATH}/{VESUVIO_CONFIG_FILE}'
+    with open(file_path, 'r') as file:
+        lines = file.readlines()
+
+    updated_lines = []
+    for line in lines:
+        match = False
+        for var in var_dict:
+            if line.startswith(var):
+                updated_lines.append(f'{var}={var_dict[var]}')
+                match = True
+                break
+        if not match:
+            updated_lines.append(line)
+
+    with open(file_path, 'w') as file:
+        file.writelines(updated_lines)
+
+
+def read_config_var(var):
+    file_path = f'{VESUVIO_CONFIG_PATH}/{VESUVIO_CONFIG_FILE}'
+    with open(file_path, 'r') as file:
+        lines = file.readlines()
+
+    result = ""
+    for line in lines:
+        if line.startswith(var):
+            result = line.split("=", 2)[1].strip('\n')
+            break
+    if not result:
+        raise ValueError(f'{var} was not found in the vesuvio config')
+    return result
diff --git a/EVSVesuvio/vesuvio_analysis/core_functions/ICHelpers.py b/EVSVesuvio/vesuvio_analysis/core_functions/ICHelpers.py
index a823bc5c..fe5bff8c 100644
--- a/EVSVesuvio/vesuvio_analysis/core_functions/ICHelpers.py
+++ b/EVSVesuvio/vesuvio_analysis/core_functions/ICHelpers.py
@@ -1,8 +1,8 @@
 from mantid.simpleapi import LoadVesuvio, SaveNexus
 from pathlib import Path
+from EVSVesuvio.scripts import handle_config
 
-currentPath = Path(__file__).absolute().parent
-experimentsPath = currentPath / ".."/ ".." / "experiments"
+experimentsPath = Path(handle_config.read_config_var('caching.location')) / "experiments"
 
 
 def completeICFromInputs(IC, scriptName, wsIC):
@@ -163,7 +163,6 @@ def setBootstrapDirs(bckwdIC, fwdIC, bootIC, yFitIC):
 
     # Select script name and experiments path
     sampleName = bckwdIC.scriptName   # Name of sample currently running
-    experimentsPath = currentPath/".."/".."/"experiments"
 
     # Used to store running times required to estimate Bootstrap total run time.
     bootIC.runTimesPath = experimentsPath / sampleName / "running_times.txt"
diff --git a/EVSVesuvio/vesuvio_analysis/core_functions/bootstrap_analysis.py b/EVSVesuvio/vesuvio_analysis/core_functions/bootstrap_analysis.py
index f143dbe7..b3e738c4 100644
--- a/EVSVesuvio/vesuvio_analysis/core_functions/bootstrap_analysis.py
+++ b/EVSVesuvio/vesuvio_analysis/core_functions/bootstrap_analysis.py
@@ -4,13 +4,8 @@
 from EVSVesuvio.vesuvio_analysis.core_functions.fit_in_yspace import selectModelAndPars
 import numpy as np
 import matplotlib .pyplot as plt
-from pathlib import Path
 from scipy import stats
 
-currentPath = Path(__file__).parent.absolute()
-experimentsPath = currentPath / ".." / ".. " / "experiments"
-IPFilesPath = currentPath / ".." / "ip_files"
-
 
 def runAnalysisOfStoredBootstrap(bckwdIC, fwdIC, yFitIC, bootIC, analysisIC, userCtr):
 

From 40ca2eea798eabe58cb1640e974c02721ea9496c Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Mon, 13 Nov 2023 12:23:44 +0000
Subject: [PATCH 5/8] add config command to cli

---
 EVSVesuvio/config/__init__.py                 |  0
 .../analysis_inputs.py}                       | 44 ++++++-------
 EVSVesuvio/scripts/__init__.py                | 56 ++++++++---------
 EVSVesuvio/scripts/handle_config.py           | 61 ++++++++++++++++---
 pyproject.toml                                |  1 +
 5 files changed, 102 insertions(+), 60 deletions(-)
 create mode 100644 EVSVesuvio/config/__init__.py
 rename EVSVesuvio/{original_inputs.py => config/analysis_inputs.py} (87%)

