cleanup tests

.github/workflows/actions.yml

@@ -39,19 +39,9 @@ jobs:
         /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -ac -screen 0 1280x1024x16
     - name: Test with pytest
       run: |
-        # sed -i '/^sdatasearch.directories=/s/.*/datasearch.directories=\/home\/cloud\/_work\/LiquidsReflectometer\/LiquidsReflectometer\/tests\/data\/liquidsreflectometer-data\/nexus/' ~/.mantid/Mantid.user.properties
-        echo datasearch.directories=/home/cloud/_work/LiquidsReflectometer/LiquidsReflectometer/tests/data/liquidsreflectometer-data/nexus/ >> ~/.mantid/Mantid.user.properties
-        cat ~/.mantid/Mantid.user.properties
-        # sudo apt-get update
-        # sudo apt-get install git-lfs
-        dpkg -l git-lfs
-        python -m pip install -e . # install the application in editable mode
         git submodule add --force https://code.ornl.gov/sns-hfir-scse/infrastructure/test-data/liquidsreflectometer-data.git tests/data/liquidsreflectometer-data
-        # git -C tests/data/liquidsreflectometer-data/ lfs install
-        # git -C tests/data/liquidsreflectometer-data/ pull
         git submodule update --init
-        ls -al tests/data/liquidsreflectometer-data/nexus/
-        xvfb-run --server-args="-screen 0 1280x1024x16" --auto-servernum python -m pytest --cov=reduction --cov=scripts --cov-report=xml --cov-report=term
+        python -m pytest --cov=reduction --cov=scripts --cov-report=xml --cov-report=term -m datarepo
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:

tests/reduction/test_reduction.py

@@ -1,13 +1,11 @@
 import unittest
 import os
 import pytest
-import sys
-print(sys.path)
 
 import mantid.simpleapi as mtd_api
 import numpy as np
 from mantid.kernel import ConfigService
-from mantid.api import FileFinder
+mantid.kernel.config.setLogLevel(3)
 
 from reduction.lr_reduction import event_reduction, template, workflow
 
@@ -23,8 +21,6 @@ def setUp(self):
         config.appendDataSearchDir(str(os.path.join(cwd, "data/liquidsreflectometer-data/nexus")))
         print(config.getDataSearchDirs())
 
-
-    @classmethod
     def test_full_reduction(self):
         """
         Test the fill reduction chain
@@ -34,21 +30,15 @@ def test_full_reduction(self):
         refl_all = []
         d_refl_all = []
         first_run = None
-        # file_prefix = "data/liquidsreflectometer-data/nexus/REF_L_{}.nxs.h5"
-        # print(oct(os.stat(filename).st_mode)[-3:])
-        # print(os.getcwd())
-        os.getcwd()
+
         for run_number in range(198409, 198417):
-            file_loc = f"data/liquidsreflectometer-data/nexus/REF_L_{run_number}.nxs.h5"
-            file_name = FileFinder.findRuns("REF_L_%d" % int(run_number))[0]
-            print(f'foundfile: {file_name}')
-            ws_sc = mtd_api.Load(Filename=file_loc)
+            ws_sc = mtd_api.Load("REF_L_%s" % run_number)
             qz_mid, refl, d_refl = template.process_from_template_ws(ws_sc, template_path)
 
             if first_run is None:
                 first_run = run_number
                 resolution = event_reduction.compute_resolution(ws_sc)
-                print(resolution)
+
             for i in range(len(qz_mid)):
                 qz_all.append(qz_mid[i])
                 refl_all.append(refl[i])
@@ -63,7 +53,7 @@ def test_full_reduction(self):
         refl_all = np.take_along_axis(refl_all, idx, axis=None)
         d_refl_all = np.take_along_axis(d_refl_all, idx, axis=None)
 
-        # assert(resolution == 0.02785205863936946)
+        assert(resolution == 0.02785205863936946)
         ref_data = np.loadtxt("data/reference_rq.txt").T
         assert len(ref_data[1]) == len(refl_all)
         assert np.fabs(np.sum(ref_data[1] - refl_all)) < 1e-10

tests/reduction/test_time_resolved.py

@@ -8,7 +8,6 @@
 
 @pytest.mark.datarepo()
 class TimeResolvedTest(unittest.TestCase):
-    @classmethod
     def setUpClass(cls):
         if os.getcwd().endswith("LiquidsReflectometer"):
             os.chdir("tests")
@@ -17,14 +16,13 @@ def setUpClass(cls):
         config.appendDataSearchDir(str(os.path.join(cwd, "data/liquidsreflectometer-data/nexus")))
         print(config.getDataSearchDirs())
 
-    @classmethod
     def test_reduce_workflow(self):
         """
         Test the time-resolved reduction that uses a measured reference.
         It is generally used at 30 Hz but it also works at 60 Hz.
         """
         template_path = "data/template.xml"
-        output_dir = "/tmp"
+        output_dir = "results"
         reduced_path = "data/reference_rq_avg_overlap.txt"
         ref_data = np.loadtxt(reduced_path).T
 

tests/scripts/test_peaks.py

@@ -11,9 +11,8 @@
 from scripts.autoreduce.peak_finding import find_peaks, peak_prominences, peak_widths
 
 
-@pytest.mark.scripts()
+@pytest.mark.datarepo()
 class ScanPeaksTest(unittest.TestCase):
-    @classmethod
     def setUpClass(cls):
         if os.getcwd().endswith("LiquidsReflectometer"):
             os.chdir("tests")
@@ -22,7 +21,6 @@ def setUpClass(cls):
         config.appendDataSearchDir(str(os.path.join(cwd, "data/liquidsreflectometer-data/nexus")))
         print(config.getDataSearchDirs())
 
-    @classmethod
     def test_peak_finding(self):
         def scan_peaks(x):
             f1 = ndimage.gaussian_filter(x, 3)

tests/scripts/test_sf.py

@@ -8,7 +8,6 @@
 
 @pytest.mark.scripts()
 class TestScalingFactor(unittest.TestCase):
-    @classmethod
     def setUpClass(cls):
         if os.getcwd().endswith("LiquidsReflectometer"):
             os.chdir("tests")
@@ -17,8 +16,7 @@ def setUpClass(cls):
         config.appendDataSearchDir(str(os.path.join(cwd, "data/liquidsreflectometer-data/nexus")))
         print(config.getDataSearchDirs())
 
-    @classmethod
     def test_scaling_factor(self):
-        sf = ScalingFactor(run_list=range(184975, 184990), sf_file="/tmp/sf_184975_air.cfg", medium="air")
+        sf = ScalingFactor(run_list=range(184975, 184990), sf_file="results/sf_184975_air.cfg", medium="air")
 
         sf.execute()