update paths to run from calibration root

mantidproject · May 2, 2023 · 1293de7 · 1293de7
1 parent 1fa741e
commit 1293de7
Show file tree

Hide file tree

Showing 12 changed files with 132 additions and 131 deletions.
diff --git a/.github/workflows/pr_workflow.yml b/.github/workflows/pr_workflow.yml
@@ -39,7 +39,8 @@ jobs:
       - name: Run EVSVesuvio Calibration Unit Tests
         run: |
           export MANTIDPROPERTIES=$(pwd)/Mantid.user.properties
-          python -m unittest discover -s ./unpackaged/vesuvio_calibration/tests/unit
+          cd unpackaged/vesuvio_calibration
+          python -m unittest discover -s ./tests/unit
 
       #DISABLED AS THEY APPEAR TOO LARGE FOR GITHUB HOSTED RUNNERS
       #- name: Run Vesuvio Calibration System Tests

diff --git a/unpackaged/vesuvio_calibration/README.md b/unpackaged/vesuvio_calibration/README.md
@@ -47,10 +47,10 @@ Upon running the script, the two calibration algorithms will be registered under
 
 1. Actviate the conda environment using `conda activate vesuvio-env`.
 
-2. From the root of the repository run `python -m unittest discover -s ./unpackaged/vesuvio_calibration/tests/unit`
+2. From `<root of the repository>/unpackaged/vesuvio_calibration` run `python -m unittest discover -s ./tests/unit`
 
 ## Running the system tests from the command line.
 
 1. Actviate the conda environment using `conda activate vesuvio-env`.
 
-2. From the root of the repository run `python -m unittest discover -s ./unpackaged/vesuvio_calibration/tests/system`
+2. From `<root of the repository>/unpackaged/vesuvio_calibration`  run `python -m unittest discover -s ./tests/system`
diff --git a/unpackaged/vesuvio_calibration/calibration_scripts/calibrate_vesuvio_analysis.py b/unpackaged/vesuvio_calibration/calibration_scripts/calibrate_vesuvio_analysis.py
@@ -3,7 +3,7 @@
 from mantid.api import FileProperty, FileAction, PythonAlgorithm,AlgorithmManager
 from mantid.simpleapi import CreateEmptyTableWorkspace, DeleteWorkspace, ReplaceSpecialValues, GroupWorkspaces, mtd,\
      ConvertTableToMatrixWorkspace, ConjoinWorkspaces, Transpose, PlotPeakByLogValue,RenameWorkspace
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions,\
+from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions,\
      InvalidDetectors
 
 import os

diff --git a/unpackaged/vesuvio_calibration/calibration_scripts/calibrate_vesuvio_fit.py b/unpackaged/vesuvio_calibration/calibration_scripts/calibrate_vesuvio_fit.py
@@ -6,7 +6,7 @@
      ReplaceSpecialValues, FindPeaks, GroupWorkspaces, mtd, Plus, LoadVesuvio, LoadRaw, ConvertToDistribution, FindPeakBackground,\
      ExtractSingleSpectrum, SumSpectra, AppendSpectra, CloneWorkspace, Fit, MaskDetectors, ExtractUnmaskedSpectra, CreateWorkspace
 from functools import partial
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions,\
+from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals, EVSMiscFunctions,\
      InvalidDetectors
 
 import os

diff --git a/unpackaged/vesuvio_calibration/load_calibration_algorithms.py b/unpackaged/vesuvio_calibration/load_calibration_algorithms.py
@@ -13,8 +13,8 @@
 """
 
 from mantid.api import AlgorithmFactory
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit import EVSCalibrationFit
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_analysis import EVSCalibrationAnalysis
+from calibration_scripts.calibrate_vesuvio_fit import EVSCalibrationFit
+from calibration_scripts.calibrate_vesuvio_analysis import EVSCalibrationAnalysis
 
 AlgorithmFactory.subscribe(EVSCalibrationFit)
 AlgorithmFactory.subscribe(EVSCalibrationAnalysis)
diff --git a/unpackaged/vesuvio_calibration/tests/system/test_system_analysis.py b/unpackaged/vesuvio_calibration/tests/system/test_system_analysis.py
@@ -4,12 +4,12 @@
 from mantid.api import AlgorithmFactory
 from mantid.simpleapi import mtd
 from mock import patch
-from unpackaged.vesuvio_calibration.tests.testhelpers.algorithms import create_algorithm
-from unpackaged.vesuvio_calibration.tests.testhelpers.system_test_base import EVSCalibrationTest, TestConstants
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals
-from unpackaged.vesuvio_calibration.tests.testhelpers.system_test_misc_functions import assert_allclose_excluding_bad_detectors
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_analysis import EVSCalibrationAnalysis
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit import EVSCalibrationFit
+from tests.testhelpers.algorithms import create_algorithm
+from tests.testhelpers.system_test_base import EVSCalibrationTest, TestConstants
+from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals
+from tests.testhelpers.system_test_misc_functions import assert_allclose_excluding_bad_detectors
+from calibration_scripts.calibrate_vesuvio_analysis import EVSCalibrationAnalysis
+from calibration_scripts.calibrate_vesuvio_fit import EVSCalibrationFit
 from copy import copy, deepcopy
 from os import path
 