diff --git a/EVSVesuvio/config/__init__.py b/EVSVesuvio/config/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/EVSVesuvio/original_inputs.py b/EVSVesuvio/config/analysis_inputs.py
similarity index 87%
rename from EVSVesuvio/original_inputs.py
rename to EVSVesuvio/config/analysis_inputs.py
index 5a7cf58e..268b1483 100644
--- a/EVSVesuvio/original_inputs.py
+++ b/EVSVesuvio/config/analysis_inputs.py
@@ -17,10 +17,10 @@ class LoadVesuvioBackParameters:
     empty_runs="41876-41923"   # 77K         # The numbers of the empty runs to be subtracted
     spectra='3-134'                          # Spectra to be analysed
     mode='DoubleDifference'
-    ipfile=ipFilesPath / "ip2019.par"   
+    ipfile=ipFilesPath / "ip2019.par"
 
     subEmptyFromRaw = True         # Flag to control wether empty ws gets subtracted from raw
-    scaleEmpty = 1       # None or scaling factor 
+    scaleEmpty = 1       # None or scaling factor
     scaleRaw = 1
 
 
@@ -29,16 +29,16 @@ class LoadVesuvioFrontParameters:
     empty_runs='43868-43911'   # 100K        # The numbers of the empty runs to be subtracted
     spectra='144-182'                        # Spectra to be analysed
     mode='SingleDifference'
-    ipfile=ipFilesPath / "ip2018_3.par" 
+    ipfile=ipFilesPath / "ip2018_3.par"
 
     subEmptyFromRaw = False         # Flag to control wether empty ws gets subtracted from raw
-    scaleEmpty = 1       # None or scaling factor 
+    scaleEmpty = 1       # None or scaling factor
     scaleRaw = 1
 
 
 class GeneralInitialConditions:
     """Used to define initial conditions shared by both Back and Forward scattering"""
-    
+
     transmission_guess =  0.8537        # Experimental value from VesuvioTransmission
     multiple_scattering_order, number_of_events = 2, 1.e5
     # Sample slab parameters
@@ -46,7 +46,7 @@ class GeneralInitialConditions:
 
 
 class BackwardInitialConditions(GeneralInitialConditions):
-    InstrParsPath = ipFilesPath / "ip2018_3.par" 
+    InstrParsPath = ipFilesPath / "ip2018_3.par"
 
     HToMassIdxRatio = 19.0620008206  # Set to zero or None when H is not present
     massIdx = 0
@@ -55,11 +55,11 @@ class BackwardInitialConditions(GeneralInitialConditions):
     masses = np.array([12, 16, 27])
     # noOfMasses = len(masses)
 
-    initPars = np.array([ 
-    # Intensities, NCP widths, NCP centers   
-            1, 12, 0.,    
-            1, 12, 0.,   
-            1, 12.5, 0.    
+    initPars = np.array([
+    # Intensities, NCP widths, NCP centers
+            1, 12, 0.,
+            1, 12, 0.,
+            1, 12.5, 0.
         ])
     bounds = np.array([
             [0, np.nan], [8, 16], [-3, 1],
@@ -81,7 +81,7 @@ class BackwardInitialConditions(GeneralInitialConditions):
     # # Parameters of workspaces in input_ws
     tofBinning='275.,1.,420'                    # Binning of ToF spectra
     maskTOFRange = None
-    
+
     # Original data uses histogram data instead of point data
     runHistData = True
     normVoigt = False
@@ -89,14 +89,14 @@ class BackwardInitialConditions(GeneralInitialConditions):
 
 class ForwardInitialConditions(GeneralInitialConditions):
 
-    masses = np.array([1.0079, 12, 16, 27]) 
+    masses = np.array([1.0079, 12, 16, 27])
 
-    initPars = np.array([ 
-    # Intensities, NCP widths, NCP centers  
-        1, 4.7, 0, 
-        1, 12.71, 0.,    
-        1, 8.76, 0.,   
-        1, 13.897, 0.    
+    initPars = np.array([
+    # Intensities, NCP widths, NCP centers
+        1, 4.7, 0,
+        1, 12.71, 0.,
+        1, 8.76, 0.,
+        1, 13.897, 0.
     ])
     bounds = np.array([
         [0, np.nan], [3, 6], [-3, 1],
@@ -118,7 +118,7 @@ class ForwardInitialConditions(GeneralInitialConditions):
 
     tofBinning="110,1,430"                 # Binning of ToF spectra
     maskTOFRange = None
-  
+
     # Original data uses histogram data instead of point data
     runHistData = True
     normVoigt = False
@@ -130,7 +130,7 @@ class YSpaceFitInitialConditions:
 
 class UserScriptControls:
     runRoutine = True
-    
+
     # Choose main procedure to run
     procedure = "BACKWARD"   # Options: None, "BACKWARD", "FORWARD", "JOINT"
 
@@ -145,7 +145,7 @@ class BootstrapInitialConditions:
 start_time = time.time()
 
 wsBackIC = LoadVesuvioBackParameters
-wsFrontIC = LoadVesuvioFrontParameters  
+wsFrontIC = LoadVesuvioFrontParameters
 bckwdIC = BackwardInitialConditions
 fwdIC = ForwardInitialConditions
 yFitIC = YSpaceFitInitialConditions
diff --git a/EVSVesuvio/scripts/__init__.py b/EVSVesuvio/scripts/__init__.py
index 85a14ea5..c6620ec7 100644
--- a/EVSVesuvio/scripts/__init__.py
+++ b/EVSVesuvio/scripts/__init__.py
@@ -1,54 +1,50 @@
 """Package defining entry points.
 """
 import argparse
-import os
-from shutil import copyfile
 from EVSVesuvio.scripts import handle_config
 
 
 def main():
     parser = __set_up_parser()
     args = parser.parse_args()
-    config_dir = handle_config.VESUVIO_CONFIG_PATH
-    cache_dir = config_dir if not args.set_cache else args.set_cache
-    experiment = "default" if not args.set_experiment else args.set_experiment
+    if args.command == "config":
+        __setup_config(args)
 
-    if __setup_config_dir(config_dir):
-        handle_config.set_config_vars({'caching.location': cache_dir,
-                                       'caching.experiment': experiment})
-    __setup_expr_dir(cache_dir, experiment)
+    if args.command == "run":
+        if not handle_config.config_set():
+            __setup_config(None)
+        __run_analysis()
 
 
 def __set_up_parser():
     parser = argparse.ArgumentParser(description="Package to analyse Vesuvio instrument data")
-    parser.add_argument("--set-cache", "-c", help="set the cache directory", default="", type=str)
-    parser.add_argument("--set-experiment", "-e", help="set the current experiment", default="", type=str)
-    return parser
+    subparsers = parser.add_subparsers(dest='command', required=True)
+    config_parser = subparsers.add_parser("config", help="set mvesuvio configuration")
+    config_parser.add_argument("--set-cache", "-c", help="set the cache directory", default="", type=str)
+    config_parser.add_argument("--set-experiment", "-e", help="set the current experiment", default="", type=str)
 
+    config_parser = subparsers.add_parser("run", help="run mvesuvio analysis")
+    return parser
 
-def __setup_config_dir(config_dir):
-    success = __mk_dir('config', config_dir)
-    if success:
-        copyfile('EVSVesuvio/config/vesuvio.user.properties', f'{config_dir}/{handle_config.VESUVIO_CONFIG_FILE}')
-    return success
 
+def __setup_config(args):
+    config_dir = handle_config.VESUVIO_CONFIG_PATH
+    handle_config.setup_config_dir(config_dir)
 
-def __setup_expr_dir(cache_dir, experiment):
-    expr_path = os.path.join(cache_dir, "experiments", experiment)
-    __mk_dir('experiment', expr_path)
+    if handle_config.config_set():
+        cache_dir = handle_config.read_config_var('caching.location') if not args or not args.set_cache else args.set_cache
+        experiment = handle_config.read_config_var('caching.experiment') if not args or not args.set_experiment else args.set_experiment
+    else:
+        cache_dir = config_dir if not args or not args.set_cache else args.set_cache
+        experiment = "default" if not args or not args.set_experiment else args.set_experiment
+    handle_config.set_config_vars({'caching.location': cache_dir,
+                                   'caching.experiment': experiment})
+    handle_config.setup_expr_dir(cache_dir, experiment)
 