@@ -40,7 +40,7 @@ def setUp(self):
         self._E1_fit = [False, True, True]
         self._L0_fit = [False]
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper(self, load_file_mock):
         self._setup_copper_test()
         self._output_workspace = "copper_analysis_test"
@@ -55,7 +55,7 @@ def test_copper(self, load_file_mock):
                                                                                            165, 167, 168, 169, 170, 182, 191, 192]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_lead(self, load_file_mock):
         self._setup_lead_test()
         self._output_workspace = "lead_analysis_test"
@@ -70,7 +70,7 @@ def test_lead(self, load_file_mock):
                                                                                            178, 180, 182, 183]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_niobium(self, load_file_mock):
         self._setup_niobium_test()
         self._output_workspace = "niobium_analysis_test"
@@ -88,7 +88,7 @@ def test_niobium(self, load_file_mock):
                                                                                            182, 186, 187, 189, 191]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper_with_uranium(self, load_file_mock):
         self._setup_copper_test()
         self._output_workspace = "copper_analysis_test"
@@ -103,7 +103,7 @@ def test_copper_with_uranium(self, load_file_mock):
                                                                                            165, 167, 168, 169, 170, 182, 191, 192]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_lead_with_uranium(self, load_file_mock):
         self._setup_lead_test()
         self._output_workspace = "lead_analysis_test"
@@ -118,7 +118,7 @@ def test_lead_with_uranium(self, load_file_mock):
                                                                                            178, 180, 182, 183]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper_with_l0_calc(self, load_file_mock):
         self._setup_copper_test()
         self._L0_fit = [True, True, True, False, False, False]
@@ -138,7 +138,7 @@ def test_copper_with_l0_calc(self, load_file_mock):
                                                                                            165, 167, 168, 169, 170, 182, 191, 192]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper_with_multiple_iterations(self, load_file_mock):
         self._setup_copper_test()
         self._iterations = 2
@@ -158,7 +158,7 @@ def test_copper_with_multiple_iterations(self, load_file_mock):
                                                                                            165, 167, 168, 169, 170, 182, 191, 192]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper_create_output(self, load_file_mock):
         self._setup_copper_test()
         self._output_workspace = "copper_analysis_test"
@@ -175,7 +175,7 @@ def test_copper_create_output(self, load_file_mock):
                                                                                            165, 167, 168, 169, 170, 182, 191, 192]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper_create_invalid_detectors_specified(self, load_file_mock):
         self._setup_copper_test()
         self._output_workspace = "copper_analysis_test"
@@ -196,7 +196,7 @@ def test_copper_create_invalid_detectors_specified(self, load_file_mock):
         detector_specific_r_tols["L1"].update({k: TestConstants.INVALID_DETECTOR for k in [0, 2, 4]})
         self._assert_parameters_match_expected(params_table, detector_specific_r_tols)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_copper_with_individual_and_global_fit(self, load_file_mock):
         self._setup_copper_test()
         self._output_workspace = "copper_analysis_test"

diff --git a/unpackaged/vesuvio_calibration/tests/system/test_system_fit.py b/unpackaged/vesuvio_calibration/tests/system/test_system_fit.py
@@ -6,11 +6,11 @@
 from mantid.api import WorkspaceGroup, AlgorithmFactory
 from mantid.simpleapi import mtd
 from mock import patch
-from unpackaged.vesuvio_calibration.tests.testhelpers.algorithms import create_algorithm
-from unpackaged.vesuvio_calibration.tests.testhelpers.system_test_base import EVSCalibrationTest, TestConstants
-from unpackaged.vesuvio_calibration.tests.testhelpers.system_test_misc_functions import assert_allclose_excluding_bad_detectors
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_helper_functions import EVSMiscFunctions, EVSGlobals
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit import EVSCalibrationFit
+from tests.testhelpers.algorithms import create_algorithm
+from tests.testhelpers.system_test_base import EVSCalibrationTest, TestConstants
+from tests.testhelpers.system_test_misc_functions import assert_allclose_excluding_bad_detectors
+from calibration_scripts.calibrate_vesuvio_helper_functions import EVSMiscFunctions, EVSGlobals
+from calibration_scripts.calibrate_vesuvio_fit import EVSCalibrationFit
 from os import path
 