 
-def __mk_dir(type, path):
-    success = False
-    if not os.path.isdir(path):
-        try:
-            os.makedirs(path)
-            success = True
-        except:
-            print(f'Unable to make {type} directory at location: {path}')
-    return success
+def __run_analysis():
+    print("RUNNING ANALYSIS")
 
 
 if __name__ == '__main__':
-    print("test")
     main()
diff --git a/EVSVesuvio/scripts/handle_config.py b/EVSVesuvio/scripts/handle_config.py
index 7ea62272..658fd178 100644
--- a/EVSVesuvio/scripts/handle_config.py
+++ b/EVSVesuvio/scripts/handle_config.py
@@ -1,22 +1,38 @@
 import os
+from shutil import copyfile
 
 VESUVIO_CONFIG_PATH = os.path.join(os.path.expanduser("~"), '.mvesuvio')
 VESUVIO_CONFIG_FILE = "vesuvio.user.properties"
+VESUVIO_INPUTS_FILE = "analysis_inputs.py"
+VESUVIO_PACKAGE_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+
+
+def __read_config(config_file_path, throw_on_not_found=True):
+    lines = ""
+    try:
+        with open(config_file_path, 'r') as file:
+            lines = file.readlines()
+    except IOError:
+        if throw_on_not_found:
+            raise RuntimeError(f"Could not read from vesuvio config file: {config_file_path}")
+    return lines
 
 
 def set_config_vars(var_dict):
-    file_path = f'{VESUVIO_CONFIG_PATH}/{VESUVIO_CONFIG_FILE}'
-    with open(file_path, 'r') as file:
-        lines = file.readlines()
+    file_path = os.path.join(VESUVIO_CONFIG_PATH, VESUVIO_CONFIG_FILE)
+    lines = __read_config(file_path)
 
     updated_lines = []
     for line in lines:
         match = False
         for var in var_dict:
             if line.startswith(var):
-                updated_lines.append(f'{var}={var_dict[var]}')
+                new_line = f'{var}={var_dict[var]}'
+                updated_lines.append(f'{new_line}\n')
                 match = True
+                print(f'Setting: {new_line}')
                 break
+
         if not match:
             updated_lines.append(line)
 
@@ -24,16 +40,45 @@ def set_config_vars(var_dict):
         file.writelines(updated_lines)
 
 
-def read_config_var(var):
+def read_config_var(var, throw_on_not_found=True):
     file_path = f'{VESUVIO_CONFIG_PATH}/{VESUVIO_CONFIG_FILE}'
-    with open(file_path, 'r') as file:
-        lines = file.readlines()
+    lines = __read_config(file_path, throw_on_not_found)
 
     result = ""
     for line in lines:
         if line.startswith(var):
             result = line.split("=", 2)[1].strip('\n')
             break
-    if not result:
+    if not result and throw_on_not_found:
         raise ValueError(f'{var} was not found in the vesuvio config')
     return result
+
+
+def setup_config_dir(config_dir):
+    success = __mk_dir('config', config_dir)
+    if success:
+        copyfile(os.path.join(VESUVIO_PACKAGE_PATH, "config", VESUVIO_CONFIG_FILE), os.path.join(config_dir, VESUVIO_CONFIG_FILE))
+
+
+def setup_expr_dir(cache_dir, experiment):
+    expr_path = os.path.join(cache_dir, "experiments", experiment)
+    __mk_dir('experiment', expr_path)
+    copyfile(os.path.join(VESUVIO_PACKAGE_PATH, "config", VESUVIO_INPUTS_FILE), os.path.join(expr_path, VESUVIO_INPUTS_FILE))
+
+
+def __mk_dir(type, path):
+    success = False
+    if not os.path.isdir(path):
+        try:
+            os.makedirs(path)
+            success = True
+        except:
+            print(f'Unable to make {type} directory at location: {path}')
+    return success
+
+
+def config_set():
+    if(not read_config_var('caching.location', False)):
+        return False
+    else:
+        return True
diff --git a/pyproject.toml b/pyproject.toml
index eed2c3ba..3cdb25f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,6 +48,7 @@ namespaces = false
 
 [tool.setuptools.package-data]
 "EVSVesuvio.vesuvio_analysis.ip_files" = ["*.OPJ", "*.par", "*.DAT", "*.DAT3", "*.DAT6", "*.txt"]
+"EVSVesuvio.config" = ["*.properties"]
 
 [tool.pytest.ini_options]
 pythonpath = ["."]

From 95bc2c8f1648f57949176ae96799ffc4fa627d84 Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Mon, 13 Nov 2023 16:59:21 +0000
Subject: [PATCH 6/8] add analysis runner

---
 EVSVesuvio/analysis_runner.py        | 51 ++++++++++++++++++++++++++++
 EVSVesuvio/config/analysis_inputs.py | 48 ++++++--------------------
 EVSVesuvio/scripts/__init__.py       |  3 +-
 EVSVesuvio/scripts/handle_config.py  | 12 ++++---
 4 files changed, 71 insertions(+), 43 deletions(-)
 create mode 100644 EVSVesuvio/analysis_runner.py

diff --git a/EVSVesuvio/analysis_runner.py b/EVSVesuvio/analysis_runner.py
new file mode 100644
index 00000000..a7aad492
--- /dev/null
+++ b/EVSVesuvio/analysis_runner.py
@@ -0,0 +1,51 @@
+import time
+from pathlib import Path
+import importlib
+import sys
+from os import path
+#from EVSVesuvio.vesuvio_analysis.core_functions.bootstrap import runBootstrap
+#from EVSVesuvio.vesuvio_analysis.core_functions.bootstrap_analysis import runAnalysisOfStoredBootstrap
+from EVSVesuvio.vesuvio_analysis.core_functions.run_script import runScript
+from mantid.api import AnalysisDataService
+from EVSVesuvio.scripts import handle_config
+
+
+def run():
+    scriptName =  handle_config.read_config_var('caching.experiment')
+    experimentsPath = Path(handle_config.read_config_var('caching.location')) / "experiments" / scriptName # Path to the repository
+    inputs_path = experimentsPath / "analysis_inputs.py"
+    ai = import_from_path(inputs_path, "analysis_inputs")
+
+    ipFilesPath = Path(path.dirname(path.dirname(handle_config.__file__))) / "vesuvio_analysis" / "ip_files"
+
+    start_time = time.time()
+
+    wsBackIC = ai.LoadVesuvioBackParameters(ipFilesPath)
+    wsFrontIC = ai.LoadVesuvioFrontParameters(ipFilesPath)
+    bckwdIC = ai.BackwardInitialConditions(ipFilesPath)
+    fwdIC = ai.ForwardInitialConditions
+    yFitIC = ai.YSpaceFitInitialConditions
+    bootIC = ai.BootstrapInitialConditions
+    userCtr = ai.UserScriptControls
+
+    runScript(userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC)
+
+    AnalysisDataService.clear()
+    userCtr.procedure = "FORWARD"
+
+    runScript(userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC)
+
+    end_time = time.time()
+    print("\nRunning time: ", end_time-start_time, " seconds")
+
+
+def import_from_path(path, name):
+    spec = importlib.util.spec_from_file_location(name, path)
+    module = importlib.util.module_from_spec(spec)
+    sys.modules[name] = module
+    spec.loader.exec_module(module)
+    return module
+
+
+if __name__ == '__main__':
+    run()
diff --git a/EVSVesuvio/config/analysis_inputs.py b/EVSVesuvio/config/analysis_inputs.py
index 268b1483..9d5a1cad 100644
--- a/EVSVesuvio/config/analysis_inputs.py
+++ b/EVSVesuvio/config/analysis_inputs.py
@@ -1,23 +1,14 @@
-import time
 import numpy as np
-from pathlib import Path
-from EVSVesuvio.vesuvio_analysis.core_functions.bootstrap import runBootstrap
-from EVSVesuvio.vesuvio_analysis.core_functions.bootstrap_analysis import runAnalysisOfStoredBootstrap
-from EVSVesuvio.vesuvio_analysis.core_functions.run_script import runScript
-from mantid.api import AnalysisDataService
-from EVSVesuvio.scripts import handle_config
-
-scriptName =  handle_config.read_config_var('caching.experiment')
-experimentsPath = Path(handle_config.read_config_var('caching.location')) / "experiments" / scriptName # Path to the repository
-ipFilesPath = Path(__file__).absolute().parent / "vesuvio_analysis" / "ip_files"
 