 
@@ -40,7 +40,7 @@ def setUp(self):
         self._E1_fit = [False]
         self._L0_fit = [False]
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_fit_bragg_peaks_copper(self, load_file_mock):
         self._setup_copper_test()
         self._spec_range = [EVSGlobals.DETECTOR_RANGE]
@@ -52,7 +52,7 @@ def test_fit_bragg_peaks_copper(self, load_file_mock):
         params_table = self._run_evs_calibration_fit("Bragg")
         self._assert_fitted_positions_match_expected(expected_values, params_table, {15: TestConstants.IGNORE_DETECTOR})
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_fit_bragg_peaks_lead(self, load_file_mock):
         self._setup_lead_test()
         self._spec_range = [EVSGlobals.DETECTOR_RANGE]
@@ -65,7 +65,7 @@ def test_fit_bragg_peaks_lead(self, load_file_mock):
         self._assert_fitted_positions_match_expected(expected_values, params_table, {145: 0.27, 158: 0.15, 190:
                                                                                     TestConstants.IGNORE_DETECTOR})
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_fit_peaks_copper_E1(self, load_file_mock):
         self._setup_copper_test()
         self._E1_fit_active = True
@@ -79,7 +79,7 @@ def test_fit_peaks_copper_E1(self, load_file_mock):
         params_table = self._run_evs_calibration_fit("Recoil")
         self._assert_fitted_positions_match_expected(expected_values, params_table, {38:  0.12})
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_fit_peaks_lead_E1(self, load_file_mock):
         self._setup_lead_test()
         self._E1_fit_active = True
@@ -93,7 +93,7 @@ def test_fit_peaks_lead_E1(self, load_file_mock):
         params_table = self._run_evs_calibration_fit("Recoil")
         self._assert_fitted_positions_match_expected(expected_values, params_table, {38:  0.12})
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_fit_frontscattering_uranium(self, load_file_mock):
         self._setup_uranium_test()
         self._run_range = EVSGlobals.U_FRONTSCATTERING_SAMPLE
@@ -107,7 +107,7 @@ def test_fit_frontscattering_uranium(self, load_file_mock):
         params_table = self._run_evs_calibration_fit("Recoil")
         self._assert_fitted_positions_match_expected(expected_values, params_table)
 
-    @patch('unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
+    @patch('calibration_scripts.calibrate_vesuvio_fit.EVSCalibrationFit._load_file')
     def test_fit_backscattering_uranium(self, load_file_mock):
         self._setup_uranium_test()
         self._run_range = EVSGlobals.U_BACKSCATTERING_SAMPLE

diff --git a/unpackaged/vesuvio_calibration/tests/testhelpers/system_test_base.py b/unpackaged/vesuvio_calibration/tests/testhelpers/system_test_base.py
@@ -1,7 +1,7 @@
 import unittest
 import numpy as np
 from mantid.simpleapi import LoadVesuvio, LoadRaw, mtd, ConvertToDistribution
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals
+from calibration_scripts.calibrate_vesuvio_helper_functions import EVSGlobals
 from os import path
 
 

diff --git a/unpackaged/vesuvio_calibration/tests/testhelpers/system_test_misc_functions.py b/unpackaged/vesuvio_calibration/tests/testhelpers/system_test_misc_functions.py
@@ -1,6 +1,6 @@
 import numpy as np
 from sys import maxsize
-from unpackaged.vesuvio_calibration.tests.testhelpers.system_test_base import TestConstants
+from tests.testhelpers.system_test_base import TestConstants
 
 
 def assert_allclose_excluding_bad_detectors(expected_position, position, rtol, default_rtol=TestConstants.DEFAULT_RELATIVE_TOLERANCE):

diff --git a/unpackaged/vesuvio_calibration/tests/unit/test_calibrate_vesuvio_analysis.py b/unpackaged/vesuvio_calibration/tests/unit/test_calibrate_vesuvio_analysis.py
@@ -1,4 +1,4 @@
-from unpackaged.vesuvio_calibration.calibration_scripts.calibrate_vesuvio_analysis import EVSCalibrationAnalysis
+from calibration_scripts.calibrate_vesuvio_analysis import EVSCalibrationAnalysis
 
 import unittest