 
 class LoadVesuvioBackParameters:
+    def __init__(self, ipFilesPath):
+        self.ipfile=ipFilesPath / "ip2019.par"
+
     runs="43066-43076"         # 77K         # The numbers of the runs to be analysed
     empty_runs="41876-41923"   # 77K         # The numbers of the empty runs to be subtracted
     spectra='3-134'                          # Spectra to be analysed
     mode='DoubleDifference'
-    ipfile=ipFilesPath / "ip2019.par"
 
     subEmptyFromRaw = True         # Flag to control wether empty ws gets subtracted from raw
     scaleEmpty = 1       # None or scaling factor
@@ -25,11 +16,13 @@ class LoadVesuvioBackParameters:
 
 
 class LoadVesuvioFrontParameters:
+    def __init__(self, ipFilesPath):
+        self.ipfile=ipFilesPath / "ip2018_3.par"
+
     runs='43066-43076'         # 100K        # The numbers of the runs to be analysed
     empty_runs='43868-43911'   # 100K        # The numbers of the empty runs to be subtracted
     spectra='144-182'                        # Spectra to be analysed
     mode='SingleDifference'
-    ipfile=ipFilesPath / "ip2018_3.par"
 
     subEmptyFromRaw = False         # Flag to control wether empty ws gets subtracted from raw
     scaleEmpty = 1       # None or scaling factor
@@ -46,7 +39,8 @@ class GeneralInitialConditions:
 
 
 class BackwardInitialConditions(GeneralInitialConditions):
-    InstrParsPath = ipFilesPath / "ip2018_3.par"
+    def __init__(self, ipFilesPath):
+        self.InstrParsPath=ipFilesPath / "ip2018_3.par"
 
     HToMassIdxRatio = 19.0620008206  # Set to zero or None when H is not present
     massIdx = 0
@@ -55,8 +49,8 @@ class BackwardInitialConditions(GeneralInitialConditions):
     masses = np.array([12, 16, 27])
     # noOfMasses = len(masses)
 
-    initPars = np.array([
     # Intensities, NCP widths, NCP centers
+    initPars = np.array([
             1, 12, 0.,
             1, 12, 0.,
             1, 12.5, 0.
@@ -91,8 +85,8 @@ class ForwardInitialConditions(GeneralInitialConditions):
 
     masses = np.array([1.0079, 12, 16, 27])
 
-    initPars = np.array([
     # Intensities, NCP widths, NCP centers
+    initPars = np.array([
         1, 4.7, 0,
         1, 12.71, 0.,
         1, 8.76, 0.,
@@ -140,25 +134,3 @@ class UserScriptControls:
 
 class BootstrapInitialConditions:
     runBootstrap = False
-
-
-start_time = time.time()
-
-wsBackIC = LoadVesuvioBackParameters
-wsFrontIC = LoadVesuvioFrontParameters
-bckwdIC = BackwardInitialConditions
-fwdIC = ForwardInitialConditions
-yFitIC = YSpaceFitInitialConditions
-bootIC = BootstrapInitialConditions
-userCtr = UserScriptControls
-
-runScript(userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC)
-
-AnalysisDataService.clear()
-userCtr.procedure = "FORWARD"
-
-runScript(userCtr, scriptName, wsBackIC, wsFrontIC, bckwdIC, fwdIC, yFitIC, bootIC)
-
-
-end_time = time.time()
-print("\nRunning time: ", end_time-start_time, " seconds")
diff --git a/EVSVesuvio/scripts/__init__.py b/EVSVesuvio/scripts/__init__.py
index c6620ec7..1baa0154 100644
--- a/EVSVesuvio/scripts/__init__.py
+++ b/EVSVesuvio/scripts/__init__.py
@@ -43,7 +43,8 @@ def __setup_config(args):
 
 
 def __run_analysis():
-    print("RUNNING ANALYSIS")
+    from EVSVesuvio import analysis_runner
+    analysis_runner.run()
 
 
 if __name__ == '__main__':
diff --git a/EVSVesuvio/scripts/handle_config.py b/EVSVesuvio/scripts/handle_config.py
index 658fd178..aae7afa0 100644
--- a/EVSVesuvio/scripts/handle_config.py
+++ b/EVSVesuvio/scripts/handle_config.py
@@ -63,7 +63,7 @@ def setup_config_dir(config_dir):
 def setup_expr_dir(cache_dir, experiment):
     expr_path = os.path.join(cache_dir, "experiments", experiment)
     __mk_dir('experiment', expr_path)
-    copyfile(os.path.join(VESUVIO_PACKAGE_PATH, "config", VESUVIO_INPUTS_FILE), os.path.join(expr_path, VESUVIO_INPUTS_FILE))
+    copyfile(os.path.join(VESUVIO_PACKAGE_PATH, "config", VESUVIO_INPUTS_FILE), input_file_path(cache_dir, experiment))
 
 
 def __mk_dir(type, path):
@@ -78,7 +78,11 @@ def __mk_dir(type, path):
 
 
 def config_set():
-    if(not read_config_var('caching.location', False)):
-        return False
-    else:
+    if(read_config_var('caching.location', False)):
         return True
+    else:
+        return False
+
+
+def input_file_path(cache_dir, experiment):
+    return os.path.join(cache_dir, "experiments", experiment, VESUVIO_INPUTS_FILE)

From e430772462850f731e425ad3b5efe3d53231a479 Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Mon, 13 Nov 2023 17:16:50 +0000
Subject: [PATCH 7/8] add mantid config file

---
 EVSVesuvio/scripts/__init__.py      | 2 ++
 EVSVesuvio/scripts/handle_config.py | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/EVSVesuvio/scripts/__init__.py b/EVSVesuvio/scripts/__init__.py
index 1baa0154..2df52d9d 100644
--- a/EVSVesuvio/scripts/__init__.py
+++ b/EVSVesuvio/scripts/__init__.py
@@ -1,6 +1,7 @@
 """Package defining entry points.
 """
 import argparse
+from os import environ, path
 from EVSVesuvio.scripts import handle_config
 
 
@@ -43,6 +44,7 @@ def __setup_config(args):
 
 
 def __run_analysis():
+    environ['MANTIDPROPERTIES'] = path.join(handle_config.VESUVIO_CONFIG_PATH, "Mantid.user.properties")
     from EVSVesuvio import analysis_runner
     analysis_runner.run()
 
diff --git a/EVSVesuvio/scripts/handle_config.py b/EVSVesuvio/scripts/handle_config.py
index aae7afa0..7e74aec9 100644
--- a/EVSVesuvio/scripts/handle_config.py
+++ b/EVSVesuvio/scripts/handle_config.py
@@ -5,6 +5,7 @@
 VESUVIO_CONFIG_FILE = "vesuvio.user.properties"
 VESUVIO_INPUTS_FILE = "analysis_inputs.py"
 VESUVIO_PACKAGE_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+MANTID_CONFIG_FILE = "Mantid.user.properties"
 
 
 def __read_config(config_file_path, throw_on_not_found=True):
@@ -58,6 +59,7 @@ def setup_config_dir(config_dir):
     success = __mk_dir('config', config_dir)
     if success:
         copyfile(os.path.join(VESUVIO_PACKAGE_PATH, "config", VESUVIO_CONFIG_FILE), os.path.join(config_dir, VESUVIO_CONFIG_FILE))
+        copyfile(os.path.join(VESUVIO_PACKAGE_PATH, "config", MANTID_CONFIG_FILE), os.path.join(config_dir, MANTID_CONFIG_FILE))
 
 
 def setup_expr_dir(cache_dir, experiment):

From 0efa30040bc126dd97116c5281bd6cef99bd4826 Mon Sep 17 00:00:00 2001
From: MialLewis <95620982+MialLewis@users.noreply.github.com>
Date: Mon, 13 Nov 2023 17:22:58 +0000
Subject: [PATCH 8/8] add mantid properties file

---
 EVSVesuvio/config/Mantid.user.properties | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100644 EVSVesuvio/config/Mantid.user.properties

diff --git a/EVSVesuvio/config/Mantid.user.properties b/EVSVesuvio/config/Mantid.user.properties
new file mode 100644
index 00000000..300b958c
--- /dev/null
+++ b/EVSVesuvio/config/Mantid.user.properties
@@ -0,0 +1,3 @@
+default.facility=ISIS
+default.instrument=Vesuvio
+datasearch.searcharchive=On